IFB-Lactam-1, a natural compound with anti-Gloeosporium kaki Hori activity

The title compound, IFB-Lactam-1 (systematic name: 2,15-dihydr­oxy-7-methyl-6-aza­bicyclo­[11.3.0]hexa­dec-3-en-5-one), C₁₆H₂₇NO₃, is a newly characterized natural anti-Gloeosporium kaki Hori compound. It was isolated from the EtOAc extract of the fermentation broth of an endophytic fungus Trichoderma sp. from cabbage. It is a 13-membered macrocyclic lactam which shares a two-atom edge with a cyclo­penta­nol ring.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.009 Å
• R factor = 0.074
• wR factor = 0.239
• Data-to-parameter ratio = 10.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.96

Alert level C
STRVA01_ALERT_4_C           Flack test results are meaningless.
           From the CIF: _refine_ls_abs_structure_Flack    0.000
           From the CIF: _refine_ls_abs_structure_Flack_su   10.000
PLAT032_ALERT_4_C Std. Uncertainty in Flack Parameter too High ...      10.00
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent .....          ?
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N1
PLAT320_ALERT_2_C Check Hybridisation of  C10    in Main Residue .          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          9
PLAT361_ALERT_2_C Long   C(sp3)-C(sp3) Bond  C5     -   C9     ...       1.65 Ang.
PLAT361_ALERT_2_C Long   C(sp3)-C(sp3) Bond  C13    -   C14    ...       1.65 Ang.
PLAT369_ALERT_2_C Long   C(sp2)-C(sp2) Bond  C1     -   C2     ...       1.54 Ang.
PLAT414_ALERT_2_C Short Intra D-H..H-X       H1A    ..  H3      ..       1.90 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       N1     -   H1A    ...          ?
PLAT850_ALERT_2_C Check Flack Parameter Exact Value 0.00 and su ..      10.00

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.49
           From the CIF: _reflns_number_total               1859
           Count of symmetry unique reflns         1942
           Completeness (_total/calc)             95.73%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C15    = .          R

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
  13 ALERT level C = Check and explain
   6 ALERT level G = General alerts; check

   7 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   8 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SMART; data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1997); software used to prepare material for publication: SHELXTL.

2,15-dihydroxy-7-methyl-6-azabicyclo[11.3.0]hexadec-3-en-5-one

Crystal data

C16H27NO3	F(000) = 620
Mr = 281.39	Dx = 1.034 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1688 reflections
a = 7.4001 (9) Å	θ = 3.8–26.5°
b = 12.9986 (13) Å	µ = 0.07 mm^−1
c = 18.860 (2) Å	T = 298 K
V = 1814.1 (4) Å^3	Prism, colourless
Z = 4	0.27 × 0.23 × 0.20 mm

Data collection

Bruker SMART CCD area-detector diffractometer	1859 independent reflections
Radiation source: fine-focus sealed tube	1583 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.038
φ and ω scans	θmax = 25.5°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −8→8
Tmin = 0.961, Tmax = 0.988	k = −8→14
9063 measured reflections	l = −22→22

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.074	H-atom parameters constrained
wR(F^2) = 0.239	w = 1/[σ^2(Fo^2) + (0.1522P)^2 + 1.1271P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
1859 reflections	Δρmax = 0.38 e Å^−3
185 parameters	Δρmin = −0.37 e Å^−3
2 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0 (10)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	−0.2937 (8)	0.5788 (5)	0.2053 (3)	0.0480 (14)
C2	−0.3015 (8)	0.5144 (5)	0.1367 (3)	0.0457 (13)
H2	−0.3544	0.4495	0.1361	0.055*
C3	−0.2289 (7)	0.5556 (4)	0.0777 (3)	0.0405 (12)
H3	−0.1943	0.6244	0.0769	0.049*
C4	−0.2032 (7)	0.4865 (5)	0.0103 (3)	0.0434 (13)
H4	−0.2520	0.5237	−0.0307	0.052*
C5	0.0022 (7)	0.4691 (4)	−0.0022 (2)	0.0395 (13)
H5	0.0494	0.4323	0.0392	0.047*
C6	0.0404 (8)	0.3974 (5)	−0.0716 (3)	0.0493 (15)
H6A	0.0306	0.3246	−0.0612	0.059*
H6B	−0.0374	0.4150	−0.1112	0.059*
C7	0.2395 (9)	0.4317 (5)	−0.0838 (3)	0.0637 (19)
H7	0.2732	0.4182	−0.1332	0.076*
C8	0.2529 (10)	0.5525 (5)	−0.0687 (3)	0.0650 (19)
H8A	0.2248	0.5909	−0.1114	0.078*
H8B	0.3744	0.5703	−0.0538	0.078*
C9	0.1110 (7)	0.5801 (4)	−0.0072 (3)	0.0437 (13)
H9	0.0282	0.6337	−0.0240	0.052*
C10	0.2096 (8)	0.6181 (5)	0.0608 (3)	0.0456 (14)
H10A	0.1871	0.5657	0.0964	0.055*
H10B	0.3375	0.6142	0.0500	0.055*
C11	0.1844 (8)	0.7169 (5)	0.0973 (3)	0.0473 (14)
H11A	0.0567	0.7215	0.1086	0.057*
H11B	0.2081	0.7699	0.0624	0.057*
C12	0.2863 (8)	0.7492 (6)	0.1647 (3)	0.0608 (17)
H12A	0.3111	0.8224	0.1628	0.073*
H12B	0.4011	0.7133	0.1667	0.073*
C13	0.1775 (9)	0.7252 (6)	0.2322 (3)	0.0620 (18)
H13A	0.2586	0.7228	0.2725	0.074*
H13B	0.1213	0.6581	0.2274	0.074*
C14	0.0199 (9)	0.8127 (6)	0.2464 (4)	0.0605 (18)
H14A	0.0537	0.8575	0.2854	0.073*
H14B	0.0005	0.8542	0.2044	0.073*
C15	−0.1557 (8)	0.7491 (7)	0.2654 (3)	0.0595 (18)
H15	−0.1314	0.7036	0.3057	0.071*
C16	−0.3078 (11)	0.8329 (8)	0.2869 (4)	0.084 (3)
H16A	−0.3258	0.8798	0.2482	0.126*
H16B	−0.2686	0.8703	0.3280	0.126*
H16C	−0.4194	0.7983	0.2973	0.126*
N1	−0.2081 (6)	0.6848 (3)	0.2001 (2)	0.0378 (10)
H1A	−0.1880	0.7100	0.1587	0.045*
O2	−0.3540 (8)	0.5386 (5)	0.2597 (2)	0.0773 (16)
O3	−0.2908 (6)	0.3723 (3)	0.0111 (2)	0.0546 (11)
H3A	−0.3897	0.3736	−0.0084	0.082*
O4	0.3517 (6)	0.3623 (4)	−0.0346 (3)	0.0678 (14)
H4A	0.3112	0.3036	−0.0356	0.102*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.033 (3)	0.057 (3)	0.053 (3)	0.003 (3)	0.004 (3)	0.005 (3)
C2	0.030 (3)	0.052 (3)	0.055 (3)	−0.005 (3)	0.004 (2)	0.002 (3)
C3	0.027 (2)	0.039 (3)	0.056 (3)	−0.002 (2)	0.000 (2)	0.004 (2)
C4	0.028 (2)	0.058 (3)	0.044 (3)	0.000 (3)	−0.005 (2)	0.004 (2)
C5	0.031 (3)	0.054 (3)	0.033 (2)	0.005 (2)	−0.004 (2)	0.001 (2)
C6	0.043 (3)	0.063 (4)	0.041 (3)	−0.004 (3)	−0.006 (2)	−0.006 (3)
C7	0.047 (4)	0.097 (5)	0.048 (3)	−0.006 (4)	0.011 (3)	−0.009 (3)
C8	0.057 (4)	0.089 (5)	0.049 (3)	−0.009 (4)	0.014 (3)	0.012 (3)
C9	0.034 (3)	0.058 (3)	0.040 (3)	0.001 (3)	−0.003 (2)	0.014 (3)
C10	0.028 (2)	0.061 (4)	0.047 (3)	−0.006 (3)	−0.002 (2)	0.008 (3)
C11	0.034 (3)	0.059 (4)	0.049 (3)	−0.005 (3)	−0.001 (2)	0.001 (3)
C12	0.029 (3)	0.089 (5)	0.064 (4)	−0.006 (4)	−0.004 (3)	−0.014 (3)
C13	0.043 (3)	0.089 (5)	0.054 (3)	−0.004 (3)	−0.011 (3)	0.003 (3)
C14	0.047 (4)	0.083 (5)	0.051 (3)	−0.011 (4)	−0.002 (3)	−0.011 (3)
C15	0.048 (3)	0.092 (5)	0.039 (3)	−0.004 (4)	0.003 (2)	−0.010 (3)
C16	0.055 (4)	0.123 (7)	0.074 (5)	0.001 (5)	0.014 (4)	−0.031 (5)
N1	0.033 (2)	0.053 (3)	0.0272 (17)	−0.008 (2)	0.0028 (18)	0.0022 (18)
O2	0.078 (4)	0.097 (4)	0.057 (2)	−0.021 (3)	0.025 (2)	0.004 (3)
O3	0.0314 (19)	0.058 (2)	0.074 (3)	−0.005 (2)	−0.011 (2)	−0.006 (2)
O4	0.032 (2)	0.075 (3)	0.096 (3)	−0.006 (2)	−0.004 (2)	−0.008 (3)

Geometric parameters (Å, º)

C1—O2	1.234 (7)	C10—C11	1.469 (8)
C1—N1	1.519 (8)	C10—H10A	0.9700
C1—C2	1.543 (8)	C10—H10B	0.9700
C2—C3	1.347 (7)	C11—C12	1.537 (8)
C2—H2	0.9300	C11—H11A	0.9700
C3—C4	1.567 (8)	C11—H11B	0.9700
C3—H3	0.9300	C12—C13	1.537 (9)
C4—C5	1.555 (7)	C12—H12A	0.9700
C4—O3	1.620 (7)	C12—H12B	0.9700
C4—H4	0.9800	C13—C14	1.651 (11)
C5—C6	1.632 (7)	C13—H13A	0.9700
C5—C9	1.655 (7)	C13—H13B	0.9700
C5—H5	0.9800	C14—C15	1.581 (10)
C6—C7	1.556 (9)	C14—H14A	0.9700
C6—H6A	0.9700	C14—H14B	0.9700
C6—H6B	0.9700	C15—N1	1.538 (7)
C7—O4	1.538 (9)	C15—C16	1.618 (11)
C7—C8	1.599 (8)	C15—H15	0.9800
C7—H7	0.9800	C16—H16A	0.9600
C8—C9	1.605 (8)	C16—H16B	0.9600
C8—H8A	0.9700	C16—H16C	0.9600
C8—H8B	0.9700	N1—H1A	0.8600
C9—C10	1.557 (7)	O3—H3A	0.8200
C9—H9	0.9800	O4—H4A	0.8200
O2—C1—N1	126.1 (5)	C11—C10—H10A	105.5
O2—C1—C2	116.9 (5)	C9—C10—H10A	105.5
N1—C1—C2	117.0 (4)	C11—C10—H10B	105.5
C3—C2—C1	117.5 (5)	C9—C10—H10B	105.5
C3—C2—H2	121.2	H10A—C10—H10B	106.1
C1—C2—H2	121.2	C10—C11—C12	124.3 (5)
C2—C3—C4	119.4 (5)	C10—C11—H11A	106.2
C2—C3—H3	120.3	C12—C11—H11A	106.2
C4—C3—H3	120.3	C10—C11—H11B	106.2
C5—C4—C3	108.9 (4)	C12—C11—H11B	106.2
C5—C4—O3	105.0 (4)	H11A—C11—H11B	106.4
C3—C4—O3	117.9 (4)	C11—C12—C13	111.8 (5)
C5—C4—H4	108.2	C11—C12—H12A	109.3
C3—C4—H4	108.2	C13—C12—H12A	109.3
O3—C4—H4	108.2	C11—C12—H12B	109.3
C4—C5—C6	112.0 (4)	C13—C12—H12B	109.3
C4—C5—C9	110.9 (4)	H12A—C12—H12B	107.9
C6—C5—C9	111.6 (4)	C12—C13—C14	111.4 (6)
C4—C5—H5	107.4	C12—C13—H13A	109.3
C6—C5—H5	107.4	C14—C13—H13A	109.3
C9—C5—H5	107.4	C12—C13—H13B	109.3
C7—C6—C5	96.8 (4)	C14—C13—H13B	109.3
C7—C6—H6A	112.4	H13A—C13—H13B	108.0
C5—C6—H6A	112.4	C15—C14—C13	104.9 (6)
C7—C6—H6B	112.4	C15—C14—H14A	110.8
C5—C6—H6B	112.4	C13—C14—H14A	110.8
H6A—C6—H6B	110.0	C15—C14—H14B	110.8
O4—C7—C6	104.7 (5)	C13—C14—H14B	110.8
O4—C7—C8	115.8 (5)	H14A—C14—H14B	108.8
C6—C7—C8	108.3 (5)	N1—C15—C14	108.1 (5)
O4—C7—H7	109.3	N1—C15—C16	113.0 (5)
C6—C7—H7	109.3	C14—C15—C16	106.1 (6)
C8—C7—H7	109.3	N1—C15—H15	109.9
C7—C8—C9	107.9 (5)	C14—C15—H15	109.9
C7—C8—H8A	110.1	C16—C15—H15	109.9
C9—C8—H8A	110.1	C15—C16—H16A	109.5
C7—C8—H8B	110.1	C15—C16—H16B	109.5
C9—C8—H8B	110.1	H16A—C16—H16B	109.5
H8A—C8—H8B	108.4	C15—C16—H16C	109.5
C10—C9—C8	111.1 (5)	H16A—C16—H16C	109.5
C10—C9—C5	117.2 (4)	H16B—C16—H16C	109.5
C8—C9—C5	99.5 (4)	C1—N1—C15	123.1 (4)
C10—C9—H9	109.5	C1—N1—H1A	118.5
C8—C9—H9	109.5	C15—N1—H1A	118.5
C5—C9—H9	109.5	C4—O3—H3A	109.5
C11—C10—C9	127.2 (5)	C7—O4—H4A	109.5
O2—C1—C2—C3	−177.1 (6)	C4—C5—C9—C10	98.6 (5)
N1—C1—C2—C3	1.4 (7)	C6—C5—C9—C10	−135.9 (5)
C1—C2—C3—C4	169.5 (5)	C4—C5—C9—C8	−141.7 (4)
C2—C3—C4—C5	−111.2 (6)	C6—C5—C9—C8	−16.1 (5)
C2—C3—C4—O3	8.3 (7)	C8—C9—C10—C11	122.5 (6)
C3—C4—C5—C6	179.9 (4)	C5—C9—C10—C11	−124.1 (6)
O3—C4—C5—C6	52.7 (5)	C9—C10—C11—C12	179.8 (5)
C3—C4—C5—C9	−54.8 (5)	C10—C11—C12—C13	−95.0 (7)
O3—C4—C5—C9	178.0 (4)	C11—C12—C13—C14	−79.4 (7)
C4—C5—C6—C7	159.3 (5)	C12—C13—C14—C15	134.5 (5)
C9—C5—C6—C7	34.4 (5)	C13—C14—C15—N1	−63.7 (6)
C5—C6—C7—O4	84.8 (5)	C13—C14—C15—C16	174.8 (5)
C5—C6—C7—C8	−39.2 (6)	O2—C1—N1—C15	10.9 (9)
O4—C7—C8—C9	−84.3 (6)	C2—C1—N1—C15	−167.4 (5)
C6—C7—C8—C9	32.9 (7)	C14—C15—N1—C1	146.2 (5)
C7—C8—C9—C10	115.1 (5)	C16—C15—N1—C1	−96.7 (7)
C7—C8—C9—C5	−9.0 (6)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3A···O4^i	0.82	1.98	2.785 (6)	167
O4—H4A···O3^ii	0.82	2.45	3.257 (7)	167

Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+1/2, −z.