# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:05:23 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: (1R,2E,6S,10E,11aS,13S,14aR)-1,13-dihydroxy-6-methyl-1,6,7,8,9,11a,12,13,14,14a-decahydro-4H-cyclopenta[f]oxacyclotridecin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC/C=C/[C@@H]2C[C@H](O)C[C@H]2[C@H](O)/C=C/C(=O)O1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 AFB  AFB  (1R,2E,6S,10E,11aS,13S,14aR)-1,13-dihydroxy-6-methyl-1,6,7,8,9,11a,12,13,14,14a-decahydro-4H-cyclopenta[f]oxacyclotridecin-4-one  ligand  44  20  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFB
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 AFB  OC7   O  OH1   0  -0.673   1.7388  -0.5275  -4.9341
 AFB  C7    C  CH1   0   0.038   1.1926  -1.8137  -4.7081
 AFB  C8    C  CH2   0  -0.474   2.0286  -2.6305  -3.7311
 AFB  C6    C  CH2   0  -0.487  -0.1080  -1.6347  -3.9445
 AFB  C5    C  CH1   0  -0.252   0.3457  -1.3070  -2.5156
 AFB  C9    C  CH1   0  -0.302   1.6720  -2.0964  -2.3206
 AFB  C10   C  C1    0  -0.176   2.7684  -1.2695  -1.7216
 AFB  C11   C  C1    0  -0.210   3.4651  -1.6016  -0.6374
 AFB  C12   C  CH2   0  -0.498   4.5763  -0.7882  -0.0507
 AFB  C13   C  CH2   0  -0.444   4.3326  -0.3033   1.3848
 AFB  C14   C  CH2   0  -0.440   4.3443  -1.4042   2.4631
 AFB  C15   C  CH1   0  -0.006   3.0461  -1.5693   3.2413
 AFB  C16   C  CH3   0  -0.667   3.1586  -2.5796   4.3654
 AFB  O16   O  O2    0  -0.468   2.0374  -2.0490   2.3287
 AFB  C1    C  C     0   0.578   1.0566  -1.2603   1.9103
 AFB  OC1   O  O     0  -0.459   0.8076  -0.1667   2.3612
 AFB  C2    C  C1    0  -0.374   0.3542  -1.8904   0.7769
 AFB  C3    C  C1    0  -0.162  -0.2516  -1.1378  -0.1348
 AFB  C4    C  CH1   0   0.014  -0.7177  -1.6439  -1.4589
 AFB  OC4   O  OH1   0  -0.679  -1.9537  -1.0185  -1.7304
 AFB  HO7   H  HOH1  0   0.448   2.6387  -0.6376  -5.2557
 AFB  HC7   H  HCH1  0   0.214   1.0427  -2.3433  -5.6578
 AFB  H81   H  HCH2  0   0.244   3.0995  -2.5844  -3.9452
 AFB  H82   H  HCH2  0   0.240   1.7388  -3.6807  -3.8129
 AFB  H61   H  HCH2  0   0.234  -0.6563  -2.5831  -3.9666
 AFB  H62   H  HCH2  0   0.250  -0.7546  -0.8730  -4.3850
 AFB  H5    H  HCH1  0   0.243   0.5527  -0.2334  -2.4506
 AFB  H9    H  HCH1  0   0.240   1.4964  -2.9492  -1.6579
 AFB  H101  H  H     0   0.226   3.0059  -0.3420  -2.2407
 AFB  H111  H  H     0   0.224   3.2202  -2.5330  -0.1327
 AFB  H121  H  HCH2  0   0.227   5.5034  -1.3731  -0.0609
 AFB  H122  H  HCH2  0   0.233   4.7575   0.0820  -0.6874
 AFB  H131  H  HCH2  0   0.239   5.1142   0.4225   1.6189
 AFB  H132  H  HCH2  0   0.231   3.3984   0.2636   1.4157
 AFB  H141  H  HCH2  0   0.232   4.6177  -2.3718   2.0291
 AFB  H142  H  HCH2  0   0.242   5.1226  -1.1862   3.1981
 AFB  H15   H  HCH1  0   0.245   2.7373  -0.6042   3.6481
 AFB  H161  H  HCH3  0   0.235   3.8955  -2.2410   5.0935
 AFB  H162  H  HCH3  0   0.242   2.2080  -2.6974   4.8861
 AFB  H163  H  HCH3  0   0.230   3.4751  -3.5563   3.9960
 AFB  H21   H  H     0   0.273   0.4712  -2.9593   0.6389
 AFB  H31   H  H     0   0.269  -0.3181  -0.0626   0.0103
 AFB  HC4   H  HCH1  0   0.222  -0.8291  -2.7381  -1.4219
 AFB  HO4   H  HOH1  0   0.458  -2.2865  -1.3507  -2.5702

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 AFB  OC7  C7    single  1.416  0.020  1.416
 AFB  OC7  HO7   single  0.850  0.020  0.980
 AFB  C7   C8    single  1.523  0.020  1.523
 AFB  C7   C6    single  1.519  0.020  1.519
 AFB  C7   HC7   single  0.970  0.020  1.090
 AFB  C8   C9    single  1.550  0.020  1.550
 AFB  C8   H81   single  0.970  0.020  1.090
 AFB  C8   H82   single  0.970  0.020  1.090
 AFB  C6   C5    single  1.535  0.020  1.535
 AFB  C6   H61   single  0.970  0.020  1.090
 AFB  C6   H62   single  0.970  0.020  1.090
 AFB  C5   C9    single  1.556  0.020  1.556
 AFB  C5   C4    single  1.537  0.020  1.537
 AFB  C5   H5    single  0.970  0.020  1.090
 AFB  C9   C10   single  1.498  0.020  1.498
 AFB  C9   H9    single  0.970  0.020  1.090
 AFB  C10  C11   double  1.331  0.020  1.331
 AFB  C10  H101  single  0.930  0.020  1.080
 AFB  C11  C12   single  1.497  0.020  1.497
 AFB  C11  H111  single  0.930  0.020  1.080
 AFB  C12  C13   single  1.535  0.020  1.535
 AFB  C12  H121  single  0.970  0.020  1.090
 AFB  C12  H122  single  0.970  0.020  1.090
 AFB  C13  C14   single  1.541  0.020  1.541
 AFB  C13  H131  single  0.970  0.020  1.090
 AFB  C13  H132  single  0.970  0.020  1.090
 AFB  C14  C15   single  1.522  0.020  1.522
 AFB  C14  H141  single  0.970  0.020  1.090
 AFB  C14  H142  single  0.970  0.020  1.090
 AFB  C15  C16   single  1.516  0.020  1.516
 AFB  C15  O16   single  1.442  0.020  1.442
 AFB  C15  H15   single  0.970  0.020  1.090
 AFB  C16  H161  single  0.970  0.020  1.090
 AFB  C16  H162  single  0.970  0.020  1.090
 AFB  C16  H163  single  0.970  0.020  1.090
 AFB  O16  C1    single  1.326  0.020  1.326
 AFB  C1   OC1   double  1.209  0.020  1.209
 AFB  C1   C2    single  1.475  0.020  1.475
 AFB  C2   C3    double  1.328  0.020  1.328
 AFB  C2   H21   single  0.930  0.020  1.080
 AFB  C3   C4    single  1.492  0.020  1.492
 AFB  C3   H31   single  0.930  0.020  1.080
 AFB  C4   OC4   single  1.412  0.020  1.412
 AFB  C4   HC4   single  0.970  0.020  1.090
 AFB  OC4  HO4   single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 AFB  HO7   OC7  C7    108.08  3.000
 AFB  HC7   C7   C6    112.02  3.000
 AFB  HC7   C7   C8    111.79  3.000
 AFB  C6    C7   C8    102.16  3.000
 AFB  HC7   C7   OC7   110.67  3.000
 AFB  C6    C7   OC7   107.67  3.000
 AFB  C8    C7   OC7   112.20  3.000
 AFB  H82   C8   H81   106.60  3.000
 AFB  H82   C8   C9    109.77  3.000
 AFB  H81   C8   C9    112.90  3.000
 AFB  H82   C8   C7    108.77  3.000
 AFB  H81   C8   C7    112.92  3.000
 AFB  C9    C8   C7    105.82  3.000
 AFB  H62   C6   H61   107.41  3.000
 AFB  H62   C6   C5    113.69  3.000
 AFB  H61   C6   C5    110.59  3.000
 AFB  H62   C6   C7    112.74  3.000
 AFB  H61   C6   C7    108.44  3.000
 AFB  C5    C6   C7    103.89  3.000
 AFB  H5    C5   C4    107.75  3.000
 AFB  H5    C5   C9    109.20  3.000
 AFB  C4    C5   C9    113.11  3.000
 AFB  H5    C5   C6    108.69  3.000
 AFB  C4    C5   C6    112.89  3.000
 AFB  C9    C5   C6    105.09  3.000
 AFB  H9    C9   C10   107.79  3.000
 AFB  H9    C9   C5    109.55  3.000
 AFB  C10   C9   C5    113.20  3.000
 AFB  H9    C9   C8    108.63  3.000
 AFB  C10   C9   C8    112.68  3.000
 AFB  C5    C9   C8    104.89  3.000
 AFB  H101  C10  C11   119.12  3.000
 AFB  H101  C10  C9    116.05  3.000
 AFB  C11   C10  C9    124.83  3.000
 AFB  H111  C11  C12   116.80  3.000
 AFB  H111  C11  C10   118.29  3.000
 AFB  C12   C11  C10   124.91  3.000
 AFB  H122  C12  H121  106.21  3.000
 AFB  H122  C12  C13   108.64  3.000
 AFB  H121  C12  C13   108.16  3.000
 AFB  H122  C12  C11   109.10  3.000
 AFB  H121  C12  C11   109.52  3.000
 AFB  C13   C12  C11   114.86  3.000
 AFB  H132  C13  H131  105.13  3.000
 AFB  H132  C13  C14   110.93  3.000
 AFB  H131  C13  C14   108.62  3.000
 AFB  H132  C13  C12   109.03  3.000
 AFB  H131  C13  C12   107.27  3.000
 AFB  C14   C13  C12   115.31  3.000
 AFB  H142  C14  H141  105.37  3.000
 AFB  H142  C14  C15   106.57  3.000
 AFB  H141  C14  C15   108.64  3.000
 AFB  H142  C14  C13   109.49  3.000
 AFB  H141  C14  C13   110.84  3.000
 AFB  C15   C14  C13   115.38  3.000
 AFB  H15   C15  O16   109.38  3.000
 AFB  H15   C15  C16   109.50  3.000
 AFB  O16   C15  C16   107.42  3.000
 AFB  H15   C15  C14   109.62  3.000
 AFB  O16   C15  C14   108.00  3.000
 AFB  C16   C15  C14   112.84  3.000
 AFB  H163  C16  H162  108.54  3.000
 AFB  H163  C16  H161  107.95  3.000
 AFB  H162  C16  H161  107.70  3.000
 AFB  H163  C16  C15   111.54  3.000
 AFB  H162  C16  C15   111.20  3.000
 AFB  H161  C16  C15   109.78  3.000
 AFB  C1    O16  C15   121.26  3.000
 AFB  C2    C1   OC1   125.11  3.000
 AFB  C2    C1   O16   109.91  3.000
 AFB  OC1   C1   O16   124.93  3.000
 AFB  H21   C2   C3    121.37  3.000
 AFB  H21   C2   C1    117.88  3.000
 AFB  C3    C2   C1    120.17  3.000
 AFB  H31   C3   C4    115.78  3.000
 AFB  H31   C3   C2    119.78  3.000
 AFB  C4    C3   C2    124.01  3.000
 AFB  HC4   C4   OC4   111.00  3.000
 AFB  HC4   C4   C3    109.82  3.000
 AFB  OC4   C4   C3    107.10  3.000
 AFB  HC4   C4   C5    108.13  3.000
 AFB  OC4   C4   C5    112.12  3.000
 AFB  C3    C4   C5    108.64  3.000
 AFB  HO4   OC4  C4    108.53  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 AFB  Var_01  C12   C11  C10  C9    178.91   0.0  0
 AFB  Var_02  C4    C3   C2   C1    165.73   0.0  0
 AFB  Var_03  C13   C12  C11  C10   118.89  30.0  1
 AFB  Var_04  C14   C13  C12  C11    69.44  30.0  1
 AFB  Var_05  C15   C14  C13  C12  -119.00  30.0  1
 AFB  Var_06  C2    C1   O16  C15   167.51  30.0  1
 AFB  Var_07  C3    C2   C1   O16  -152.27  30.0  1
 AFB  Var_08  H101  C10  C11  C12     0.11   0.0  0
 AFB  Var_09  H31   C3   C2   C1     -6.37   0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AFB  chir_01  C7   OC7  C8   C6   negativ
 AFB  chir_02  C5   C6   C9   C4   positiv
 AFB  chir_03  C9   C8   C5   C10  positiv
 AFB  chir_04  C15  O16  C14  C16  positiv
 AFB  chir_05  C4   C5   C3   OC4  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AFB  plan-1  C9    0.020
 AFB  plan-1  C10   0.020
 AFB  plan-1  C11   0.020
 AFB  plan-1  C12   0.020
 AFB  plan-1  H101  0.020
 AFB  plan-1  H111  0.020
 AFB  plan-2  O16   0.020
 AFB  plan-2  C1    0.020
 AFB  plan-2  OC1   0.020
 AFB  plan-2  C2    0.020
 AFB  plan-3  C1    0.020
 AFB  plan-3  C2    0.020
 AFB  plan-3  C3    0.020
 AFB  plan-3  C4    0.020
 AFB  plan-3  H21   0.020
 AFB  plan-3  H31   0.020

