# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 14:05:28 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxodecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12C[C@@]34CCC(=O)[C@@](C)(CCC(=O)Nc5c(O)ccc(C(O)=O)c5O)[C@@H]3[C@H](C[C@@H]1C4)O2
#
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
 P9A  P9A  '3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxodecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid'  ligand  61  32  .  2021-08-19  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P9A
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
 P9A  O16   O  O2    0  -0.502  -25.2515  30.2437   5.3821
 P9A  O19   O  O     0  -0.396  -23.4871  33.5553   0.8580
 P9A  O20   O  O     0  -0.452  -23.8637  36.6426   3.9344
 P9A  O30   O  OH1   0  -0.599  -26.1495  37.1352   6.4571
 P9A  O32   O  O     0  -0.443  -20.0821  37.7434   8.3958
 P9A  O33   O  OH1   0  -0.605  -21.1114  39.4902   9.3092
 P9A  N28   N  NH1   0  -0.741  -24.0504  35.5015   5.8767
 P9A  C1    C  C     0   0.524  -24.1080  35.6035   4.5131
 P9A  C2    C  CH2   0  -0.590  -24.4160  34.3058   3.8058
 P9A  C3    C  CH2   0  -0.415  -23.1206  33.5122   3.6020
 P9A  C4    C  CT    0  -0.213  -23.2198  32.1900   2.8162
 P9A  C5    C  C     0   0.448  -23.5451  32.4484   1.3459
 P9A  C6    C  CH2   0  -0.556  -23.9052  31.2384   0.5237
 P9A  C7    C  CH2   0  -0.441  -25.1021  30.5228   1.1454
 P9A  C8    C  CT    0  -0.108  -24.8225  30.0795   2.5686
 P9A  C9    C  CH1   0  -0.213  -24.3157  31.2725   3.4290
 P9A  C10   C  CH1   0  -0.018  -24.0428  30.7835   4.8703
 P9A  C11   C  CH2   0  -0.423  -23.1412  29.5552   4.9465
 P9A  C12   C  CH1   0  -0.304  -24.0390  28.5599   4.2174
 P9A  C13   C  CH2   0  -0.415  -23.9249  28.8421   2.7149
 P9A  C14   C  CH2   0  -0.392  -26.0687  29.5282   3.2758
 P9A  C15   C  CT    0   0.253  -25.4775  29.0617   4.6050
 P9A  C17   C  CH3   0  -0.694  -26.3201  28.0977   5.4038
 P9A  C18   C  CH3   0  -0.678  -21.7870  31.6180   2.8026
 P9A  C22   C  CR6   0  -0.234  -22.4194  38.0583   8.0129
 P9A  C23   C  CR6   0   0.370  -22.6182  36.9262   7.2016
 P9A  C24   C  CR6   0   0.105  -23.8888  36.6422   6.6929
 P9A  C25   C  CR6   0   0.358  -24.9698  37.4716   6.9780
 P9A  C26   C  CR16  0  -0.406  -24.7834  38.5966   7.7829
 P9A  C27   C  CR16  0  -0.249  -23.5288  38.8690   8.2795
 P9A  HO30  H  HOH1  0   0.486  -26.8287  37.7700   6.7146
 P9A  HO31  H  HOH1  0   0.470  -21.9491  35.3738   6.3851
 P9A  HO33  H  HOH1  0   0.483  -20.2213  39.6588   9.6506
 P9A  HN28  H  HNH1  0   0.412  -24.4319  34.6684   6.3025
 P9A  H2    H  HCH2  0   0.257  -25.1382  33.7332   4.3911
 P9A  H2A   H  HCH2  0   0.275  -24.8796  34.5443   2.8498
 P9A  H3    H  HCH2  0   0.257  -22.3903  34.1527   3.1028
 P9A  H3A   H  HCH2  0   0.243  -22.6908  33.2839   4.5808
 P9A  H6    H  HCH2  0   0.265  -24.1160  31.5495  -0.4998
 P9A  H6A   H  HCH2  0   0.263  -23.0491  30.5574   0.4884
 P9A  H7    H  HCH2  0   0.236  -25.9659  31.1966   1.1386
 P9A  H7A   H  HCH2  0   0.245  -25.3806  29.6612   0.5324
 P9A  H9    H  HCH1  0   0.258  -25.1947  31.9238   3.5131
 P9A  H10   H  HCH1  0   0.237  -23.7313  31.6033   5.5231
 P9A  H11   H  HCH2  0   0.241  -22.1631  29.6529   4.4814
 P9A  H11A  H  HCH2  0   0.247  -22.9850  29.2890   5.9944
 P9A  H12   H  HCH1  0   0.241  -23.8553  27.5196   4.4867
 P9A  H13   H  HCH2  0   0.239  -24.3456  28.0263   2.1191
 P9A  H13A  H  HCH2  0   0.240  -22.8897  28.9624   2.3919
 P9A  H14   H  HCH2  0   0.239  -26.8635  30.2655   3.4134
 P9A  H14A  H  HCH2  0   0.230  -26.4780  28.6924   2.6994
 P9A  H17   H  HCH3  0   0.232  -25.8167  27.8094   6.3281
 P9A  H17A  H  HCH3  0   0.232  -27.2865  28.5348   5.6619
 P9A  H17B  H  HCH3  0   0.229  -26.5084  27.1910   4.8286
 P9A  H18   H  HCH3  0   0.253  -21.1213  32.3054   2.2768
 P9A  H18A  H  HCH3  0   0.250  -21.4036  31.5196   3.8172
 P9A  H18B  H  HCH3  0   0.248  -21.7039  30.6508   2.3139
 P9A  H26   H  HCR6  0   0.282  -25.6154  39.2492   8.0167
 P9A  H27   H  HCR6  0   0.278  -23.4114  39.7451   8.9008
 P9A  O31   O  OH1   0  -0.584  -21.6067  36.1128   6.9106
 P9A  C21   C  C     0   0.543  -21.0941  38.3820   8.5679

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
 P9A  C15  O16   single    1.433  0.020  1.433
 P9A  C10  O16   single    1.419  0.020  1.419
 P9A  O19  C5    double    1.211  0.020  1.211
 P9A  O20  C1    double    1.214  0.020  1.214
 P9A  O30  C25   single    1.333  0.020  1.333
 P9A  O30  HO30  single    0.850  0.020  0.980
 P9A  O31  C23   single    1.330  0.020  1.330
 P9A  O31  HO31  single    0.850  0.020  0.980
 P9A  O32  C21   double    1.209  0.020  1.209
 P9A  C21  O33   single    1.333  0.020  1.333
 P9A  O33  HO33  single    0.850  0.020  0.980
 P9A  C1   N28   single    1.369  0.020  1.369
 P9A  N28  C24   single    1.412  0.020  1.412
 P9A  N28  HN28  single    0.890  0.020  1.040
 P9A  C2   C1    single    1.510  0.020  1.510
 P9A  C2   C3    single    1.533  0.020  1.533
 P9A  C2   H2    single    0.970  0.020  1.090
 P9A  C2   H2A   single    0.970  0.020  1.090
 P9A  C4   C3    single    1.541  0.020  1.541
 P9A  C3   H3    single    0.970  0.020  1.090
 P9A  C3   H3A   single    0.970  0.020  1.090
 P9A  C5   C4    single    1.528  0.020  1.528
 P9A  C4   C18   single    1.543  0.020  1.543
 P9A  C4   C9    single    1.555  0.020  1.555
 P9A  C6   C5    single    1.507  0.020  1.507
 P9A  C6   C7    single    1.527  0.020  1.527
 P9A  C6   H6    single    0.970  0.020  1.090
 P9A  C6   H6A   single    0.970  0.020  1.090
 P9A  C7   C8    single    1.517  0.020  1.517
 P9A  C7   H7    single    0.970  0.020  1.090
 P9A  C7   H7A   single    0.970  0.020  1.090
 P9A  C8   C13   single    1.536  0.020  1.536
 P9A  C8   C14   single    1.535  0.020  1.535
 P9A  C8   C9    single    1.556  0.020  1.556
 P9A  C9   C10   single    1.546  0.020  1.546
 P9A  C9   H9    single    0.970  0.020  1.090
 P9A  C10  C11   single    1.526  0.020  1.526
 P9A  C10  H10   single    0.970  0.020  1.090
 P9A  C12  C11   single    1.526  0.020  1.526
 P9A  C11  H11   single    0.970  0.020  1.090
 P9A  C11  H11A  single    0.970  0.020  1.090
 P9A  C13  C12   single    1.533  0.020  1.533
 P9A  C12  C15   single    1.572  0.020  1.572
 P9A  C12  H12   single    0.970  0.020  1.090
 P9A  C13  H13   single    0.970  0.020  1.090
 P9A  C13  H13A  single    0.970  0.020  1.090
 P9A  C14  C15   single    1.528  0.020  1.528
 P9A  C14  H14   single    0.970  0.020  1.090
 P9A  C14  H14A  single    0.970  0.020  1.090
 P9A  C15  C17   single    1.509  0.020  1.509
 P9A  C17  H17   single    0.970  0.020  1.090
 P9A  C17  H17A  single    0.970  0.020  1.090
 P9A  C17  H17B  single    0.970  0.020  1.090
 P9A  C18  H18   single    0.970  0.020  1.090
 P9A  C18  H18A  single    0.970  0.020  1.090
 P9A  C18  H18B  single    0.970  0.020  1.090
 P9A  C22  C21   single    1.473  0.020  1.473
 P9A  C23  C22   aromatic  1.407  0.020  1.407
 P9A  C22  C27   aromatic  1.400  0.020  1.400
 P9A  C24  C23   aromatic  1.398  0.020  1.398
 P9A  C24  C25   aromatic  1.392  0.020  1.392
 P9A  C25  C26   aromatic  1.396  0.020  1.396
 P9A  C26  C27   aromatic  1.377  0.020  1.377
 P9A  C26  H26   single    0.930  0.020  1.080
 P9A  C27  H27   single    0.930  0.020  1.080

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
 P9A  C15   O16  C10   104.62  3.000
 P9A  HO30  O30  C25   110.66  3.000
 P9A  HO33  O33  C21   109.20  3.000
 P9A  HN28  N28  C24   117.76  3.000
 P9A  HN28  N28  C1    117.74  3.000
 P9A  C24   N28  C1    121.37  3.000
 P9A  C2    C1   N28   114.29  3.000
 P9A  C2    C1   O20   123.59  3.000
 P9A  N28   C1   O20   122.02  3.000
 P9A  H2A   C2   H2    107.69  3.000
 P9A  H2A   C2   C3    110.89  3.000
 P9A  H2    C2   C3    111.02  3.000
 P9A  H2A   C2   C1    108.06  3.000
 P9A  H2    C2   C1    109.55  3.000
 P9A  C3    C2   C1    109.57  3.000
 P9A  H3A   C3   H3    105.60  3.000
 P9A  H3A   C3   C4    107.61  3.000
 P9A  H3    C3   C4    108.25  3.000
 P9A  H3A   C3   C2    108.75  3.000
 P9A  H3    C3   C2    108.80  3.000
 P9A  C4    C3   C2    117.23  3.000
 P9A  C18   C4   C9    116.05  3.000
 P9A  C9    C4   C5    109.20  3.000
 P9A  C18   C4   C5    104.59  3.000
 P9A  C9    C4   C3    110.52  3.000
 P9A  C18   C4   C3    105.24  3.000
 P9A  C5    C4   C3    111.05  3.000
 P9A  C6    C5   C4    116.12  3.000
 P9A  C6    C5   O19   121.72  3.000
 P9A  C4    C5   O19   122.14  3.000
 P9A  H6A   C6   H6    107.37  3.000
 P9A  H6A   C6   C7    109.55  3.000
 P9A  H6    C6   C7    111.37  3.000
 P9A  H6A   C6   C5    109.30  3.000
 P9A  H6    C6   C5    109.22  3.000
 P9A  C7    C6   C5    109.98  3.000
 P9A  H7A   C7   H7    106.28  3.000
 P9A  H7A   C7   C8    110.04  3.000
 P9A  H7    C7   C8    109.32  3.000
 P9A  H7A   C7   C6    109.92  3.000
 P9A  H7    C7   C6    109.11  3.000
 P9A  C8    C7   C6    111.99  3.000
 P9A  C14   C8   C13    98.12  3.000
 P9A  C14   C8   C9    106.56  3.000
 P9A  C13   C8   C9    112.01  3.000
 P9A  C9    C8   C7    110.79  3.000
 P9A  C14   C8   C7    112.80  3.000
 P9A  C13   C8   C7    115.64  3.000
 P9A  H9    C9   C10   104.94  3.000
 P9A  H9    C9   C8    103.68  3.000
 P9A  C10   C9   C8    109.30  3.000
 P9A  H9    C9   C4    104.15  3.000
 P9A  C10   C9   C4    115.44  3.000
 P9A  C8    C9   C4    117.65  3.000
 P9A  H10   C10  C11   113.93  3.000
 P9A  H10   C10  C9    111.69  3.000
 P9A  C11   C10  C9    113.92  3.000
 P9A  H10   C10  O16   108.21  3.000
 P9A  C11   C10  O16   100.32  3.000
 P9A  C9    C10  O16   107.82  3.000
 P9A  H11A  C11  H11   107.68  3.000
 P9A  H11A  C11  C12   112.56  3.000
 P9A  H11   C11  C12   112.55  3.000
 P9A  H11A  C11  C10   109.18  3.000
 P9A  H11   C11  C10   115.96  3.000
 P9A  C12   C11  C10    98.83  3.000
 P9A  H12   C12  C15   113.45  3.000
 P9A  H12   C12  C13   113.91  3.000
 P9A  C15   C12  C13   104.54  3.000
 P9A  H12   C12  C11   113.90  3.000
 P9A  C15   C12  C11   102.26  3.000
 P9A  C13   C12  C11   107.73  3.000
 P9A  H13A  C13  H13   106.60  3.000
 P9A  H13A  C13  C12   112.40  3.000
 P9A  H13   C13  C12   111.58  3.000
 P9A  H13A  C13  C8    115.95  3.000
 P9A  H13   C13  C8    108.91  3.000
 P9A  C12   C13  C8    101.43  3.000
 P9A  H14A  C14  H14   108.03  3.000
 P9A  H14A  C14  C15   111.70  3.000
 P9A  H14   C14  C15   112.21  3.000
 P9A  H14A  C14  C8    109.58  3.000
 P9A  H14   C14  C8    113.95  3.000
 P9A  C15   C14  C8    101.32  3.000
 P9A  C17   C15  C14   116.07  3.000
 P9A  C17   C15  C12   115.95  3.000
 P9A  C14   C15  C12   103.71  3.000
 P9A  C17   C15  O16   109.15  3.000
 P9A  C14   C15  O16   106.33  3.000
 P9A  C12   C15  O16   104.64  3.000
 P9A  H17B  C17  H17A  107.75  3.000
 P9A  H17B  C17  H17   107.87  3.000
 P9A  H17A  C17  H17   108.29  3.000
 P9A  H17B  C17  C15   110.39  3.000
 P9A  H17A  C17  C15   111.32  3.000
 P9A  H17   C17  C15   111.07  3.000
 P9A  H18B  C18  H18A  108.15  3.000
 P9A  H18B  C18  H18   107.29  3.000
 P9A  H18A  C18  H18   106.91  3.000
 P9A  H18B  C18  C4    113.89  3.000
 P9A  H18A  C18  C4    110.62  3.000
 P9A  H18   C18  C4    109.70  3.000
 P9A  C27   C22  C23   117.64  3.000
 P9A  C27   C22  C21   120.94  3.000
 P9A  C23   C22  C21   121.42  3.000
 P9A  C24   C23  C22   120.12  3.000
 P9A  C24   C23  O31   119.16  3.000
 P9A  C22   C23  O31   120.72  3.000
 P9A  C25   C24  C23   120.68  3.000
 P9A  C25   C24  N28   120.72  3.000
 P9A  C23   C24  N28   118.59  3.000
 P9A  C26   C25  C24   119.65  3.000
 P9A  C26   C25  O30   123.17  3.000
 P9A  C24   C25  O30   117.19  3.000
 P9A  H26   C26  C27   120.20  3.000
 P9A  H26   C26  C25   120.50  3.000
 P9A  C27   C26  C25   119.29  3.000
 P9A  H27   C27  C26   117.84  3.000
 P9A  H27   C27  C22   119.54  3.000
 P9A  C26   C27  C22   122.62  3.000
 P9A  HO31  O31  C23   108.44  3.000
 P9A  C22   C21  O33   112.37  3.000
 P9A  C22   C21  O32   125.70  3.000
 P9A  O33   C21  O32   121.94  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
 P9A  CONST_01  C25   C24  C23  C22     0.00   0.0  0
 P9A  CONST_02  C25   C26  C27  C22     0.00   0.0  0
 P9A  CONST_03  C26   C27  C22  C23     0.00   0.0  0
 P9A  CONST_04  C26   C25  C24  C23     0.00   0.0  0
 P9A  CONST_05  C27   C22  C23  C24     0.00   0.0  0
 P9A  CONST_06  C27   C26  C25  C24     0.00   0.0  0
 P9A  CONST_07  C23   C24  C25  O30   180.00   0.0  0
 P9A  CONST_08  C27   C26  C25  O30   180.00   0.0  0
 P9A  CONST_09  C27   C22  C23  O31   180.00   0.0  0
 P9A  CONST_10  C25   C24  C23  O31   180.00   0.0  0
 P9A  CONST_11  C22   C23  C24  N28   180.00   0.0  0
 P9A  CONST_12  C26   C25  C24  N28   180.00   0.0  0
 P9A  CONST_13  C24   C23  C22  C21   180.00   0.0  0
 P9A  CONST_14  C26   C27  C22  C21   180.00   0.0  0
 P9A  CONST_15  H26   C26  C27  C22   180.00   0.0  0
 P9A  CONST_16  H27   C27  C22  C23   180.00   0.0  0
 P9A  CONST_20  C24   N28  C1   O20     0.00   0.0  0
 P9A  CONST_21  C24   N28  C1   C2    180.00   0.0  0
 P9A  CONST_22  HO33  O33  C21  C22   180.00   0.0  0
 P9A  Var_01    C7    C6   C5   C4     57.41  30.0  1
 P9A  Var_02    C8    C7   C6   C5    -58.96  30.0  1
 P9A  Var_03    C23   C22  C21  O32     0.03  30.0  2
 P9A  Var_04    C4    C3   C2   C1   -176.38  30.0  3
 P9A  Var_05    C3    C2   C1   O20    91.78  30.0  2

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
 P9A  chir_01  C4   C5   C18  C9   positiv
 P9A  chir_02  C8   C7   C14  C9   positiv
 P9A  chir_03  C9   C4   C8   C10  negativ
 P9A  chir_04  C10  O16  C11  C9   negativ
 P9A  chir_05  C12  C15  C13  C11  negativ
 P9A  chir_06  C15  C12  O16  C17  positiv

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
 P9A  plan-1  O30   0.020
 P9A  plan-1  N28   0.020
 P9A  plan-1  C22   0.020
 P9A  plan-1  C23   0.020
 P9A  plan-1  C24   0.020
 P9A  plan-1  C25   0.020
 P9A  plan-1  C26   0.020
 P9A  plan-1  C27   0.020
 P9A  plan-1  H26   0.020
 P9A  plan-1  H27   0.020
 P9A  plan-1  O31   0.020
 P9A  plan-1  C21   0.020
 P9A  plan-2  O20   0.020
 P9A  plan-2  N28   0.020
 P9A  plan-2  C1    0.020
 P9A  plan-2  C2    0.020
 P9A  plan-2  C24   0.020
 P9A  plan-2  HN28  0.020
 P9A  plan-3  O19   0.020
 P9A  plan-3  C4    0.020
 P9A  plan-3  C5    0.020
 P9A  plan-3  C6    0.020
 P9A  plan-4  O32   0.020
 P9A  plan-4  O33   0.020
 P9A  plan-4  C22   0.020
 P9A  plan-4  HO33  0.020
 P9A  plan-4  C21   0.020

