# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:15:50 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S,3S,4S)-1,2,3,4-tetrahydrobenzo[c]phenanthrene-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1Cc2c(ccc3ccc4ccccc4c23)[C@H](O)[C@H]1O
#
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
 BPJ  BPJ  (2S,3S,4S)-1,2,3,4-tetrahydrobenzo[c]phenanthrene-2,3,4-triol  ligand  37  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BPJ
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
 BPJ  C1    C  CH2   0  -0.631  -1.4267  -0.0104  -0.8551
 BPJ  C2    C  CH1   0  -0.001  -1.7067  -0.5175  -2.2626
 BPJ  O2    O  OH1   0  -0.667  -1.3208  -1.8598  -2.4484
 BPJ  C3    C  CH1   0   0.049  -0.9298   0.3437  -3.2313
 BPJ  O3    O  OH1   0  -0.674  -1.3179   0.0538  -4.5505
 BPJ  C4    C  CH1   0  -0.069   0.5578   0.1207  -3.0201
 BPJ  O4    O  OH1   0  -0.669   1.2402   1.1480  -3.7182
 BPJ  C5    C  CR16  0  -0.302   2.3348   0.0429  -1.2979
 BPJ  C6    C  CR16  0  -0.315   2.7955  -0.1013  -0.0220
 BPJ  C7    C  CR16  0  -0.312   2.4213  -0.3629   2.3660
 BPJ  C8    C  CR16  0  -0.326   1.6078  -0.4319   3.4376
 BPJ  C9    C  CR16  0  -0.302  -0.5825  -0.0914   4.4595
 BPJ  C10   C  CR16  0  -0.265  -1.8927   0.3120   4.4025
 BPJ  C11   C  CR16  0  -0.246  -2.4219   0.7104   3.1720
 BPJ  C12   C  CR16  0  -0.355  -1.6629   0.6419   2.0260
 BPJ  C13   C  CR6   0   0.055   0.0421   0.0760  -0.5098
 BPJ  C14   C  CR6   0   0.052   0.9565   0.0976  -1.5548
 BPJ  C15   C  CR66  0   0.059   1.8997  -0.1188   1.0584
 BPJ  C16   C  CR66  0   0.103   0.5099   0.0538   0.8423
 BPJ  C17   C  CR66  0   0.086  -0.3331   0.1675   2.0302
 BPJ  C18   C  CR66  0   0.081   0.2173  -0.1402   3.3031
 BPJ  H11A  H  HCH2  0   0.264  -1.9041   0.9702  -0.7718
 BPJ  H12A  H  HCH2  0   0.276  -1.9456  -0.6576  -0.1434
 BPJ  H2    H  HCH1  0   0.236  -2.7824  -0.3905  -2.4501
 BPJ  HO2   H  HOH1  0   0.453  -1.7659  -2.3969  -1.7857
 BPJ  H3    H  HCH1  0   0.218  -1.1570   1.3913  -2.9791
 BPJ  HO3   H  HOH1  0   0.448  -0.8316   0.6414  -5.1382
 BPJ  H4    H  HCH1  0   0.240   0.8181  -0.8549  -3.4482
 BPJ  HO4   H  HOH1  0   0.462   2.0453   0.7886  -4.0994
 BPJ  H5    H  HCR6  0   0.247   3.0411   0.0597  -2.1184
 BPJ  H6    H  HCR6  0   0.255   3.8554  -0.2127   0.1712
 BPJ  H7    H  HCR6  0   0.256   3.4877  -0.5215   2.4703
 BPJ  H8    H  HCR6  0   0.256   2.0006  -0.6601   4.4207
 BPJ  H9    H  HCR6  0   0.256  -0.1340  -0.3559   5.4094
 BPJ  H10   H  HCR6  0   0.259  -2.4964   0.3550   5.2994
 BPJ  H11   H  HCR6  0   0.259  -3.4333   1.0909   3.1141
 BPJ  H12   H  HCR6  0   0.267  -2.1119   1.0124   1.1222

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
 BPJ  C1   C2    single    1.522  0.020  1.522
 BPJ  C1   C13   single    1.511  0.020  1.511
 BPJ  C1   H11A  single    0.970  0.020  1.090
 BPJ  C1   H12A  single    0.970  0.020  1.090
 BPJ  C2   O2    single    1.409  0.020  1.409
 BPJ  C2   C3    single    1.511  0.020  1.511
 BPJ  C2   H2    single    0.970  0.020  1.090
 BPJ  O2   HO2   single    0.850  0.020  0.980
 BPJ  C3   O3    single    1.405  0.020  1.405
 BPJ  C3   C4    single    1.519  0.020  1.519
 BPJ  C3   H3    single    0.970  0.020  1.090
 BPJ  O3   HO3   single    0.850  0.020  0.980
 BPJ  C4   O4    single    1.417  0.020  1.417
 BPJ  C4   C14   single    1.519  0.020  1.519
 BPJ  C4   H4    single    0.970  0.020  1.090
 BPJ  O4   HO4   single    0.850  0.020  0.980
 BPJ  C5   C6    aromatic  1.364  0.020  1.364
 BPJ  C5   C14   aromatic  1.403  0.020  1.403
 BPJ  C5   H5    single    0.930  0.020  1.080
 BPJ  C6   C15   aromatic  1.404  0.020  1.404
 BPJ  C6   H6    single    0.930  0.020  1.080
 BPJ  C7   C8    aromatic  1.347  0.020  1.347
 BPJ  C7   C15   aromatic  1.429  0.020  1.429
 BPJ  C7   H7    single    0.930  0.020  1.080
 BPJ  C8   C18   aromatic  1.427  0.020  1.427
 BPJ  C8   H8    single    0.930  0.020  1.080
 BPJ  C9   C10   aromatic  1.372  0.020  1.372
 BPJ  C9   C18   aromatic  1.407  0.020  1.407
 BPJ  C9   H9    single    0.930  0.020  1.080
 BPJ  C10  C11   aromatic  1.397  0.020  1.397
 BPJ  C10  H10   single    0.930  0.020  1.080
 BPJ  C11  C12   aromatic  1.376  0.020  1.376
 BPJ  C11  H11   single    0.930  0.020  1.080
 BPJ  C12  C17   aromatic  1.412  0.020  1.412
 BPJ  C12  H12   single    0.930  0.020  1.080
 BPJ  C13  C14   aromatic  1.389  0.020  1.389
 BPJ  C13  C16   aromatic  1.431  0.020  1.431
 BPJ  C15  C16   aromatic  1.417  0.020  1.417
 BPJ  C16  C17   aromatic  1.461  0.020  1.461
 BPJ  C17  C18   aromatic  1.421  0.020  1.421

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
 BPJ  H12A  C1   H11A  105.91  3.000
 BPJ  H12A  C1   C13   110.27  3.000
 BPJ  H11A  C1   C13   110.83  3.000
 BPJ  H12A  C1   C2    108.52  3.000
 BPJ  H11A  C1   C2    106.78  3.000
 BPJ  C13   C1   C2    114.15  3.000
 BPJ  H2    C2   C3    109.14  3.000
 BPJ  H2    C2   O2    110.82  3.000
 BPJ  C3    C2   O2    108.52  3.000
 BPJ  H2    C2   C1    107.42  3.000
 BPJ  C3    C2   C1    107.96  3.000
 BPJ  O2    C2   C1    112.89  3.000
 BPJ  HO2   O2   C2    108.32  3.000
 BPJ  H3    C3   C4    108.05  3.000
 BPJ  H3    C3   O3    110.75  3.000
 BPJ  C4    C3   O3    111.76  3.000
 BPJ  H3    C3   C2    106.81  3.000
 BPJ  C4    C3   C2    109.31  3.000
 BPJ  O3    C3   C2    110.01  3.000
 BPJ  HO3   O3   C3    107.91  3.000
 BPJ  H4    C4   C14   107.51  3.000
 BPJ  H4    C4   O4    109.77  3.000
 BPJ  C14   C4   O4    111.09  3.000
 BPJ  H4    C4   C3    107.99  3.000
 BPJ  C14   C4   C3    113.17  3.000
 BPJ  O4    C4   C3    107.25  3.000
 BPJ  HO4   O4   C4    109.14  3.000
 BPJ  H5    C5   C14   120.10  3.000
 BPJ  H5    C5   C6    119.35  3.000
 BPJ  C14   C5   C6    120.47  3.000
 BPJ  H6    C6   C15   119.08  3.000
 BPJ  H6    C6   C5    120.55  3.000
 BPJ  C15   C6   C5    120.38  3.000
 BPJ  H7    C7   C15   118.20  3.000
 BPJ  H7    C7   C8    120.69  3.000
 BPJ  C15   C7   C8    121.09  3.000
 BPJ  H8    C8   C18   118.82  3.000
 BPJ  H8    C8   C7    120.92  3.000
 BPJ  C18   C8   C7    120.19  3.000
 BPJ  H9    C9   C18   118.49  3.000
 BPJ  H9    C9   C10   120.23  3.000
 BPJ  C18   C9   C10   121.26  3.000
 BPJ  H10   C10  C11   120.48  3.000
 BPJ  H10   C10  C9    120.67  3.000
 BPJ  C11   C10  C9    118.81  3.000
 BPJ  H11   C11  C12   119.23  3.000
 BPJ  H11   C11  C10   120.09  3.000
 BPJ  C12   C11  C10   120.68  3.000
 BPJ  H12   C12  C17   120.78  3.000
 BPJ  H12   C12  C11   116.91  3.000
 BPJ  C17   C12  C11   122.25  3.000
 BPJ  C16   C13  C14   119.74  3.000
 BPJ  C16   C13  C1    122.19  3.000
 BPJ  C14   C13  C1    117.96  3.000
 BPJ  C13   C14  C5    120.56  3.000
 BPJ  C13   C14  C4    123.60  3.000
 BPJ  C5    C14  C4    115.79  3.000
 BPJ  C16   C15  C7    121.22  3.000
 BPJ  C16   C15  C6    120.47  3.000
 BPJ  C7    C15  C6    118.27  3.000
 BPJ  C17   C16  C15   116.83  3.000
 BPJ  C17   C16  C13   125.34  3.000
 BPJ  C15   C16  C13   117.82  3.000
 BPJ  C18   C17  C16   119.22  3.000
 BPJ  C18   C17  C12   116.13  3.000
 BPJ  C16   C17  C12   124.55  3.000
 BPJ  C17   C18  C9    120.58  3.000
 BPJ  C17   C18  C8    120.41  3.000
 BPJ  C9    C18  C8    118.92  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
 BPJ  CONST_01  C7   C15  C6   C5   180.00   0.0  0
 BPJ  CONST_02  C16  C15  C6   C5     0.00   0.0  0
 BPJ  CONST_03  C16  C13  C14  C5     0.00   0.0  0
 BPJ  CONST_04  C13  C14  C5   C6     0.00   0.0  0
 BPJ  CONST_05  C8   C7   C15  C6   180.00   0.0  0
 BPJ  CONST_06  C13  C16  C15  C6     0.00   0.0  0
 BPJ  CONST_07  C17  C16  C15  C6   180.00   0.0  0
 BPJ  CONST_08  C9   C18  C8   C7   180.00   0.0  0
 BPJ  CONST_09  C17  C18  C8   C7     0.00   0.0  0
 BPJ  CONST_10  C13  C16  C15  C7   180.00   0.0  0
 BPJ  CONST_11  C17  C16  C15  C7     0.00   0.0  0
 BPJ  CONST_12  C16  C15  C7   C8     0.00   0.0  0
 BPJ  CONST_13  C10  C9   C18  C8   180.00   0.0  0
 BPJ  CONST_14  C12  C17  C18  C8   180.00   0.0  0
 BPJ  CONST_15  C16  C17  C18  C8     0.00   0.0  0
 BPJ  CONST_16  C12  C11  C10  C9     0.00   0.0  0
 BPJ  CONST_17  C12  C17  C18  C9     0.00   0.0  0
 BPJ  CONST_18  C16  C17  C18  C9   180.00   0.0  0
 BPJ  CONST_19  C17  C18  C9   C10    0.00   0.0  0
 BPJ  CONST_20  C17  C12  C11  C10    0.00   0.0  0
 BPJ  CONST_21  C18  C9   C10  C11    0.00   0.0  0
 BPJ  CONST_22  C16  C17  C12  C11  180.00   0.0  0
 BPJ  CONST_23  C18  C17  C12  C11    0.00   0.0  0
 BPJ  CONST_26  C18  C17  C16  C13  180.00   0.0  0
 BPJ  CONST_27  C15  C6   C5   C14    0.00   0.0  0
 BPJ  CONST_28  C15  C16  C13  C14    0.00   0.0  0
 BPJ  CONST_29  C17  C16  C13  C14  180.00   0.0  0
 BPJ  CONST_30  C18  C8   C7   C15    0.00   0.0  0
 BPJ  CONST_31  C18  C17  C16  C15    0.00   0.0  0
 BPJ  CONST_32  H5   C5   C14  C4     0.00   0.0  0
 BPJ  CONST_33  H7   C7   C15  C6     0.00   0.0  0
 BPJ  CONST_34  H6   C6   C15  C7     0.00   0.0  0
 BPJ  CONST_35  H9   C9   C18  C8     0.00   0.0  0
 BPJ  CONST_36  H11  C11  C10  C9   180.00   0.0  0
 BPJ  CONST_37  H8   C8   C18  C9     0.00   0.0  0
 BPJ  CONST_38  H12  C12  C11  C10  180.00   0.0  0
 BPJ  CONST_39  H10  C10  C11  C12  180.00   0.0  0
 BPJ  Var_01    C14  C13  C1   C2    19.15  30.0  1

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
 BPJ  chir_01  C2  C1  O2  C3   positiv
 BPJ  chir_02  C3  O3  C4  C2   positiv
 BPJ  chir_03  C4  O4  C3  C14  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
 BPJ  plan-1  C1   0.020
 BPJ  plan-1  C4   0.020
 BPJ  plan-1  C5   0.020
 BPJ  plan-1  C6   0.020
 BPJ  plan-1  C7   0.020
 BPJ  plan-1  C8   0.020
 BPJ  plan-1  C9   0.020
 BPJ  plan-1  C10  0.020
 BPJ  plan-1  C11  0.020
 BPJ  plan-1  C12  0.020
 BPJ  plan-1  C13  0.020
 BPJ  plan-1  C14  0.020
 BPJ  plan-1  C15  0.020
 BPJ  plan-1  C16  0.020
 BPJ  plan-1  C17  0.020
 BPJ  plan-1  C18  0.020
 BPJ  plan-1  H5   0.020
 BPJ  plan-1  H6   0.020
 BPJ  plan-1  H7   0.020
 BPJ  plan-1  H8   0.020
 BPJ  plan-1  H9   0.020
 BPJ  plan-1  H10  0.020
 BPJ  plan-1  H11  0.020
 BPJ  plan-1  H12  0.020

