# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 01:42:42 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (7R,8R,9R)-7,8,9,10-tetrahydrobenzo[pqr]tetraphene-7,8,9-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cc2c(cc3ccc4cccc5ccc2c3c45)[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
 BAP  BAP  (7R,8R,9R)-7,8,9,10-tetrahydrobenzo[pqr]tetraphene-7,8,9-triol  ligand  39  23  .  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_BAP
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
 BAP  C1    C  CR16  0  -0.343  -0.7759   0.0869  -4.8314
 BAP  C2    C  CR16  0  -0.252   0.5231  -0.0269  -5.3061
 BAP  C3    C  CR16  0  -0.342   1.5866  -0.1390  -4.4250
 BAP  C3A   C  CR66  0   0.082   1.3671  -0.1364  -3.0456
 BAP  C4    C  CR16  0  -0.318   2.4352  -0.2552  -2.1026
 BAP  C5    C  CR16  0  -0.360   2.2036  -0.2449  -0.7695
 BAP  C5A   C  CR66  0   0.093   0.8789  -0.1123  -0.2331
 BAP  C6    C  CR6   0   0.031   0.6269  -0.0924   1.1526
 BAP  C7    C  CR6   0   0.024  -0.6890   0.0035   1.6091
 BAP  C8    C  CR16  0  -0.402  -1.7388   0.0950   0.7017
 BAP  C8A   C  CR66  0   0.086  -1.5204   0.1008  -0.6702
 BAP  C9    C  CR16  0  -0.329  -2.5978   0.2075  -1.6103
 BAP  C10   C  CR16  0  -0.338  -2.3671   0.2065  -2.9416
 BAP  C1A   C  CR66  0   0.090  -1.0358   0.0932  -3.4610
 BAP  C3B   C  C     0   0.124   0.0464  -0.0170  -2.5521
 BAP  C5B   C  C     0   0.109  -0.1945  -0.0089  -1.1509
 BAP  C1'   C  CH1   0  -0.053  -1.0153   0.0425   3.0898
 BAP  O1'   O  OH1   0  -0.669  -2.1844  -0.7001   3.3796
 BAP  C2'   C  CH1   0   0.049   0.1199  -0.5259   3.9321
 BAP  O2'   O  OH1   0  -0.675  -0.1195  -0.3524   5.3047
 BAP  C3'   C  CH1   0  -0.005   1.4249   0.1456   3.5575
 BAP  O3'   O  OH1   0  -0.669   1.2692   1.5370   3.7275
 BAP  C4'   C  CH2   0  -0.568   1.7728  -0.2240   2.1229
 BAP  H1    H  HCR6  0   0.259  -1.6008   0.1704  -5.5282
 BAP  H2    H  HCR6  0   0.260   0.7051  -0.0297  -6.3728
 BAP  H3    H  HCR6  0   0.259   2.5979  -0.2304  -4.8027
 BAP  H4    H  HCR6  0   0.257   3.4476  -0.3567  -2.4744
 BAP  H5    H  HCR6  0   0.257   3.0442  -0.3444  -0.0973
 BAP  H8    H  HCR6  0   0.245  -2.7579   0.1681   1.0628
 BAP  H9    H  HCR6  0   0.255  -3.6091   0.2920  -1.2310
 BAP  H10   H  HCR6  0   0.257  -3.1899   0.2891  -3.6413
 BAP  H1'   H  HCH1  0   0.246  -1.1624   1.0910   3.3741
 BAP  HO1   H  HOH1  0   0.465  -2.9072  -0.0914   3.5501
 BAP  H2'   H  HCH1  0   0.217   0.2263  -1.5944   3.6837
 BAP  HO2   H  HOH1  0   0.446  -0.9730  -0.7511   5.5059
 BAP  H3'   H  HCH1  0   0.236   2.2228  -0.2384   4.2087
 BAP  HO3   H  HOH1  0   0.453   2.0776   1.9684   3.4342
 BAP  H4'1  H  HCH2  0   0.263   2.6215   0.3886   1.8057
 BAP  H4'2  H  HCH2  0   0.264   2.1411  -1.2554   2.1088

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
 BAP  C1   C2    aromatic  1.388  0.020  1.388
 BAP  C1   C1A   aromatic  1.395  0.020  1.395
 BAP  C1   H1    single    0.930  0.020  1.080
 BAP  C2   C3    aromatic  1.386  0.020  1.386
 BAP  C2   H2    single    0.930  0.020  1.080
 BAP  C3   C3A   aromatic  1.397  0.020  1.397
 BAP  C3   H3    single    0.930  0.020  1.080
 BAP  C3A  C4    aromatic  1.430  0.020  1.430
 BAP  C3A  C3B   aromatic  1.415  0.020  1.415
 BAP  C4   C5    aromatic  1.353  0.020  1.353
 BAP  C4   H4    single    0.930  0.020  1.080
 BAP  C5   C5A   aromatic  1.435  0.020  1.435
 BAP  C5   H5    single    0.930  0.020  1.080
 BAP  C5A  C6    aromatic  1.409  0.020  1.409
 BAP  C5A  C5B   aromatic  1.416  0.020  1.416
 BAP  C6   C7    aromatic  1.396  0.020  1.396
 BAP  C6   C4'   single    1.507  0.020  1.507
 BAP  C7   C8    aromatic  1.391  0.020  1.391
 BAP  C7   C1'   single    1.517  0.020  1.517
 BAP  C8   C8A   aromatic  1.389  0.020  1.389
 BAP  C8   H8    single    0.930  0.020  1.080
 BAP  C8A  C9    aromatic  1.434  0.020  1.434
 BAP  C8A  C5B   aromatic  1.415  0.020  1.415
 BAP  C9   C10   aromatic  1.351  0.020  1.351
 BAP  C9   H9    single    0.930  0.020  1.080
 BAP  C10  C1A   aromatic  1.434  0.020  1.434
 BAP  C10  H10   single    0.930  0.020  1.080
 BAP  C1A  C3B   aromatic  1.418  0.020  1.418
 BAP  C3B  C5B   aromatic  1.422  0.020  1.422
 BAP  C1'  O1'   single    1.415  0.020  1.415
 BAP  C1'  C2'   single    1.524  0.020  1.524
 BAP  C1'  H1'   single    0.970  0.020  1.090
 BAP  O1'  HO1   single    0.850  0.020  0.980
 BAP  C2'  O2'   single    1.404  0.020  1.404
 BAP  C2'  C3'   single    1.515  0.020  1.515
 BAP  C2'  H2'   single    0.970  0.020  1.090
 BAP  O2'  HO2   single    0.850  0.020  0.980
 BAP  C3'  O3'   single    1.410  0.020  1.410
 BAP  C3'  C4'   single    1.522  0.020  1.522
 BAP  C3'  H3'   single    0.970  0.020  1.090
 BAP  O3'  HO3   single    0.850  0.020  0.980
 BAP  C4'  H4'1  single    0.970  0.020  1.090
 BAP  C4'  H4'2  single    0.970  0.020  1.090

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
 BAP  H1    C1   C1A   119.33  3.000
 BAP  H1    C1   C2    119.95  3.000
 BAP  C1A   C1   C2    120.72  3.000
 BAP  H2    C2   C3    119.84  3.000
 BAP  H2    C2   C1    119.66  3.000
 BAP  C3    C2   C1    120.50  3.000
 BAP  H3    C3   C3A   119.42  3.000
 BAP  H3    C3   C2    120.11  3.000
 BAP  C3A   C3   C2    120.48  3.000
 BAP  C3B   C3A  C4    118.31  3.000
 BAP  C3B   C3A  C3    119.42  3.000
 BAP  C4    C3A  C3    122.26  3.000
 BAP  H4    C4   C5    119.92  3.000
 BAP  H4    C4   C3A   118.66  3.000
 BAP  C5    C4   C3A   121.42  3.000
 BAP  H5    C5   C5A   119.59  3.000
 BAP  H5    C5   C4    118.62  3.000
 BAP  C5A   C5   C4    121.79  3.000
 BAP  C5B   C5A  C6    120.06  3.000
 BAP  C5B   C5A  C5    117.66  3.000
 BAP  C6    C5A  C5    122.28  3.000
 BAP  C4'   C6   C7    120.81  3.000
 BAP  C4'   C6   C5A   119.74  3.000
 BAP  C7    C6   C5A   119.42  3.000
 BAP  C1'   C7   C8    118.22  3.000
 BAP  C1'   C7   C6    121.58  3.000
 BAP  C8    C7   C6    120.18  3.000
 BAP  H8    C8   C8A   118.47  3.000
 BAP  H8    C8   C7    119.79  3.000
 BAP  C8A   C8   C7    121.73  3.000
 BAP  C5B   C8A  C9    119.16  3.000
 BAP  C5B   C8A  C8    118.86  3.000
 BAP  C9    C8A  C8    121.98  3.000
 BAP  H9    C9   C10   120.29  3.000
 BAP  H9    C9   C8A   118.53  3.000
 BAP  C10   C9   C8A   121.18  3.000
 BAP  H10   C10  C1A   118.52  3.000
 BAP  H10   C10  C9    120.44  3.000
 BAP  C1A   C10  C9    121.04  3.000
 BAP  C3B   C1A  C10   118.87  3.000
 BAP  C3B   C1A  C1    119.17  3.000
 BAP  C10   C1A  C1    121.96  3.000
 BAP  C5B   C3B  C1A   120.14  3.000
 BAP  C5B   C3B  C3A   120.15  3.000
 BAP  C1A   C3B  C3A   119.70  3.000
 BAP  C3B   C5B  C8A   119.61  3.000
 BAP  C3B   C5B  C5A   120.66  3.000
 BAP  C8A   C5B  C5A   119.73  3.000
 BAP  H1'   C1'  C2'   108.27  3.000
 BAP  H1'   C1'  O1'   109.76  3.000
 BAP  C2'   C1'  O1'   107.86  3.000
 BAP  H1'   C1'  C7    107.85  3.000
 BAP  C2'   C1'  C7    111.70  3.000
 BAP  O1'   C1'  C7    111.36  3.000
 BAP  HO1   O1'  C1'   109.00  3.000
 BAP  H2'   C2'  C3'   106.91  3.000
 BAP  H2'   C2'  O2'   110.89  3.000
 BAP  C3'   C2'  O2'   109.51  3.000
 BAP  H2'   C2'  C1'   108.00  3.000
 BAP  C3'   C2'  C1'   109.87  3.000
 BAP  O2'   C2'  C1'   111.55  3.000
 BAP  HO2   O2'  C2'   107.71  3.000
 BAP  H3'   C3'  C4'   107.92  3.000
 BAP  H3'   C3'  O3'   110.70  3.000
 BAP  C4'   C3'  O3'   112.24  3.000
 BAP  H3'   C3'  C2'   108.91  3.000
 BAP  C4'   C3'  C2'   108.81  3.000
 BAP  O3'   C3'  C2'   108.21  3.000
 BAP  HO3   O3'  C3'   108.23  3.000
 BAP  H4'2  C4'  H4'1  105.24  3.000
 BAP  H4'2  C4'  C3'   108.53  3.000
 BAP  H4'1  C4'  C3'   108.35  3.000
 BAP  H4'2  C4'  C6    109.24  3.000
 BAP  H4'1  C4'  C6    110.75  3.000
 BAP  C3'   C4'  C6    114.32  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
 BAP  CONST_01  C3A  C3   C2   C1     0.00   0.0  0
 BAP  CONST_02  C9   C10  C1A  C1   180.00   0.0  0
 BAP  CONST_03  C3A  C3B  C1A  C1     0.00   0.0  0
 BAP  CONST_04  C5B  C3B  C1A  C1   180.00   0.0  0
 BAP  CONST_05  C10  C1A  C1   C2   180.00   0.0  0
 BAP  CONST_06  C3B  C1A  C1   C2     0.00   0.0  0
 BAP  CONST_07  C4   C3A  C3   C2   180.00   0.0  0
 BAP  CONST_08  C3B  C3A  C3   C2     0.00   0.0  0
 BAP  CONST_09  C1A  C1   C2   C3     0.00   0.0  0
 BAP  CONST_10  C5   C4   C3A  C3   180.00   0.0  0
 BAP  CONST_11  C1A  C3B  C3A  C3     0.00   0.0  0
 BAP  CONST_12  C5B  C3B  C3A  C3   180.00   0.0  0
 BAP  CONST_13  C5A  C5   C4   C3A    0.00   0.0  0
 BAP  CONST_14  C10  C1A  C3B  C3A  180.00   0.0  0
 BAP  CONST_15  C5A  C5B  C3B  C3A    0.00   0.0  0
 BAP  CONST_16  C8A  C5B  C3B  C3A  180.00   0.0  0
 BAP  CONST_17  C1A  C3B  C3A  C4   180.00   0.0  0
 BAP  CONST_18  C5B  C3B  C3A  C4     0.00   0.0  0
 BAP  CONST_19  C6   C5A  C5   C4   180.00   0.0  0
 BAP  CONST_20  C5B  C5A  C5   C4     0.00   0.0  0
 BAP  CONST_21  C3B  C3A  C4   C5     0.00   0.0  0
 BAP  CONST_22  C7   C6   C5A  C5   180.00   0.0  0
 BAP  CONST_23  C8A  C5B  C5A  C5   180.00   0.0  0
 BAP  CONST_24  C3B  C5B  C5A  C5     0.00   0.0  0
 BAP  CONST_25  C8   C7   C6   C5A    0.00   0.0  0
 BAP  CONST_26  C8   C8A  C5B  C5A    0.00   0.0  0
 BAP  CONST_27  C9   C8A  C5B  C5A  180.00   0.0  0
 BAP  CONST_28  C1A  C3B  C5B  C5A  180.00   0.0  0
 BAP  CONST_29  C8A  C5B  C5A  C6     0.00   0.0  0
 BAP  CONST_30  C3B  C5B  C5A  C6   180.00   0.0  0
 BAP  CONST_31  C8A  C8   C7   C6     0.00   0.0  0
 BAP  CONST_32  C5B  C5A  C6   C7     0.00   0.0  0
 BAP  CONST_33  C9   C8A  C8   C7   180.00   0.0  0
 BAP  CONST_34  C5B  C8A  C8   C7     0.00   0.0  0
 BAP  CONST_35  C10  C9   C8A  C8   180.00   0.0  0
 BAP  CONST_36  C3B  C5B  C8A  C8   180.00   0.0  0
 BAP  CONST_37  C1A  C10  C9   C8A    0.00   0.0  0
 BAP  CONST_38  C1A  C3B  C5B  C8A    0.00   0.0  0
 BAP  CONST_39  C3B  C5B  C8A  C9     0.00   0.0  0
 BAP  CONST_40  C3B  C1A  C10  C9     0.00   0.0  0
 BAP  CONST_41  C5B  C8A  C9   C10    0.00   0.0  0
 BAP  CONST_42  C5B  C3B  C1A  C10    0.00   0.0  0
 BAP  CONST_43  H3   C3   C2   C1   180.00   0.0  0
 BAP  CONST_44  H10  C10  C1A  C1     0.00   0.0  0
 BAP  CONST_45  H1   C1   C2   C3   180.00   0.0  0
 BAP  CONST_46  H4   C4   C3A  C3     0.00   0.0  0
 BAP  CONST_47  H2   C2   C3   C3A  180.00   0.0  0
 BAP  CONST_48  H5   C5   C4   C3A  180.00   0.0  0
 BAP  CONST_49  H8   C8   C7   C6   180.00   0.0  0
 BAP  CONST_50  H9   C9   C8A  C8     0.00   0.0  0
 BAP  Var_01    C3'  C4'  C6   C5A  165.92  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
 BAP  chir_01  C1'  C7   O1'  C2'  negativ
 BAP  chir_02  C2'  O2'  C1'  C3'  negativ
 BAP  chir_03  C3'  O3'  C2'  C4'  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
 BAP  plan-1  C1   0.020
 BAP  plan-1  C2   0.020
 BAP  plan-1  C3   0.020
 BAP  plan-1  C3A  0.020
 BAP  plan-1  C4   0.020
 BAP  plan-1  C5   0.020
 BAP  plan-1  C5A  0.020
 BAP  plan-1  C6   0.020
 BAP  plan-1  C7   0.020
 BAP  plan-1  C8   0.020
 BAP  plan-1  C8A  0.020
 BAP  plan-1  C9   0.020
 BAP  plan-1  C10  0.020
 BAP  plan-1  C1A  0.020
 BAP  plan-1  C3B  0.020
 BAP  plan-1  C5B  0.020
 BAP  plan-1  C1'  0.020
 BAP  plan-1  C4'  0.020
 BAP  plan-1  H1   0.020
 BAP  plan-1  H2   0.020
 BAP  plan-1  H3   0.020
 BAP  plan-1  H4   0.020
 BAP  plan-1  H5   0.020
 BAP  plan-1  H8   0.020
 BAP  plan-1  H9   0.020
 BAP  plan-1  H10  0.020

