# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:31:55 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
 BPC  BPC  (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_BPC
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
 BPC  C1    C  CR16  0  -0.343  -4.8467  -0.7706   0.0729
 BPC  C2    C  CR16  0  -0.252  -5.3206   0.5276  -0.0536
 BPC  C3    C  CR16  0  -0.342  -4.4389   1.5899  -0.1709
 BPC  C3A   C  CR66  0   0.082  -3.0595   1.3702  -0.1611
 BPC  C4    C  CR16  0  -0.318  -2.1160   2.4372  -0.2844
 BPC  C5    C  CR16  0  -0.360  -0.7829   2.2055  -0.2670
 BPC  C5A   C  CR66  0   0.093  -0.2474   0.8816  -0.1224
 BPC  C6    C  CR6   0   0.031   1.1383   0.6295  -0.0965
 BPC  C7    C  CR6   0   0.024   1.5940  -0.6860   0.0090
 BPC  C8    C  CR16  0  -0.402   0.6861  -1.7348   0.1065
 BPC  C8A   C  CR66  0   0.086  -0.6857  -1.5160   0.1074
 BPC  C9    C  CR16  0  -0.328  -1.6265  -2.5922   0.2197
 BPC  C10   C  CR16  0  -0.338  -2.9577  -2.3612   0.2123
 BPC  C1A   C  CR66  0   0.090  -3.4764  -1.0307   0.0864
 BPC  C3B   C  C     0   0.124  -2.5668   0.0503  -0.0291
 BPC  C5B   C  C     0   0.109  -1.1657  -0.1907  -0.0142
 BPC  C1'   C  CH1   0  -0.054   3.0743  -1.0135   0.0503
 BPC  O1'   O  OH1   0  -0.669   3.3625  -2.1851  -0.6894
 BPC  C2'   C  CH1   0   0.049   3.9187   0.1193  -0.5200
 BPC  O2'   O  OH1   0  -0.675   5.2907  -0.1203  -0.3423
 BPC  C3'   C  CH1   0  -0.005   3.5426   1.4268   0.1455
 BPC  O3'   O  OH1   0  -0.669   3.7068   1.2751   1.5379
 BPC  C4'   C  CH2   0  -0.568   2.1097   1.7741  -0.2314
 BPC  H1    H  HCR6  0   0.259  -5.5440  -1.5947   0.1603
 BPC  H2    H  HCR6  0   0.260  -6.3873   0.7098  -0.0618
 BPC  H3    H  HCR6  0   0.259  -4.8161   2.6004  -0.2720
 BPC  H4    H  HCR6  0   0.257  -2.4873   3.4487  -0.3956
 BPC  H5    H  HCR6  0   0.257  -0.1100   3.0450  -0.3702
 BPC  H8    H  HCR6  0   0.245   1.0470  -2.7533   0.1878
 BPC  H9    H  HCR6  0   0.255  -1.2477  -3.6028   0.3137
 BPC  H10   H  HCR6  0   0.257  -3.6579  -3.1831   0.2992
 BPC  H1'   H  HCH1  0   0.246   3.3574  -1.1588   1.0993
 BPC  HA    H  HOH1  0   0.465   3.5409  -2.9038  -0.0783
 BPC  H2'   H  HCH1  0   0.217   3.6732   0.2215  -1.5896
 BPC  HB    H  HOH1  0   0.446   5.4934  -0.9738  -0.7404
 BPC  H3'   H  HCH1  0   0.236   4.1957   2.2231  -0.2385
 BPC  HC    H  HOH1  0   0.453   3.4213   2.0883   1.9655
 BPC  H4'1  H  HCH2  0   0.263   1.7909   2.6265   0.3751
 BPC  H4'2  H  HCH2  0   0.264   2.0999   2.1368  -1.2649

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
 BPC  C1   C2    aromatic  1.388  0.020  1.388
 BPC  C1   C1A   aromatic  1.395  0.020  1.395
 BPC  C1   H1    single    0.930  0.020  1.080
 BPC  C2   C3    aromatic  1.386  0.020  1.386
 BPC  C2   H2    single    0.930  0.020  1.080
 BPC  C3   C3A   aromatic  1.397  0.020  1.397
 BPC  C3   H3    single    0.930  0.020  1.080
 BPC  C3A  C4    aromatic  1.430  0.020  1.430
 BPC  C3A  C3B   aromatic  1.415  0.020  1.415
 BPC  C4   C5    aromatic  1.353  0.020  1.353
 BPC  C4   H4    single    0.930  0.020  1.080
 BPC  C5   C5A   aromatic  1.435  0.020  1.435
 BPC  C5   H5    single    0.930  0.020  1.080
 BPC  C5A  C6    aromatic  1.409  0.020  1.409
 BPC  C5A  C5B   aromatic  1.416  0.020  1.416
 BPC  C6   C7    aromatic  1.396  0.020  1.396
 BPC  C6   C4'   single    1.507  0.020  1.507
 BPC  C7   C8    aromatic  1.391  0.020  1.391
 BPC  C7   C1'   single    1.517  0.020  1.517
 BPC  C8   C8A   aromatic  1.389  0.020  1.389
 BPC  C8   H8    single    0.930  0.020  1.080
 BPC  C8A  C9    aromatic  1.434  0.020  1.434
 BPC  C8A  C5B   aromatic  1.415  0.020  1.415
 BPC  C9   C10   aromatic  1.351  0.020  1.351
 BPC  C9   H9    single    0.930  0.020  1.080
 BPC  C10  C1A   aromatic  1.434  0.020  1.434
 BPC  C10  H10   single    0.930  0.020  1.080
 BPC  C1A  C3B   aromatic  1.418  0.020  1.418
 BPC  C3B  C5B   aromatic  1.422  0.020  1.422
 BPC  C1'  O1'   single    1.415  0.020  1.415
 BPC  C1'  C2'   single    1.524  0.020  1.524
 BPC  C1'  H1'   single    0.970  0.020  1.090
 BPC  O1'  HA    single    0.850  0.020  0.980
 BPC  C2'  O2'   single    1.404  0.020  1.404
 BPC  C2'  C3'   single    1.515  0.020  1.515
 BPC  C2'  H2'   single    0.970  0.020  1.090
 BPC  O2'  HB    single    0.850  0.020  0.980
 BPC  C3'  O3'   single    1.410  0.020  1.410
 BPC  C3'  C4'   single    1.522  0.020  1.522
 BPC  C3'  H3'   single    0.970  0.020  1.090
 BPC  O3'  HC    single    0.850  0.020  0.980
 BPC  C4'  H4'1  single    0.970  0.020  1.090
 BPC  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
 BPC  H1    C1   C1A   119.33  3.000
 BPC  H1    C1   C2    119.95  3.000
 BPC  C1A   C1   C2    120.72  3.000
 BPC  H2    C2   C3    119.84  3.000
 BPC  H2    C2   C1    119.66  3.000
 BPC  C3    C2   C1    120.50  3.000
 BPC  H3    C3   C3A   119.42  3.000
 BPC  H3    C3   C2    120.10  3.000
 BPC  C3A   C3   C2    120.48  3.000
 BPC  C3B   C3A  C4    118.32  3.000
 BPC  C3B   C3A  C3    119.43  3.000
 BPC  C4    C3A  C3    122.26  3.000
 BPC  H4    C4   C5    119.93  3.000
 BPC  H4    C4   C3A   118.65  3.000
 BPC  C5    C4   C3A   121.42  3.000
 BPC  H5    C5   C5A   119.59  3.000
 BPC  H5    C5   C4    118.62  3.000
 BPC  C5A   C5   C4    121.79  3.000
 BPC  C5B   C5A  C6    120.07  3.000
 BPC  C5B   C5A  C5    117.66  3.000
 BPC  C6    C5A  C5    122.27  3.000
 BPC  C4'   C6   C7    120.79  3.000
 BPC  C4'   C6   C5A   119.76  3.000
 BPC  C7    C6   C5A   119.41  3.000
 BPC  C1'   C7   C8    118.19  3.000
 BPC  C1'   C7   C6    121.61  3.000
 BPC  C8    C7   C6    120.19  3.000
 BPC  H8    C8   C8A   118.49  3.000
 BPC  H8    C8   C7    119.78  3.000
 BPC  C8A   C8   C7    121.73  3.000
 BPC  C5B   C8A  C9    119.15  3.000
 BPC  C5B   C8A  C8    118.85  3.000
 BPC  C9    C8A  C8    121.99  3.000
 BPC  H9    C9   C10   120.29  3.000
 BPC  H9    C9   C8A   118.52  3.000
 BPC  C10   C9   C8A   121.18  3.000
 BPC  H10   C10  C1A   118.51  3.000
 BPC  H10   C10  C9    120.45  3.000
 BPC  C1A   C10  C9    121.04  3.000
 BPC  C3B   C1A  C10   118.87  3.000
 BPC  C3B   C1A  C1    119.17  3.000
 BPC  C10   C1A  C1    121.97  3.000
 BPC  C5B   C3B  C1A   120.15  3.000
 BPC  C5B   C3B  C3A   120.15  3.000
 BPC  C1A   C3B  C3A   119.70  3.000
 BPC  C3B   C5B  C8A   119.61  3.000
 BPC  C3B   C5B  C5A   120.66  3.000
 BPC  C8A   C5B  C5A   119.73  3.000
 BPC  H1'   C1'  C2'   108.28  3.000
 BPC  H1'   C1'  O1'   109.74  3.000
 BPC  C2'   C1'  O1'   107.88  3.000
 BPC  H1'   C1'  C7    107.87  3.000
 BPC  C2'   C1'  C7    111.73  3.000
 BPC  O1'   C1'  C7    111.30  3.000
 BPC  HA    O1'  C1'   108.96  3.000
 BPC  H2'   C2'  C3'   106.92  3.000
 BPC  H2'   C2'  O2'   110.88  3.000
 BPC  C3'   C2'  O2'   109.53  3.000
 BPC  H2'   C2'  C1'   107.99  3.000
 BPC  C3'   C2'  C1'   109.86  3.000
 BPC  O2'   C2'  C1'   111.55  3.000
 BPC  HB    O2'  C2'   107.72  3.000
 BPC  H3'   C3'  C4'   107.91  3.000
 BPC  H3'   C3'  O3'   110.71  3.000
 BPC  C4'   C3'  O3'   112.26  3.000
 BPC  H3'   C3'  C2'   108.93  3.000
 BPC  C4'   C3'  C2'   108.78  3.000
 BPC  O3'   C3'  C2'   108.18  3.000
 BPC  HC    O3'  C3'   108.26  3.000
 BPC  H4'2  C4'  H4'1  105.23  3.000
 BPC  H4'2  C4'  C3'   108.52  3.000
 BPC  H4'1  C4'  C3'   108.36  3.000
 BPC  H4'2  C4'  C6    109.28  3.000
 BPC  H4'1  C4'  C6    110.76  3.000
 BPC  C3'   C4'  C6    114.29  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
 BPC  CONST_01  C3A  C3   C2   C1     0.00   0.0  0
 BPC  CONST_02  C9   C10  C1A  C1   180.00   0.0  0
 BPC  CONST_03  C3A  C3B  C1A  C1     0.00   0.0  0
 BPC  CONST_04  C5B  C3B  C1A  C1   180.00   0.0  0
 BPC  CONST_05  C10  C1A  C1   C2   180.00   0.0  0
 BPC  CONST_06  C3B  C1A  C1   C2     0.00   0.0  0
 BPC  CONST_07  C4   C3A  C3   C2   180.00   0.0  0
 BPC  CONST_08  C3B  C3A  C3   C2     0.00   0.0  0
 BPC  CONST_09  C1A  C1   C2   C3     0.00   0.0  0
 BPC  CONST_10  C5   C4   C3A  C3   180.00   0.0  0
 BPC  CONST_11  C1A  C3B  C3A  C3     0.00   0.0  0
 BPC  CONST_12  C5B  C3B  C3A  C3   180.00   0.0  0
 BPC  CONST_13  C5A  C5   C4   C3A    0.00   0.0  0
 BPC  CONST_14  C10  C1A  C3B  C3A  180.00   0.0  0
 BPC  CONST_15  C5A  C5B  C3B  C3A    0.00   0.0  0
 BPC  CONST_16  C8A  C5B  C3B  C3A  180.00   0.0  0
 BPC  CONST_17  C1A  C3B  C3A  C4   180.00   0.0  0
 BPC  CONST_18  C5B  C3B  C3A  C4     0.00   0.0  0
 BPC  CONST_19  C6   C5A  C5   C4   180.00   0.0  0
 BPC  CONST_20  C5B  C5A  C5   C4     0.00   0.0  0
 BPC  CONST_21  C3B  C3A  C4   C5     0.00   0.0  0
 BPC  CONST_22  C7   C6   C5A  C5   180.00   0.0  0
 BPC  CONST_23  C8A  C5B  C5A  C5   180.00   0.0  0
 BPC  CONST_24  C3B  C5B  C5A  C5     0.00   0.0  0
 BPC  CONST_25  C8   C7   C6   C5A    0.00   0.0  0
 BPC  CONST_26  C8   C8A  C5B  C5A    0.00   0.0  0
 BPC  CONST_27  C9   C8A  C5B  C5A  180.00   0.0  0
 BPC  CONST_28  C1A  C3B  C5B  C5A  180.00   0.0  0
 BPC  CONST_29  C8A  C5B  C5A  C6     0.00   0.0  0
 BPC  CONST_30  C3B  C5B  C5A  C6   180.00   0.0  0
 BPC  CONST_31  C8A  C8   C7   C6     0.00   0.0  0
 BPC  CONST_32  C5B  C5A  C6   C7     0.00   0.0  0
 BPC  CONST_33  C9   C8A  C8   C7   180.00   0.0  0
 BPC  CONST_34  C5B  C8A  C8   C7     0.00   0.0  0
 BPC  CONST_35  C10  C9   C8A  C8   180.00   0.0  0
 BPC  CONST_36  C3B  C5B  C8A  C8   180.00   0.0  0
 BPC  CONST_37  C1A  C10  C9   C8A    0.00   0.0  0
 BPC  CONST_38  C1A  C3B  C5B  C8A    0.00   0.0  0
 BPC  CONST_39  C3B  C5B  C8A  C9     0.00   0.0  0
 BPC  CONST_40  C3B  C1A  C10  C9     0.00   0.0  0
 BPC  CONST_41  C5B  C8A  C9   C10    0.00   0.0  0
 BPC  CONST_42  C5B  C3B  C1A  C10    0.00   0.0  0
 BPC  CONST_43  H3   C3   C2   C1   180.00   0.0  0
 BPC  CONST_44  H10  C10  C1A  C1     0.00   0.0  0
 BPC  CONST_45  H1   C1   C2   C3   180.00   0.0  0
 BPC  CONST_46  H4   C4   C3A  C3     0.00   0.0  0
 BPC  CONST_47  H2   C2   C3   C3A  180.00   0.0  0
 BPC  CONST_48  H5   C5   C4   C3A  180.00   0.0  0
 BPC  CONST_49  H8   C8   C7   C6   180.00   0.0  0
 BPC  CONST_50  H9   C9   C8A  C8     0.00   0.0  0
 BPC  Var_01    C3'  C4'  C6   C5A  165.90  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
 BPC  chir_01  C1'  C7   O1'  C2'  negativ
 BPC  chir_02  C2'  O2'  C1'  C3'  negativ
 BPC  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
 BPC  plan-1  C1   0.020
 BPC  plan-1  C2   0.020
 BPC  plan-1  C3   0.020
 BPC  plan-1  C3A  0.020
 BPC  plan-1  C4   0.020
 BPC  plan-1  C5   0.020
 BPC  plan-1  C5A  0.020
 BPC  plan-1  C6   0.020
 BPC  plan-1  C7   0.020
 BPC  plan-1  C8   0.020
 BPC  plan-1  C8A  0.020
 BPC  plan-1  C9   0.020
 BPC  plan-1  C10  0.020
 BPC  plan-1  C1A  0.020
 BPC  plan-1  C3B  0.020
 BPC  plan-1  C5B  0.020
 BPC  plan-1  C1'  0.020
 BPC  plan-1  C4'  0.020
 BPC  plan-1  H1   0.020
 BPC  plan-1  H2   0.020
 BPC  plan-1  H3   0.020
 BPC  plan-1  H4   0.020
 BPC  plan-1  H5   0.020
 BPC  plan-1  H8   0.020
 BPC  plan-1  H9   0.020
 BPC  plan-1  H10  0.020

