# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:48:18 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,4R)-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
 BPI  BPI  (2R,3R,4R)-1,2,3,4-tetrahydrobenzo[c]phenanthrene-2,3,4-triol  ligand  37  21  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BPI
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
 BPI  C1    C  CH2   0  -0.621   1.2762   0.1966  -1.0152
 BPI  C2    C  CH1   0   0.064   1.4440   0.6858  -2.4493
 BPI  O2    O  OH1   0  -0.674   2.8020   0.6911  -2.8271
 BPI  C3    C  CH1   0  -0.005   0.6753  -0.2066  -3.3988
 BPI  O3    O  OH1   0  -0.670   1.1030  -1.5334  -3.2152
 BPI  C4    C  CH1   0  -0.096  -0.8068  -0.0595  -3.0814
 BPI  O4    O  OH1   0  -0.662  -1.2093   1.1993  -3.5893
 BPI  C5    C  CR16  0  -0.314  -2.4715  -0.3207  -1.2810
 BPI  C6    C  CR16  0  -0.313  -2.8883  -0.2486   0.0161
 BPI  C7    C  CR16  0  -0.311  -2.4405   0.0851   2.3807
 BPI  C8    C  CR16  0  -0.324  -1.5956   0.2714   3.4129
 BPI  C9    C  CR16  0  -0.301   0.6640   0.2371   4.3327
 BPI  C10   C  CR16  0  -0.265   2.0128   0.0145   4.2169
 BPI  C11   C  CR16  0  -0.246   2.5348  -0.3200   2.9647
 BPI  C12   C  CR16  0  -0.350   1.7226  -0.3657   1.8544
 BPI  C13   C  CR6   0   0.048  -0.1564  -0.0420  -0.6038
 BPI  C14   C  CR6   0   0.053  -1.1143  -0.1692  -1.6020
 BPI  C15   C  CR66  0   0.061  -1.9512  -0.0962   1.0501
 BPI  C16   C  CR66  0   0.113  -0.5613  -0.0832   0.7689
 BPI  C17   C  CR66  0   0.080   0.3423  -0.0762   1.9181
 BPI  C18   C  CR66  0   0.081  -0.1862   0.1662   3.2142
 BPI  H11A  H  HCH2  0   0.262   1.8601  -0.7218  -0.9162
 BPI  H12A  H  HCH2  0   0.266   1.7324   0.9334  -0.3488
 BPI  H2    H  HCH1  0   0.224   1.0184   1.6938  -2.5353
 BPI  HO2   H  HOH1  0   0.451   3.2574   1.3578  -2.3037
 BPI  H3    H  HCH1  0   0.236   0.8425   0.1252  -4.4335
 BPI  HO3   H  HOH1  0   0.454   0.6498  -2.0908  -3.8554
 BPI  H4    H  HCH1  0   0.236  -1.3535  -0.8627  -3.5986
 BPI  HO4   H  HOH1  0   0.455  -2.1477   1.3222  -3.4156
 BPI  H5    H  HCR6  0   0.261  -3.1977  -0.4664  -2.0732
 BPI  H6    H  HCR6  0   0.256  -3.9419  -0.3002   0.2613
 BPI  H7    H  HCR6  0   0.256  -3.5129   0.1032   2.5323
 BPI  H8    H  HCR6  0   0.256  -1.9697   0.4555   4.4124
 BPI  H9    H  HCR6  0   0.256   0.2273   0.4506   5.3009
 BPI  H10   H  HCR6  0   0.259   2.6574   0.0657   5.0844
 BPI  H11   H  HCR6  0   0.259   3.5856  -0.5565   2.8606
 BPI  H12   H  HCR6  0   0.264   2.1752  -0.6797   0.9316

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
 BPI  C1   C2    single    1.525  0.020  1.525
 BPI  C1   C13   single    1.509  0.020  1.509
 BPI  C1   H11A  single    0.970  0.020  1.090
 BPI  C1   H12A  single    0.970  0.020  1.090
 BPI  C2   O2    single    1.409  0.020  1.409
 BPI  C2   C3    single    1.513  0.020  1.513
 BPI  C2   H2    single    0.970  0.020  1.090
 BPI  O2   HO2   single    0.850  0.020  0.980
 BPI  C3   O3    single    1.406  0.020  1.406
 BPI  C3   C4    single    1.523  0.020  1.523
 BPI  C3   H3    single    0.970  0.020  1.090
 BPI  O3   HO3   single    0.850  0.020  0.980
 BPI  C4   O4    single    1.416  0.020  1.416
 BPI  C4   C14   single    1.515  0.020  1.515
 BPI  C4   H4    single    0.970  0.020  1.090
 BPI  O4   HO4   single    0.850  0.020  0.980
 BPI  C5   C6    aromatic  1.364  0.020  1.364
 BPI  C5   C14   aromatic  1.403  0.020  1.403
 BPI  C5   H5    single    0.930  0.020  1.080
 BPI  C6   C15   aromatic  1.404  0.020  1.404
 BPI  C6   H6    single    0.930  0.020  1.080
 BPI  C7   C8    aromatic  1.347  0.020  1.347
 BPI  C7   C15   aromatic  1.429  0.020  1.429
 BPI  C7   H7    single    0.930  0.020  1.080
 BPI  C8   C18   aromatic  1.427  0.020  1.427
 BPI  C8   H8    single    0.930  0.020  1.080
 BPI  C9   C10   aromatic  1.372  0.020  1.372
 BPI  C9   C18   aromatic  1.407  0.020  1.407
 BPI  C9   H9    single    0.930  0.020  1.080
 BPI  C10  C11   aromatic  1.397  0.020  1.397
 BPI  C10  H10   single    0.930  0.020  1.080
 BPI  C11  C12   aromatic  1.376  0.020  1.376
 BPI  C11  H11   single    0.930  0.020  1.080
 BPI  C12  C17   aromatic  1.412  0.020  1.412
 BPI  C12  H12   single    0.930  0.020  1.080
 BPI  C13  C14   aromatic  1.389  0.020  1.389
 BPI  C13  C16   aromatic  1.432  0.020  1.432
 BPI  C15  C16   aromatic  1.418  0.020  1.418
 BPI  C16  C17   aromatic  1.462  0.020  1.462
 BPI  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
 BPI  H12A  C1   H11A  106.75  3.000
 BPI  H12A  C1   C13   109.66  3.000
 BPI  H11A  C1   C13   110.46  3.000
 BPI  H12A  C1   C2    108.13  3.000
 BPI  H11A  C1   C2    107.22  3.000
 BPI  C13   C1   C2    114.31  3.000
 BPI  H2    C2   C3    107.19  3.000
 BPI  H2    C2   O2    110.44  3.000
 BPI  C3    C2   O2    108.88  3.000
 BPI  H2    C2   C1    109.01  3.000
 BPI  C3    C2   C1    110.19  3.000
 BPI  O2    C2   C1    111.06  3.000
 BPI  HO2   O2   C2    108.23  3.000
 BPI  H3    C3   C4    108.36  3.000
 BPI  H3    C3   O3    111.19  3.000
 BPI  C4    C3   O3    111.09  3.000
 BPI  H3    C3   C2    109.60  3.000
 BPI  C4    C3   C2    107.87  3.000
 BPI  O3    C3   C2    108.67  3.000
 BPI  HO3   O3   C3    108.45  3.000
 BPI  H4    C4   C14   107.77  3.000
 BPI  H4    C4   O4    109.82  3.000
 BPI  C14   C4   O4    110.92  3.000
 BPI  H4    C4   C3    108.36  3.000
 BPI  C14   C4   C3    113.21  3.000
 BPI  O4    C4   C3    106.72  3.000
 BPI  HO4   O4   C4    109.03  3.000
 BPI  H5    C5   C14   119.68  3.000
 BPI  H5    C5   C6    119.80  3.000
 BPI  C14   C5   C6    120.49  3.000
 BPI  H6    C6   C15   119.20  3.000
 BPI  H6    C6   C5    120.66  3.000
 BPI  C15   C6   C5    120.14  3.000
 BPI  H7    C7   C15   118.13  3.000
 BPI  H7    C7   C8    120.76  3.000
 BPI  C15   C7   C8    121.08  3.000
 BPI  H8    C8   C18   118.83  3.000
 BPI  H8    C8   C7    120.93  3.000
 BPI  C18   C8   C7    120.17  3.000
 BPI  H9    C9   C18   118.48  3.000
 BPI  H9    C9   C10   120.24  3.000
 BPI  C18   C9   C10   121.26  3.000
 BPI  H10   C10  C11   120.48  3.000
 BPI  H10   C10  C9    120.69  3.000
 BPI  C11   C10  C9    118.80  3.000
 BPI  H11   C11  C12   119.22  3.000
 BPI  H11   C11  C10   120.08  3.000
 BPI  C12   C11  C10   120.69  3.000
 BPI  H12   C12  C17   120.69  3.000
 BPI  H12   C12  C11   116.99  3.000
 BPI  C17   C12  C11   122.25  3.000
 BPI  C16   C13  C14   119.42  3.000
 BPI  C16   C13  C1    122.29  3.000
 BPI  C14   C13  C1    118.23  3.000
 BPI  C13   C14  C5    120.83  3.000
 BPI  C13   C14  C4    123.71  3.000
 BPI  C5    C14  C4    115.32  3.000
 BPI  C16   C15  C7    121.27  3.000
 BPI  C16   C15  C6    120.61  3.000
 BPI  C7    C15  C6    118.09  3.000
 BPI  C17   C16  C15   116.74  3.000
 BPI  C17   C16  C13   125.37  3.000
 BPI  C15   C16  C13   117.88  3.000
 BPI  C18   C17  C16   119.22  3.000
 BPI  C18   C17  C12   116.10  3.000
 BPI  C16   C17  C12   124.60  3.000
 BPI  C17   C18  C9    120.61  3.000
 BPI  C17   C18  C8    120.47  3.000
 BPI  C9    C18  C8    118.84  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
 BPI  CONST_01  C7   C15  C6   C5   180.00   0.0  0
 BPI  CONST_02  C16  C15  C6   C5     0.00   0.0  0
 BPI  CONST_03  C16  C13  C14  C5     0.00   0.0  0
 BPI  CONST_04  C13  C14  C5   C6     0.00   0.0  0
 BPI  CONST_05  C8   C7   C15  C6   180.00   0.0  0
 BPI  CONST_06  C13  C16  C15  C6     0.00   0.0  0
 BPI  CONST_07  C17  C16  C15  C6   180.00   0.0  0
 BPI  CONST_08  C9   C18  C8   C7   180.00   0.0  0
 BPI  CONST_09  C17  C18  C8   C7     0.00   0.0  0
 BPI  CONST_10  C13  C16  C15  C7   180.00   0.0  0
 BPI  CONST_11  C17  C16  C15  C7     0.00   0.0  0
 BPI  CONST_12  C16  C15  C7   C8     0.00   0.0  0
 BPI  CONST_13  C10  C9   C18  C8   180.00   0.0  0
 BPI  CONST_14  C12  C17  C18  C8   180.00   0.0  0
 BPI  CONST_15  C16  C17  C18  C8     0.00   0.0  0
 BPI  CONST_16  C12  C11  C10  C9     0.00   0.0  0
 BPI  CONST_17  C12  C17  C18  C9     0.00   0.0  0
 BPI  CONST_18  C16  C17  C18  C9   180.00   0.0  0
 BPI  CONST_19  C17  C18  C9   C10    0.00   0.0  0
 BPI  CONST_20  C17  C12  C11  C10    0.00   0.0  0
 BPI  CONST_21  C18  C9   C10  C11    0.00   0.0  0
 BPI  CONST_22  C16  C17  C12  C11  180.00   0.0  0
 BPI  CONST_23  C18  C17  C12  C11    0.00   0.0  0
 BPI  CONST_26  C18  C17  C16  C13  180.00   0.0  0
 BPI  CONST_27  C15  C6   C5   C14    0.00   0.0  0
 BPI  CONST_28  C15  C16  C13  C14    0.00   0.0  0
 BPI  CONST_29  C17  C16  C13  C14  180.00   0.0  0
 BPI  CONST_30  C18  C8   C7   C15    0.00   0.0  0
 BPI  CONST_31  C18  C17  C16  C15    0.00   0.0  0
 BPI  CONST_32  H5   C5   C14  C4     0.00   0.0  0
 BPI  CONST_33  H7   C7   C15  C6     0.00   0.0  0
 BPI  CONST_34  H6   C6   C15  C7     0.00   0.0  0
 BPI  CONST_35  H9   C9   C18  C8     0.00   0.0  0
 BPI  CONST_36  H11  C11  C10  C9   180.00   0.0  0
 BPI  CONST_37  H8   C8   C18  C9     0.00   0.0  0
 BPI  CONST_38  H12  C12  C11  C10  180.00   0.0  0
 BPI  CONST_39  H10  C10  C11  C12  180.00   0.0  0
 BPI  Var_01    C14  C13  C1   C2    17.62  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
 BPI  chir_01  C2  C1  O2  C3   negativ
 BPI  chir_02  C3  O3  C4  C2   negativ
 BPI  chir_03  C4  O4  C3  C14  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
 BPI  plan-1  C1   0.020
 BPI  plan-1  C4   0.020
 BPI  plan-1  C5   0.020
 BPI  plan-1  C6   0.020
 BPI  plan-1  C7   0.020
 BPI  plan-1  C8   0.020
 BPI  plan-1  C9   0.020
 BPI  plan-1  C10  0.020
 BPI  plan-1  C11  0.020
 BPI  plan-1  C12  0.020
 BPI  plan-1  C13  0.020
 BPI  plan-1  C14  0.020
 BPI  plan-1  C15  0.020
 BPI  plan-1  C16  0.020
 BPI  plan-1  C17  0.020
 BPI  plan-1  C18  0.020
 BPI  plan-1  H5   0.020
 BPI  plan-1  H6   0.020
 BPI  plan-1  H7   0.020
 BPI  plan-1  H8   0.020
 BPI  plan-1  H9   0.020
 BPI  plan-1  H10  0.020
 BPI  plan-1  H11  0.020
 BPI  plan-1  H12  0.020

