# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:53:23 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-benzo[pqr]tetraphen-6-yl-3-methylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)Nc1c2ccccc2c3ccc4cccc5ccc1c3c45
#
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
 BPL  BPL  1-benzo[pqr]tetraphen-6-yl-3-methylurea  ligand  41  25  .  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_BPL
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
 BPL  C1   C  CR16  0  -0.334  -0.0026  -0.3219  -4.8660
 BPL  C2   C  CR16  0  -0.253   1.3568  -0.2273  -5.0825
 BPL  C3   C  CR16  0  -0.341   2.2263  -0.0335  -4.0119
 BPL  C4   C  CR66  0   0.094   1.7424   0.0710  -2.7138
 BPL  C5   C  C     0   0.130   0.3475  -0.0202  -2.4763
 BPL  C6   C  C     0   0.089  -0.1712   0.0871  -1.1542
 BPL  C7   C  CR66  0   0.047   0.7321   0.2949  -0.0614
 BPL  C8   C  CR6   0   0.201   0.2373   0.4179   1.2217
 BPL  C9   C  CR66  0   0.068  -1.1561   0.3341   1.4777
 BPL  C10  C  CR66  0   0.067  -2.0586   0.0934   0.4079
 BPL  C11  C  CR66  0   0.074  -1.5536  -0.0179  -0.9274
 BPL  C12  C  CR16  0  -0.375  -2.4101  -0.2221  -2.0500
 BPL  C13  C  CR16  0  -0.315  -1.9223  -0.3176  -3.3114
 BPL  C14  C  CR66  0   0.077  -0.5267  -0.2218  -3.5693
 BPL  C15  C  CR16  0  -0.326   2.6202   0.2607  -1.5934
 BPL  C16  C  CR16  0  -0.323   2.1430   0.3647  -0.3379
 BPL  C17  C  CR16  0  -0.302  -1.6684   0.4937   2.7885
 BPL  C18  C  CR16  0  -0.259  -3.0083   0.3962   3.0389
 BPL  C19  C  CR16  0  -0.242  -3.9029   0.1299   1.9863
 BPL  C20  C  CR16  0  -0.347  -3.4375  -0.0115   0.7076
 BPL  N21  N  NH1   0  -0.792   1.1164   0.6685   2.2926
 BPL  C22  C  C     0   0.699   1.4746  -0.3193   3.1747
 BPL  O23  O  O     0  -0.524   1.0476  -1.4626   3.0781
 BPL  N24  N  NH1   0  -0.668   2.3186   0.0726   4.1515
 BPL  C25  C  CH3   0  -0.507   2.7840  -0.8445   5.1625
 BPL  H1   H  HCR6  0   0.261  -0.6785  -0.4754  -5.6982
 BPL  H2   H  HCR6  0   0.262   1.7510  -0.3060  -6.0872
 BPL  H3   H  HCR6  0   0.261   3.2932   0.0356  -4.1856
 BPL  H12  H  HCR6  0   0.258  -3.4786  -0.2974  -1.9105
 BPL  H13  H  HCR6  0   0.261  -2.5992  -0.4671  -4.1434
 BPL  H15  H  HCR6  0   0.259   3.6868   0.3131  -1.7750
 BPL  H16  H  HCR6  0   0.249   2.8302   0.4984   0.4860
 BPL  H17  H  HCR6  0   0.254  -0.9903   0.7148   3.6006
 BPL  H18  H  HCR6  0   0.261  -3.3821   0.5254   4.0461
 BPL  H19  H  HCR6  0   0.262  -4.9630   0.0451   2.1851
 BPL  H20  H  HCR6  0   0.257  -4.1525  -0.2054  -0.0790
 BPL  H21  H  HNH1  0   0.402   1.5843   1.5614   2.3242
 BPL  H24  H  HNH1  0   0.400   2.6048   1.0349   4.2144
 BPL  H26  H  HCH3  0   0.248   3.4213  -0.2953   5.8499
 BPL  H27  H  HCH3  0   0.233   1.9620  -1.2760   5.7353
 BPL  H28  H  HCH3  0   0.233   3.3700  -1.6607   4.7377

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
 BPL  C1   C2   aromatic  1.380  0.020  1.380
 BPL  C1   C14  aromatic  1.402  0.020  1.402
 BPL  C1   H1   single    0.930  0.020  1.080
 BPL  C2   C3   aromatic  1.393  0.020  1.393
 BPL  C2   H2   single    0.930  0.020  1.080
 BPL  C3   C4   aromatic  1.389  0.020  1.389
 BPL  C3   H3   single    0.930  0.020  1.080
 BPL  C4   C5   aromatic  1.418  0.020  1.418
 BPL  C4   C15  aromatic  1.436  0.020  1.436
 BPL  C5   C6   aromatic  1.424  0.020  1.424
 BPL  C5   C14  aromatic  1.414  0.020  1.414
 BPL  C6   C7   aromatic  1.433  0.020  1.433
 BPL  C6   C11  aromatic  1.405  0.020  1.405
 BPL  C7   C8   aromatic  1.381  0.020  1.381
 BPL  C7   C16  aromatic  1.439  0.020  1.439
 BPL  C8   C9   aromatic  1.419  0.020  1.419
 BPL  C8   N21  single    1.408  0.020  1.408
 BPL  C9   C10  aromatic  1.420  0.020  1.420
 BPL  C9   C17  aromatic  1.416  0.020  1.416
 BPL  C10  C11  aromatic  1.432  0.020  1.432
 BPL  C10  C20  aromatic  1.415  0.020  1.415
 BPL  C11  C12  aromatic  1.427  0.020  1.427
 BPL  C12  C13  aromatic  1.356  0.020  1.356
 BPL  C12  H12  single    0.930  0.020  1.080
 BPL  C13  C14  aromatic  1.422  0.020  1.422
 BPL  C13  H13  single    0.930  0.020  1.080
 BPL  C15  C16  aromatic  1.347  0.020  1.347
 BPL  C15  H15  single    0.930  0.020  1.080
 BPL  C16  H16  single    0.930  0.020  1.080
 BPL  C17  C18  aromatic  1.367  0.020  1.367
 BPL  C17  H17  single    0.930  0.020  1.080
 BPL  C18  C19  aromatic  1.407  0.020  1.407
 BPL  C18  H18  single    0.930  0.020  1.080
 BPL  C19  C20  aromatic  1.368  0.020  1.368
 BPL  C19  H19  single    0.930  0.020  1.080
 BPL  C20  H20  single    0.930  0.020  1.080
 BPL  N21  C22  single    1.372  0.020  1.372
 BPL  N21  H21  single    0.860  0.020  1.020
 BPL  C22  O23  double    1.224  0.020  1.224
 BPL  C22  N24  single    1.349  0.020  1.349
 BPL  N24  C25  single    1.442  0.020  1.442
 BPL  N24  H24  single    0.860  0.020  1.020
 BPL  C25  H26  single    0.970  0.020  1.090
 BPL  C25  H27  single    0.970  0.020  1.090
 BPL  C25  H28  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
 BPL  H1   C1   C14  119.17  3.000
 BPL  H1   C1   C2   120.26  3.000
 BPL  C14  C1   C2   120.57  3.000
 BPL  H2   C2   C3   119.76  3.000
 BPL  H2   C2   C1   119.98  3.000
 BPL  C3   C2   C1   120.26  3.000
 BPL  H3   C3   C4   119.22  3.000
 BPL  H3   C3   C2   120.03  3.000
 BPL  C4   C3   C2   120.75  3.000
 BPL  C15  C4   C5   118.64  3.000
 BPL  C15  C4   C3   121.74  3.000
 BPL  C5   C4   C3   119.62  3.000
 BPL  C14  C5   C6   120.21  3.000
 BPL  C14  C5   C4   119.20  3.000
 BPL  C6   C5   C4   120.59  3.000
 BPL  C11  C6   C7   120.54  3.000
 BPL  C11  C6   C5   120.17  3.000
 BPL  C7   C6   C5   119.29  3.000
 BPL  C16  C7   C8   121.70  3.000
 BPL  C16  C7   C6   118.58  3.000
 BPL  C8   C7   C6   119.72  3.000
 BPL  N21  C8   C9   119.10  3.000
 BPL  N21  C8   C7   119.93  3.000
 BPL  C9   C8   C7   120.95  3.000
 BPL  C17  C9   C10  119.10  3.000
 BPL  C17  C9   C8   121.03  3.000
 BPL  C10  C9   C8   119.87  3.000
 BPL  C20  C10  C11  122.37  3.000
 BPL  C20  C10  C9   118.19  3.000
 BPL  C11  C10  C9   119.44  3.000
 BPL  C12  C11  C10  122.22  3.000
 BPL  C12  C11  C6   118.32  3.000
 BPL  C10  C11  C6   119.45  3.000
 BPL  H12  C12  C13  118.10  3.000
 BPL  H12  C12  C11  120.15  3.000
 BPL  C13  C12  C11  121.75  3.000
 BPL  H13  C13  C14  118.91  3.000
 BPL  H13  C13  C12  119.97  3.000
 BPL  C14  C13  C12  121.12  3.000
 BPL  C13  C14  C5   118.43  3.000
 BPL  C13  C14  C1   121.98  3.000
 BPL  C5   C14  C1   119.59  3.000
 BPL  H15  C15  C16  120.09  3.000
 BPL  H15  C15  C4   118.52  3.000
 BPL  C16  C15  C4   121.39  3.000
 BPL  H16  C16  C15  119.65  3.000
 BPL  H16  C16  C7   118.86  3.000
 BPL  C15  C16  C7   121.50  3.000
 BPL  H17  C17  C18  119.48  3.000
 BPL  H17  C17  C9   119.44  3.000
 BPL  C18  C17  C9   121.07  3.000
 BPL  H18  C18  C19  119.96  3.000
 BPL  H18  C18  C17  120.05  3.000
 BPL  C19  C18  C17  120.00  3.000
 BPL  H19  C19  C20  119.80  3.000
 BPL  H19  C19  C18  120.03  3.000
 BPL  C20  C19  C18  120.17  3.000
 BPL  H20  C20  C19  118.28  3.000
 BPL  H20  C20  C10  120.27  3.000
 BPL  C19  C20  C10  121.45  3.000
 BPL  H21  N21  C22  119.74  3.000
 BPL  H21  N21  C8   118.11  3.000
 BPL  C22  N21  C8   121.59  3.000
 BPL  N24  C22  O23  123.13  3.000
 BPL  N24  C22  N21  114.82  3.000
 BPL  O23  C22  N21  122.04  3.000
 BPL  H24  N24  C25  118.21  3.000
 BPL  H24  N24  C22  120.07  3.000
 BPL  C25  N24  C22  121.65  3.000
 BPL  H28  C25  H27  108.26  3.000
 BPL  H28  C25  H26  108.03  3.000
 BPL  H27  C25  H26  108.04  3.000
 BPL  H28  C25  N24  112.10  3.000
 BPL  H27  C25  N24  112.12  3.000
 BPL  H26  C25  N24  108.14  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
 BPL  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 BPL  CONST_02  C4   C5   C14  C1      0.00   0.0  0
 BPL  CONST_03  C6   C5   C14  C1    180.00   0.0  0
 BPL  CONST_04  C12  C13  C14  C1    180.00   0.0  0
 BPL  CONST_05  C5   C14  C1   C2      0.00   0.0  0
 BPL  CONST_06  C13  C14  C1   C2    180.00   0.0  0
 BPL  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 BPL  CONST_08  C15  C4   C3   C2    180.00   0.0  0
 BPL  CONST_09  C14  C1   C2   C3      0.00   0.0  0
 BPL  CONST_10  C6   C5   C4   C3    180.00   0.0  0
 BPL  CONST_11  C14  C5   C4   C3      0.00   0.0  0
 BPL  CONST_12  C16  C15  C4   C3    180.00   0.0  0
 BPL  CONST_13  C7   C6   C5   C4      0.00   0.0  0
 BPL  CONST_14  C11  C6   C5   C4    180.00   0.0  0
 BPL  CONST_15  C13  C14  C5   C4    180.00   0.0  0
 BPL  CONST_16  C7   C16  C15  C4      0.00   0.0  0
 BPL  CONST_17  C16  C15  C4   C5      0.00   0.0  0
 BPL  CONST_18  C8   C7   C6   C5    180.00   0.0  0
 BPL  CONST_19  C16  C7   C6   C5      0.00   0.0  0
 BPL  CONST_20  C10  C11  C6   C5    180.00   0.0  0
 BPL  CONST_21  C12  C11  C6   C5      0.00   0.0  0
 BPL  CONST_22  C12  C13  C14  C5      0.00   0.0  0
 BPL  CONST_23  C15  C4   C5   C6      0.00   0.0  0
 BPL  CONST_24  C13  C14  C5   C6      0.00   0.0  0
 BPL  CONST_25  C9   C8   C7   C6      0.00   0.0  0
 BPL  CONST_26  C15  C16  C7   C6      0.00   0.0  0
 BPL  CONST_27  C9   C10  C11  C6      0.00   0.0  0
 BPL  CONST_28  C20  C10  C11  C6    180.00   0.0  0
 BPL  CONST_29  C13  C12  C11  C6      0.00   0.0  0
 BPL  CONST_30  C14  C5   C6   C7    180.00   0.0  0
 BPL  CONST_31  C10  C11  C6   C7      0.00   0.0  0
 BPL  CONST_32  C12  C11  C6   C7    180.00   0.0  0
 BPL  CONST_33  C10  C9   C8   C7      0.00   0.0  0
 BPL  CONST_34  C17  C9   C8   C7    180.00   0.0  0
 BPL  CONST_35  C11  C6   C7   C8      0.00   0.0  0
 BPL  CONST_36  C15  C16  C7   C8    180.00   0.0  0
 BPL  CONST_37  C11  C10  C9   C8      0.00   0.0  0
 BPL  CONST_38  C20  C10  C9   C8    180.00   0.0  0
 BPL  CONST_39  C18  C17  C9   C8    180.00   0.0  0
 BPL  CONST_40  C16  C7   C8   C9    180.00   0.0  0
 BPL  CONST_41  C12  C11  C10  C9    180.00   0.0  0
 BPL  CONST_42  C19  C20  C10  C9      0.00   0.0  0
 BPL  CONST_43  C19  C18  C17  C9      0.00   0.0  0
 BPL  CONST_44  C18  C17  C9   C10     0.00   0.0  0
 BPL  CONST_45  C13  C12  C11  C10   180.00   0.0  0
 BPL  CONST_46  C18  C19  C20  C10     0.00   0.0  0
 BPL  CONST_47  C14  C5   C6   C11     0.00   0.0  0
 BPL  CONST_48  C16  C7   C6   C11   180.00   0.0  0
 BPL  CONST_49  C17  C9   C10  C11   180.00   0.0  0
 BPL  CONST_50  C19  C20  C10  C11   180.00   0.0  0
 BPL  CONST_51  C14  C13  C12  C11     0.00   0.0  0
 BPL  CONST_52  C20  C10  C11  C12     0.00   0.0  0
 BPL  CONST_53  C15  C4   C5   C14   180.00   0.0  0
 BPL  CONST_54  C20  C10  C9   C17     0.00   0.0  0
 BPL  CONST_55  C20  C19  C18  C17     0.00   0.0  0
 BPL  CONST_56  N21  C8   C7   C6    180.00   0.0  0
 BPL  CONST_57  N21  C8   C9   C10   180.00   0.0  0
 BPL  CONST_58  N21  C8   C7   C16     0.00   0.0  0
 BPL  CONST_59  N21  C8   C9   C17     0.00   0.0  0
 BPL  CONST_60  H3   C3   C2   C1    180.00   0.0  0
 BPL  CONST_61  H13  C13  C14  C1      0.00   0.0  0
 BPL  CONST_62  H1   C1   C2   C3    180.00   0.0  0
 BPL  CONST_63  H15  C15  C4   C3      0.00   0.0  0
 BPL  CONST_64  H2   C2   C3   C4    180.00   0.0  0
 BPL  CONST_65  H16  C16  C15  C4    180.00   0.0  0
 BPL  CONST_66  H12  C12  C11  C6    180.00   0.0  0
 BPL  CONST_67  H17  C17  C9   C8      0.00   0.0  0
 BPL  CONST_68  H20  C20  C10  C9    180.00   0.0  0
 BPL  CONST_69  H18  C18  C17  C9    180.00   0.0  0
 BPL  CONST_70  H19  C19  C20  C10   180.00   0.0  0
 BPL  CONST_74  O23  C22  N21  C8      0.00   0.0  0
 BPL  CONST_75  N24  C22  N21  C8    180.00   0.0  0
 BPL  CONST_76  C25  N24  C22  O23     0.00   0.0  0
 BPL  CONST_77  C25  N24  C22  N21   180.00   0.0  0
 BPL  CONST_78  H24  N24  C22  O23   180.00   0.0  0
 BPL  Var_01    H26  C25  N24  C22  -178.22  30.0  3

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
 BPL  plan-1  C1   0.020
 BPL  plan-1  C2   0.020
 BPL  plan-1  C3   0.020
 BPL  plan-1  C4   0.020
 BPL  plan-1  C5   0.020
 BPL  plan-1  C6   0.020
 BPL  plan-1  C7   0.020
 BPL  plan-1  C8   0.020
 BPL  plan-1  C9   0.020
 BPL  plan-1  C10  0.020
 BPL  plan-1  C11  0.020
 BPL  plan-1  C12  0.020
 BPL  plan-1  C13  0.020
 BPL  plan-1  C14  0.020
 BPL  plan-1  C15  0.020
 BPL  plan-1  C16  0.020
 BPL  plan-1  C17  0.020
 BPL  plan-1  C18  0.020
 BPL  plan-1  C19  0.020
 BPL  plan-1  C20  0.020
 BPL  plan-1  N21  0.020
 BPL  plan-1  H1   0.020
 BPL  plan-1  H2   0.020
 BPL  plan-1  H3   0.020
 BPL  plan-1  H12  0.020
 BPL  plan-1  H13  0.020
 BPL  plan-1  H15  0.020
 BPL  plan-1  H16  0.020
 BPL  plan-1  H17  0.020
 BPL  plan-1  H18  0.020
 BPL  plan-1  H19  0.020
 BPL  plan-1  H20  0.020
 BPL  plan-2  C8   0.020
 BPL  plan-2  N21  0.020
 BPL  plan-2  C22  0.020
 BPL  plan-2  O23  0.020
 BPL  plan-2  N24  0.020
 BPL  plan-2  C25  0.020
 BPL  plan-2  H21  0.020
 BPL  plan-2  H24  0.020

