# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:36:04 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(Cc1cccc2ccccc12)Cc3cccc4ccccc34
#
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
 BNA  BNA  '3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanoic acid'  ligand  45  26  .  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_BNA
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
 BNA  OXT   O  OC    -1  -0.609   3.2046  30.7927  17.7459
 BNA  C     C  C      0   0.412   3.4080  29.5735  17.5661
 BNA  O     O  O      0  -0.595   3.1229  28.9096  16.5505
 BNA  CA    C  CH1    0  -0.364   4.1542  28.8314  18.7006
 BNA  CB1   C  CH2    0  -0.476   3.6858  27.3998  18.9061
 BNA  C1A   C  CR6    0   0.114   2.2693  27.2265  19.3892
 BNA  C2A   C  CR16   0  -0.355   1.4699  28.2909  19.7241
 BNA  C3A   C  CR16   0  -0.237   0.1490  28.1132  20.1872
 BNA  C4A   C  CR16   0  -0.335  -0.3802  26.8618  20.3122
 BNA  C11   C  CR66   0   0.111   0.4006  25.7288  19.9828
 BNA  C5A   C  CR16   0  -0.311  -0.1253  24.4212  20.1043
 BNA  C6A   C  CR16   0  -0.261   0.6316  23.3259  19.7901
 BNA  C7A   C  CR16   0  -0.247   1.9553  23.4952  19.3405
 BNA  C8A   C  CR16   0  -0.333   2.4898  24.7499  19.2128
 BNA  C12   C  CR66   0   0.081   1.7339  25.9069  19.5242
 BNA  CB2   C  CH2    0  -0.544   5.6573  28.8658  18.3472
 BNA  C1B   C  C      0   0.131   6.5629  28.4185  19.4587
 BNA  C2B   C  C1     0  -0.337   7.1509  27.1786  19.4094
 BNA  C3B   C  C1     0  -0.241   7.9859  26.7073  20.4417
 BNA  C4B   C  C1     0  -0.337   8.2341  27.4882  21.5342
 BNA  C13   C  CR6    0   0.115   7.6587  28.7770  21.6322
 BNA  C5B   C  CR16   0  -0.310   7.9123  29.6023  22.7533
 BNA  C6B   C  CR16   0  -0.259   7.3619  30.8507  22.8458
 BNA  C7B   C  CR16   0  -0.252   6.5336  31.3307  21.8120
 BNA  C8B   C  CR16   0  -0.335   6.2697  30.5546  20.7153
 BNA  C14   C  CR6    0   0.076   6.8176  29.2531  20.5893
 BNA  HA    H  HCH1   0   0.219   4.0186  29.3913  19.6305
 BNA  HB11  H  HCH2   0   0.243   4.3502  26.9018  19.6209
 BNA  HB12  H  HCH2   0   0.231   3.8125  26.8574  17.9644
 BNA  H2A   H  HCR6   0   0.247   1.8409  29.3024  19.6273
 BNA  H3A   H  HCR6   0   0.249  -0.4433  28.9837  20.4387
 BNA  H4A   H  HCR6   0   0.248  -1.3958  26.7204  20.6624
 BNA  H5A   H  HCR6   0   0.251  -1.1443  24.3005  20.4531
 BNA  H6A   H  HCR6   0   0.253   0.2179  22.3304  19.8869
 BNA  H7A   H  HCR6   0   0.253   2.5535  22.6272  19.0947
 BNA  H8A   H  HCR6   0   0.253   3.5095  24.8514  18.8669
 BNA  HB21  H  HCH2   0   0.248   5.9217  29.8812  18.0381
 BNA  HB22  H  HCH2   0   0.247   5.8262  28.2288  17.4755
 BNA  H2B   H  H      0   0.248   6.9702  26.5416  18.5513
 BNA  H3B   H  H      0   0.251   8.4286  25.7227  20.3614
 BNA  H4B   H  H      0   0.250   8.8739  27.1357  22.3345
 BNA  H5B   H  HCR6   0   0.252   8.5542  29.2269  23.5415
 BNA  H6B   H  HCR6   0   0.254   7.5619  31.4733  23.7081
 BNA  H7B   H  HCR6   0   0.254   6.1030  32.3209  21.8868
 BNA  H8B   H  HCR6   0   0.246   5.6302  30.9482  19.9359

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
 BNA  OXT  C     deloc     1.249  0.020  1.249
 BNA  C    O     deloc     1.246  0.020  1.246
 BNA  C    CA    single    1.547  0.020  1.547
 BNA  CA   CB1   single    1.520  0.020  1.520
 BNA  CA   CB2   single    1.544  0.020  1.544
 BNA  CA   HA    single    0.970  0.020  1.090
 BNA  CB1  C1A   single    1.507  0.020  1.507
 BNA  CB1  HB11  single    0.970  0.020  1.090
 BNA  CB1  HB12  single    0.970  0.020  1.090
 BNA  C1A  C2A   aromatic  1.373  0.020  1.373
 BNA  C1A  C12   aromatic  1.430  0.020  1.430
 BNA  C2A  C3A   aromatic  1.411  0.020  1.411
 BNA  C2A  H2A   single    0.930  0.020  1.080
 BNA  C3A  C4A   aromatic  1.364  0.020  1.364
 BNA  C3A  H3A   single    0.930  0.020  1.080
 BNA  C4A  C11   aromatic  1.415  0.020  1.415
 BNA  C4A  H4A   single    0.930  0.020  1.080
 BNA  C11  C5A   aromatic  1.415  0.020  1.415
 BNA  C11  C12   aromatic  1.421  0.020  1.421
 BNA  C5A  C6A   aromatic  1.368  0.020  1.368
 BNA  C5A  H5A   single    0.930  0.020  1.080
 BNA  C6A  C7A   aromatic  1.408  0.020  1.408
 BNA  C6A  H6A   single    0.930  0.020  1.080
 BNA  C7A  C8A   aromatic  1.370  0.020  1.370
 BNA  C7A  H7A   single    0.930  0.020  1.080
 BNA  C8A  C12   aromatic  1.417  0.020  1.417
 BNA  C8A  H8A   single    0.930  0.020  1.080
 BNA  CB2  C1B   single    1.502  0.020  1.502
 BNA  CB2  HB21  single    0.970  0.020  1.090
 BNA  CB2  HB22  single    0.970  0.020  1.090
 BNA  C1B  C2B   aromatic  1.373  0.020  1.373
 BNA  C1B  C14   aromatic  1.428  0.020  1.428
 BNA  C2B  C3B   aromatic  1.409  0.020  1.409
 BNA  C2B  H2B   single    0.930  0.020  1.080
 BNA  C3B  C4B   aromatic  1.366  0.020  1.366
 BNA  C3B  H3B   single    0.930  0.020  1.080
 BNA  C4B  C13   aromatic  1.415  0.020  1.415
 BNA  C4B  H4B   single    0.930  0.020  1.080
 BNA  C13  C5B   aromatic  1.415  0.020  1.415
 BNA  C13  C14   aromatic  1.422  0.020  1.422
 BNA  C5B  C6B   aromatic  1.367  0.020  1.367
 BNA  C5B  H5B   single    0.930  0.020  1.080
 BNA  C6B  C7B   aromatic  1.409  0.020  1.409
 BNA  C6B  H6B   single    0.930  0.020  1.080
 BNA  C7B  C8B   aromatic  1.369  0.020  1.369
 BNA  C7B  H7B   single    0.930  0.020  1.080
 BNA  C8B  C14   aromatic  1.418  0.020  1.418
 BNA  C8B  H8B   single    0.930  0.020  1.080

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
 BNA  CA    C    O     116.89  3.000
 BNA  CA    C    OXT   116.18  3.000
 BNA  O     C    OXT   126.86  3.000
 BNA  HA    CA   CB2   107.68  3.000
 BNA  HA    CA   CB1   109.20  3.000
 BNA  CB2   CA   CB1   110.60  3.000
 BNA  HA    CA   C     108.54  3.000
 BNA  CB2   CA   C     106.91  3.000
 BNA  CB1   CA   C     113.71  3.000
 BNA  HB12  CB1  HB11  105.43  3.000
 BNA  HB12  CB1  C1A   109.13  3.000
 BNA  HB11  CB1  C1A   107.97  3.000
 BNA  HB12  CB1  CA    108.35  3.000
 BNA  HB11  CB1  CA    109.24  3.000
 BNA  C1A   CB1  CA    116.19  3.000
 BNA  C12   C1A  C2A   118.31  3.000
 BNA  C12   C1A  CB1   119.23  3.000
 BNA  C2A   C1A  CB1   122.46  3.000
 BNA  H2A   C2A  C3A   117.92  3.000
 BNA  H2A   C2A  C1A   120.23  3.000
 BNA  C3A   C2A  C1A   121.85  3.000
 BNA  H3A   C3A  C4A   120.26  3.000
 BNA  H3A   C3A  C2A   119.16  3.000
 BNA  C4A   C3A  C2A   120.58  3.000
 BNA  H4A   C4A  C11   119.21  3.000
 BNA  H4A   C4A  C3A   120.85  3.000
 BNA  C11   C4A  C3A   119.93  3.000
 BNA  C12   C11  C5A   119.49  3.000
 BNA  C12   C11  C4A   119.51  3.000
 BNA  C5A   C11  C4A   121.00  3.000
 BNA  H5A   C5A  C6A   120.33  3.000
 BNA  H5A   C5A  C11   118.70  3.000
 BNA  C6A   C5A  C11   120.98  3.000
 BNA  H6A   C6A  C7A   119.89  3.000
 BNA  H6A   C6A  C5A   120.30  3.000
 BNA  C7A   C6A  C5A   119.81  3.000
 BNA  H7A   C7A  C8A   119.85  3.000
 BNA  H7A   C7A  C6A   119.70  3.000
 BNA  C8A   C7A  C6A   120.44  3.000
 BNA  H8A   C8A  C12   119.78  3.000
 BNA  H8A   C8A  C7A   118.93  3.000
 BNA  C12   C8A  C7A   121.29  3.000
 BNA  C8A   C12  C11   117.98  3.000
 BNA  C8A   C12  C1A   122.20  3.000
 BNA  C11   C12  C1A   119.82  3.000
 BNA  HB22  CB2  HB21  106.17  3.000
 BNA  HB22  CB2  C1B   108.87  3.000
 BNA  HB21  CB2  C1B   109.86  3.000
 BNA  HB22  CB2  CA    108.66  3.000
 BNA  HB21  CB2  CA    108.70  3.000
 BNA  C1B   CB2  CA    114.26  3.000
 BNA  C14   C1B  C2B   118.67  3.000
 BNA  C14   C1B  CB2   121.29  3.000
 BNA  C2B   C1B  CB2   120.03  3.000
 BNA  H2B   C2B  C3B   118.83  3.000
 BNA  H2B   C2B  C1B   119.20  3.000
 BNA  C3B   C2B  C1B   121.97  3.000
 BNA  H3B   C3B  C4B   120.34  3.000
 BNA  H3B   C3B  C2B   119.49  3.000
 BNA  C4B   C3B  C2B   120.17  3.000
 BNA  H4B   C4B  C13   119.03  3.000
 BNA  H4B   C4B  C3B   120.81  3.000
 BNA  C13   C4B  C3B   120.16  3.000
 BNA  C14   C13  C5B   119.46  3.000
 BNA  C14   C13  C4B   119.66  3.000
 BNA  C5B   C13  C4B   120.89  3.000
 BNA  H5B   C5B  C6B   120.36  3.000
 BNA  H5B   C5B  C13   118.71  3.000
 BNA  C6B   C5B  C13   120.93  3.000
 BNA  H6B   C6B  C7B   119.82  3.000
 BNA  H6B   C6B  C5B   120.31  3.000
 BNA  C7B   C6B  C5B   119.87  3.000
 BNA  H7B   C7B  C8B   119.82  3.000
 BNA  H7B   C7B  C6B   119.66  3.000
 BNA  C8B   C7B  C6B   120.52  3.000
 BNA  H8B   C8B  C14   119.88  3.000
 BNA  H8B   C8B  C7B   118.98  3.000
 BNA  C14   C8B  C7B   121.14  3.000
 BNA  C8B   C14  C13   118.09  3.000
 BNA  C8B   C14  C1B   122.54  3.000
 BNA  C13   C14  C1B   119.37  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
 BNA  CONST_01  C4A  C3A  C2A  C1A    0.00   0.0  0
 BNA  CONST_02  C4A  C11  C12  C1A    0.00   0.0  0
 BNA  CONST_03  C5A  C11  C12  C1A  180.00   0.0  0
 BNA  CONST_04  C7A  C8A  C12  C1A  180.00   0.0  0
 BNA  CONST_05  C11  C12  C1A  C2A    0.00   0.0  0
 BNA  CONST_06  C8A  C12  C1A  C2A  180.00   0.0  0
 BNA  CONST_07  C11  C4A  C3A  C2A    0.00   0.0  0
 BNA  CONST_08  C12  C1A  C2A  C3A    0.00   0.0  0
 BNA  CONST_09  C5A  C11  C4A  C3A  180.00   0.0  0
 BNA  CONST_10  C12  C11  C4A  C3A    0.00   0.0  0
 BNA  CONST_11  C6A  C5A  C11  C4A  180.00   0.0  0
 BNA  CONST_12  C8A  C12  C11  C4A  180.00   0.0  0
 BNA  CONST_13  C7A  C6A  C5A  C11    0.00   0.0  0
 BNA  CONST_14  C7A  C8A  C12  C11    0.00   0.0  0
 BNA  CONST_15  C8A  C12  C11  C5A    0.00   0.0  0
 BNA  CONST_16  C8A  C7A  C6A  C5A    0.00   0.0  0
 BNA  CONST_17  C12  C11  C5A  C6A    0.00   0.0  0
 BNA  CONST_18  C12  C8A  C7A  C6A    0.00   0.0  0
 BNA  CONST_19  C4B  C3B  C2B  C1B    0.00   0.0  0
 BNA  CONST_20  C4B  C13  C14  C1B    0.00   0.0  0
 BNA  CONST_21  C5B  C13  C14  C1B  180.00   0.0  0
 BNA  CONST_22  C7B  C8B  C14  C1B  180.00   0.0  0
 BNA  CONST_23  C13  C14  C1B  C2B    0.00   0.0  0
 BNA  CONST_24  C8B  C14  C1B  C2B  180.00   0.0  0
 BNA  CONST_25  C13  C4B  C3B  C2B    0.00   0.0  0
 BNA  CONST_26  C14  C1B  C2B  C3B    0.00   0.0  0
 BNA  CONST_27  C5B  C13  C4B  C3B  180.00   0.0  0
 BNA  CONST_28  C14  C13  C4B  C3B    0.00   0.0  0
 BNA  CONST_29  C6B  C5B  C13  C4B  180.00   0.0  0
 BNA  CONST_30  C8B  C14  C13  C4B  180.00   0.0  0
 BNA  CONST_31  C7B  C6B  C5B  C13    0.00   0.0  0
 BNA  CONST_32  C7B  C8B  C14  C13    0.00   0.0  0
 BNA  CONST_33  C8B  C14  C13  C5B    0.00   0.0  0
 BNA  CONST_34  C8B  C7B  C6B  C5B    0.00   0.0  0
 BNA  CONST_35  C14  C13  C5B  C6B    0.00   0.0  0
 BNA  CONST_36  C14  C8B  C7B  C6B    0.00   0.0  0
 BNA  CONST_37  C3A  C2A  C1A  CB1  180.00   0.0  0
 BNA  CONST_38  C11  C12  C1A  CB1  180.00   0.0  0
 BNA  CONST_39  C8A  C12  C1A  CB1    0.00   0.0  0
 BNA  CONST_40  C3B  C2B  C1B  CB2  180.00   0.0  0
 BNA  CONST_41  C13  C14  C1B  CB2  180.00   0.0  0
 BNA  CONST_42  C8B  C14  C1B  CB2    0.00   0.0  0
 BNA  CONST_43  H3A  C3A  C2A  C1A  180.00   0.0  0
 BNA  CONST_44  H8A  C8A  C12  C1A    0.00   0.0  0
 BNA  CONST_45  H4A  C4A  C3A  C2A  180.00   0.0  0
 BNA  CONST_46  H2A  C2A  C3A  C4A  180.00   0.0  0
 BNA  CONST_47  H5A  C5A  C11  C4A    0.00   0.0  0
 BNA  CONST_48  H6A  C6A  C5A  C11  180.00   0.0  0
 BNA  CONST_49  H7A  C7A  C6A  C5A  180.00   0.0  0
 BNA  CONST_50  H3B  C3B  C2B  C1B  180.00   0.0  0
 BNA  CONST_51  H8B  C8B  C14  C1B    0.00   0.0  0
 BNA  CONST_52  H4B  C4B  C3B  C2B  180.00   0.0  0
 BNA  CONST_53  H2B  C2B  C3B  C4B  180.00   0.0  0
 BNA  CONST_54  H5B  C5B  C13  C4B    0.00   0.0  0
 BNA  CONST_55  H6B  C6B  C5B  C13  180.00   0.0  0
 BNA  CONST_56  H7B  C7B  C6B  C5B  180.00   0.0  0
 BNA  Var_01    C2A  C1A  CB1  CA    -4.74  30.0  2
 BNA  Var_02    C2B  C1B  CB2  CA   104.61  30.0  2
 BNA  Var_03    C1A  CB1  CA   C    -65.51  30.0  3
 BNA  Var_04    C1B  CB2  CA   C    169.14  30.0  3
 BNA  Var_05    CB1  CA   C    OXT  144.89  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
 BNA  plan-1  CB1  0.020
 BNA  plan-1  C1A  0.020
 BNA  plan-1  C2A  0.020
 BNA  plan-1  C3A  0.020
 BNA  plan-1  C4A  0.020
 BNA  plan-1  C11  0.020
 BNA  plan-1  C5A  0.020
 BNA  plan-1  C6A  0.020
 BNA  plan-1  C7A  0.020
 BNA  plan-1  C8A  0.020
 BNA  plan-1  C12  0.020
 BNA  plan-1  H2A  0.020
 BNA  plan-1  H3A  0.020
 BNA  plan-1  H4A  0.020
 BNA  plan-1  H5A  0.020
 BNA  plan-1  H6A  0.020
 BNA  plan-1  H7A  0.020
 BNA  plan-1  H8A  0.020
 BNA  plan-2  CB2  0.020
 BNA  plan-2  C1B  0.020
 BNA  plan-2  C2B  0.020
 BNA  plan-2  C3B  0.020
 BNA  plan-2  C4B  0.020
 BNA  plan-2  C13  0.020
 BNA  plan-2  C5B  0.020
 BNA  plan-2  C6B  0.020
 BNA  plan-2  C7B  0.020
 BNA  plan-2  C8B  0.020
 BNA  plan-2  C14  0.020
 BNA  plan-2  H2B  0.020
 BNA  plan-2  H3B  0.020
 BNA  plan-2  H4B  0.020
 BNA  plan-2  H5B  0.020
 BNA  plan-2  H6B  0.020
 BNA  plan-2  H7B  0.020
 BNA  plan-2  H8B  0.020
 BNA  plan-3  OXT  0.020
 BNA  plan-3  C    0.020
 BNA  plan-3  O    0.020
 BNA  plan-3  CA   0.020

