# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 09:08:20 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-(naphthalen-1-ylmethoxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1OCc2cccc3ccccc23
#
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
 5B9  5B9  '2-(naphthalen-1-ylmethoxy)benzoic acid'  ligand  34  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5B9
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
 5B9  C1   C  CR66   0   0.118  -2.7323  -0.2703   0.0303
 5B9  C2   C  CR6    0   0.014  -1.3944   0.2179  -0.0348
 5B9  C3   C  CR66   0   0.109  -3.8092   0.6564   0.0125
 5B9  C11  C  CR16   0  -0.244  -2.2440   2.4819  -0.1424
 5B9  C12  C  CR16   0  -0.262  -5.4016  -1.1613   0.1595
 5B9  C13  C  CR6    0   0.381   2.1214  -0.7243  -0.0099
 5B9  C14  C  CR6    0  -0.166   3.2891   0.0506   0.0762
 5B9  C15  C  CR16   0  -0.386   2.2024  -2.1115  -0.1203
 5B9  C16  C  CR16   0  -0.279   4.5121  -0.6094   0.0607
 5B9  C17  C  C      0   0.380   3.2795   1.5731   0.1710
 5B9  C18  C  CR16   0  -0.255   3.4433  -2.7358  -0.1662
 5B9  C19  C  CR16   0  -0.274   4.6057  -1.9888  -0.0790
 5B9  C4   C  CR16   0  -0.345  -3.0403  -1.6511   0.1096
 5B9  C5   C  CH2    0  -0.223  -0.2581  -0.7686  -0.0226
 5B9  C6   C  CR16   0  -0.350  -1.1697   1.5678  -0.1234
 5B9  C7   C  CR16   0  -0.326  -3.5339   2.0414  -0.0743
 5B9  C8   C  CR16   0  -0.311  -5.1386   0.1788   0.0805
 5B9  C9   C  CR16   0  -0.246  -4.3378  -2.0844   0.1725
 5B9  O10  O  O2     0  -0.463   0.9501  -0.0615   0.0650
 5B9  O20  O  OC    -1  -0.600   4.1013   2.0679   0.9661
 5B9  O21  O  O      0  -0.586   2.4931   2.1872  -0.5719
 5B9  H1   H  HCR6   0   0.256  -2.0341   3.5414  -0.2116
 5B9  H2   H  HCR6   0   0.258  -6.4230  -1.5151   0.2121
 5B9  H3   H  HCR6   0   0.276   1.3124  -2.7245  -0.1689
 5B9  H4   H  HCR6   0   0.246   5.4164  -0.0209   0.1510
 5B9  H5   H  HCR6   0   0.254   3.4888  -3.8131  -0.2608
 5B9  H6   H  HCR6   0   0.245   5.5741  -2.4711  -0.1084
 5B9  H7   H  HCR6   0   0.253  -2.2478  -2.3875   0.1197
 5B9  H8   H  HCH2   0   0.236  -0.3642  -1.4587   0.8243
 5B9  H9   H  HCH2   0   0.242  -0.2910  -1.3789  -0.9352
 5B9  H10  H  HCR6   0   0.278  -0.1579   1.9468  -0.1846
 5B9  H11  H  HCR6   0   0.254  -4.3592   2.7426  -0.0877
 5B9  H12  H  HCR6   0   0.257  -5.9500   0.8966   0.0681
 5B9  H13  H  HCR6   0   0.260  -4.5471  -3.1445   0.2329

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
 5B9  O21  C17  deloc     1.244  0.020  1.244
 5B9  O20  C17  deloc     1.246  0.020  1.246
 5B9  C17  C14  single    1.525  0.020  1.525
 5B9  C14  C16  aromatic  1.390  0.020  1.390
 5B9  C14  C13  aromatic  1.404  0.020  1.404
 5B9  C11  C7   aromatic  1.365  0.020  1.365
 5B9  C11  C6   aromatic  1.411  0.020  1.411
 5B9  C7   C3   aromatic  1.415  0.020  1.415
 5B9  C16  C19  aromatic  1.390  0.020  1.390
 5B9  O10  C13  single    1.348  0.020  1.348
 5B9  O10  C5   single    1.403  0.020  1.403
 5B9  C6   C2   aromatic  1.371  0.020  1.371
 5B9  C3   C8   aromatic  1.414  0.020  1.414
 5B9  C3   C1   aromatic  1.421  0.020  1.421
 5B9  C8   C12  aromatic  1.368  0.020  1.368
 5B9  C13  C15  aromatic  1.394  0.020  1.394
 5B9  C2   C1   aromatic  1.426  0.020  1.426
 5B9  C2   C5   single    1.505  0.020  1.505
 5B9  C1   C4   aromatic  1.417  0.020  1.417
 5B9  C12  C9   aromatic  1.409  0.020  1.409
 5B9  C19  C18  aromatic  1.384  0.020  1.384
 5B9  C4   C9   aromatic  1.369  0.020  1.369
 5B9  C15  C18  aromatic  1.390  0.020  1.390
 5B9  C11  H1   single    0.930  0.020  1.080
 5B9  C12  H2   single    0.930  0.020  1.080
 5B9  C15  H3   single    0.930  0.020  1.080
 5B9  C16  H4   single    0.930  0.020  1.080
 5B9  C18  H5   single    0.930  0.020  1.080
 5B9  C19  H6   single    0.930  0.020  1.080
 5B9  C4   H7   single    0.930  0.020  1.080
 5B9  C5   H8   single    0.970  0.020  1.090
 5B9  C5   H9   single    0.970  0.020  1.090
 5B9  C6   H10  single    0.930  0.020  1.080
 5B9  C7   H11  single    0.930  0.020  1.080
 5B9  C8   H12  single    0.930  0.020  1.080
 5B9  C9   H13  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
 5B9  C4   C1   C3   118.14  3.000
 5B9  C4   C1   C2   122.69  3.000
 5B9  C3   C1   C2   119.17  3.000
 5B9  C6   C2   C5   121.47  3.000
 5B9  C5   C2   C1   118.94  3.000
 5B9  C6   C2   C1   119.59  3.000
 5B9  C8   C3   C7   121.10  3.000
 5B9  C8   C3   C1   119.44  3.000
 5B9  C7   C3   C1   119.46  3.000
 5B9  H1   C11  C7   120.16  3.000
 5B9  H1   C11  C6   119.18  3.000
 5B9  C7   C11  C6   120.66  3.000
 5B9  H2   C12  C9   119.87  3.000
 5B9  H2   C12  C8   120.30  3.000
 5B9  C9   C12  C8   119.82  3.000
 5B9  O10  C13  C15  122.97  3.000
 5B9  C15  C13  C14  120.38  3.000
 5B9  O10  C13  C14  116.61  3.000
 5B9  C17  C14  C16  118.70  3.000
 5B9  C16  C14  C13  117.97  3.000
 5B9  C17  C14  C13  123.33  3.000
 5B9  H3   C15  C18  118.59  3.000
 5B9  H3   C15  C13  121.31  3.000
 5B9  C18  C15  C13  120.10  3.000
 5B9  H4   C16  C19  119.45  3.000
 5B9  H4   C16  C14  118.42  3.000
 5B9  C19  C16  C14  122.13  3.000
 5B9  O21  C17  O20  127.01  3.000
 5B9  O20  C17  C14  115.59  3.000
 5B9  O21  C17  C14  117.36  3.000
 5B9  H5   C18  C19  120.47  3.000
 5B9  H5   C18  C15  119.17  3.000
 5B9  C19  C18  C15  120.35  3.000
 5B9  H6   C19  C18  120.61  3.000
 5B9  H6   C19  C16  120.35  3.000
 5B9  C18  C19  C16  119.03  3.000
 5B9  H7   C4   C9   118.57  3.000
 5B9  H7   C4   C1   120.31  3.000
 5B9  C9   C4   C1   121.12  3.000
 5B9  H9   C5   H8   106.79  3.000
 5B9  H9   C5   O10  110.97  3.000
 5B9  H8   C5   O10  110.61  3.000
 5B9  H9   C5   C2   109.56  3.000
 5B9  H8   C5   C2   110.21  3.000
 5B9  O10  C5   C2   108.69  3.000
 5B9  H10  C6   C11  118.96  3.000
 5B9  H10  C6   C2   120.11  3.000
 5B9  C11  C6   C2   120.93  3.000
 5B9  H11  C7   C11  120.70  3.000
 5B9  H11  C7   C3   119.10  3.000
 5B9  C11  C7   C3   120.20  3.000
 5B9  H12  C8   C12  120.38  3.000
 5B9  H12  C8   C3   118.66  3.000
 5B9  C12  C8   C3   120.96  3.000
 5B9  H13  C9   C4   119.72  3.000
 5B9  H13  C9   C12  119.76  3.000
 5B9  C4   C9   C12  120.52  3.000
 5B9  C5   O10  C13  119.81  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
 5B9  CONST_01  C11  C7   C3   C1      0.00   0.0  0
 5B9  CONST_02  C12  C8   C3   C1      0.00   0.0  0
 5B9  CONST_03  C11  C6   C2   C1      0.00   0.0  0
 5B9  CONST_04  C12  C9   C4   C1      0.00   0.0  0
 5B9  CONST_05  C7   C11  C6   C2      0.00   0.0  0
 5B9  CONST_06  C7   C3   C1   C2      0.00   0.0  0
 5B9  CONST_07  C8   C3   C1   C2    180.00   0.0  0
 5B9  CONST_08  C9   C4   C1   C2    180.00   0.0  0
 5B9  CONST_09  C6   C11  C7   C3      0.00   0.0  0
 5B9  CONST_10  C9   C12  C8   C3      0.00   0.0  0
 5B9  CONST_11  C6   C2   C1   C3      0.00   0.0  0
 5B9  CONST_12  C9   C4   C1   C3      0.00   0.0  0
 5B9  CONST_13  C8   C3   C7   C11   180.00   0.0  0
 5B9  CONST_14  C7   C3   C8   C12   180.00   0.0  0
 5B9  CONST_15  C19  C16  C14  C13     0.00   0.0  0
 5B9  CONST_16  C19  C18  C15  C13     0.00   0.0  0
 5B9  CONST_17  C18  C19  C16  C14     0.00   0.0  0
 5B9  CONST_18  C18  C15  C13  C14     0.00   0.0  0
 5B9  CONST_19  C16  C14  C13  C15     0.00   0.0  0
 5B9  CONST_20  C16  C19  C18  C15     0.00   0.0  0
 5B9  CONST_21  C7   C3   C1   C4    180.00   0.0  0
 5B9  CONST_22  C8   C3   C1   C4      0.00   0.0  0
 5B9  CONST_23  C6   C2   C1   C4    180.00   0.0  0
 5B9  CONST_24  C8   C12  C9   C4      0.00   0.0  0
 5B9  CONST_25  C5   C2   C1   C3    180.00   0.0  0
 5B9  CONST_26  C5   C2   C6   C11   180.00   0.0  0
 5B9  CONST_27  C17  C14  C13  C15   180.00   0.0  0
 5B9  CONST_28  O10  C13  C14  C16   180.00   0.0  0
 5B9  CONST_29  C19  C16  C14  C17   180.00   0.0  0
 5B9  CONST_30  O10  C13  C15  C18   180.00   0.0  0
 5B9  CONST_31  C5   C2   C1   C4      0.00   0.0  0
 5B9  CONST_32  H11  C7   C3   C1    180.00   0.0  0
 5B9  CONST_33  H12  C8   C3   C1    180.00   0.0  0
 5B9  CONST_34  H10  C6   C2   C1    180.00   0.0  0
 5B9  CONST_35  H13  C9   C4   C1    180.00   0.0  0
 5B9  CONST_36  H1   C11  C6   C2    180.00   0.0  0
 5B9  CONST_37  H7   C4   C1   C2      0.00   0.0  0
 5B9  CONST_38  H2   C12  C8   C3    180.00   0.0  0
 5B9  CONST_39  H4   C16  C14  C13   180.00   0.0  0
 5B9  CONST_40  H5   C18  C15  C13   180.00   0.0  0
 5B9  CONST_41  H6   C19  C16  C14   180.00   0.0  0
 5B9  CONST_42  H3   C15  C13  C14   180.00   0.0  0
 5B9  Var_01    O10  C5   C2   C1   -173.13  30.0  2
 5B9  Var_02    O21  C17  C14  C13   -43.03  30.0  2

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
 5B9  plan-1  C13  0.020
 5B9  plan-1  C14  0.020
 5B9  plan-1  C15  0.020
 5B9  plan-1  C16  0.020
 5B9  plan-1  C17  0.020
 5B9  plan-1  C18  0.020
 5B9  plan-1  C19  0.020
 5B9  plan-1  O10  0.020
 5B9  plan-1  H3   0.020
 5B9  plan-1  H4   0.020
 5B9  plan-1  H5   0.020
 5B9  plan-1  H6   0.020
 5B9  plan-2  C1   0.020
 5B9  plan-2  C2   0.020
 5B9  plan-2  C3   0.020
 5B9  plan-2  C11  0.020
 5B9  plan-2  C12  0.020
 5B9  plan-2  C4   0.020
 5B9  plan-2  C5   0.020
 5B9  plan-2  C6   0.020
 5B9  plan-2  C7   0.020
 5B9  plan-2  C8   0.020
 5B9  plan-2  C9   0.020
 5B9  plan-2  H1   0.020
 5B9  plan-2  H2   0.020
 5B9  plan-2  H7   0.020
 5B9  plan-2  H10  0.020
 5B9  plan-2  H11  0.020
 5B9  plan-2  H12  0.020
 5B9  plan-2  H13  0.020
 5B9  plan-3  C14  0.020
 5B9  plan-3  C17  0.020
 5B9  plan-3  O20  0.020
 5B9  plan-3  O21  0.020

