# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:23:18 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: benzyl pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(OCc1ccccc1)c2cccnc2
#
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
 0OM  0OM  'benzyl pyridine-3-carboxylate'  ligand  27  16  .  2022-03-09  2022-03-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0OM
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
 0OM  CAG  C  CR16  0  -0.291  -3.0290  -0.0975   1.2086
 0OM  CAC  C  CR16  0  -0.242  -4.1151   0.7672   1.1996
 0OM  CAB  C  CR16  0  -0.261  -4.6197   1.2355  -0.0065
 0OM  CAD  C  CR16  0  -0.242  -4.0366   0.8349  -1.2021
 0OM  CAH  C  CR16  0  -0.288  -2.9520  -0.0309  -1.1895
 0OM  CAO  C  CR6   0   0.079  -2.4408  -0.5052   0.0152
 0OM  CAK  C  CH2   0  -0.253  -1.2615  -1.4272   0.0264
 0OM  OAM  O  O2    0  -0.455  -0.0816  -0.6036   0.0265
 0OM  CAN  C  C     0   0.608   1.0922  -1.2103   0.0227
 0OM  OAA  O  O     0  -0.446   1.2342  -2.4089   0.0293
 0OM  CAP  C  CR6   0  -0.176   2.2263  -0.2534   0.0106
 0OM  CAI  C  CR16  0  -0.140   3.5271  -0.7460   0.0432
 0OM  CAE  C  CR16  0  -0.316   4.5798   0.1504   0.0306
 0OM  CAF  C  CR16  0  -0.048   4.2902   1.5067  -0.0165
 0OM  NAL  N  N     0  -0.400   3.0535   1.9903  -0.0502
 0OM  CAJ  C  CR16  0  -0.051   2.0472   1.1279  -0.0360
 0OM  H1   H  HCR6  0   0.257  -2.6401  -0.4629   2.1517
 0OM  H2   H  HCR6  0   0.259  -4.5694   1.0708   2.1338
 0OM  H3   H  HCR6  0   0.260  -5.4686   1.9067  -0.0153
 0OM  H4   H  HCR6  0   0.260  -4.4297   1.1923  -2.1450
 0OM  H5   H  HCR6  0   0.256  -2.5039  -0.3451  -2.1248
 0OM  H6   H  HCH2  0   0.258  -1.2664  -2.0617   0.9145
 0OM  H7   H  HCH2  0   0.258  -1.2576  -2.0711  -0.8550
 0OM  H8   H  HCR6  0   0.281   3.7098  -1.8117   0.0788
 0OM  H9   H  HCR6  0   0.281   5.6056  -0.1885   0.0562
 0OM  H10  H  HCR6  0   0.277   5.0935   2.2342  -0.0279
 0OM  H11  H  HCR6  0   0.274   1.0527   1.5563  -0.0653

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
 0OM  NAL  CAJ  aromatic  1.325  0.020  1.325
 0OM  NAL  CAF  aromatic  1.328  0.020  1.328
 0OM  CAJ  CAP  aromatic  1.394  0.020  1.394
 0OM  OAA  CAN  double    1.207  0.020  1.207
 0OM  CAF  CAE  aromatic  1.388  0.020  1.388
 0OM  CAP  CAN  single    1.484  0.020  1.484
 0OM  CAP  CAI  aromatic  1.391  0.020  1.391
 0OM  CAN  OAM  single    1.321  0.020  1.321
 0OM  CAE  CAI  aromatic  1.383  0.020  1.383
 0OM  OAM  CAK  single    1.439  0.020  1.439
 0OM  CAK  CAO  single    1.497  0.020  1.497
 0OM  CAO  CAH  aromatic  1.392  0.020  1.392
 0OM  CAO  CAG  aromatic  1.392  0.020  1.392
 0OM  CAH  CAD  aromatic  1.388  0.020  1.388
 0OM  CAG  CAC  aromatic  1.388  0.020  1.388
 0OM  CAD  CAB  aromatic  1.389  0.020  1.389
 0OM  CAC  CAB  aromatic  1.389  0.020  1.389
 0OM  CAG  H1   single    0.930  0.020  1.080
 0OM  CAC  H2   single    0.930  0.020  1.080
 0OM  CAB  H3   single    0.930  0.020  1.080
 0OM  CAD  H4   single    0.930  0.020  1.080
 0OM  CAH  H5   single    0.930  0.020  1.080
 0OM  CAK  H6   single    0.970  0.020  1.090
 0OM  CAK  H7   single    0.970  0.020  1.090
 0OM  CAI  H8   single    0.930  0.020  1.080
 0OM  CAE  H9   single    0.930  0.020  1.080
 0OM  CAF  H10  single    0.930  0.020  1.080
 0OM  CAJ  H11  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
 0OM  H1   CAG  CAO  119.73  3.000
 0OM  H1   CAG  CAC  119.77  3.000
 0OM  CAO  CAG  CAC  120.51  3.000
 0OM  H2   CAC  CAB  120.17  3.000
 0OM  H2   CAC  CAG  119.84  3.000
 0OM  CAB  CAC  CAG  119.99  3.000
 0OM  H3   CAB  CAD  120.07  3.000
 0OM  H3   CAB  CAC  120.08  3.000
 0OM  CAD  CAB  CAC  119.85  3.000
 0OM  H4   CAD  CAH  119.85  3.000
 0OM  H4   CAD  CAB  120.14  3.000
 0OM  CAH  CAD  CAB  120.01  3.000
 0OM  H5   CAH  CAO  119.76  3.000
 0OM  H5   CAH  CAD  119.75  3.000
 0OM  CAO  CAH  CAD  120.49  3.000
 0OM  CAK  CAO  CAH  120.37  3.000
 0OM  CAH  CAO  CAG  119.16  3.000
 0OM  CAK  CAO  CAG  120.47  3.000
 0OM  H7   CAK  H6   108.31  3.000
 0OM  H7   CAK  OAM  109.56  3.000
 0OM  H6   CAK  OAM  109.66  3.000
 0OM  H7   CAK  CAO  111.11  3.000
 0OM  H6   CAK  CAO  111.13  3.000
 0OM  OAM  CAK  CAO  107.06  3.000
 0OM  CAN  OAM  CAK  117.75  3.000
 0OM  CAP  CAN  OAA  123.40  3.000
 0OM  CAP  CAN  OAM  112.51  3.000
 0OM  OAA  CAN  OAM  124.09  3.000
 0OM  CAJ  CAP  CAI  118.15  3.000
 0OM  CAI  CAP  CAN  119.08  3.000
 0OM  CAJ  CAP  CAN  122.77  3.000
 0OM  H8   CAI  CAE  120.69  3.000
 0OM  H8   CAI  CAP  120.49  3.000
 0OM  CAE  CAI  CAP  118.82  3.000
 0OM  H9   CAE  CAF  120.36  3.000
 0OM  H9   CAE  CAI  121.28  3.000
 0OM  CAF  CAE  CAI  118.37  3.000
 0OM  H10  CAF  NAL  116.45  3.000
 0OM  H10  CAF  CAE  120.12  3.000
 0OM  NAL  CAF  CAE  123.44  3.000
 0OM  CAJ  NAL  CAF  118.01  3.000
 0OM  H11  CAJ  NAL  116.07  3.000
 0OM  H11  CAJ  CAP  120.72  3.000
 0OM  NAL  CAJ  CAP  123.21  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
 0OM  CONST_01  CAD  CAH  CAO  CAG    0.00   0.0  0
 0OM  CONST_02  CAD  CAB  CAC  CAG    0.00   0.0  0
 0OM  CONST_03  CAH  CAO  CAG  CAC    0.00   0.0  0
 0OM  CONST_04  CAH  CAD  CAB  CAC    0.00   0.0  0
 0OM  CONST_05  CAO  CAH  CAD  CAB    0.00   0.0  0
 0OM  CONST_06  CAO  CAG  CAC  CAB    0.00   0.0  0
 0OM  CONST_07  CAF  NAL  CAJ  CAP    0.00   0.0  0
 0OM  CONST_08  CAF  CAE  CAI  CAP    0.00   0.0  0
 0OM  CONST_09  NAL  CAJ  CAP  CAI    0.00   0.0  0
 0OM  CONST_10  NAL  CAF  CAE  CAI    0.00   0.0  0
 0OM  CONST_11  CAJ  NAL  CAF  CAE    0.00   0.0  0
 0OM  CONST_12  CAJ  CAP  CAI  CAE    0.00   0.0  0
 0OM  CONST_13  CAK  CAO  CAG  CAC  180.00   0.0  0
 0OM  CONST_14  CAK  CAO  CAH  CAD  180.00   0.0  0
 0OM  CONST_15  NAL  CAJ  CAP  CAN  180.00   0.0  0
 0OM  CONST_16  CAE  CAI  CAP  CAN  180.00   0.0  0
 0OM  CONST_17  H5   CAH  CAO  CAG  180.00   0.0  0
 0OM  CONST_18  H3   CAB  CAC  CAG  180.00   0.0  0
 0OM  CONST_19  H4   CAD  CAB  CAC  180.00   0.0  0
 0OM  CONST_20  H1   CAG  CAC  CAB  180.00   0.0  0
 0OM  CONST_21  H2   CAC  CAB  CAD  180.00   0.0  0
 0OM  CONST_22  H9   CAE  CAI  CAP  180.00   0.0  0
 0OM  CONST_23  H11  CAJ  CAP  CAI  180.00   0.0  0
 0OM  CONST_24  H10  CAF  CAE  CAI  180.00   0.0  0
 0OM  CONST_25  H8   CAI  CAE  CAF  180.00   0.0  0
 0OM  Var_01    OAM  CAK  CAO  CAG  -92.09  30.0  2
 0OM  Var_02    CAJ  CAP  CAN  OAM   -1.96  30.0  2
 0OM  Var_03    CAP  CAN  OAM  CAK  179.47  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
 0OM  plan-1  CAG  0.020
 0OM  plan-1  CAC  0.020
 0OM  plan-1  CAB  0.020
 0OM  plan-1  CAD  0.020
 0OM  plan-1  CAH  0.020
 0OM  plan-1  CAO  0.020
 0OM  plan-1  CAK  0.020
 0OM  plan-1  H1   0.020
 0OM  plan-1  H2   0.020
 0OM  plan-1  H3   0.020
 0OM  plan-1  H4   0.020
 0OM  plan-1  H5   0.020
 0OM  plan-2  CAN  0.020
 0OM  plan-2  CAP  0.020
 0OM  plan-2  CAI  0.020
 0OM  plan-2  CAE  0.020
 0OM  plan-2  CAF  0.020
 0OM  plan-2  NAL  0.020
 0OM  plan-2  CAJ  0.020
 0OM  plan-2  H8   0.020
 0OM  plan-2  H9   0.020
 0OM  plan-2  H10  0.020
 0OM  plan-2  H11  0.020
 0OM  plan-3  OAM  0.020
 0OM  plan-3  CAN  0.020
 0OM  plan-3  OAA  0.020
 0OM  plan-3  CAP  0.020

