# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:21:35 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-hydroxy-3-methoxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)C([O-])=O
#
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
 VNL  VNL  4-hydroxy-3-methoxybenzoate  ligand  19  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VNL
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
 VNL  C1   C  CR6    0  -0.108  -1.1652  -0.2590   0.0591
 VNL  CO1  C  CR16   0  -0.312  -0.8331  -1.6062   0.0417
 VNL  CO2  C  CR16   0  -0.424  -0.1351   0.6841   0.0120
 VNL  CM1  C  CR16   0  -0.333   0.4943  -2.0138  -0.0218
 VNL  CM2  C  CR6    0   0.312   1.1895   0.2892  -0.0524
 VNL  OM   O  O2     0  -0.494   2.2570   1.1217  -0.1016
 VNL  CZ   C  CR6    0   0.272   1.5135  -1.0778  -0.0702
 VNL  CC   C  C      0   0.396  -2.6142   0.1945   0.1272
 VNL  CV   C  CH3    0  -0.428   2.0254   2.5144  -0.0757
 VNL  O1   O  OC    -1  -0.598  -3.4819  -0.7007   0.1404
 VNL  O2   O  O      0  -0.598  -2.8169   1.4251   0.1634
 VNL  O3   O  OH1    0  -0.633   2.7950  -1.4949  -0.1320
 VNL  HO1  H  HCR6   0   0.240  -1.6156  -2.3515   0.0771
 VNL  HO2  H  HCR6   0   0.269  -0.3961   1.7342   0.0269
 VNL  HM1  H  HCR6   0   0.256   0.7464  -3.0676  -0.0351
 VNL  HV1  H  HCH3   0   0.228   1.5153   2.8240   0.8401
 VNL  HV2  H  HCH3   0   0.259   3.0010   2.9928  -0.1139
 VNL  HV3  H  HCH3   0   0.228   1.4366   2.8445  -0.9357
 VNL  HO3  H  HOH1   0   0.470   3.3882  -0.7345  -0.1630

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
 VNL  C1   CO1  aromatic  1.388  0.020  1.388
 VNL  C1   CO2  aromatic  1.397  0.020  1.397
 VNL  C1   CC   single    1.520  0.020  1.520
 VNL  CO1  CM1  aromatic  1.390  0.020  1.390
 VNL  CO1  HO1  single    0.930  0.020  1.080
 VNL  CO2  CM2  aromatic  1.384  0.020  1.384
 VNL  CO2  HO2  single    0.930  0.020  1.080
 VNL  CM1  CZ   aromatic  1.385  0.020  1.385
 VNL  CM1  HM1  single    0.930  0.020  1.080
 VNL  CM2  OM   single    1.355  0.020  1.355
 VNL  CM2  CZ   aromatic  1.405  0.020  1.405
 VNL  OM   CV   single    1.412  0.020  1.412
 VNL  CZ   O3   single    1.349  0.020  1.349
 VNL  CC   O1   deloc     1.247  0.020  1.247
 VNL  CC   O2   deloc     1.248  0.020  1.248
 VNL  CV   HV1  single    0.970  0.020  1.090
 VNL  CV   HV2  single    0.970  0.020  1.090
 VNL  CV   HV3  single    0.970  0.020  1.090
 VNL  O3   HO3  single    0.850  0.020  0.980

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
 VNL  CC   C1   CO2  120.19  3.000
 VNL  CC   C1   CO1  121.23  3.000
 VNL  CO2  C1   CO1  118.58  3.000
 VNL  HO1  CO1  CM1  119.37  3.000
 VNL  HO1  CO1  C1   119.71  3.000
 VNL  CM1  CO1  C1   120.92  3.000
 VNL  HO2  CO2  CM2  120.57  3.000
 VNL  HO2  CO2  C1   118.47  3.000
 VNL  CM2  CO2  C1   120.97  3.000
 VNL  HM1  CM1  CZ   119.06  3.000
 VNL  HM1  CM1  CO1  120.52  3.000
 VNL  CZ   CM1  CO1  120.42  3.000
 VNL  CZ   CM2  OM   114.57  3.000
 VNL  CZ   CM2  CO2  119.94  3.000
 VNL  OM   CM2  CO2  125.49  3.000
 VNL  CV   OM   CM2  118.44  3.000
 VNL  O3   CZ   CM2  121.36  3.000
 VNL  O3   CZ   CM1  119.46  3.000
 VNL  CM2  CZ   CM1  119.17  3.000
 VNL  O2   CC   O1   126.50  3.000
 VNL  O2   CC   C1   116.78  3.000
 VNL  O1   CC   C1   116.73  3.000
 VNL  HV3  CV   HV2  108.83  3.000
 VNL  HV3  CV   HV1  108.79  3.000
 VNL  HV2  CV   HV1  108.88  3.000
 VNL  HV3  CV   OM   111.82  3.000
 VNL  HV2  CV   OM   106.63  3.000
 VNL  HV1  CV   OM   111.80  3.000
 VNL  HO3  O3   CZ   109.99  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
 VNL  CONST_01  CZ   CM1  CO1  C1     0.00   0.0  0
 VNL  CONST_02  CZ   CM2  CO2  C1     0.00   0.0  0
 VNL  CONST_03  CM2  CO2  C1   CO1    0.00   0.0  0
 VNL  CONST_04  CM2  CZ   CM1  CO1    0.00   0.0  0
 VNL  CONST_05  CM1  CO1  C1   CO2    0.00   0.0  0
 VNL  CONST_06  CM1  CZ   CM2  CO2    0.00   0.0  0
 VNL  CONST_07  OM   CM2  CO2  C1   180.00   0.0  0
 VNL  CONST_08  O3   CZ   CM1  CO1  180.00   0.0  0
 VNL  CONST_09  O3   CZ   CM2  CO2  180.00   0.0  0
 VNL  CONST_10  CC   C1   CO1  CM1  180.00   0.0  0
 VNL  CONST_11  OM   CM2  CZ   CM1  180.00   0.0  0
 VNL  CONST_12  CC   C1   CO2  CM2  180.00   0.0  0
 VNL  CONST_13  HM1  CM1  CO1  C1   180.00   0.0  0
 VNL  CONST_14  HO2  CO2  C1   CO1  180.00   0.0  0
 VNL  CONST_15  HO1  CO1  C1   CO2  180.00   0.0  0
 VNL  Var_01    O1   CC   C1   CO1   -1.32  30.0  2
 VNL  Var_02    HV1  CV   OM   CM2   60.60  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
 VNL  plan-1  C1   0.020
 VNL  plan-1  CO1  0.020
 VNL  plan-1  CO2  0.020
 VNL  plan-1  CM1  0.020
 VNL  plan-1  CM2  0.020
 VNL  plan-1  OM   0.020
 VNL  plan-1  CZ   0.020
 VNL  plan-1  CC   0.020
 VNL  plan-1  O3   0.020
 VNL  plan-1  HO1  0.020
 VNL  plan-1  HO2  0.020
 VNL  plan-1  HM1  0.020
 VNL  plan-2  C1   0.020
 VNL  plan-2  CC   0.020
 VNL  plan-2  O1   0.020
 VNL  plan-2  O2   0.020

