# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:42:38 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: methyl 2-[(3-hydroxy-2-methylphenoxy)methyl]pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccnc1COc2cccc(O)c2C
#
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
 V2D  V2D  'methyl 2-[(3-hydroxy-2-methylphenoxy)methyl]pyridine-3-carboxylate'  ligand  35  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_V2D
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
 V2D  C1   C  CH3   0  -0.712  12.3224  -12.7459  -22.0987
 V2D  C2   C  CR6   0  -0.123  12.2253  -12.2815  -20.6734
 V2D  C3   C  CR6   0   0.336  13.2240  -11.4700  -20.1324
 V2D  C4   C  CR16  0  -0.403  13.1661  -11.0204  -18.8146
 V2D  C5   C  CR16  0  -0.244  12.0930  -11.3884  -18.0247
 V2D  C6   C  CR16  0  -0.400  11.0855  -12.2020  -18.5218
 V2D  C7   C  CR6   0   0.399  11.1643  -12.6521  -19.8379
 V2D  C10  C  CH2   0  -0.276   9.2498  -14.0569  -19.5795
 V2D  C11  C  CR6   0   0.256   8.6705  -15.2162  -20.3436
 V2D  C12  C  CR6   0  -0.093   9.4714  -16.1559  -21.0020
 V2D  C13  C  CR16  0  -0.141   8.8444  -17.1421  -21.7535
 V2D  C14  C  CR16  0  -0.319   7.4621  -17.2018  -21.7780
 V2D  O8   O  OH1   0  -0.628  14.2524  -11.1474  -20.9452
 V2D  O9   O  O2    0  -0.486  10.2332  -13.4579  -20.3964
 V2D  C15  C  CR16  0  -0.058   6.7585  -16.2504  -21.0593
 V2D  N16  N  N     0  -0.424   7.3466  -15.2730  -20.3804
 V2D  C17  C  C     0   0.527  10.9605  -16.1583  -20.9686
 V2D  O18  O  O     0  -0.437  11.6386  -16.3974  -21.9356
 V2D  O19  O  O2    0  -0.446  11.4400  -15.9345  -19.7594
 V2D  C20  C  CH3   0  -0.430  12.8583  -15.8468  -19.6166
 V2D  H1   H  HCH3  0   0.242  13.0503  -13.5535  -22.2086
 V2D  H2   H  HCH3  0   0.247  11.3733  -13.1189  -22.4728
 V2D  H3   H  HCH3  0   0.245  12.6412  -11.9382  -22.7571
 V2D  H4   H  HCR6  0   0.263  13.9516  -10.3895  -18.4150
 V2D  H5   H  HCR6  0   0.259  12.0350  -11.0376  -17.0028
 V2D  H6   H  HCR6  0   0.275  10.2557  -12.4637  -17.8807
 V2D  H7   H  HCH2  0   0.254   9.6738  -14.4073  -18.6336
 V2D  H8   H  HCH2  0   0.259   8.4467  -13.3525  -19.3441
 V2D  H9   H  HCR6  0   0.285   9.4330  -17.8711  -22.2949
 V2D  H10  H  HCR6  0   0.281   6.9425  -17.9665  -22.3372
 V2D  H11  H  HOH1  0   0.474  14.8802  -10.5850  -20.4792
 V2D  H12  H  HCR6  0   0.275   5.6750  -16.2658  -21.0402
 V2D  H13  H  HCH3  0   0.254  13.0364  -15.6022  -18.5741
 V2D  H14  H  HCH3  0   0.247  13.3395  -16.7937  -19.8594
 V2D  H15  H  HCH3  0   0.244  13.2698  -15.0588  -20.2465

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
 V2D  O18  C17  double    1.205  0.020  1.205
 V2D  C1   C2   single    1.502  0.020  1.502
 V2D  C13  C14  aromatic  1.384  0.020  1.384
 V2D  C13  C12  aromatic  1.389  0.020  1.389
 V2D  C14  C15  aromatic  1.384  0.020  1.384
 V2D  C17  C12  single    1.489  0.020  1.489
 V2D  C17  O19  single    1.320  0.020  1.320
 V2D  C12  C11  aromatic  1.399  0.020  1.399
 V2D  C15  N16  aromatic  1.327  0.020  1.327
 V2D  O8   C3   single    1.350  0.020  1.350
 V2D  C2   C3   aromatic  1.396  0.020  1.396
 V2D  C2   C7   aromatic  1.400  0.020  1.400
 V2D  O9   C7   single    1.352  0.020  1.352
 V2D  O9   C10  single    1.412  0.020  1.412
 V2D  C11  N16  aromatic  1.326  0.020  1.326
 V2D  C11  C10  single    1.504  0.020  1.504
 V2D  C3   C4   aromatic  1.394  0.020  1.394
 V2D  C20  O19  single    1.428  0.020  1.428
 V2D  C7   C6   aromatic  1.393  0.020  1.393
 V2D  C4   C5   aromatic  1.382  0.020  1.382
 V2D  C6   C5   aromatic  1.387  0.020  1.387
 V2D  C1   H1   single    0.970  0.020  1.090
 V2D  C1   H2   single    0.970  0.020  1.090
 V2D  C1   H3   single    0.970  0.020  1.090
 V2D  C4   H4   single    0.930  0.020  1.080
 V2D  C5   H5   single    0.930  0.020  1.080
 V2D  C6   H6   single    0.930  0.020  1.080
 V2D  C10  H7   single    0.970  0.020  1.090
 V2D  C10  H8   single    0.970  0.020  1.090
 V2D  C13  H9   single    0.930  0.020  1.080
 V2D  C14  H10  single    0.930  0.020  1.080
 V2D  O8   H11  single    0.850  0.020  0.980
 V2D  C15  H12  single    0.930  0.020  1.080
 V2D  C20  H13  single    0.970  0.020  1.090
 V2D  C20  H14  single    0.970  0.020  1.090
 V2D  C20  H15  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
 V2D  H3   C1   H2   107.58  3.000
 V2D  H3   C1   H1   106.99  3.000
 V2D  H2   C1   H1   107.07  3.000
 V2D  H3   C1   C2   111.29  3.000
 V2D  H2   C1   C2   112.12  3.000
 V2D  H1   C1   C2   111.53  3.000
 V2D  C7   C2   C3   117.69  3.000
 V2D  C7   C2   C1   122.22  3.000
 V2D  C3   C2   C1   120.08  3.000
 V2D  O8   C3   C4   121.60  3.000
 V2D  C4   C3   C2   121.62  3.000
 V2D  O8   C3   C2   116.78  3.000
 V2D  H4   C4   C5   120.47  3.000
 V2D  H4   C4   C3   120.41  3.000
 V2D  C5   C4   C3   119.12  3.000
 V2D  H5   C5   C6   119.32  3.000
 V2D  H5   C5   C4   119.67  3.000
 V2D  C6   C5   C4   121.02  3.000
 V2D  H6   C6   C7   121.70  3.000
 V2D  H6   C6   C5   119.16  3.000
 V2D  C7   C6   C5   119.14  3.000
 V2D  O9   C7   C6   122.95  3.000
 V2D  C6   C7   C2   121.39  3.000
 V2D  O9   C7   C2   115.66  3.000
 V2D  H8   C10  H7   107.73  3.000
 V2D  H8   C10  O9   111.27  3.000
 V2D  H7   C10  O9   111.48  3.000
 V2D  H8   C10  C11  108.84  3.000
 V2D  H7   C10  C11  109.97  3.000
 V2D  O9   C10  C11  107.54  3.000
 V2D  N16  C11  C12  121.99  3.000
 V2D  N16  C11  C10  115.57  3.000
 V2D  C12  C11  C10  122.42  3.000
 V2D  C17  C12  C13  117.53  3.000
 V2D  C17  C12  C11  124.24  3.000
 V2D  C13  C12  C11  118.22  3.000
 V2D  H9   C13  C14  120.37  3.000
 V2D  H9   C13  C12  120.21  3.000
 V2D  C14  C13  C12  119.40  3.000
 V2D  H10  C14  C15  120.71  3.000
 V2D  H10  C14  C13  121.33  3.000
 V2D  C15  C14  C13  117.96  3.000
 V2D  H11  O8   C3   110.17  3.000
 V2D  C10  O9   C7   119.58  3.000
 V2D  H12  C15  N16  116.38  3.000
 V2D  H12  C15  C14  120.50  3.000
 V2D  N16  C15  C14  123.12  3.000
 V2D  C15  N16  C11  119.22  3.000
 V2D  O19  C17  O18  124.36  3.000
 V2D  O19  C17  C12  112.55  3.000
 V2D  O18  C17  C12  123.02  3.000
 V2D  C20  O19  C17  117.57  3.000
 V2D  H15  C20  H14  109.44  3.000
 V2D  H15  C20  H13  109.30  3.000
 V2D  H14  C20  H13  109.72  3.000
 V2D  H15  C20  O19  111.20  3.000
 V2D  H14  C20  O19  111.28  3.000
 V2D  H13  C20  O19  105.83  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
 V2D  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 V2D  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 V2D  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 V2D  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 V2D  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 V2D  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 V2D  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 V2D  CONST_08  C14  C15  N16  C11     0.00   0.0  0
 V2D  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 V2D  CONST_10  C15  N16  C11  C12     0.00   0.0  0
 V2D  CONST_11  N16  C15  C14  C13     0.00   0.0  0
 V2D  CONST_12  N16  C11  C12  C13     0.00   0.0  0
 V2D  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 V2D  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 V2D  CONST_15  O9   C7   C2   C3    180.00   0.0  0
 V2D  CONST_16  O8   C3   C4   C5    180.00   0.0  0
 V2D  CONST_17  O9   C7   C6   C5    180.00   0.0  0
 V2D  CONST_18  O8   C3   C2   C7    180.00   0.0  0
 V2D  CONST_19  C13  C12  C11  C10   180.00   0.0  0
 V2D  CONST_20  C15  N16  C11  C10   180.00   0.0  0
 V2D  CONST_21  C17  C12  C13  C14   180.00   0.0  0
 V2D  CONST_22  C17  C12  C11  N16   180.00   0.0  0
 V2D  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 V2D  CONST_24  H6   C6   C7   C2    180.00   0.0  0
 V2D  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 V2D  CONST_26  H9   C13  C12  C11   180.00   0.0  0
 V2D  CONST_27  H12  C15  N16  C11   180.00   0.0  0
 V2D  CONST_28  H10  C14  C13  C12   180.00   0.0  0
 V2D  Var_01    C11  C10  O9   C7   -161.29  30.0  3
 V2D  Var_02    O18  C17  C12  C11  -139.40  30.0  2
 V2D  Var_03    O9   C10  C11  C12    47.14  30.0  2
 V2D  Var_04    H1   C1   C2   C3     76.21  30.0  2
 V2D  Var_05    H13  C20  O19  C17   176.64  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
 V2D  plan-1  C1   0.020
 V2D  plan-1  C2   0.020
 V2D  plan-1  C3   0.020
 V2D  plan-1  C4   0.020
 V2D  plan-1  C5   0.020
 V2D  plan-1  C6   0.020
 V2D  plan-1  C7   0.020
 V2D  plan-1  O8   0.020
 V2D  plan-1  O9   0.020
 V2D  plan-1  H4   0.020
 V2D  plan-1  H5   0.020
 V2D  plan-1  H6   0.020
 V2D  plan-2  C10  0.020
 V2D  plan-2  C11  0.020
 V2D  plan-2  C12  0.020
 V2D  plan-2  C13  0.020
 V2D  plan-2  C14  0.020
 V2D  plan-2  C15  0.020
 V2D  plan-2  N16  0.020
 V2D  plan-2  C17  0.020
 V2D  plan-2  H9   0.020
 V2D  plan-2  H10  0.020
 V2D  plan-2  H12  0.020
 V2D  plan-3  C12  0.020
 V2D  plan-3  C17  0.020
 V2D  plan-3  O18  0.020
 V2D  plan-3  O19  0.020

