# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:53:46 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-[2-amino-5-(4-hydroxy-3-methoxyphenyl)pyridin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)c2cnc(N)c(c2)c3ccc(cc3)C(N)=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
 VGM  VGM  4-[2-amino-5-(4-hydroxy-3-methoxyphenyl)pyridin-3-yl]benzamide  ligand  42  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VGM
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
 VGM  C01   C  CH3   0  -0.433   6.2432   1.0687  -1.2366
 VGM  O02   O  O2    0  -0.490   6.0789  -0.2046  -0.6445
 VGM  C03   C  CR6   0   0.320   4.8787  -0.5209  -0.1126
 VGM  C04   C  CR16  0  -0.452   3.7607   0.2957  -0.1189
 VGM  C05   C  CR6   0   0.086   2.5558  -0.1303   0.4539
 VGM  C06   C  CR6   0  -0.003   1.3740   0.7477   0.4355
 VGM  C07   C  CR16  0  -0.111   1.4693   2.1216   0.6161
 VGM  N08   N  N     0  -0.445   0.4374   2.9514   0.5908
 VGM  C09   C  CR6   0   0.400  -0.7873   2.4689   0.3998
 VGM  N10   N  NH2   0  -0.828  -1.8040   3.3782   0.3901
 VGM  C11   C  CR6   0  -0.034  -1.0203   1.0823   0.2403
 VGM  C12   C  CR6   0   0.048  -2.3695   0.5169   0.0407
 VGM  C13   C  CR16  0  -0.290  -3.4262   0.8215   0.9017
 VGM  C14   C  CR16  0  -0.251  -4.6726   0.2474   0.7232
 VGM  C15   C  CR6   0  -0.048  -4.8960  -0.6620  -0.3075
 VGM  C16   C  C     0   0.486  -6.2640  -1.2483  -0.4543
 VGM  N17   N  NH2   0  -0.812  -6.3404  -2.4165  -1.1095
 VGM  O18   O  O     0  -0.481  -7.2457  -0.6779   0.0024
 VGM  C19   C  CR16  0  -0.267  -3.8482  -0.9629  -1.1742
 VGM  C20   C  CR16  0  -0.287  -2.6043  -0.3779  -1.0032
 VGM  C21   C  CR16  0  -0.247   0.0835   0.2499   0.2483
 VGM  C22   C  CR16  0  -0.336   2.5039  -1.3954   1.0272
 VGM  C23   C  CR16  0  -0.329   3.6212  -2.2215   1.0308
 VGM  C24   C  CR6   0   0.269   4.8119  -1.7994   0.4666
 VGM  O25   O  OH1   0  -0.631   5.8799  -2.6224   0.4821
 VGM  H011  H  HCH3  0   0.264   7.2714   1.1183  -1.5849
 VGM  H012  H  HCH3  0   0.231   5.5735   1.2088  -2.0885
 VGM  H013  H  HCH3  0   0.231   6.0725   1.8728  -0.5165
 VGM  H04   H  HCR6  0   0.277   3.8025   1.2673  -0.5943
 VGM  H22   H  HCR6  0   0.251   1.5928  -1.7456   1.4955
 VGM  H07   H  HCR6  0   0.255   2.4359   2.5798   0.8033
 VGM  H21   H  HCR6  0   0.263  -0.0648  -0.8145   0.1064
 VGM  H101  H  HNH2  0   0.386  -1.5200   4.3368   0.2663
 VGM  H102  H  HNH2  0   0.394  -2.6497   3.1381  -0.1007
 VGM  H13   H  HCR6  0   0.267  -3.2718   1.5011   1.7297
 VGM  H20   H  HCR6  0   0.263  -1.8094  -0.6094  -1.7009
 VGM  H14   H  HCR6  0   0.264  -5.4750   0.4968   1.4049
 VGM  H19   H  HCR6  0   0.262  -3.9904  -1.6355  -2.0106
 VGM  H171  H  HNH2  0   0.413  -5.5272  -2.9582  -1.3444
 VGM  H172  H  HNH2  0   0.406  -7.2338  -2.8683  -1.2181
 VGM  H23   H  HCR6  0   0.265   3.5717  -3.2030   1.4861
 VGM  H25   H  HOH1  0   0.472   6.6288  -2.2061   0.0385

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
 VGM  C01  O02   single    1.414  0.020  1.414
 VGM  O02  C03   single    1.350  0.020  1.350
 VGM  C03  C04   aromatic  1.385  0.020  1.385
 VGM  C03  C24   aromatic  1.405  0.020  1.405
 VGM  C04  C05   aromatic  1.400  0.020  1.400
 VGM  C05  C06   single    1.472  0.020  1.472
 VGM  C05  C22   aromatic  1.390  0.020  1.390
 VGM  C06  C07   aromatic  1.389  0.020  1.389
 VGM  C06  C21   aromatic  1.396  0.020  1.396
 VGM  C07  N08   aromatic  1.324  0.020  1.324
 VGM  N08  C09   aromatic  1.330  0.020  1.330
 VGM  C09  N10   single    1.364  0.020  1.364
 VGM  C09  C11   aromatic  1.415  0.020  1.415
 VGM  C11  C12   single    1.476  0.020  1.476
 VGM  C11  C21   aromatic  1.383  0.020  1.383
 VGM  C12  C13   aromatic  1.397  0.020  1.397
 VGM  C12  C20   aromatic  1.395  0.020  1.395
 VGM  C13  C14   aromatic  1.384  0.020  1.384
 VGM  C14  C15   aromatic  1.393  0.020  1.393
 VGM  C15  C16   single    1.496  0.020  1.496
 VGM  C15  C19   aromatic  1.393  0.020  1.393
 VGM  C16  N17   single    1.342  0.020  1.342
 VGM  C16  O18   double    1.224  0.020  1.224
 VGM  C19  C20   aromatic  1.385  0.020  1.385
 VGM  C22  C23   aromatic  1.389  0.020  1.389
 VGM  C23  C24   aromatic  1.384  0.020  1.384
 VGM  C24  O25   single    1.348  0.020  1.348
 VGM  C01  H011  single    0.970  0.020  1.090
 VGM  C01  H012  single    0.970  0.020  1.090
 VGM  C01  H013  single    0.970  0.020  1.090
 VGM  C04  H04   single    0.930  0.020  1.080
 VGM  C22  H22   single    0.930  0.020  1.080
 VGM  C07  H07   single    0.930  0.020  1.080
 VGM  C21  H21   single    0.930  0.020  1.080
 VGM  N10  H101  single    0.890  0.020  1.040
 VGM  N10  H102  single    0.890  0.020  1.040
 VGM  C13  H13   single    0.930  0.020  1.080
 VGM  C20  H20   single    0.930  0.020  1.080
 VGM  C14  H14   single    0.930  0.020  1.080
 VGM  C19  H19   single    0.930  0.020  1.080
 VGM  N17  H171  single    0.860  0.020  1.020
 VGM  N17  H172  single    0.860  0.020  1.020
 VGM  C23  H23   single    0.930  0.020  1.080
 VGM  O25  H25   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
 VGM  H013  C01  H012  108.89  3.000
 VGM  H013  C01  H011  108.99  3.000
 VGM  H012  C01  H011  108.91  3.000
 VGM  H013  C01  O02   111.62  3.000
 VGM  H012  C01  O02   111.76  3.000
 VGM  H011  C01  O02   106.57  3.000
 VGM  C03   O02  C01   118.64  3.000
 VGM  C24   C03  C04   120.01  3.000
 VGM  C24   C03  O02   114.70  3.000
 VGM  C04   C03  O02   125.29  3.000
 VGM  H04   C04  C05   119.07  3.000
 VGM  H04   C04  C03   120.01  3.000
 VGM  C05   C04  C03   120.90  3.000
 VGM  C22   C05  C06   121.20  3.000
 VGM  C22   C05  C04   118.53  3.000
 VGM  C06   C05  C04   120.27  3.000
 VGM  C21   C06  C07   115.70  3.000
 VGM  C21   C06  C05   122.08  3.000
 VGM  C07   C06  C05   122.22  3.000
 VGM  H07   C07  N08   115.62  3.000
 VGM  H07   C07  C06   120.06  3.000
 VGM  N08   C07  C06   124.32  3.000
 VGM  C09   N08  C07   119.53  3.000
 VGM  C11   C09  N10   121.98  3.000
 VGM  C11   C09  N08   121.55  3.000
 VGM  N10   C09  N08   116.45  3.000
 VGM  H102  N10  H101  113.81  3.000
 VGM  H102  N10  C09   118.07  3.000
 VGM  H101  N10  C09   115.15  3.000
 VGM  C21   C11  C12   119.98  3.000
 VGM  C21   C11  C09   117.25  3.000
 VGM  C12   C11  C09   122.75  3.000
 VGM  C20   C12  C13   118.29  3.000
 VGM  C20   C12  C11   120.05  3.000
 VGM  C13   C12  C11   121.64  3.000
 VGM  H13   C13  C14   119.19  3.000
 VGM  H13   C13  C12   120.04  3.000
 VGM  C14   C13  C12   120.76  3.000
 VGM  H14   C14  C15   119.86  3.000
 VGM  H14   C14  C13   119.41  3.000
 VGM  C15   C14  C13   120.72  3.000
 VGM  C19   C15  C16   122.85  3.000
 VGM  C19   C15  C14   118.75  3.000
 VGM  C16   C15  C14   118.38  3.000
 VGM  O18   C16  N17   122.85  3.000
 VGM  O18   C16  C15   120.96  3.000
 VGM  N17   C16  C15   116.19  3.000
 VGM  H172  N17  H171  116.80  3.000
 VGM  H172  N17  C16   119.60  3.000
 VGM  H171  N17  C16   122.51  3.000
 VGM  H19   C19  C20   118.40  3.000
 VGM  H19   C19  C15   121.08  3.000
 VGM  C20   C19  C15   120.50  3.000
 VGM  H20   C20  C19   119.30  3.000
 VGM  H20   C20  C12   119.73  3.000
 VGM  C19   C20  C12   120.97  3.000
 VGM  H21   C21  C11   118.76  3.000
 VGM  H21   C21  C06   119.63  3.000
 VGM  C11   C21  C06   121.61  3.000
 VGM  H22   C22  C23   118.90  3.000
 VGM  H22   C22  C05   120.28  3.000
 VGM  C23   C22  C05   120.81  3.000
 VGM  H23   C23  C24   119.16  3.000
 VGM  H23   C23  C22   120.20  3.000
 VGM  C24   C23  C22   120.64  3.000
 VGM  O25   C24  C23   119.39  3.000
 VGM  O25   C24  C03   121.49  3.000
 VGM  C23   C24  C03   119.12  3.000
 VGM  H25   O25  C24   110.25  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
 VGM  CONST_01  C06   C05  C04  C03   180.00   0.0  0
 VGM  CONST_02  C22   C05  C04  C03     0.00   0.0  0
 VGM  CONST_03  C22   C23  C24  C03     0.00   0.0  0
 VGM  CONST_04  C23   C24  C03  C04     0.00   0.0  0
 VGM  CONST_07  C23   C22  C05  C04     0.00   0.0  0
 VGM  CONST_08  C24   C03  C04  C05     0.00   0.0  0
 VGM  CONST_09  N08   C07  C06  C05   180.00   0.0  0
 VGM  CONST_10  C11   C21  C06  C05   180.00   0.0  0
 VGM  CONST_11  C24   C23  C22  C05     0.00   0.0  0
 VGM  CONST_12  C23   C22  C05  C06   180.00   0.0  0
 VGM  CONST_13  C09   N08  C07  C06     0.00   0.0  0
 VGM  CONST_14  C09   C11  C21  C06     0.00   0.0  0
 VGM  CONST_15  C12   C11  C21  C06   180.00   0.0  0
 VGM  CONST_17  C11   C21  C06  C07     0.00   0.0  0
 VGM  CONST_18  C11   C09  N08  C07     0.00   0.0  0
 VGM  CONST_19  C21   C06  C07  N08     0.00   0.0  0
 VGM  CONST_20  C12   C11  C09  N08   180.00   0.0  0
 VGM  CONST_21  C21   C11  C09  N08     0.00   0.0  0
 VGM  CONST_24  C14   C13  C12  C11   180.00   0.0  0
 VGM  CONST_25  C19   C20  C12  C11   180.00   0.0  0
 VGM  CONST_26  C15   C14  C13  C12     0.00   0.0  0
 VGM  CONST_27  C15   C19  C20  C12     0.00   0.0  0
 VGM  CONST_29  C19   C20  C12  C13     0.00   0.0  0
 VGM  CONST_30  C19   C15  C14  C13     0.00   0.0  0
 VGM  CONST_31  C20   C12  C13  C14     0.00   0.0  0
 VGM  CONST_32  C20   C19  C15  C14     0.00   0.0  0
 VGM  CONST_35  C05   C04  C03  O02   180.00   0.0  0
 VGM  CONST_36  C23   C24  C03  O02   180.00   0.0  0
 VGM  CONST_37  O25   C24  C03  C04   180.00   0.0  0
 VGM  CONST_38  N10   C09  N08  C07   180.00   0.0  0
 VGM  CONST_39  C12   C11  C09  N10     0.00   0.0  0
 VGM  CONST_40  C21   C11  C09  N10   180.00   0.0  0
 VGM  CONST_41  C16   C15  C14  C13   180.00   0.0  0
 VGM  CONST_42  C20   C19  C15  C16   180.00   0.0  0
 VGM  CONST_43  O25   C24  C23  C22   180.00   0.0  0
 VGM  CONST_44  H23   C23  C24  C03   180.00   0.0  0
 VGM  CONST_45  H22   C22  C05  C04   180.00   0.0  0
 VGM  CONST_46  H07   C07  C06  C05     0.00   0.0  0
 VGM  CONST_47  H21   C21  C06  C05     0.00   0.0  0
 VGM  CONST_48  H04   C04  C05  C06     0.00   0.0  0
 VGM  CONST_49  H13   C13  C12  C11     0.00   0.0  0
 VGM  CONST_50  H20   C20  C12  C11     0.00   0.0  0
 VGM  CONST_51  H14   C14  C13  C12   180.00   0.0  0
 VGM  CONST_52  H19   C19  C20  C12   180.00   0.0  0
 VGM  CONST_55  H171  N17  C16  C15     0.00   0.0  0
 VGM  CONST_56  H172  N17  C16  C15   180.00   0.0  0
 VGM  Var_01    C04   C03  O02  C01     1.46  30.0  2
 VGM  Var_02    N17   C16  C15  C14  -157.51  30.0  2
 VGM  Var_03    H011  C01  O02  C03   179.32  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
 VGM  plan-1  O02   0.020
 VGM  plan-1  C03   0.020
 VGM  plan-1  C04   0.020
 VGM  plan-1  C05   0.020
 VGM  plan-1  C06   0.020
 VGM  plan-1  C22   0.020
 VGM  plan-1  C23   0.020
 VGM  plan-1  C24   0.020
 VGM  plan-1  O25   0.020
 VGM  plan-1  H04   0.020
 VGM  plan-1  H22   0.020
 VGM  plan-1  H23   0.020
 VGM  plan-2  C05   0.020
 VGM  plan-2  C06   0.020
 VGM  plan-2  C07   0.020
 VGM  plan-2  N08   0.020
 VGM  plan-2  C09   0.020
 VGM  plan-2  N10   0.020
 VGM  plan-2  C11   0.020
 VGM  plan-2  C12   0.020
 VGM  plan-2  C21   0.020
 VGM  plan-2  H07   0.020
 VGM  plan-2  H21   0.020
 VGM  plan-3  C11   0.020
 VGM  plan-3  C12   0.020
 VGM  plan-3  C13   0.020
 VGM  plan-3  C14   0.020
 VGM  plan-3  C15   0.020
 VGM  plan-3  C16   0.020
 VGM  plan-3  C19   0.020
 VGM  plan-3  C20   0.020
 VGM  plan-3  H13   0.020
 VGM  plan-3  H20   0.020
 VGM  plan-3  H14   0.020
 VGM  plan-3  H19   0.020
 VGM  plan-4  C15   0.020
 VGM  plan-4  C16   0.020
 VGM  plan-4  N17   0.020
 VGM  plan-4  O18   0.020
 VGM  plan-4  H171  0.020
 VGM  plan-4  H172  0.020
 VGM  plan-5  C09   0.020
 VGM  plan-5  N10   0.020
 VGM  plan-5  H101  0.020
 VGM  plan-5  H102  0.020

