# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:32:33 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-amino-5-(1-methyl-1H-pyrazol-4-yl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)C2=CNC(=O)C(=C2)N
#
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
 3D7  3D7  3-amino-5-(1-methyl-1H-pyrazol-4-yl)pyridin-2(1H)-one  ligand  24  14  .  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_3D7
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
 3D7  O     O  O     0  -0.517  -4.1620  -0.7713   0.0599
 3D7  C4    C  CR6   0   0.486  -2.9538  -0.5293   0.0378
 3D7  C     C  CR6   0   0.147  -2.4046   0.8210   0.0055
 3D7  N     N  NH2   0  -0.846  -3.3261   1.8346  -0.0711
 3D7  N1    N  NR16  0  -0.652  -2.0167  -1.5178   0.0507
 3D7  C3    C  CR16  0  -0.059  -0.6651  -1.3425   0.0349
 3D7  C2    C  CR6   0  -0.030  -0.1409  -0.0901   0.0270
 3D7  C1    C  CR16  0  -0.291  -1.0517   1.0057   0.0160
 3D7  C5    C  CR5   0  -0.149   1.3013   0.1362   0.0318
 3D7  C7    C  CR15  0  -0.101   2.0106   1.2494  -0.4599
 3D7  N3    N  N     0  -0.281   3.3130   1.1073  -0.2968
 3D7  N2    N  NR5   0  -0.264   3.4681  -0.0735   0.2895
 3D7  C8    C  CH3   0  -0.506   4.7861  -0.5351   0.6537
 3D7  C6    C  CR15  0   0.007   2.2974  -0.6921   0.5140
 3D7  H1    H  HNR6  0   0.420  -2.3691  -2.4653   0.0657
 3D7  HN1   H  HNH2  0   0.379  -4.2382   1.6148   0.2965
 3D7  HN2   H  HNH2  0   0.382  -3.0039   2.7475   0.2065
 3D7  HA    H  HCR6  0   0.259  -0.6606   2.0172   0.0230
 3D7  H3    H  HCR6  0   0.291  -0.0750  -2.2465   0.0202
 3D7  H7    H  HCR5  0   0.257   1.6167   2.1358  -0.9348
 3D7  H6    H  HCR5  0   0.289   2.2480  -1.6521   1.0032
 3D7  H81C  H  HCH3  0   0.260   5.2070   0.0886   1.4403
 3D7  H82C  H  HCH3  0   0.258   4.7162  -1.5575   1.0131
 3D7  H83C  H  HCH3  0   0.262   5.4423  -0.5097  -0.2131

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
 3D7  O   C4    double    1.232  0.020  1.232
 3D7  C4  C     single    1.458  0.020  1.458
 3D7  C4  N1    single    1.362  0.020  1.362
 3D7  C   N     single    1.372  0.020  1.372
 3D7  C   C1    double    1.365  0.020  1.365
 3D7  N1  C3    single    1.363  0.020  1.363
 3D7  C3  C2    double    1.358  0.020  1.358
 3D7  C2  C1    single    1.425  0.020  1.425
 3D7  C2  C5    single    1.460  0.020  1.460
 3D7  C5  C7    aromatic  1.409  0.020  1.409
 3D7  C5  C6    aromatic  1.382  0.020  1.382
 3D7  C7  N3    aromatic  1.320  0.020  1.320
 3D7  N3  N2    aromatic  1.327  0.020  1.327
 3D7  N2  C8    single    1.443  0.020  1.443
 3D7  N2  C6    aromatic  1.343  0.020  1.343
 3D7  N1  H1    single    0.860  0.020  1.020
 3D7  N   HN1   single    0.890  0.020  1.040
 3D7  N   HN2   single    0.890  0.020  1.040
 3D7  C1  HA    single    0.930  0.020  1.080
 3D7  C3  H3    single    0.930  0.020  1.080
 3D7  C7  H7    single    0.930  0.020  1.080
 3D7  C6  H6    single    0.930  0.020  1.080
 3D7  C8  H81C  single    0.970  0.020  1.090
 3D7  C8  H82C  single    0.970  0.020  1.090
 3D7  C8  H83C  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
 3D7  N1    C4  C     114.40  3.000
 3D7  N1    C4  O     122.13  3.000
 3D7  C     C4  O     123.47  3.000
 3D7  C1    C   N     124.47  3.000
 3D7  C1    C   C4    119.88  3.000
 3D7  N     C   C4    115.62  3.000
 3D7  HN2   N   HN1   112.75  3.000
 3D7  HN2   N   C     116.07  3.000
 3D7  HN1   N   C     115.24  3.000
 3D7  H1    N1  C3    117.79  3.000
 3D7  H1    N1  C4    116.13  3.000
 3D7  C3    N1  C4    126.07  3.000
 3D7  H3    C3  C2    124.14  3.000
 3D7  H3    C3  N1    115.75  3.000
 3D7  C2    C3  N1    120.10  3.000
 3D7  C5    C2  C1    120.81  3.000
 3D7  C5    C2  C3    121.63  3.000
 3D7  C1    C2  C3    117.55  3.000
 3D7  HA    C1  C2    119.12  3.000
 3D7  HA    C1  C     118.91  3.000
 3D7  C2    C1  C     121.96  3.000
 3D7  C6    C5  C7    103.45  3.000
 3D7  C6    C5  C2    128.32  3.000
 3D7  C7    C5  C2    128.23  3.000
 3D7  H7    C7  N3    120.17  3.000
 3D7  H7    C7  C5    128.20  3.000
 3D7  N3    C7  C5    111.62  3.000
 3D7  N2    N3  C7    105.40  3.000
 3D7  C6    N2  C8    127.34  3.000
 3D7  C6    N2  N3    112.44  3.000
 3D7  C8    N2  N3    120.18  3.000
 3D7  H83C  C8  H82C  108.94  3.000
 3D7  H83C  C8  H81C  109.22  3.000
 3D7  H82C  C8  H81C  108.98  3.000
 3D7  H83C  C8  N2    110.03  3.000
 3D7  H82C  C8  N2    109.02  3.000
 3D7  H81C  C8  N2    110.62  3.000
 3D7  H6    C6  N2    121.72  3.000
 3D7  H6    C6  C5    131.19  3.000
 3D7  N2    C6  C5    107.08  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
 3D7  CONST_01  N2    N3  C7  C5    0.00   0.0  0
 3D7  CONST_02  N3    N2  C6  C5    0.00   0.0  0
 3D7  CONST_03  N2    C6  C5  C7    0.00   0.0  0
 3D7  CONST_04  C6    N2  N3  C7    0.00   0.0  0
 3D7  CONST_05  C6    C5  C7  N3    0.00   0.0  0
 3D7  CONST_06  N3    C7  C5  C2  180.00   0.0  0
 3D7  CONST_07  N2    C6  C5  C2  180.00   0.0  0
 3D7  CONST_08  C3    N1  C4  C     0.00   0.0  0
 3D7  CONST_09  C8    N2  C6  C5  180.00   0.0  0
 3D7  CONST_10  C8    N2  N3  C7  180.00   0.0  0
 3D7  CONST_11  C3    N1  C4  O   180.00   0.0  0
 3D7  CONST_12  H7    C7  C5  C2    0.00   0.0  0
 3D7  CONST_13  H6    C6  C5  C2    0.00   0.0  0
 3D7  CONST_14  H1    N1  C4  C   180.00   0.0  0
 3D7  Var_01    C7    C5  C2  C3  153.95  30.0  2
 3D7  Var_02    HN1   N   C   C4   25.61  30.0  2
 3D7  Var_03    H81C  C8  N2  N3   66.52  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
 3D7  plan-1  C2  0.020
 3D7  plan-1  C5  0.020
 3D7  plan-1  C7  0.020
 3D7  plan-1  N3  0.020
 3D7  plan-1  N2  0.020
 3D7  plan-1  C8  0.020
 3D7  plan-1  C6  0.020
 3D7  plan-1  H7  0.020
 3D7  plan-1  H6  0.020
 3D7  plan-2  O   0.020
 3D7  plan-2  C4  0.020
 3D7  plan-2  C   0.020
 3D7  plan-2  N   0.020
 3D7  plan-2  N1  0.020
 3D7  plan-2  C3  0.020
 3D7  plan-2  C2  0.020
 3D7  plan-2  C1  0.020
 3D7  plan-2  C5  0.020
 3D7  plan-2  H1  0.020
 3D7  plan-2  HA  0.020
 3D7  plan-2  H3  0.020

