# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:50:36 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-(3-methyl-1H-pyrazol-5-yl)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([nH]n1)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
 VRM  VRM  3-(3-methyl-1H-pyrazol-5-yl)pyridine  ligand  21  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VRM
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
 VRM  C4    C  CR5   0   0.419  22.9709  -11.4254   -9.0464
 VRM  C8    C  CR6   0  -0.020  23.1452  -10.1769   -8.3144
 VRM  C10   C  CR16  0  -0.311  22.2504   -8.3105   -7.1097
 VRM  N12   N  N     0  -0.395  24.6072   -8.4909   -7.4323
 VRM  C13   C  CR16  0  -0.093  24.4066   -9.6253   -8.0861
 VRM  C11   C  CR16  0  -0.068  23.5491   -7.8467   -6.9554
 VRM  C2    C  CR5   0   0.238  22.3423  -13.3603   -9.9182
 VRM  C3    C  CR15  0  -0.541  21.9584  -12.3620   -9.0034
 VRM  C9    C  CR16  0  -0.201  22.0459   -9.4896   -7.8025
 VRM  N5    N  NR15  0  -0.514  23.8622  -11.8964   -9.9422
 VRM  N7    N  N     0  -0.281  23.5000  -13.0554  -10.4806
 VRM  H101  H  HCR6  0   0.277  21.4190   -7.7520   -6.7026
 VRM  H131  H  HCR6  0   0.261  25.2997  -10.1322   -8.4375
 VRM  H13   H  HCH3  0   0.246  22.1869  -15.2138  -10.9686
 VRM  H12   H  HCH3  0   0.246  21.4252  -15.2177   -9.3769
 VRM  H11   H  HCH3  0   0.247  20.6454  -14.3949  -10.7171
 VRM  H111  H  HCR6  0   0.270  23.7411   -6.9208   -6.4255
 VRM  H31   H  HCR5  0   0.264  21.0770  -12.3444   -8.3831
 VRM  H91   H  HCR6  0   0.273  21.0430   -9.8671   -7.9551
 VRM  H1    H  HNR5  0   0.420  24.7052  -11.4471  -10.2625
 VRM  C1    C  CH3   0  -0.737  21.6136  -14.6128  -10.2645

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
 VRM  N7   C2    aromatic  1.323  0.020  1.323
 VRM  N7   N5    aromatic  1.328  0.020  1.328
 VRM  C1   C2    single    1.490  0.020  1.490
 VRM  C2   C3    aromatic  1.407  0.020  1.407
 VRM  N5   C4    aromatic  1.349  0.020  1.349
 VRM  C4   C3    aromatic  1.380  0.020  1.380
 VRM  C4   C8    single    1.458  0.020  1.458
 VRM  C8   C13   aromatic  1.396  0.020  1.396
 VRM  C8   C9    aromatic  1.394  0.020  1.394
 VRM  C13  N12   aromatic  1.325  0.020  1.325
 VRM  C9   C10   aromatic  1.383  0.020  1.383
 VRM  N12  C11   aromatic  1.327  0.020  1.327
 VRM  C10  C11   aromatic  1.388  0.020  1.388
 VRM  C10  H101  single    0.930  0.020  1.080
 VRM  C13  H131  single    0.930  0.020  1.080
 VRM  C1   H13   single    0.970  0.020  1.090
 VRM  C1   H12   single    0.970  0.020  1.090
 VRM  C1   H11   single    0.970  0.020  1.090
 VRM  C11  H111  single    0.930  0.020  1.080
 VRM  C3   H31   single    0.930  0.020  1.080
 VRM  C9   H91   single    0.930  0.020  1.080
 VRM  N5   H1    single    0.860  0.020  1.020

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
 VRM  N5    C4   C3   105.58  3.000
 VRM  C3    C4   C8   130.80  3.000
 VRM  N5    C4   C8   123.62  3.000
 VRM  C9    C8   C13  117.25  3.000
 VRM  C9    C8   C4   120.83  3.000
 VRM  C13   C8   C4   121.92  3.000
 VRM  H101  C10  C9   121.02  3.000
 VRM  H101  C10  C11  120.35  3.000
 VRM  C9    C10  C11  118.62  3.000
 VRM  C11   N12  C13  118.17  3.000
 VRM  H131  C13  N12  115.79  3.000
 VRM  H131  C13  C8   120.41  3.000
 VRM  N12   C13  C8   123.79  3.000
 VRM  H111  C11  N12  116.67  3.000
 VRM  H111  C11  C10  120.38  3.000
 VRM  N12   C11  C10  122.95  3.000
 VRM  N7    C2   C3   110.58  3.000
 VRM  C3    C2   C1   127.88  3.000
 VRM  N7    C2   C1   121.54  3.000
 VRM  H31   C3   C2   127.49  3.000
 VRM  H31   C3   C4   127.35  3.000
 VRM  C2    C3   C4   105.13  3.000
 VRM  H91   C9   C10  120.33  3.000
 VRM  H91   C9   C8   120.47  3.000
 VRM  C10   C9   C8   119.20  3.000
 VRM  H1    N5   N7   119.23  3.000
 VRM  H1    N5   C4   127.48  3.000
 VRM  N7    N5   C4   113.19  3.000
 VRM  N5    N7   C2   105.52  3.000
 VRM  H11   C1   H12  107.17  3.000
 VRM  H11   C1   H13  108.02  3.000
 VRM  H12   C1   H13  108.13  3.000
 VRM  H11   C1   C2   111.26  3.000
 VRM  H12   C1   C2   111.20  3.000
 VRM  H13   C1   C2   110.90  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
 VRM  CONST_01  C2    N7   N5   C4      0.00   0.0  0
 VRM  CONST_02  N7    C2   C3   C4      0.00   0.0  0
 VRM  CONST_03  N12   C13  C8   C4    180.00   0.0  0
 VRM  CONST_04  C10   C9   C8   C4    180.00   0.0  0
 VRM  CONST_05  N7    N5   C4   C8    180.00   0.0  0
 VRM  CONST_06  C2    C3   C4   C8    180.00   0.0  0
 VRM  CONST_07  C11   N12  C13  C8      0.00   0.0  0
 VRM  CONST_08  C11   C10  C9   C8      0.00   0.0  0
 VRM  CONST_09  C13   C8   C9   C10     0.00   0.0  0
 VRM  CONST_10  C13   N12  C11  C10     0.00   0.0  0
 VRM  CONST_11  C9    C8   C13  N12     0.00   0.0  0
 VRM  CONST_12  C9    C10  C11  N12     0.00   0.0  0
 VRM  CONST_15  N5    C4   C3   C2      0.00   0.0  0
 VRM  CONST_16  N5    N7   C2   C3      0.00   0.0  0
 VRM  CONST_17  N7    N5   C4   C3      0.00   0.0  0
 VRM  CONST_20  C1    C2   C3   C4    180.00   0.0  0
 VRM  CONST_21  N5    N7   C2   C1    180.00   0.0  0
 VRM  CONST_22  H131  C13  C8   C4      0.00   0.0  0
 VRM  CONST_23  H91   C9   C8   C4      0.00   0.0  0
 VRM  CONST_24  H1    N5   C4   C8      0.00   0.0  0
 VRM  CONST_25  H31   C3   C4   C8      0.00   0.0  0
 VRM  CONST_26  H101  C10  C9   C8    180.00   0.0  0
 VRM  CONST_27  H111  C11  N12  C13   180.00   0.0  0
 VRM  Var_01    H13   C1   C2   C3   -176.99  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
 VRM  plan-1  C4    0.020
 VRM  plan-1  C8    0.020
 VRM  plan-1  C2    0.020
 VRM  plan-1  C3    0.020
 VRM  plan-1  N5    0.020
 VRM  plan-1  N7    0.020
 VRM  plan-1  H31   0.020
 VRM  plan-1  H1    0.020
 VRM  plan-1  C1    0.020
 VRM  plan-2  C4    0.020
 VRM  plan-2  C8    0.020
 VRM  plan-2  C10   0.020
 VRM  plan-2  N12   0.020
 VRM  plan-2  C13   0.020
 VRM  plan-2  C11   0.020
 VRM  plan-2  C9    0.020
 VRM  plan-2  H101  0.020
 VRM  plan-2  H131  0.020
 VRM  plan-2  H111  0.020
 VRM  plan-2  H91   0.020

