# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:36:49 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 1-[2-(1H-pyrazol-1-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccccc1n2cccn2
#
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
 Z5P  Z5P  1-[2-(1H-pyrazol-1-yl)phenyl]methanamine  ligand  24  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z5P
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
 Z5P  N13   N  NH2   0  -0.801  -0.1082  -2.7754   0.5522
 Z5P  C10   C  CR16  0  -0.307  -2.4447  -0.6625  -0.1949
 Z5P  N4    N  NR5   0  -0.380   1.0239   0.5760   0.0781
 Z5P  C9    C  CR16  0  -0.238  -3.1568   0.4828   0.1253
 Z5P  C8    C  CR16  0  -0.271  -2.4779   1.6565   0.4226
 Z5P  C7    C  CR16  0  -0.275  -1.0930   1.6667   0.4112
 Z5P  C6    C  CR6   0   0.290  -0.3904   0.5118   0.0845
 Z5P  C3    C  CR15  0   0.029   1.7886   1.4809  -0.5713
 Z5P  C12   C  CH2   0  -0.374  -0.3308  -1.9400  -0.6210
 Z5P  C2    C  CR15  0  -0.509   3.0935   1.1957  -0.2550
 Z5P  C1    C  CR15  0  -0.036   3.0074   0.0880   0.6059
 Z5P  C11   C  CR6   0   0.121  -1.0524  -0.6729  -0.2411
 Z5P  N5    N  N     0  -0.289   1.7552  -0.2740   0.8033
 Z5P  H9    H  HCR6  0   0.261  -4.2383   0.4603   0.1391
 Z5P  H8    H  HCR6  0   0.264  -3.0205   2.5574   0.6758
 Z5P  H10   H  HCR6  0   0.256  -2.9795  -1.5721  -0.4407
 Z5P  H7    H  HCR6  0   0.275  -0.5532   2.5683   0.6714
 Z5P  H2    H  HCR5  0   0.268   3.9775   1.7083  -0.5948
 Z5P  H1    H  HCR5  0   0.266   3.8090  -0.4502   1.0884
 Z5P  H3    H  HCR5  0   0.298   1.3548   2.2342  -1.2088
 Z5P  H121  H  HCH2  0   0.214   0.5842  -1.6939  -1.1726
 Z5P  H122  H  HCH2  0   0.243  -0.9674  -2.4933  -1.3140
 Z5P  H131  H  HNH2  0   0.347   0.2942  -3.6550   0.2521
 Z5P  H132  H  HNH2  0   0.348   0.5980  -2.3259   1.1237

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
 Z5P  C9   C8    aromatic  1.388  0.020  1.388
 Z5P  C9   C10   aromatic  1.386  0.020  1.386
 Z5P  C8   C7    aromatic  1.385  0.020  1.385
 Z5P  C10  C11   aromatic  1.393  0.020  1.393
 Z5P  C7   C6    aromatic  1.391  0.020  1.391
 Z5P  C2   C1    aromatic  1.406  0.020  1.406
 Z5P  C2   C3    aromatic  1.373  0.020  1.373
 Z5P  C1   N5    aromatic  1.318  0.020  1.318
 Z5P  C3   N4    aromatic  1.351  0.020  1.351
 Z5P  C11  C6    aromatic  1.396  0.020  1.396
 Z5P  C11  C12   single    1.507  0.020  1.507
 Z5P  C6   N4    single    1.416  0.020  1.416
 Z5P  C12  N13   single    1.457  0.020  1.457
 Z5P  N5   N4    aromatic  1.335  0.020  1.335
 Z5P  C9   H9    single    0.930  0.020  1.080
 Z5P  C8   H8    single    0.930  0.020  1.080
 Z5P  C10  H10   single    0.930  0.020  1.080
 Z5P  C7   H7    single    0.930  0.020  1.080
 Z5P  C2   H2    single    0.930  0.020  1.080
 Z5P  C1   H1    single    0.930  0.020  1.080
 Z5P  C3   H3    single    0.930  0.020  1.080
 Z5P  C12  H121  single    0.970  0.020  1.090
 Z5P  C12  H122  single    0.970  0.020  1.090
 Z5P  N13  H131  single    0.890  0.020  1.040
 Z5P  N13  H132  single    0.890  0.020  1.040

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
 Z5P  H132  N13  H131  105.99  3.000
 Z5P  H132  N13  C12   107.82  3.000
 Z5P  H131  N13  C12   108.67  3.000
 Z5P  H10   C10  C11   118.66  3.000
 Z5P  H10   C10  C9    119.51  3.000
 Z5P  C11   C10  C9    121.82  3.000
 Z5P  N5    N4   C3    112.17  3.000
 Z5P  N5    N4   C6    121.05  3.000
 Z5P  C3    N4   C6    126.72  3.000
 Z5P  H9    C9   C8    120.25  3.000
 Z5P  H9    C9   C10   119.96  3.000
 Z5P  C8    C9   C10   119.79  3.000
 Z5P  H8    C8   C7    119.83  3.000
 Z5P  H8    C8   C9    120.59  3.000
 Z5P  C7    C8   C9    119.57  3.000
 Z5P  H7    C7   C6    119.75  3.000
 Z5P  H7    C7   C8    120.18  3.000
 Z5P  C6    C7   C8    120.06  3.000
 Z5P  C11   C6   C7    121.34  3.000
 Z5P  C11   C6   N4    120.75  3.000
 Z5P  C7    C6   N4    117.91  3.000
 Z5P  H3    C3   C2    131.61  3.000
 Z5P  H3    C3   N4    121.64  3.000
 Z5P  C2    C3   N4    106.75  3.000
 Z5P  H122  C12  H121  106.32  3.000
 Z5P  H122  C12  C11   107.88  3.000
 Z5P  H121  C12  C11   109.74  3.000
 Z5P  H122  C12  N13   108.03  3.000
 Z5P  H121  C12  N13   113.97  3.000
 Z5P  C11   C12  N13   110.62  3.000
 Z5P  H2    C2   C1    128.22  3.000
 Z5P  H2    C2   C3    127.50  3.000
 Z5P  C1    C2   C3    104.28  3.000
 Z5P  H1    C1   N5    120.10  3.000
 Z5P  H1    C1   C2    128.41  3.000
 Z5P  N5    C1   C2    111.49  3.000
 Z5P  C12   C11  C6    123.06  3.000
 Z5P  C12   C11  C10   119.55  3.000
 Z5P  C6    C11  C10   117.39  3.000
 Z5P  C1    N5   N4    105.31  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
 Z5P  CONST_01  C7    C8   C9   C10    0.00   0.0  0
 Z5P  CONST_02  C7    C6   C11  C10    0.00   0.0  0
 Z5P  CONST_03  N4    C6   C11  C10  180.00   0.0  0
 Z5P  CONST_04  C1    C2   C3   N4     0.00   0.0  0
 Z5P  CONST_05  C8    C7   C6   N4   180.00   0.0  0
 Z5P  CONST_06  C2    C1   N5   N4     0.00   0.0  0
 Z5P  CONST_07  C6    C7   C8   C9     0.00   0.0  0
 Z5P  CONST_08  C6    C11  C10  C9     0.00   0.0  0
 Z5P  CONST_09  C11   C10  C9   C8     0.00   0.0  0
 Z5P  CONST_10  C11   C6   C7   C8     0.00   0.0  0
 Z5P  CONST_13  C2    C3   N4   C6   180.00   0.0  0
 Z5P  CONST_14  C1    N5   N4   C6   180.00   0.0  0
 Z5P  CONST_15  N5    C1   C2   C3     0.00   0.0  0
 Z5P  CONST_17  C1    N5   N4   C3     0.00   0.0  0
 Z5P  CONST_18  N5    N4   C3   C2     0.00   0.0  0
 Z5P  CONST_20  C12   C11  C6   N4     0.00   0.0  0
 Z5P  CONST_21  C12   C11  C10  C9   180.00   0.0  0
 Z5P  CONST_22  C12   C11  C6   C7   180.00   0.0  0
 Z5P  CONST_23  H8    C8   C9   C10  180.00   0.0  0
 Z5P  CONST_24  H2    C2   C3   N4   180.00   0.0  0
 Z5P  CONST_25  H7    C7   C6   N4     0.00   0.0  0
 Z5P  CONST_26  H1    C1   N5   N4   180.00   0.0  0
 Z5P  CONST_27  H10   C10  C9   C8   180.00   0.0  0
 Z5P  CONST_28  H9    C9   C8   C7   180.00   0.0  0
 Z5P  CONST_29  H3    C3   N4   C6     0.00   0.0  0
 Z5P  Var_01    C10   C11  C12  N13  -86.94  30.0  2
 Z5P  Var_02    H131  N13  C12  C11  174.49  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
 Z5P  plan-1  N4   0.020
 Z5P  plan-1  C6   0.020
 Z5P  plan-1  C3   0.020
 Z5P  plan-1  C2   0.020
 Z5P  plan-1  C1   0.020
 Z5P  plan-1  N5   0.020
 Z5P  plan-1  H2   0.020
 Z5P  plan-1  H1   0.020
 Z5P  plan-1  H3   0.020
 Z5P  plan-2  C10  0.020
 Z5P  plan-2  N4   0.020
 Z5P  plan-2  C9   0.020
 Z5P  plan-2  C8   0.020
 Z5P  plan-2  C7   0.020
 Z5P  plan-2  C6   0.020
 Z5P  plan-2  C12  0.020
 Z5P  plan-2  C11  0.020
 Z5P  plan-2  H9   0.020
 Z5P  plan-2  H8   0.020
 Z5P  plan-2  H10  0.020
 Z5P  plan-2  H7   0.020

