# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:39:37 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(C)cc1CN
#
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
 47J  47J  1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine  ligand  20  9  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_47J
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
 47J  C4   C  CH2   0  -0.398   1.9456   0.8017  -0.5139
 47J  N1   N  NR5   0  -0.315   0.1216  -0.8557  -0.0587
 47J  N2   N  N     0  -0.314  -1.1965  -0.9490   0.1235
 47J  C1   C  CR5   0   0.264  -1.6655   0.2825   0.0145
 47J  C    C  CH3   0  -0.736  -3.1195   0.5740   0.1670
 47J  C3   C  CR5   0   0.438   0.5208   0.4113  -0.2968
 47J  C2   C  CR15  0  -0.565  -0.6191   1.1838  -0.2500
 47J  N    N  NH2   0  -0.791   2.6292   1.0367   0.7543
 47J  H1   H  HCH2  0   0.227   2.4405   0.0605  -1.1554
 47J  H2   H  HCH2  0   0.257   1.9482   1.7359  -1.0764
 47J  H3   H  HCH3  0   0.255   1.0366  -2.4429  -1.0922
 47J  H4   H  HCH3  0   0.252   1.9132  -1.8603   0.3311
 47J  H5   H  HCH3  0   0.268   0.4420  -2.8080   0.5358
 47J  H6   H  HCH3  0   0.243  -3.2978   1.3117   0.9504
 47J  H7   H  HCH3  0   0.243  -3.5430   0.9761  -0.7544
 47J  H8   H  HCH3  0   0.243  -3.6714  -0.3293   0.4233
 47J  H9   H  HCR5  0   0.254  -0.6824   2.2523  -0.3839
 47J  H10  H  HNH2  0   0.345   2.7676   0.1576   1.2373
 47J  H11  H  HNH2  0   0.356   3.5586   1.3883   0.5603
 47J  C5   C  CH3   0  -0.526   0.9252  -2.0547  -0.0796

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
 47J  N   C4   single    1.460  0.020  1.460
 47J  C   C1   single    1.491  0.020  1.491
 47J  C2  C1   aromatic  1.406  0.020  1.406
 47J  C2  C3   aromatic  1.378  0.020  1.378
 47J  C1  N2   aromatic  1.322  0.020  1.322
 47J  C3  C4   single    1.493  0.020  1.493
 47J  C3  N1   aromatic  1.350  0.020  1.350
 47J  N2  N1   aromatic  1.334  0.020  1.334
 47J  N1  C5   single    1.443  0.020  1.443
 47J  C4  H1   single    0.970  0.020  1.090
 47J  C4  H2   single    0.970  0.020  1.090
 47J  C5  H3   single    0.970  0.020  1.090
 47J  C5  H4   single    0.970  0.020  1.090
 47J  C5  H5   single    0.970  0.020  1.090
 47J  C   H6   single    0.970  0.020  1.090
 47J  C   H7   single    0.970  0.020  1.090
 47J  C   H8   single    0.970  0.020  1.090
 47J  C2  H9   single    0.930  0.020  1.080
 47J  N   H10  single    0.890  0.020  1.040
 47J  N   H11  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
 47J  H2   C4  H1   106.01  3.000
 47J  H2   C4  N    108.01  3.000
 47J  H1   C4  N    113.90  3.000
 47J  H2   C4  C3   107.53  3.000
 47J  H1   C4  C3   109.78  3.000
 47J  N    C4  C3   111.26  3.000
 47J  C3   N1  N2   112.46  3.000
 47J  N2   N1  C5   119.60  3.000
 47J  C3   N1  C5   127.78  3.000
 47J  C1   N2  N1   105.91  3.000
 47J  C2   C1  C    128.30  3.000
 47J  C2   C1  N2   110.40  3.000
 47J  C    C1  N2   121.30  3.000
 47J  H8   C   H7   107.92  3.000
 47J  H8   C   H6   108.01  3.000
 47J  H7   C   H6   107.09  3.000
 47J  H8   C   C1   110.87  3.000
 47J  H7   C   C1   111.36  3.000
 47J  H6   C   C1   111.42  3.000
 47J  C2   C3  N1   106.00  3.000
 47J  N1   C3  C4   123.60  3.000
 47J  C2   C3  C4   130.37  3.000
 47J  H9   C2  C3   126.85  3.000
 47J  H9   C2  C1   127.93  3.000
 47J  C3   C2  C1   105.23  3.000
 47J  H11  N   H10  105.51  3.000
 47J  H11  N   C4   108.62  3.000
 47J  H10  N   C4   109.80  3.000
 47J  H5   C5  H4   108.31  3.000
 47J  H5   C5  H3   108.95  3.000
 47J  H4   C5  H3   108.75  3.000
 47J  H5   C5  N1   108.68  3.000
 47J  H4   C5  N1   110.60  3.000
 47J  H3   C5  N1   111.47  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
 47J  CONST_01  C1   C2  C3  N1    0.00   0.0  0
 47J  CONST_02  C2   C1  N2  N1    0.00   0.0  0
 47J  CONST_03  C3   C2  C1  N2    0.00   0.0  0
 47J  CONST_04  C2   C3  N1  N2    0.00   0.0  0
 47J  CONST_05  C3   N1  N2  C1    0.00   0.0  0
 47J  CONST_06  C1   C2  C3  C4  180.00   0.0  0
 47J  CONST_07  N2   N1  C3  C4  180.00   0.0  0
 47J  CONST_08  C2   C3  N1  C5  180.00   0.0  0
 47J  CONST_09  C1   N2  N1  C5  180.00   0.0  0
 47J  CONST_10  C    C1  N2  N1  180.00   0.0  0
 47J  CONST_11  C3   C2  C1  C   180.00   0.0  0
 47J  CONST_12  H9   C2  C3  N1  180.00   0.0  0
 47J  Var_01    N    C4  C3  N1  -85.25  30.0  2
 47J  Var_02    H6   C   C1  N2  123.50  30.0  2
 47J  Var_03    H3   C5  N1  N2   91.57  30.0  2
 47J  Var_04    H10  N   C4  C3   70.77  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
 47J  plan-1  C4  0.020
 47J  plan-1  N1  0.020
 47J  plan-1  N2  0.020
 47J  plan-1  C1  0.020
 47J  plan-1  C   0.020
 47J  plan-1  C3  0.020
 47J  plan-1  C2  0.020
 47J  plan-1  H9  0.020
 47J  plan-1  C5  0.020

