# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:54:27 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 1-(1,5-dimethyl-1H-pyrazol-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(CN)cc1C
#
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
 SW3  SW3  1-(1,5-dimethyl-1H-pyrazol-3-yl)methanamine  ligand  20  9  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SW3
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
 SW3  C1    C  CH3   0  -0.747   2.4470   1.5229  -0.2217
 SW3  N1    N  NH2   0  -0.796  -3.0601  -0.1574  -0.8411
 SW3  C2    C  CR5   0   0.411   1.1664   0.7897  -0.0377
 SW3  N2    N  N     0  -0.311  -0.1719  -0.9853   0.1787
 SW3  C3    C  CR15  0  -0.569  -0.1181   1.2563   0.1483
 SW3  N3    N  NR5   0  -0.310   1.0751  -0.5566  -0.0172
 SW3  C4    C  CR5   0   0.271  -0.9130   0.1045   0.2772
 SW3  C5    C  CH2   0  -0.367  -2.3962   0.0302   0.4463
 SW3  C6    C  CH3   0  -0.520   2.1558  -1.5084  -0.0900
 SW3  H1    H  HCH3  0   0.256   3.1537   1.3197   0.5846
 SW3  H1A   H  HCH3  0   0.256   2.9368   1.2599  -1.1607
 SW3  H1B   H  HCH3  0   0.264   2.2586   2.5941  -0.2344
 SW3  HN1   H  HNH2  0   0.349  -4.0605  -0.2016  -0.6889
 SW3  HN1A  H  HNH2  0   0.339  -2.9108   0.6635  -1.4152
 SW3  H3    H  HCR5  0   0.256  -0.4331   2.2871   0.1854
 SW3  H5    H  HCH2  0   0.210  -2.7281   0.9276   0.9841
 SW3  H5A   H  HCH2  0   0.233  -2.6436  -0.8231   1.0813
 SW3  H6    H  HCH3  0   0.254   2.5005  -1.7947   0.9036
 SW3  H6A   H  HCH3  0   0.264   1.8169  -2.3956  -0.6182
 SW3  H6B   H  HCH3  0   0.258   2.9905  -1.0787  -0.6375

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
 SW3  C1  C2    single    1.487  0.020  1.487
 SW3  N1  C5    single    1.461  0.020  1.461
 SW3  C2  C3    aromatic  1.379  0.020  1.379
 SW3  C2  N3    aromatic  1.350  0.020  1.350
 SW3  N2  N3    aromatic  1.333  0.020  1.333
 SW3  N2  C4    aromatic  1.322  0.020  1.322
 SW3  C3  C4    aromatic  1.405  0.020  1.405
 SW3  N3  C6    single    1.442  0.020  1.442
 SW3  C4  C5    single    1.495  0.020  1.495
 SW3  C1  H1    single    0.970  0.020  1.090
 SW3  C1  H1A   single    0.970  0.020  1.090
 SW3  C1  H1B   single    0.970  0.020  1.090
 SW3  N1  HN1   single    0.890  0.020  1.040
 SW3  N1  HN1A  single    0.890  0.020  1.040
 SW3  C3  H3    single    0.930  0.020  1.080
 SW3  C5  H5    single    0.970  0.020  1.090
 SW3  C5  H5A   single    0.970  0.020  1.090
 SW3  C6  H6    single    0.970  0.020  1.090
 SW3  C6  H6A   single    0.970  0.020  1.090
 SW3  C6  H6B   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
 SW3  H1B   C1  H1A  107.77  3.000
 SW3  H1B   C1  H1   107.71  3.000
 SW3  H1A   C1  H1   107.47  3.000
 SW3  H1B   C1  C2   109.75  3.000
 SW3  H1A   C1  C2   111.97  3.000
 SW3  H1    C1  C2   111.99  3.000
 SW3  HN1A  N1  HN1  105.43  3.000
 SW3  HN1A  N1  C5   109.18  3.000
 SW3  HN1   N1  C5   108.79  3.000
 SW3  N3    C2  C3   105.81  3.000
 SW3  N3    C2  C1   123.51  3.000
 SW3  C3    C2  C1   130.68  3.000
 SW3  C4    N2  N3   105.68  3.000
 SW3  H3    C3  C4   127.94  3.000
 SW3  H3    C3  C2   126.87  3.000
 SW3  C4    C3  C2   105.18  3.000
 SW3  C6    N3  N2   119.75  3.000
 SW3  C6    N3  C2   127.37  3.000
 SW3  N2    N3  C2   112.73  3.000
 SW3  C5    C4  C3   127.77  3.000
 SW3  C5    C4  N2   121.59  3.000
 SW3  C3    C4  N2   110.60  3.000
 SW3  H5A   C5  H5   106.59  3.000
 SW3  H5A   C5  C4   109.23  3.000
 SW3  H5    C5  C4   108.35  3.000
 SW3  H5A   C5  N1   108.01  3.000
 SW3  H5    C5  N1   113.55  3.000
 SW3  C4    C5  N1   110.96  3.000
 SW3  H6B   C6  H6A  108.51  3.000
 SW3  H6B   C6  H6   108.68  3.000
 SW3  H6A   C6  H6   109.10  3.000
 SW3  H6B   C6  N3   109.88  3.000
 SW3  H6A   C6  N3   109.25  3.000
 SW3  H6    C6  N3   111.37  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
 SW3  CONST_01  N2   C4  C3  C2     0.00   0.0  0
 SW3  CONST_02  C4   N2  N3  C2     0.00   0.0  0
 SW3  CONST_03  C3   C2  N3  N2     0.00   0.0  0
 SW3  CONST_04  N3   N2  C4  C3     0.00   0.0  0
 SW3  CONST_05  C4   C3  C2  N3     0.00   0.0  0
 SW3  CONST_06  C4   C3  C2  C1   180.00   0.0  0
 SW3  CONST_07  N2   N3  C2  C1   180.00   0.0  0
 SW3  CONST_08  C5   C4  C3  C2   180.00   0.0  0
 SW3  CONST_09  C6   N3  C2  C3   180.00   0.0  0
 SW3  CONST_10  C5   C4  N2  N3   180.00   0.0  0
 SW3  CONST_11  C6   N3  N2  C4   180.00   0.0  0
 SW3  CONST_12  H3   C3  C4  N2   180.00   0.0  0
 SW3  Var_01    N2   C4  C5  N1   -82.48  30.0  1
 SW3  Var_02    H6   C6  N3  C2    92.58  30.0  2
 SW3  Var_03    H1   C1  C2  C3   117.29  30.0  2
 SW3  Var_04    HN1  N1  C5  C4  -179.90  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
 SW3  plan-1  C1  0.020
 SW3  plan-1  C2  0.020
 SW3  plan-1  N2  0.020
 SW3  plan-1  C3  0.020
 SW3  plan-1  N3  0.020
 SW3  plan-1  C4  0.020
 SW3  plan-1  C5  0.020
 SW3  plan-1  C6  0.020
 SW3  plan-1  H3  0.020

