# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:45:17 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-chloranyl-4-(cyclopropylmethylamino)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1nccc(NCC2CC2)c1C#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
 NQH  NQH  2-chloranyl-4-(cyclopropylmethylamino)pyridine-3-carbonitrile  ligand  24  14  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NQH
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
 NQH  N1   N   NS    0  -0.237  -27.0173  26.4414  -13.9147
 NQH  C2   C   CR16  0  -0.399  -26.5759  31.1910  -13.3328
 NQH  C3   C   CR6   0   0.550  -26.7440  29.8132  -13.0762
 NQH  C7   C   CH1   0  -0.245  -28.4553  30.3534  -10.2621
 NQH  C6   C   CH2   0  -0.327  -27.0236  30.0467  -10.6155
 NQH  C5   C   CSP   0   0.030  -26.8849  27.5754  -14.0809
 NQH  C4   C   CR6   0  -0.102  -26.7265  28.9744  -14.2233
 NQH  C9   C   CH2   0  -0.492  -28.7511  31.4986   -9.3450
 NQH  C    C   CR6   0   0.144  -26.5507  29.5580  -15.4788
 NQH  CL   CL  CL    0  -0.071  -26.5334  28.5174  -16.8602
 NQH  C1   C   CR16  0  -0.057  -26.4105  31.6240  -14.6212
 NQH  N    N   N     0  -0.417  -26.3971  30.8295  -15.7031
 NQH  N2   N   NH1   0  -0.680  -26.8877  29.3013  -11.8533
 NQH  C8   C   CH2   0  -0.484  -29.1383  31.5761  -10.7913
 NQH  H1   H   HCR6  0   0.290  -26.5683  31.9161  -12.5346
 NQH  H2   H   HCH1  0   0.262  -29.0793  29.4732  -10.1441
 NQH  H3   H   HCH2  0   0.278  -26.5721  29.4359   -9.8331
 NQH  H4   H   HCH2  0   0.255  -26.4311  30.9614  -10.6651
 NQH  H5   H   HCH2  0   0.248  -27.9199  32.1090   -9.0126
 NQH  H6   H   HCH2  0   0.256  -29.5305  31.3737   -8.6052
 NQH  H7   H   HCR6  0   0.287  -26.2802  32.6820  -14.8127
 NQH  H8   H   HNH1  0   0.411  -27.0216  28.3051  -11.7710
 NQH  H9   H   HCH2  0   0.245  -28.5793  32.2514  -11.4270
 NQH  H10  H   HCH2  0   0.255  -30.1874  31.4995  -11.0462

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
 NQH  CL  C    single    1.730  0.020  1.730
 NQH  N   C    aromatic  1.300  0.020  1.300
 NQH  N   C1   aromatic  1.342  0.020  1.342
 NQH  C   C4   aromatic  1.396  0.020  1.396
 NQH  C1  C2   aromatic  1.369  0.020  1.369
 NQH  C4  C5   single    1.415  0.020  1.415
 NQH  C4  C3   aromatic  1.421  0.020  1.421
 NQH  C5  N1   triple    1.154  0.020  1.154
 NQH  C2  C3   aromatic  1.412  0.020  1.412
 NQH  C3  N2   single    1.333  0.020  1.333
 NQH  N2  C6   single    1.451  0.020  1.451
 NQH  C6  C7   single    1.506  0.020  1.506
 NQH  C8  C7   single    1.497  0.020  1.497
 NQH  C8  C9   single    1.499  0.020  1.499
 NQH  C7  C9   single    1.497  0.020  1.497
 NQH  C2  H1   single    0.930  0.020  1.080
 NQH  C7  H2   single    0.970  0.020  1.090
 NQH  C6  H3   single    0.970  0.020  1.090
 NQH  C6  H4   single    0.970  0.020  1.090
 NQH  C9  H5   single    0.970  0.020  1.090
 NQH  C9  H6   single    0.970  0.020  1.090
 NQH  C1  H7   single    0.930  0.020  1.080
 NQH  N2  H8   single    0.860  0.020  1.020
 NQH  C8  H9   single    0.970  0.020  1.090
 NQH  C8  H10  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
 NQH  H1   C2  C1  118.88  3.000
 NQH  H1   C2  C3  121.51  3.000
 NQH  C1   C2  C3  119.61  3.000
 NQH  N2   C3  C4  121.00  3.000
 NQH  N2   C3  C2  123.66  3.000
 NQH  C4   C3  C2  115.33  3.000
 NQH  H2   C7  C8  116.00  3.000
 NQH  H2   C7  C9  116.12  3.000
 NQH  C8   C7  C9   60.10  3.000
 NQH  H2   C7  C6  114.01  3.000
 NQH  C9   C7  C6  119.17  3.000
 NQH  C8   C7  C6  121.13  3.000
 NQH  H4   C6  H3  106.11  3.000
 NQH  H4   C6  N2  109.93  3.000
 NQH  H3   C6  N2  106.59  3.000
 NQH  H4   C6  C7  110.87  3.000
 NQH  H3   C6  C7  109.83  3.000
 NQH  N2   C6  C7  113.18  3.000
 NQH  C4   C5  N1  180.00  3.000
 NQH  C    C4  C5  121.20  3.000
 NQH  C5   C4  C3  120.06  3.000
 NQH  C    C4  C3  118.74  3.000
 NQH  H6   C9  H5  114.08  3.000
 NQH  H6   C9  C8  118.66  3.000
 NQH  H5   C9  C8  117.71  3.000
 NQH  H6   C9  C7  118.23  3.000
 NQH  H5   C9  C7  117.87  3.000
 NQH  C8   C9  C7   59.97  3.000
 NQH  N    C   CL  116.71  3.000
 NQH  N    C   C4  125.38  3.000
 NQH  CL   C   C4  117.92  3.000
 NQH  H7   C1  N   115.75  3.000
 NQH  H7   C1  C2  119.33  3.000
 NQH  N    C1  C2  124.92  3.000
 NQH  C1   N   C   116.02  3.000
 NQH  H8   N2  C6  115.17  3.000
 NQH  H8   N2  C3  117.93  3.000
 NQH  C6   N2  C3  126.52  3.000
 NQH  H10  C8  H9  113.97  3.000
 NQH  H10  C8  C9  118.29  3.000
 NQH  H9   C8  C9  117.72  3.000
 NQH  H10  C8  C7  117.88  3.000
 NQH  H9   C8  C7  118.77  3.000
 NQH  C9   C8  C7   59.93  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
 NQH  CONST_01  C   N   C1  C2     0.00   0.0  0
 NQH  CONST_02  C   C4  C3  C2     0.00   0.0  0
 NQH  CONST_03  N   C   C4  C3     0.00   0.0  0
 NQH  CONST_04  N   C1  C2  C3     0.00   0.0  0
 NQH  CONST_05  C1  N   C   C4     0.00   0.0  0
 NQH  CONST_06  C1  C2  C3  C4     0.00   0.0  0
 NQH  CONST_07  C5  C4  C3  C2   180.00   0.0  0
 NQH  CONST_08  CL  C   C4  C3   180.00   0.0  0
 NQH  CONST_09  N   C   C4  C5   180.00   0.0  0
 NQH  CONST_10  N2  C3  C4  C    180.00   0.0  0
 NQH  CONST_11  C1  N   C   CL   180.00   0.0  0
 NQH  CONST_12  N2  C3  C2  C1   180.00   0.0  0
 NQH  CONST_13  H7  C1  C2  C3   180.00   0.0  0
 NQH  CONST_14  H1  C2  C3  C4   180.00   0.0  0
 NQH  CONST_15  C6  N2  C3  C2     0.00   0.0  0
 NQH  CONST_16  C4  C3  N2  C6   180.00   0.0  0
 NQH  CONST_17  H8  N2  C3  C2   180.00   0.0  0
 NQH  Var_01    C9  C8  C7  C6  -108.03  30.0  1
 NQH  Var_02    H5  C9  C8  C7   107.83  30.0  1
 NQH  Var_03    C7  C6  N2  C3    90.40  30.0  3
 NQH  Var_04    N2  C6  C7  C9  -157.63  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NQH  chir_01  C7  C6  C8  C9  both

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
 NQH  plan-1  N1  0.020
 NQH  plan-1  C2  0.020
 NQH  plan-1  C3  0.020
 NQH  plan-1  C5  0.020
 NQH  plan-1  C4  0.020
 NQH  plan-1  C   0.020
 NQH  plan-1  CL  0.020
 NQH  plan-1  C1  0.020
 NQH  plan-1  N   0.020
 NQH  plan-1  N2  0.020
 NQH  plan-1  H1  0.020
 NQH  plan-1  H7  0.020
 NQH  plan-2  C3  0.020
 NQH  plan-2  C6  0.020
 NQH  plan-2  N2  0.020
 NQH  plan-2  H8  0.020

