# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 14:12:31 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: ~{N}-methylpyrimidine-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=N)c1ncccn1
#
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
 IQL  IQL  "N-methylpyrimidine-2-carboximidamide"  ligand  18  10  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IQL
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
 IQL  C01  C  CH3   0  -0.503  22.0873  44.5533  -10.0568
 IQL  C03  C  C     0   0.359  23.3496  42.4823   -9.8610
 IQL  C05  C  CR6   0   0.335  24.7299  41.8840   -9.8878
 IQL  C07  C  CR16  0  -0.006  26.0237  40.0417   -9.7123
 IQL  C08  C  CR16  0  -0.349  27.1598  40.8056   -9.9231
 IQL  C09  C  CR16  0  -0.004  26.9623  42.1617  -10.1151
 IQL  N02  N  NH1   0  -0.630  23.3163  43.8102  -10.0686
 IQL  N04  N  N     0  -0.655  22.2913  41.7943   -9.6592
 IQL  N06  N  N     0  -0.415  24.8113  40.5771   -9.6940
 IQL  N10  N  N     0  -0.423  25.7505  42.7013  -10.0983
 IQL  H1   H  HCH3  0   0.244  22.3083  45.5987  -10.2556
 IQL  H2   H  HCH3  0   0.228  21.3944  44.1960  -10.8211
 IQL  H3   H  HCH3  0   0.226  21.5780  44.4865   -9.0924
 IQL  H4   H  HCR6  0   0.285  26.0902  38.9716   -9.5541
 IQL  H5   H  HCR6  0   0.292  28.1463  40.3667   -9.9367
 IQL  H6   H  HCR6  0   0.286  27.7960  42.8325  -10.2862
 IQL  H7   H  HNH1  0   0.399  24.1900  44.2922  -10.1915
 IQL  H8   H  H     0   0.331  22.5430  40.8202   -9.5338

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
 IQL  C09  N10  aromatic  1.327  0.020  1.327
 IQL  C09  C08  aromatic  1.384  0.020  1.384
 IQL  N10  C05  aromatic  1.324  0.020  1.324
 IQL  N02  C01  single    1.436  0.020  1.436
 IQL  N02  C03  single    1.344  0.020  1.344
 IQL  C08  C07  aromatic  1.385  0.020  1.385
 IQL  C05  C03  single    1.505  0.020  1.505
 IQL  C05  N06  aromatic  1.324  0.020  1.324
 IQL  C03  N04  double    1.278  0.020  1.278
 IQL  N06  C07  aromatic  1.326  0.020  1.326
 IQL  C01  H1   single    0.970  0.020  1.090
 IQL  C01  H2   single    0.970  0.020  1.090
 IQL  C01  H3   single    0.970  0.020  1.090
 IQL  C07  H4   single    0.930  0.020  1.080
 IQL  C08  H5   single    0.930  0.020  1.080
 IQL  C09  H6   single    0.930  0.020  1.080
 IQL  N02  H7   single    0.860  0.020  1.020
 IQL  N04  H8   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
 IQL  H3   C01  H2   107.58  3.000
 IQL  H3   C01  H1   108.37  3.000
 IQL  H2   C01  H1   108.41  3.000
 IQL  H3   C01  N02  111.99  3.000
 IQL  H2   C01  N02  111.59  3.000
 IQL  H1   C01  N02  108.79  3.000
 IQL  N04  C03  N02  122.38  3.000
 IQL  N04  C03  C05  123.25  3.000
 IQL  N02  C03  C05  114.38  3.000
 IQL  N10  C05  N06  125.82  3.000
 IQL  N06  C05  C03  116.52  3.000
 IQL  N10  C05  C03  117.67  3.000
 IQL  H4   C07  N06  116.93  3.000
 IQL  H4   C07  C08  121.10  3.000
 IQL  N06  C07  C08  121.97  3.000
 IQL  H5   C08  C09  121.81  3.000
 IQL  H5   C08  C07  121.80  3.000
 IQL  C09  C08  C07  116.39  3.000
 IQL  H6   C09  N10  116.93  3.000
 IQL  H6   C09  C08  121.25  3.000
 IQL  N10  C09  C08  121.82  3.000
 IQL  H7   N02  C03  118.09  3.000
 IQL  H7   N02  C01  119.78  3.000
 IQL  C03  N02  C01  122.07  3.000
 IQL  H8   N04  C03  109.34  3.000
 IQL  C07  N06  C05  116.94  3.000
 IQL  C09  N10  C05  117.06  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
 IQL  CONST_01  C08  C09  N10  C05     0.00   0.0  0
 IQL  CONST_02  C08  C07  N06  C05     0.00   0.0  0
 IQL  CONST_03  N10  C09  C08  C07     0.00   0.0  0
 IQL  CONST_04  N10  C05  N06  C07     0.00   0.0  0
 IQL  CONST_05  N06  C05  N10  C09     0.00   0.0  0
 IQL  CONST_06  N06  C07  C08  C09     0.00   0.0  0
 IQL  CONST_07  C09  N10  C05  C03   180.00   0.0  0
 IQL  CONST_08  C07  N06  C05  C03   180.00   0.0  0
 IQL  CONST_09  H6   C09  N10  C05   180.00   0.0  0
 IQL  CONST_10  H4   C07  N06  C05   180.00   0.0  0
 IQL  CONST_11  H6   C09  C08  C07   180.00   0.0  0
 IQL  CONST_12  H4   C07  C08  C09   180.00   0.0  0
 IQL  CONST_13  H5   C08  C07  N06   180.00   0.0  0
 IQL  CONST_14  H5   C08  C09  N10   180.00   0.0  0
 IQL  CONST_15  C05  C03  N02  C01   180.00   0.0  0
 IQL  CONST_16  H7   N02  C03  C05     0.00   0.0  0
 IQL  CONST_17  H8   N04  C03  C05     0.00   0.0  0
 IQL  CONST_18  N04  C03  N02  C01     0.00   0.0  0
 IQL  CONST_19  H8   N04  C03  N02   180.00   0.0  0
 IQL  CONST_20  H7   N02  C03  N04   180.00   0.0  0
 IQL  Var_01    N10  C05  C03  N02     0.44  30.0  2
 IQL  Var_02    N06  C05  C03  N02  -179.70  30.0  2
 IQL  Var_03    N10  C05  C03  N04  -179.60  30.0  2
 IQL  Var_04    N06  C05  C03  N04     0.27  30.0  2
 IQL  Var_05    H1   C01  N02  C03  -179.49  30.0  3
 IQL  Var_06    H2   C01  N02  C03   -59.93  30.0  3
 IQL  Var_07    H3   C01  N02  C03    60.74  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
 IQL  plan-1  C03  0.020
 IQL  plan-1  C05  0.020
 IQL  plan-1  C07  0.020
 IQL  plan-1  C08  0.020
 IQL  plan-1  C09  0.020
 IQL  plan-1  N06  0.020
 IQL  plan-1  N10  0.020
 IQL  plan-1  H4   0.020
 IQL  plan-1  H5   0.020
 IQL  plan-1  H6   0.020
 IQL  plan-2  C01  0.020
 IQL  plan-2  C03  0.020
 IQL  plan-2  C05  0.020
 IQL  plan-2  N02  0.020
 IQL  plan-2  N04  0.020
 IQL  plan-2  H7   0.020
 IQL  plan-2  H8   0.020

