# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:03:00 2021
#   Inital geometry file: a 54 line input string
#   Ligand name: N~4~,N~4~-dimethylpyridine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccnc(N)c1
#
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
 X4V  X4V  N~4~,N~4~-dimethylpyridine-2,4-diamine  ligand  21  10  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X4V
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
 X4V  C1   C  CH3   0  -0.537   9.3452  -3.5051  -15.9624
 X4V  C2   C  CH3   0  -0.536   9.3292  -1.0073  -15.9203
 X4V  C3   C  CR6   0   0.486   7.3039  -2.2658  -16.3781
 X4V  C4   C  CR16  0  -0.444   6.5629  -1.0647  -16.4865
 X4V  C5   C  CR16  0  -0.076   5.2166  -1.1487  -16.7546
 X4V  C6   C  CR6   0   0.439   5.2164  -3.4140  -16.7992
 X4V  C7   C  CR16  0  -0.502   6.5873  -3.4596  -16.5317
 X4V  N1   N  NT    0  -0.501   8.6388  -2.2580  -16.1418
 X4V  N2   N  N     0  -0.484   4.5285  -2.2768  -16.9170
 X4V  N3   N  NH2   0  -0.839   4.4959  -4.5748  -16.9085
 X4V  H1   H  HCH3  0   0.258  10.4038  -3.3053  -15.8247
 X4V  H2   H  HCH3  0   0.234   8.9929  -4.0603  -15.0879
 X4V  H3   H  HCH3  0   0.239   9.2434  -4.1547  -16.8347
 X4V  H4   H  HCH3  0   0.257  10.3933  -1.1976  -15.8147
 X4V  H5   H  HCH3  0   0.240   9.2012  -0.3221  -16.7605
 X4V  H6   H  HCH3  0   0.234   8.9891  -0.4964  -15.0147
 X4V  H7   H  HCR6  0   0.263   7.0180  -0.0931  -16.3666
 X4V  H8   H  HCR6  0   0.246   4.6442  -0.2308  -16.8476
 X4V  H9   H  HCR6  0   0.266   7.0708  -4.4231  -16.4475
 X4V  H10  H  HNH2  0   0.375   3.6178  -4.4938  -17.3951
 X4V  H11  H  HNH2  0   0.382   5.0063  -5.4103  -17.1420

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
 X4V  N2  C5   aromatic  1.331  0.020  1.331
 X4V  N2  C6   aromatic  1.334  0.020  1.334
 X4V  N3  C6   single    1.371  0.020  1.371
 X4V  C5  C4   aromatic  1.375  0.020  1.375
 X4V  C6  C7   aromatic  1.397  0.020  1.397
 X4V  C4  C3   aromatic  1.415  0.020  1.415
 X4V  C7  C3   aromatic  1.401  0.020  1.401
 X4V  C3  N1   single    1.356  0.020  1.356
 X4V  N1  C1   single    1.444  0.020  1.444
 X4V  N1  C2   single    1.446  0.020  1.446
 X4V  C1  H1   single    0.970  0.020  1.090
 X4V  C1  H2   single    0.970  0.020  1.090
 X4V  C1  H3   single    0.970  0.020  1.090
 X4V  C2  H4   single    0.970  0.020  1.090
 X4V  C2  H5   single    0.970  0.020  1.090
 X4V  C2  H6   single    0.970  0.020  1.090
 X4V  C4  H7   single    0.930  0.020  1.080
 X4V  C5  H8   single    0.930  0.020  1.080
 X4V  C7  H9   single    0.930  0.020  1.080
 X4V  N3  H10  single    0.890  0.020  1.040
 X4V  N3  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
 X4V  H3   C1  H2   107.85  3.000
 X4V  H3   C1  H1   107.55  3.000
 X4V  H2   C1  H1   107.81  3.000
 X4V  H3   C1  N1   111.64  3.000
 X4V  H2   C1  N1   112.32  3.000
 X4V  H1   C1  N1   109.48  3.000
 X4V  H6   C2  H5   107.91  3.000
 X4V  H6   C2  H4   107.81  3.000
 X4V  H5   C2  H4   107.44  3.000
 X4V  H6   C2  N1   112.48  3.000
 X4V  H5   C2  N1   111.66  3.000
 X4V  H4   C2  N1   109.34  3.000
 X4V  N1   C3  C7   121.85  3.000
 X4V  N1   C3  C4   121.60  3.000
 X4V  C7   C3  C4   116.55  3.000
 X4V  H7   C4  C5   119.29  3.000
 X4V  H7   C4  C3   122.31  3.000
 X4V  C5   C4  C3   118.40  3.000
 X4V  H8   C5  N2   115.69  3.000
 X4V  H8   C5  C4   118.76  3.000
 X4V  N2   C5  C4   125.55  3.000
 X4V  N3   C6  N2   116.34  3.000
 X4V  N3   C6  C7   120.22  3.000
 X4V  N2   C6  C7   123.40  3.000
 X4V  H9   C7  C6   118.86  3.000
 X4V  H9   C7  C3   121.47  3.000
 X4V  C6   C7  C3   119.67  3.000
 X4V  C3   N1  C2   120.13  3.000
 X4V  C2   N1  C1   119.63  3.000
 X4V  C3   N1  C1   119.88  3.000
 X4V  C6   N2  C5   116.42  3.000
 X4V  H11  N3  H10  113.38  3.000
 X4V  H11  N3  C6   117.06  3.000
 X4V  H10  N3  C6   115.38  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
 X4V  CONST_01  N2  C5  C4  C3     0.00   0.0  0
 X4V  CONST_02  N2  C6  C7  C3     0.00   0.0  0
 X4V  CONST_03  C6  N2  C5  C4     0.00   0.0  0
 X4V  CONST_04  C6  C7  C3  C4     0.00   0.0  0
 X4V  CONST_05  C7  C6  N2  C5     0.00   0.0  0
 X4V  CONST_06  C7  C3  C4  C5     0.00   0.0  0
 X4V  CONST_07  N3  C6  C7  C3   180.00   0.0  0
 X4V  CONST_08  N3  C6  N2  C5   180.00   0.0  0
 X4V  CONST_09  N1  C3  C4  C5   180.00   0.0  0
 X4V  CONST_10  N1  C3  C7  C6   180.00   0.0  0
 X4V  CONST_11  H8  C5  C4  C3   180.00   0.0  0
 X4V  CONST_12  H9  C7  C3  C4   180.00   0.0  0
 X4V  CONST_13  H7  C4  C3  C7   180.00   0.0  0
 X4V  CONST_14  C4  C3  N1  C1   180.00   0.0  0
 X4V  CONST_15  C7  C3  N1  C1     0.00   0.0  0
 X4V  CONST_16  C4  C3  N1  C2     0.00   0.0  0
 X4V  CONST_17  C7  C3  N1  C2   180.00   0.0  0
 X4V  Var_01    H1  C1  N1  C3   177.73  30.0  3
 X4V  Var_02    H4  C2  N1  C3  -176.31  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
 X4V  plan-1  C3   0.020
 X4V  plan-1  C4   0.020
 X4V  plan-1  C5   0.020
 X4V  plan-1  C6   0.020
 X4V  plan-1  C7   0.020
 X4V  plan-1  N1   0.020
 X4V  plan-1  N2   0.020
 X4V  plan-1  N3   0.020
 X4V  plan-1  H7   0.020
 X4V  plan-1  H8   0.020
 X4V  plan-1  H9   0.020
 X4V  plan-2  C1   0.020
 X4V  plan-2  C2   0.020
 X4V  plan-2  C3   0.020
 X4V  plan-2  N1   0.020
 X4V  plan-3  C6   0.020
 X4V  plan-3  N3   0.020
 X4V  plan-3  H10  0.020
 X4V  plan-3  H11  0.020

