# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:57:21 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: 6-methyl-N~4~-[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(NCc2cccnc2)nc(N)n1
#
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
 RE4  RE4  6-methyl-N~4~-[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine  ligand  29  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RE4
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
 RE4  C4   C  CR6   0   0.519  24.6272   2.4906  59.8655
 RE4  C5   C  CH2   0  -0.391  21.3777   0.2984  61.0746
 RE4  C6   C  CR6   0   0.027  20.6604   0.5311  59.7682
 RE4  N1   N  N     0  -0.513  25.8263   2.0081  59.5501
 RE4  C7   C  CR16  0  -0.171  20.5239   1.7967  59.2132
 RE4  C8   C  CR16  0  -0.323  19.8766   1.9351  57.9945
 RE4  N2   N  NH2   0  -0.824  24.4558   3.8311  59.7661
 RE4  C9   C  CR16  0  -0.073  19.3918   0.7967  57.3695
 RE4  C10  C  CR16  0  -0.095  20.1283  -0.5389  59.0549
 RE4  N3   N  NH1   0  -0.660  22.7071  -0.2412  60.9023
 RE4  N4   N  N     0  -0.404  19.5107  -0.4216  57.8867
 RE4  C1   C  CR6   0   0.285  25.9886   0.6873  59.6974
 RE4  C    C  CH3   0  -0.721  27.3326   0.1403  59.3330
 RE4  N    N  N     0  -0.516  23.5773   1.7917  60.3014
 RE4  C3   C  CR6   0   0.575  23.7473   0.4829  60.4445
 RE4  C2   C  CR16  0  -0.480  24.9800  -0.1333  60.1476
 RE4  H1   H  HCH2  0   0.264  21.4293   1.2286  61.6407
 RE4  H2   H  HCH2  0   0.277  20.8217  -0.4152  61.6828
 RE4  H3   H  HCR6  0   0.264  20.9242   2.6607  59.7272
 RE4  H4   H  HCR6  0   0.269  19.7504   2.9054  57.5339
 RE4  H5   H  HNH2  0   0.386  25.1323   4.3503  59.2334
 RE4  H6   H  HNH2  0   0.387  23.5141   4.1833  59.7498
 RE4  H7   H  HCR6  0   0.262  18.8828   0.8715  56.4147
 RE4  H8   H  HCR6  0   0.256  20.2059  -1.5456  59.4567
 RE4  H9   H  HNH1  0   0.399  22.8090  -1.2419  60.9210
 RE4  H10  H  HCH3  0   0.252  27.5313   0.3018  58.2723
 RE4  H11  H  HCH3  0   0.250  28.1182   0.6537  59.8884
 RE4  H12  H  HCH3  0   0.243  27.4071  -0.9264  59.5356
 RE4  H13  H  HCR6  0   0.258  25.1199  -1.1995  60.2613

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
 RE4  C9   C8   aromatic  1.386  0.020  1.386
 RE4  C9   N4   aromatic  1.329  0.020  1.329
 RE4  C8   C7   aromatic  1.387  0.020  1.387
 RE4  N4   C10  aromatic  1.327  0.020  1.327
 RE4  C7   C6   aromatic  1.389  0.020  1.389
 RE4  C10  C6   aromatic  1.392  0.020  1.392
 RE4  C    C1   single    1.496  0.020  1.496
 RE4  N1   C1   aromatic  1.339  0.020  1.339
 RE4  N1   C4   aromatic  1.331  0.020  1.331
 RE4  C1   C2   aromatic  1.376  0.020  1.376
 RE4  C6   C5   single    1.508  0.020  1.508
 RE4  C2   C3   aromatic  1.410  0.020  1.410
 RE4  N2   C4   single    1.355  0.020  1.355
 RE4  C4   N    aromatic  1.334  0.020  1.334
 RE4  C3   N    aromatic  1.328  0.020  1.328
 RE4  C3   N3   single    1.348  0.020  1.348
 RE4  N3   C5   single    1.445  0.020  1.445
 RE4  C5   H1   single    0.970  0.020  1.090
 RE4  C5   H2   single    0.970  0.020  1.090
 RE4  C7   H3   single    0.930  0.020  1.080
 RE4  C8   H4   single    0.930  0.020  1.080
 RE4  N2   H5   single    0.890  0.020  1.040
 RE4  N2   H6   single    0.890  0.020  1.040
 RE4  C9   H7   single    0.930  0.020  1.080
 RE4  C10  H8   single    0.930  0.020  1.080
 RE4  N3   H9   single    0.860  0.020  1.020
 RE4  C    H10  single    0.970  0.020  1.090
 RE4  C    H11  single    0.970  0.020  1.090
 RE4  C    H12  single    0.970  0.020  1.090
 RE4  C2   H13  single    0.930  0.020  1.080

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
 RE4  N    C4   N2   116.27  3.000
 RE4  N    C4   N1   126.62  3.000
 RE4  N2   C4   N1   117.09  3.000
 RE4  H2   C5   H1   107.04  3.000
 RE4  H2   C5   N3   106.94  3.000
 RE4  H1   C5   N3   109.69  3.000
 RE4  H2   C5   C6   109.98  3.000
 RE4  H1   C5   C6   109.91  3.000
 RE4  N3   C5   C6   113.07  3.000
 RE4  C10  C6   C7   117.28  3.000
 RE4  C10  C6   C5   120.47  3.000
 RE4  C7   C6   C5   122.24  3.000
 RE4  C1   N1   C4   116.16  3.000
 RE4  H3   C7   C8   120.69  3.000
 RE4  H3   C7   C6   120.10  3.000
 RE4  C8   C7   C6   119.21  3.000
 RE4  H4   C8   C9   120.27  3.000
 RE4  H4   C8   C7   121.21  3.000
 RE4  C9   C8   C7   118.52  3.000
 RE4  H6   N2   H5   116.15  3.000
 RE4  H6   N2   C4   117.78  3.000
 RE4  H5   N2   C4   117.68  3.000
 RE4  H7   C9   N4   116.61  3.000
 RE4  H7   C9   C8   120.29  3.000
 RE4  N4   C9   C8   123.10  3.000
 RE4  H8   C10  N4   116.15  3.000
 RE4  H8   C10  C6   119.70  3.000
 RE4  N4   C10  C6   124.15  3.000
 RE4  H9   N3   C3   117.55  3.000
 RE4  H9   N3   C5   117.54  3.000
 RE4  C3   N3   C5   123.37  3.000
 RE4  C10  N4   C9   117.74  3.000
 RE4  C2   C1   C    121.34  3.000
 RE4  C2   C1   N1   122.38  3.000
 RE4  C    C1   N1   116.28  3.000
 RE4  H12  C    H11  108.50  3.000
 RE4  H12  C    H10  108.27  3.000
 RE4  H11  C    H10  107.11  3.000
 RE4  H12  C    C1   112.00  3.000
 RE4  H11  C    C1   110.54  3.000
 RE4  H10  C    C1   110.26  3.000
 RE4  C3   N    C4   116.80  3.000
 RE4  C2   C3   N    121.35  3.000
 RE4  N    C3   N3   117.87  3.000
 RE4  C2   C3   N3   120.78  3.000
 RE4  H13  C2   C3   121.46  3.000
 RE4  H13  C2   C1   121.84  3.000
 RE4  C3   C2   C1   116.69  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
 RE4  CONST_01  C2   C1   N1   C4     0.00   0.0  0
 RE4  CONST_02  C2   C3   N    C4     0.00   0.0  0
 RE4  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 RE4  CONST_04  C9   N4   C10  C6     0.00   0.0  0
 RE4  CONST_05  C3   C2   C1   N1     0.00   0.0  0
 RE4  CONST_06  C3   N    C4   N1     0.00   0.0  0
 RE4  CONST_07  N4   C9   C8   C7     0.00   0.0  0
 RE4  CONST_08  N4   C10  C6   C7     0.00   0.0  0
 RE4  CONST_09  C10  N4   C9   C8     0.00   0.0  0
 RE4  CONST_10  C10  C6   C7   C8     0.00   0.0  0
 RE4  CONST_11  N    C4   N1   C1     0.00   0.0  0
 RE4  CONST_12  N    C3   C2   C1     0.00   0.0  0
 RE4  CONST_13  C    C1   N1   C4   180.00   0.0  0
 RE4  CONST_14  N3   C3   N    C4   180.00   0.0  0
 RE4  CONST_15  C8   C7   C6   C5   180.00   0.0  0
 RE4  CONST_16  N4   C10  C6   C5   180.00   0.0  0
 RE4  CONST_17  C1   N1   C4   N2   180.00   0.0  0
 RE4  CONST_18  C3   N    C4   N2   180.00   0.0  0
 RE4  CONST_19  C1   C2   C3   N3   180.00   0.0  0
 RE4  CONST_20  C3   C2   C1   C    180.00   0.0  0
 RE4  CONST_21  H4   C8   C7   C6   180.00   0.0  0
 RE4  CONST_22  H13  C2   C1   N1   180.00   0.0  0
 RE4  CONST_23  H7   C9   C8   C7   180.00   0.0  0
 RE4  CONST_24  H8   C10  C6   C7   180.00   0.0  0
 RE4  CONST_25  H3   C7   C8   C9   180.00   0.0  0
 RE4  CONST_26  C2   C3   N3   C5   180.00   0.0  0
 RE4  CONST_27  N    C3   N3   C5     0.00   0.0  0
 RE4  CONST_30  H9   N3   C3   N    180.00   0.0  0
 RE4  Var_01    C3   N3   C5   C6    72.93  30.0  1
 RE4  Var_02    N3   C5   C6   C7  -102.93  30.0  2
 RE4  Var_03    H10  C    C1   N1   -62.82  30.0  2

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
 RE4  plan-1  C4   0.020
 RE4  plan-1  N1   0.020
 RE4  plan-1  N2   0.020
 RE4  plan-1  N3   0.020
 RE4  plan-1  C1   0.020
 RE4  plan-1  C    0.020
 RE4  plan-1  N    0.020
 RE4  plan-1  C3   0.020
 RE4  plan-1  C2   0.020
 RE4  plan-1  H13  0.020
 RE4  plan-2  C5   0.020
 RE4  plan-2  C6   0.020
 RE4  plan-2  C7   0.020
 RE4  plan-2  C8   0.020
 RE4  plan-2  C9   0.020
 RE4  plan-2  C10  0.020
 RE4  plan-2  N4   0.020
 RE4  plan-2  H3   0.020
 RE4  plan-2  H4   0.020
 RE4  plan-2  H7   0.020
 RE4  plan-2  H8   0.020
 RE4  plan-3  C4   0.020
 RE4  plan-3  N2   0.020
 RE4  plan-3  H5   0.020
 RE4  plan-3  H6   0.020
 RE4  plan-4  C5   0.020
 RE4  plan-4  N3   0.020
 RE4  plan-4  C3   0.020
 RE4  plan-4  H9   0.020

