# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:32:40 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-(2,4-dichloro-5-methoxyphenyl)-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c(Cl)cc1Cl)c2cc(C)nc(N)n2
#
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
 3RP  3RP  4-(2,4-dichloro-5-methoxyphenyl)-6-methylpyrimidin-2-amine  ligand  29  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3RP
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
 3RP  N1    N   N     0  -0.475  -4.1054  -0.5601   0.1238
 3RP  N3    N   NH2   0  -0.829  -4.1736   1.1521   1.6382
 3RP  C4    C   CR6   0   0.292  -3.3906  -1.3382  -0.6736
 3RP  C5    C   CH3   0  -0.730  -4.1267  -2.3552  -1.4852
 3RP  C6    C   CR6   0   0.164   0.0385   0.0214  -0.0598
 3RP  C7    C   CR6   0  -0.151   0.6072   1.2390  -0.4108
 3RP  C8    C   CR16  0  -0.143   1.9855   1.3949  -0.4344
 3RP  C10   C   CR6   0   0.490   2.2617  -0.9091   0.2556
 3RP  C11   C   CR16  0  -0.448   0.8782  -1.0422   0.2640
 3RP  C3    C   CR16  0  -0.398  -2.0080  -1.1963  -0.7800
 3RP  C9    C   CR6   0  -0.170   2.7996   0.3327  -0.0975
 3RP  C2    C   CR6   0   0.250  -1.4271  -0.1960  -0.0168
 3RP  C1    C   CR6   0   0.537  -3.4464   0.3724   0.8241
 3RP  C12   C   CH3   0  -0.444   2.6149  -3.1529   0.9231
 3RP  N2    N   N     0  -0.459  -2.1283   0.5884   0.7867
 3RP  O1    O   O2    0  -0.452   3.1247  -1.8795   0.5640
 3RP  CL1   CL  CL    0  -0.120  -0.3718   2.5809  -0.8938
 3RP  CL2   CL  CL    0  -0.093   4.5122   0.5276  -0.1169
 3RP  HN3   H   HNH2  0   0.399  -5.1689   1.0353   1.6997
 3RP  HN3A  H   HNH2  0   0.399  -3.7354   1.8814   2.1716
 3RP  H5    H   HCH3  0   0.263  -4.4013  -1.9276  -2.4519
 3RP  H5A   H   HCH3  0   0.251  -3.5137  -3.2335  -1.6801
 3RP  H5B   H   HCH3  0   0.254  -5.0443  -2.6612  -0.9867
 3RP  H8    H   HCR6  0   0.303   2.4243   2.3410  -0.7194
 3RP  H11   H   HCR6  0   0.299   0.4236  -1.9833   0.5435
 3RP  H3    H   HCR6  0   0.266  -1.4224  -1.8242  -1.4362
 3RP  H12   H   HCH3  0   0.238   2.0060  -3.1034   1.8289
 3RP  H12A  H   HCH3  0   0.238   2.0231  -3.5935   0.1175
 3RP  H12B  H   HCH3  0   0.269   3.4788  -3.7833   1.1139

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
 3RP  N1   C1    aromatic  1.340  0.020  1.340
 3RP  N1   C4    aromatic  1.324  0.020  1.324
 3RP  N3   C1    single    1.341  0.020  1.341
 3RP  N3   HN3   single    0.860  0.020  1.020
 3RP  N3   HN3A  single    0.860  0.020  1.020
 3RP  C5   C4    single    1.495  0.020  1.495
 3RP  C4   C3    aromatic  1.394  0.020  1.394
 3RP  C5   H5    single    0.970  0.020  1.090
 3RP  C5   H5A   single    0.970  0.020  1.090
 3RP  C5   H5B   single    0.970  0.020  1.090
 3RP  C7   C6    aromatic  1.389  0.020  1.389
 3RP  C2   C6    single    1.482  0.020  1.482
 3RP  C6   C11   aromatic  1.393  0.020  1.393
 3RP  CL1  C7    single    1.730  0.020  1.730
 3RP  C7   C8    aromatic  1.387  0.020  1.387
 3RP  C8   C9    aromatic  1.380  0.020  1.380
 3RP  C8   H8    single    0.930  0.020  1.080
 3RP  C9   C10   aromatic  1.399  0.020  1.399
 3RP  C11  C10   aromatic  1.390  0.020  1.390
 3RP  C10  O1    single    1.335  0.020  1.335
 3RP  C11  H11   single    0.930  0.020  1.080
 3RP  C3   C2    aromatic  1.386  0.020  1.386
 3RP  C3   H3    single    0.930  0.020  1.080
 3RP  C9   CL2   single    1.724  0.020  1.724
 3RP  N2   C2    aromatic  1.324  0.020  1.324
 3RP  C1   N2    aromatic  1.336  0.020  1.336
 3RP  O1   C12   single    1.418  0.020  1.418
 3RP  C12  H12   single    0.970  0.020  1.090
 3RP  C12  H12A  single    0.970  0.020  1.090
 3RP  C12  H12B  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
 3RP  C1    N1   C4    117.28  3.000
 3RP  HN3A  N3   HN3   118.98  3.000
 3RP  HN3A  N3   C1    120.52  3.000
 3RP  HN3   N3   C1    120.46  3.000
 3RP  C3    C4   C5    121.08  3.000
 3RP  C3    C4   N1    121.45  3.000
 3RP  C5    C4   N1    117.45  3.000
 3RP  H5B   C5   H5A   109.27  3.000
 3RP  H5B   C5   H5    107.68  3.000
 3RP  H5A   C5   H5    107.40  3.000
 3RP  H5B   C5   C4    110.96  3.000
 3RP  H5A   C5   C4    111.64  3.000
 3RP  H5    C5   C4    109.75  3.000
 3RP  C2    C6   C11   118.50  3.000
 3RP  C11   C6   C7    118.76  3.000
 3RP  C2    C6   C7    122.73  3.000
 3RP  CL1   C7   C8    118.06  3.000
 3RP  C8    C7   C6    120.64  3.000
 3RP  CL1   C7   C6    121.26  3.000
 3RP  H8    C8   C9    119.90  3.000
 3RP  H8    C8   C7    120.40  3.000
 3RP  C9    C8   C7    119.70  3.000
 3RP  O1    C10  C9    117.08  3.000
 3RP  O1    C10  C11   124.93  3.000
 3RP  C9    C10  C11   117.99  3.000
 3RP  H11   C11  C10   120.20  3.000
 3RP  H11   C11  C6    118.09  3.000
 3RP  C10   C11  C6    121.70  3.000
 3RP  H3    C3   C2    121.78  3.000
 3RP  H3    C3   C4    121.65  3.000
 3RP  C2    C3   C4    116.56  3.000
 3RP  CL2   C9   C10   119.04  3.000
 3RP  CL2   C9   C8    119.76  3.000
 3RP  C10   C9   C8    121.20  3.000
 3RP  N2    C2   C3    122.68  3.000
 3RP  N2    C2   C6    117.02  3.000
 3RP  C3    C2   C6    120.29  3.000
 3RP  N2    C1   N3    117.24  3.000
 3RP  N2    C1   N1    125.68  3.000
 3RP  N3    C1   N1    117.08  3.000
 3RP  H12B  C12  H12A  109.04  3.000
 3RP  H12B  C12  H12   108.90  3.000
 3RP  H12A  C12  H12   109.14  3.000
 3RP  H12B  C12  O1    106.24  3.000
 3RP  H12A  C12  O1    111.73  3.000
 3RP  H12   C12  O1    111.69  3.000
 3RP  C1    N2   C2    116.34  3.000
 3RP  C12   O1   C10   118.62  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
 3RP  CONST_01  C2    N2   C1   N1     0.00   0.0  0
 3RP  CONST_02  C2    C3   C4   N1     0.00   0.0  0
 3RP  CONST_03  N2    C1   N1   C4     0.00   0.0  0
 3RP  CONST_04  C6    C2   C3   C4   180.00   0.0  0
 3RP  CONST_05  N2    C2   C3   C4     0.00   0.0  0
 3RP  CONST_06  C9    C8   C7   C6     0.00   0.0  0
 3RP  CONST_07  C1    N2   C2   C6   180.00   0.0  0
 3RP  CONST_08  C9    C10  C11  C6     0.00   0.0  0
 3RP  CONST_11  C10   C11  C6   C7     0.00   0.0  0
 3RP  CONST_12  C10   C9   C8   C7     0.00   0.0  0
 3RP  CONST_13  C2    C6   C7   C8   180.00   0.0  0
 3RP  CONST_14  C11   C6   C7   C8     0.00   0.0  0
 3RP  CONST_15  C11   C10  C9   C8     0.00   0.0  0
 3RP  CONST_16  C2    C6   C11  C10  180.00   0.0  0
 3RP  CONST_19  C1    N1   C4   C3     0.00   0.0  0
 3RP  CONST_20  C1    N2   C2   C3     0.00   0.0  0
 3RP  CONST_21  C4    N1   C1   N3   180.00   0.0  0
 3RP  CONST_22  C2    N2   C1   N3   180.00   0.0  0
 3RP  CONST_23  C1    N1   C4   C5   180.00   0.0  0
 3RP  CONST_24  C2    C3   C4   C5   180.00   0.0  0
 3RP  CONST_25  O1    C10  C11  C6   180.00   0.0  0
 3RP  CONST_26  CL2   C9   C8   C7   180.00   0.0  0
 3RP  CONST_27  O1    C10  C9   C8   180.00   0.0  0
 3RP  CONST_28  CL1   C7   C6   C11  180.00   0.0  0
 3RP  CONST_29  CL2   C9   C10  C11  180.00   0.0  0
 3RP  CONST_30  CL1   C7   C8   C9   180.00   0.0  0
 3RP  CONST_31  CL1   C7   C6   C2     0.00   0.0  0
 3RP  CONST_32  H3    C3   C4   N1   180.00   0.0  0
 3RP  CONST_33  H8    C8   C7   C6   180.00   0.0  0
 3RP  CONST_34  H11   C11  C6   C7   180.00   0.0  0
 3RP  CONST_35  HN3   N3   C1   N1     0.00   0.0  0
 3RP  CONST_36  HN3A  N3   C1   N1   180.00   0.0  0
 3RP  Var_01    H5    C5   C4   N1    90.79  30.0  2
 3RP  Var_02    H12   C12  O1   C10  -62.33  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
 3RP  plan-1  N1    0.020
 3RP  plan-1  N3    0.020
 3RP  plan-1  C4    0.020
 3RP  plan-1  C5    0.020
 3RP  plan-1  C6    0.020
 3RP  plan-1  C3    0.020
 3RP  plan-1  C2    0.020
 3RP  plan-1  C1    0.020
 3RP  plan-1  N2    0.020
 3RP  plan-1  H3    0.020
 3RP  plan-2  C6    0.020
 3RP  plan-2  C7    0.020
 3RP  plan-2  C8    0.020
 3RP  plan-2  C10   0.020
 3RP  plan-2  C11   0.020
 3RP  plan-2  C9    0.020
 3RP  plan-2  C2    0.020
 3RP  plan-2  O1    0.020
 3RP  plan-2  CL1   0.020
 3RP  plan-2  CL2   0.020
 3RP  plan-2  H8    0.020
 3RP  plan-2  H11   0.020
 3RP  plan-3  N3    0.020
 3RP  plan-3  C1    0.020
 3RP  plan-3  HN3   0.020
 3RP  plan-3  HN3A  0.020

