# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 22:21:06 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc(Cl)cc2
#
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
 CP6  CP6  5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine  ligand  30  17  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CP6
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
 CP6  N1    N   N     0  -0.506  -1.3973   0.2152  -3.0248
 CP6  C2    C   CR6   0   0.530  -0.2205   0.1457  -3.6419
 CP6  C3    C   CR6   0   0.490  -1.3763   0.2170  -1.6978
 CP6  C4    C   CR6   0  -0.140  -0.1677   0.1375  -0.9659
 CP6  C5    C   CR6   0   0.289   0.9892   0.0626  -1.7252
 CP6  N6    N   N     0  -0.499   0.9704   0.0679  -3.0601
 CP6  C7    C   CR6   0  -0.002  -0.1828   0.1353   0.5127
 CP6  C8    C   CR16  0  -0.280   0.1214  -1.0160   1.2376
 CP6  C9    C   CR16  0  -0.175   0.1077  -1.0172   2.6241
 CP6  C10   C   CR6   0  -0.048  -0.2283   0.1457   3.2976
 CP6  C11   C   CR16  0  -0.174  -0.5460   1.3034   2.6056
 CP6  C12   C   CR16  0  -0.272  -0.5200   1.2894   1.2198
 CP6  N13   N   NH2   0  -0.806  -2.5667   0.3220  -1.0719
 CP6  N14   N   NH2   0  -0.802  -0.2421   0.1959  -4.9983
 CP6  C15   C   CH2   0  -0.496   2.3536  -0.0449  -1.1074
 CP6  C16   C   CH3   0  -0.644   2.9645  -1.4279  -1.3194
 CP6  CL1   CL  CL    0  -0.128  -0.2545   0.1514   5.0295
 CP6  H8    H   HCR6  0   0.261   0.3722  -1.9300   0.7145
 CP6  H9    H   HCR6  0   0.259   0.3523  -1.9176   3.1699
 CP6  H11   H   HCR6  0   0.258  -0.8071   2.2086   3.1357
 CP6  H12   H   HCR6  0   0.243  -0.7593   2.1983   0.6828
 CP6  H131  H   HNH2  0   0.370  -3.3987   0.1942  -1.6198
 CP6  H132  H   HNH2  0   0.387  -2.6447   0.1085  -0.0938
 CP6  H141  H   HNH2  0   0.366  -1.1107  -0.0148  -5.4558
 CP6  H142  H   HNH2  0   0.367   0.5828  -0.1112  -5.4818
 CP6  H151  H   HCH2  0   0.240   2.3166   0.1862  -0.0435
 CP6  H152  H   HCH2  0   0.242   2.9953   0.7050  -1.5754
 CP6  H161  H   HCH3  0   0.228   3.9735  -1.4673  -0.9105
 CP6  H162  H   HCH3  0   0.217   2.3763  -2.2029  -0.8273
 CP6  H163  H   HCH3  0   0.226   3.0187  -1.6720  -2.3796

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
 CP6  N1   C2    aromatic  1.331  0.020  1.331
 CP6  N1   C3    aromatic  1.327  0.020  1.327
 CP6  C2   N6    aromatic  1.328  0.020  1.328
 CP6  C2   N14   single    1.357  0.020  1.357
 CP6  C3   C4    aromatic  1.415  0.020  1.415
 CP6  C3   N13   single    1.349  0.020  1.349
 CP6  C4   C5    aromatic  1.386  0.020  1.386
 CP6  C4   C7    single    1.479  0.020  1.479
 CP6  C5   N6    aromatic  1.335  0.020  1.335
 CP6  C5   C15   single    1.502  0.020  1.502
 CP6  C7   C8    aromatic  1.394  0.020  1.394
 CP6  C7   C12   aromatic  1.395  0.020  1.395
 CP6  C8   C9    aromatic  1.387  0.020  1.387
 CP6  C8   H8    single    0.930  0.020  1.080
 CP6  C9   C10   aromatic  1.385  0.020  1.385
 CP6  C9   H9    single    0.930  0.020  1.080
 CP6  C10  C11   aromatic  1.386  0.020  1.386
 CP6  C10  CL1   single    1.732  0.020  1.732
 CP6  C11  C12   aromatic  1.386  0.020  1.386
 CP6  C11  H11   single    0.930  0.020  1.080
 CP6  C12  H12   single    0.930  0.020  1.080
 CP6  N13  H131  single    0.890  0.020  1.040
 CP6  N13  H132  single    0.890  0.020  1.040
 CP6  N14  H141  single    0.890  0.020  1.040
 CP6  N14  H142  single    0.890  0.020  1.040
 CP6  C15  C16   single    1.527  0.020  1.527
 CP6  C15  H151  single    0.970  0.020  1.090
 CP6  C15  H152  single    0.970  0.020  1.090
 CP6  C16  H161  single    0.970  0.020  1.090
 CP6  C16  H162  single    0.970  0.020  1.090
 CP6  C16  H163  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
 CP6  C3    N1   C2    116.73  3.000
 CP6  N14   C2   N6    117.02  3.000
 CP6  N14   C2   N1    116.58  3.000
 CP6  N6    C2   N1    126.37  3.000
 CP6  N13   C3   C4    121.20  3.000
 CP6  N13   C3   N1    116.75  3.000
 CP6  C4    C3   N1    122.04  3.000
 CP6  C7    C4   C5    123.80  3.000
 CP6  C7    C4   C3    120.56  3.000
 CP6  C5    C4   C3    115.63  3.000
 CP6  C15   C5   N6    115.11  3.000
 CP6  C15   C5   C4    122.48  3.000
 CP6  N6    C5   C4    122.41  3.000
 CP6  C5    N6   C2    116.81  3.000
 CP6  C12   C7   C8    118.20  3.000
 CP6  C12   C7   C4    120.54  3.000
 CP6  C8    C7   C4    121.26  3.000
 CP6  H8    C8   C9    118.99  3.000
 CP6  H8    C8   C7    119.78  3.000
 CP6  C9    C8   C7    121.23  3.000
 CP6  H9    C9   C10   120.58  3.000
 CP6  H9    C9   C8    120.23  3.000
 CP6  C10   C9   C8    119.20  3.000
 CP6  CL1   C10  C11   119.55  3.000
 CP6  CL1   C10  C9    119.51  3.000
 CP6  C11   C10  C9    120.94  3.000
 CP6  H11   C11  C12   120.22  3.000
 CP6  H11   C11  C10   120.67  3.000
 CP6  C12   C11  C10   119.11  3.000
 CP6  H12   C12  C11   118.90  3.000
 CP6  H12   C12  C7    119.79  3.000
 CP6  C11   C12  C7    121.31  3.000
 CP6  H132  N13  H131  116.10  3.000
 CP6  H132  N13  C3    120.26  3.000
 CP6  H131  N13  C3    117.90  3.000
 CP6  H142  N14  H141  115.28  3.000
 CP6  H142  N14  C2    117.18  3.000
 CP6  H141  N14  C2    117.47  3.000
 CP6  H152  C15  H151  107.02  3.000
 CP6  H152  C15  C16   109.10  3.000
 CP6  H151  C15  C16   109.96  3.000
 CP6  H152  C15  C5    107.97  3.000
 CP6  H151  C15  C5    110.84  3.000
 CP6  C16   C15  C5    111.79  3.000
 CP6  H163  C16  H162  107.87  3.000
 CP6  H163  C16  H161  108.13  3.000
 CP6  H162  C16  H161  107.73  3.000
 CP6  H163  C16  C15   110.98  3.000
 CP6  H162  C16  C15   111.43  3.000
 CP6  H161  C16  C15   110.57  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
 CP6  CONST_01  C5    N6   C2   N1     0.00   0.0  0
 CP6  CONST_02  C5    C4   C3   N1     0.00   0.0  0
 CP6  CONST_03  C7    C4   C3   N1   180.00   0.0  0
 CP6  CONST_04  C4    C3   N1   C2     0.00   0.0  0
 CP6  CONST_05  C4    C5   N6   C2     0.00   0.0  0
 CP6  CONST_06  N6    C2   N1   C3     0.00   0.0  0
 CP6  CONST_07  N6    C5   C4   C3     0.00   0.0  0
 CP6  CONST_10  C9    C8   C7   C4   180.00   0.0  0
 CP6  CONST_11  C11   C12  C7   C4   180.00   0.0  0
 CP6  CONST_14  C7    C4   C5   N6   180.00   0.0  0
 CP6  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 CP6  CONST_16  C10   C11  C12  C7     0.00   0.0  0
 CP6  CONST_17  C11   C12  C7   C8     0.00   0.0  0
 CP6  CONST_18  C11   C10  C9   C8     0.00   0.0  0
 CP6  CONST_19  C12   C7   C8   C9     0.00   0.0  0
 CP6  CONST_20  C12   C11  C10  C9     0.00   0.0  0
 CP6  CONST_21  N13   C3   N1   C2   180.00   0.0  0
 CP6  CONST_22  C15   C5   N6   C2   180.00   0.0  0
 CP6  CONST_23  N14   C2   N1   C3   180.00   0.0  0
 CP6  CONST_24  C15   C5   C4   C3   180.00   0.0  0
 CP6  CONST_25  N13   C3   C4   C5   180.00   0.0  0
 CP6  CONST_26  N14   C2   N6   C5   180.00   0.0  0
 CP6  CONST_27  N13   C3   C4   C7     0.00   0.0  0
 CP6  CONST_28  C15   C5   C4   C7     0.00   0.0  0
 CP6  CONST_29  CL1   C10  C9   C8   180.00   0.0  0
 CP6  CONST_30  CL1   C10  C11  C12  180.00   0.0  0
 CP6  CONST_31  H8    C8   C7   C4     0.00   0.0  0
 CP6  CONST_32  H12   C12  C7   C4     0.00   0.0  0
 CP6  CONST_33  H9    C9   C8   C7   180.00   0.0  0
 CP6  CONST_34  H11   C11  C12  C7   180.00   0.0  0
 CP6  CONST_37  H131  N13  C3   N1     0.00   0.0  0
 CP6  CONST_38  H132  N13  C3   N1   180.00   0.0  0
 CP6  Var_01    C16   C15  C5   C4   109.36  30.0  2
 CP6  Var_02    H161  C16  C15  C5   176.99  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
 CP6  plan-1  N1    0.020
 CP6  plan-1  C2    0.020
 CP6  plan-1  C3    0.020
 CP6  plan-1  C4    0.020
 CP6  plan-1  C5    0.020
 CP6  plan-1  N6    0.020
 CP6  plan-1  C7    0.020
 CP6  plan-1  N13   0.020
 CP6  plan-1  N14   0.020
 CP6  plan-1  C15   0.020
 CP6  plan-2  C4    0.020
 CP6  plan-2  C7    0.020
 CP6  plan-2  C8    0.020
 CP6  plan-2  C9    0.020
 CP6  plan-2  C10   0.020
 CP6  plan-2  C11   0.020
 CP6  plan-2  C12   0.020
 CP6  plan-2  CL1   0.020
 CP6  plan-2  H8    0.020
 CP6  plan-2  H9    0.020
 CP6  plan-2  H11   0.020
 CP6  plan-2  H12   0.020
 CP6  plan-3  C3    0.020
 CP6  plan-3  N13   0.020
 CP6  plan-3  H131  0.020
 CP6  plan-3  H132  0.020
 CP6  plan-4  C2    0.020
 CP6  plan-4  N14   0.020
 CP6  plan-4  H141  0.020
 CP6  plan-4  H142  0.020

