# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 03:45:16 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-(3,4-dichlorophenyl)-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc(N)c1c2ccc(Cl)c(Cl)c2
#
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
 C2M  C2M  5-(3,4-dichlorophenyl)-6-methylpyrimidine-2,4-diamine  ligand  27  17  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C2M
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
 C2M  N1    N   N     0  -0.507   3.5273   1.0874   0.5637
 C2M  C2    C   CR6   0   0.531   4.1849   0.1548  -0.1240
 C2M  N2    N   N     0  -0.508   3.6473  -0.9041  -0.7252
 C2M  C3    C   CR6   0   0.482   2.3290  -1.0436  -0.6376
 C2M  C4    C   CR6   0  -0.136   1.5270  -0.1135   0.0666
 C2M  C5    C   CR6   0   0.266   2.2045   0.9460   0.6529
 C2M  C6    C   CR6   0   0.004   0.0632  -0.2849   0.1587
 C2M  C7    C   CR16  0  -0.247  -0.7954   0.6226  -0.4555
 C2M  C8    C   CR6   0   0.023  -2.1704   0.4757  -0.3585
 C2M  C9    C   CR6   0  -0.016  -2.7099  -0.5943   0.3460
 C2M  C10   C   CR16  0  -0.197  -1.8643  -1.5115   0.9514
 C2M  C11   C   CR16  0  -0.293  -0.4919  -1.3561   0.8589
 C2M  N3    N   NH2   0  -0.823   5.5210   0.3154  -0.2504
 C2M  N4    N   NH2   0  -0.825   1.7930  -2.1251  -1.2358
 C2M  C12   C   CH3   0  -0.742   1.4922   2.0104   1.4301
 C2M  CL1   CL  CL    0  -0.097  -4.4153  -0.7929   0.4768
 C2M  CL2   CL  CL    0  -0.098  -3.1970   1.6256  -1.1280
 C2M  H7    H   HCR6  0   0.282  -0.3902   1.4540  -1.0175
 C2M  H10   H   HCR6  0   0.290  -2.2826  -2.3439   1.5004
 C2M  H11   H   HCR6  0   0.272   0.1525  -2.0732   1.3507
 C2M  HN31  H   HNH2  0   0.390   5.9766   0.9740   0.3571
 C2M  HN32  H   HNH2  0   0.390   6.0705  -0.4679  -0.5585
 C2M  HN41  H   HNH2  0   0.394   2.3773  -2.6566  -1.8587
 C2M  HN42  H   HNH2  0   0.402   0.8028  -2.1789  -1.3991
 C2M  H121  H   HCH3  0   0.259   1.2771   2.8674   0.7882
 C2M  H122  H   HCH3  0   0.247   0.5469   1.6683   1.8457
 C2M  H123  H   HCH3  0   0.256   2.1252   2.3666   2.2413

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
 C2M  N1   C2    aromatic  1.332  0.020  1.332
 C2M  N1   C5    aromatic  1.333  0.020  1.333
 C2M  C2   N2    aromatic  1.331  0.020  1.331
 C2M  C2   N3    single    1.352  0.020  1.352
 C2M  N2   C3    aromatic  1.329  0.020  1.329
 C2M  C3   C4    aromatic  1.416  0.020  1.416
 C2M  C3   N4    single    1.347  0.020  1.347
 C2M  C4   C5    aromatic  1.388  0.020  1.388
 C2M  C4   C6    single    1.477  0.020  1.477
 C2M  C5   C12   single    1.498  0.020  1.498
 C2M  C6   C7    aromatic  1.392  0.020  1.392
 C2M  C6   C11   aromatic  1.395  0.020  1.395
 C2M  C7   C8    aromatic  1.386  0.020  1.386
 C2M  C7   H7    single    0.930  0.020  1.080
 C2M  C8   C9    aromatic  1.390  0.020  1.390
 C2M  C8   CL2   single    1.723  0.020  1.723
 C2M  C9   C10   aromatic  1.387  0.020  1.387
 C2M  C9   CL1   single    1.722  0.020  1.722
 C2M  C10  C11   aromatic  1.384  0.020  1.384
 C2M  C10  H10   single    0.930  0.020  1.080
 C2M  C11  H11   single    0.930  0.020  1.080
 C2M  N3   HN31  single    0.890  0.020  1.040
 C2M  N3   HN32  single    0.890  0.020  1.040
 C2M  N4   HN41  single    0.890  0.020  1.040
 C2M  N4   HN42  single    0.890  0.020  1.040
 C2M  C12  H121  single    0.970  0.020  1.090
 C2M  C12  H122  single    0.970  0.020  1.090
 C2M  C12  H123  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
 C2M  C5    N1   C2    116.74  3.000
 C2M  N3    C2   N2    116.84  3.000
 C2M  N3    C2   N1    116.94  3.000
 C2M  N2    C2   N1    126.20  3.000
 C2M  C3    N2   C2    117.04  3.000
 C2M  N4    C3   C4    121.53  3.000
 C2M  N4    C3   N2    116.73  3.000
 C2M  C4    C3   N2    121.73  3.000
 C2M  C6    C4   C5    123.11  3.000
 C2M  C6    C4   C3    121.09  3.000
 C2M  C5    C4   C3    115.80  3.000
 C2M  C12   C5   C4    121.98  3.000
 C2M  C12   C5   N1    115.53  3.000
 C2M  C4    C5   N1    122.49  3.000
 C2M  C11   C6   C7    118.47  3.000
 C2M  C11   C6   C4    120.99  3.000
 C2M  C7    C6   C4    120.54  3.000
 C2M  H7    C7   C8    119.29  3.000
 C2M  H7    C7   C6    119.93  3.000
 C2M  C8    C7   C6    120.79  3.000
 C2M  CL2   C8   C9    120.58  3.000
 C2M  CL2   C8   C7    119.28  3.000
 C2M  C9    C8   C7    120.13  3.000
 C2M  CL1   C9   C10   119.64  3.000
 C2M  CL1   C9   C8    120.78  3.000
 C2M  C10   C9   C8    119.58  3.000
 C2M  H10   C10  C11   120.26  3.000
 C2M  H10   C10  C9    119.66  3.000
 C2M  C11   C10  C9    120.08  3.000
 C2M  H11   C11  C10   119.05  3.000
 C2M  H11   C11  C6    120.00  3.000
 C2M  C10   C11  C6    120.95  3.000
 C2M  HN32  N3   HN31  116.62  3.000
 C2M  HN32  N3   C2    118.45  3.000
 C2M  HN31  N3   C2    117.99  3.000
 C2M  HN42  N4   HN41  116.32  3.000
 C2M  HN42  N4   C3    120.47  3.000
 C2M  HN41  N4   C3    117.91  3.000
 C2M  H123  C12  H122  108.88  3.000
 C2M  H123  C12  H121  107.20  3.000
 C2M  H122  C12  H121  107.47  3.000
 C2M  H123  C12  C5    110.03  3.000
 C2M  H122  C12  C5    112.82  3.000
 C2M  H121  C12  C5    110.26  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
 C2M  CONST_01  C3    N2   C2   N1     0.00   0.0  0
 C2M  CONST_02  C3    C4   C5   N1     0.00   0.0  0
 C2M  CONST_03  C6    C4   C5   N1   180.00   0.0  0
 C2M  CONST_04  C4    C5   N1   C2     0.00   0.0  0
 C2M  CONST_05  C4    C3   N2   C2     0.00   0.0  0
 C2M  CONST_06  C5    N1   C2   N2     0.00   0.0  0
 C2M  CONST_07  C5    C4   C3   N2     0.00   0.0  0
 C2M  CONST_08  C6    C4   C3   N2   180.00   0.0  0
 C2M  CONST_11  C8    C7   C6   C4   180.00   0.0  0
 C2M  CONST_12  C10   C11  C6   C4   180.00   0.0  0
 C2M  CONST_15  C9    C8   C7   C6     0.00   0.0  0
 C2M  CONST_16  C9    C10  C11  C6     0.00   0.0  0
 C2M  CONST_17  C10   C11  C6   C7     0.00   0.0  0
 C2M  CONST_18  C10   C9   C8   C7     0.00   0.0  0
 C2M  CONST_19  C11   C6   C7   C8     0.00   0.0  0
 C2M  CONST_20  C11   C10  C9   C8     0.00   0.0  0
 C2M  CONST_21  C12   C5   N1   C2   180.00   0.0  0
 C2M  CONST_22  N4    C3   N2   C2   180.00   0.0  0
 C2M  CONST_23  N3    C2   N2   C3   180.00   0.0  0
 C2M  CONST_24  C12   C5   C4   C3   180.00   0.0  0
 C2M  CONST_25  N3    C2   N1   C5   180.00   0.0  0
 C2M  CONST_26  N4    C3   C4   C5   180.00   0.0  0
 C2M  CONST_27  N4    C3   C4   C6     0.00   0.0  0
 C2M  CONST_28  C12   C5   C4   C6     0.00   0.0  0
 C2M  CONST_29  CL2   C8   C7   C6   180.00   0.0  0
 C2M  CONST_30  CL1   C9   C8   C7   180.00   0.0  0
 C2M  CONST_31  CL2   C8   C9   C10  180.00   0.0  0
 C2M  CONST_32  CL1   C9   C10  C11  180.00   0.0  0
 C2M  CONST_33  H7    C7   C6   C4     0.00   0.0  0
 C2M  CONST_34  H11   C11  C6   C4     0.00   0.0  0
 C2M  CONST_35  H10   C10  C11  C6   180.00   0.0  0
 C2M  CONST_37  HN32  N3   C2   N1   180.00   0.0  0
 C2M  CONST_38  HN41  N4   C3   N2     0.00   0.0  0
 C2M  CONST_39  HN42  N4   C3   N2   180.00   0.0  0
 C2M  Var_01    H121  C12  C5   N1    84.83  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
 C2M  plan-1  N1    0.020
 C2M  plan-1  C2    0.020
 C2M  plan-1  N2    0.020
 C2M  plan-1  C3    0.020
 C2M  plan-1  C4    0.020
 C2M  plan-1  C5    0.020
 C2M  plan-1  C6    0.020
 C2M  plan-1  N3    0.020
 C2M  plan-1  N4    0.020
 C2M  plan-1  C12   0.020
 C2M  plan-2  C4    0.020
 C2M  plan-2  C6    0.020
 C2M  plan-2  C7    0.020
 C2M  plan-2  C8    0.020
 C2M  plan-2  C9    0.020
 C2M  plan-2  C10   0.020
 C2M  plan-2  C11   0.020
 C2M  plan-2  CL1   0.020
 C2M  plan-2  CL2   0.020
 C2M  plan-2  H7    0.020
 C2M  plan-2  H10   0.020
 C2M  plan-2  H11   0.020
 C2M  plan-3  C2    0.020
 C2M  plan-3  N3    0.020
 C2M  plan-3  HN31  0.020
 C2M  plan-3  HN32  0.020
 C2M  plan-4  C3    0.020
 C2M  plan-4  N4    0.020
 C2M  plan-4  HN41  0.020
 C2M  plan-4  HN42  0.020

