# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 19:27:23 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-ethyl-5-phenylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccccc2
#
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
 CP7  CP7  6-ethyl-5-phenylpyrimidine-2,4-diamine  ligand  30  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CP7
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
 CP7  N1    N  N     0  -0.511  -1.3545   0.1019  -2.2843
 CP7  C2    C  CR6   0   0.518  -0.1654   0.1268  -2.8824
 CP7  C3    C  CR6   0   0.490  -1.3586   0.1031  -0.9542
 CP7  C4    C  CR6   0  -0.150  -0.1587   0.1312  -0.2044
 CP7  C5    C  CR6   0   0.275   1.0111   0.1583  -0.9426
 CP7  N6    N  N     0  -0.507   1.0199   0.1557  -2.2789
 CP7  C7    C  CR6   0  -0.007  -0.1932   0.1205   1.2765
 CP7  C8    C  CR16  0  -0.274  -0.1719  -1.0837   1.9798
 CP7  C9    C  CR16  0  -0.242  -0.2104  -1.0954   3.3677
 CP7  C10   C  CR16  0  -0.264  -0.2772   0.0998   4.0720
 CP7  C11   C  CR16  0  -0.242  -0.3084   1.3051   3.3829
 CP7  C12   C  CR16  0  -0.275  -0.2687   1.3137   1.9949
 CP7  N13   N  NH2   0  -0.829  -2.5548   0.0619  -0.3462
 CP7  N14   N  NH2   0  -0.825  -0.1671   0.1642  -4.2386
 CP7  C15   C  CH2   0  -0.504   2.3597   0.1476  -0.2830
 CP7  C16   C  CH3   0  -0.661   2.9506  -1.2610  -0.2460
 CP7  H8    H  HCR6  0   0.248  -0.1222  -2.0176   1.4330
 CP7  H9    H  HCR6  0   0.256  -0.1885  -2.0379   3.8997
 CP7  H10   H  HCR6  0   0.257  -0.3069   0.0920   5.1538
 CP7  H11   H  HCR6  0   0.256  -0.3637   2.2395   3.9266
 CP7  H12   H  HCR6  0   0.250  -0.2918   2.2549   1.4589
 CP7  H131  H  HNH2  0   0.394  -3.3956   0.1090  -0.8945
 CP7  H132  H  HNH2  0   0.403  -2.6386   0.1247   0.6525
 CP7  H141  H  HNH2  0   0.386  -1.0117  -0.1102  -4.7108
 CP7  H142  H  HNH2  0   0.386   0.6903  -0.0736  -4.7073
 CP7  H151  H  HCH2  0   0.241   2.2919   0.5440   0.7303
 CP7  H152  H  HCH2  0   0.244   3.0256   0.8050  -0.8454
 CP7  H161  H  HCH3  0   0.235   3.9441  -1.2473   0.2024
 CP7  H162  H  HCH3  0   0.226   2.3275  -1.9357   0.3420
 CP7  H163  H  HCH3  0   0.228   3.0408  -1.6754  -1.2504

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
 CP7  N1   C2    aromatic  1.331  0.020  1.331
 CP7  N1   C3    aromatic  1.330  0.020  1.330
 CP7  C2   N6    aromatic  1.330  0.020  1.330
 CP7  C2   N14   single    1.357  0.020  1.357
 CP7  C3   C4    aromatic  1.415  0.020  1.415
 CP7  C3   N13   single    1.342  0.020  1.342
 CP7  C4   C5    aromatic  1.383  0.020  1.383
 CP7  C4   C7    single    1.481  0.020  1.481
 CP7  C5   N6    aromatic  1.336  0.020  1.336
 CP7  C5   C15   single    1.501  0.020  1.501
 CP7  C7   C8    aromatic  1.395  0.020  1.395
 CP7  C7   C12   aromatic  1.395  0.020  1.395
 CP7  C8   C9    aromatic  1.388  0.020  1.388
 CP7  C8   H8    single    0.930  0.020  1.080
 CP7  C9   C10   aromatic  1.389  0.020  1.389
 CP7  C9   H9    single    0.930  0.020  1.080
 CP7  C10  C11   aromatic  1.389  0.020  1.389
 CP7  C10  H10   single    0.930  0.020  1.080
 CP7  C11  C12   aromatic  1.389  0.020  1.389
 CP7  C11  H11   single    0.930  0.020  1.080
 CP7  C12  H12   single    0.930  0.020  1.080
 CP7  N13  H131  single    0.860  0.020  1.020
 CP7  N13  H132  single    0.860  0.020  1.020
 CP7  N14  H141  single    0.890  0.020  1.040
 CP7  N14  H142  single    0.890  0.020  1.040
 CP7  C15  C16   single    1.528  0.020  1.528
 CP7  C15  H151  single    0.970  0.020  1.090
 CP7  C15  H152  single    0.970  0.020  1.090
 CP7  C16  H161  single    0.970  0.020  1.090
 CP7  C16  H162  single    0.970  0.020  1.090
 CP7  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
 CP7  C3    N1   C2    116.87  3.000
 CP7  N14   C2   N6    117.00  3.000
 CP7  N14   C2   N1    116.64  3.000
 CP7  N6    C2   N1    126.33  3.000
 CP7  N13   C3   C4    121.08  3.000
 CP7  N13   C3   N1    117.10  3.000
 CP7  C4    C3   N1    121.81  3.000
 CP7  C7    C4   C5    123.59  3.000
 CP7  C7    C4   C3    120.65  3.000
 CP7  C5    C4   C3    115.76  3.000
 CP7  C15   C5   N6    115.68  3.000
 CP7  C15   C5   C4    121.67  3.000
 CP7  N6    C5   C4    122.62  3.000
 CP7  C5    N6   C2    116.60  3.000
 CP7  C12   C7   C8    118.67  3.000
 CP7  C12   C7   C4    120.66  3.000
 CP7  C8    C7   C4    120.66  3.000
 CP7  H8    C8   C9    119.90  3.000
 CP7  H8    C8   C7    119.37  3.000
 CP7  C9    C8   C7    120.72  3.000
 CP7  H9    C9   C10   120.07  3.000
 CP7  H9    C9   C8    119.87  3.000
 CP7  C10   C9   C8    120.06  3.000
 CP7  H10   C10  C11   120.11  3.000
 CP7  H10   C10  C9    120.13  3.000
 CP7  C11   C10  C9    119.76  3.000
 CP7  H11   C11  C12   119.88  3.000
 CP7  H11   C11  C10   120.07  3.000
 CP7  C12   C11  C10   120.05  3.000
 CP7  H12   C12  C11   119.95  3.000
 CP7  H12   C12  C7    119.31  3.000
 CP7  C11   C12  C7    120.74  3.000
 CP7  H132  N13  H131  118.03  3.000
 CP7  H132  N13  C3    121.52  3.000
 CP7  H131  N13  C3    119.80  3.000
 CP7  H142  N14  H141  115.64  3.000
 CP7  H142  N14  C2    117.27  3.000
 CP7  H141  N14  C2    117.57  3.000
 CP7  H152  C15  H151  107.33  3.000
 CP7  H152  C15  C16   109.37  3.000
 CP7  H151  C15  C16   109.68  3.000
 CP7  H152  C15  C5    108.50  3.000
 CP7  H151  C15  C5    110.48  3.000
 CP7  C16   C15  C5    111.38  3.000
 CP7  H163  C16  H162  107.99  3.000
 CP7  H163  C16  H161  107.96  3.000
 CP7  H162  C16  H161  107.87  3.000
 CP7  H163  C16  C15   111.10  3.000
 CP7  H162  C16  C15   111.25  3.000
 CP7  H161  C16  C15   110.54  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
 CP7  CONST_01  C5    N6   C2   N1    0.00   0.0  0
 CP7  CONST_02  C5    C4   C3   N1    0.00   0.0  0
 CP7  CONST_03  C7    C4   C3   N1  180.00   0.0  0
 CP7  CONST_04  C4    C3   N1   C2    0.00   0.0  0
 CP7  CONST_05  C4    C5   N6   C2    0.00   0.0  0
 CP7  CONST_06  N6    C2   N1   C3    0.00   0.0  0
 CP7  CONST_07  N6    C5   C4   C3    0.00   0.0  0
 CP7  CONST_10  C9    C8   C7   C4  180.00   0.0  0
 CP7  CONST_11  C11   C12  C7   C4  180.00   0.0  0
 CP7  CONST_14  C7    C4   C5   N6  180.00   0.0  0
 CP7  CONST_15  C10   C9   C8   C7    0.00   0.0  0
 CP7  CONST_16  C10   C11  C12  C7    0.00   0.0  0
 CP7  CONST_17  C11   C12  C7   C8    0.00   0.0  0
 CP7  CONST_18  C11   C10  C9   C8    0.00   0.0  0
 CP7  CONST_19  C12   C7   C8   C9    0.00   0.0  0
 CP7  CONST_20  C12   C11  C10  C9    0.00   0.0  0
 CP7  CONST_21  N13   C3   N1   C2  180.00   0.0  0
 CP7  CONST_22  C15   C5   N6   C2  180.00   0.0  0
 CP7  CONST_23  N14   C2   N1   C3  180.00   0.0  0
 CP7  CONST_24  C15   C5   C4   C3  180.00   0.0  0
 CP7  CONST_25  N13   C3   C4   C5  180.00   0.0  0
 CP7  CONST_26  N14   C2   N6   C5  180.00   0.0  0
 CP7  CONST_27  N13   C3   C4   C7    0.00   0.0  0
 CP7  CONST_28  C15   C5   C4   C7    0.00   0.0  0
 CP7  CONST_29  H8    C8   C7   C4    0.00   0.0  0
 CP7  CONST_30  H12   C12  C7   C4    0.00   0.0  0
 CP7  CONST_31  H9    C9   C8   C7  180.00   0.0  0
 CP7  CONST_32  H11   C11  C12  C7  180.00   0.0  0
 CP7  CONST_33  H10   C10  C9   C8  180.00   0.0  0
 CP7  CONST_36  H131  N13  C3   N1    0.00   0.0  0
 CP7  CONST_37  H132  N13  C3   N1  180.00   0.0  0
 CP7  Var_01    C16   C15  C5   C4   97.59  30.0  2
 CP7  Var_02    H161  C16  C15  C5  177.94  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
 CP7  plan-1  N1    0.020
 CP7  plan-1  C2    0.020
 CP7  plan-1  C3    0.020
 CP7  plan-1  C4    0.020
 CP7  plan-1  C5    0.020
 CP7  plan-1  N6    0.020
 CP7  plan-1  C7    0.020
 CP7  plan-1  N13   0.020
 CP7  plan-1  N14   0.020
 CP7  plan-1  C15   0.020
 CP7  plan-2  C4    0.020
 CP7  plan-2  C7    0.020
 CP7  plan-2  C8    0.020
 CP7  plan-2  C9    0.020
 CP7  plan-2  C10   0.020
 CP7  plan-2  C11   0.020
 CP7  plan-2  C12   0.020
 CP7  plan-2  H8    0.020
 CP7  plan-2  H9    0.020
 CP7  plan-2  H10   0.020
 CP7  plan-2  H11   0.020
 CP7  plan-2  H12   0.020
 CP7  plan-3  C3    0.020
 CP7  plan-3  N13   0.020
 CP7  plan-3  H131  0.020
 CP7  plan-3  H132  0.020
 CP7  plan-4  C2    0.020
 CP7  plan-4  N14   0.020
 CP7  plan-4  H141  0.020
 CP7  plan-4  H142  0.020

