# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:43:56 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-chloranyl-N4-[(4-methylphenyl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNc2cc(Cl)nc(N)n2)cc1
#
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
 IEE  IEE  6-chloranyl-N4-[(4-methylphenyl)methyl]pyrimidine-2,4-diamine  ligand  30  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IEE
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
 IEE  C16   C   CR16  0  -0.411  -1.9525  -0.7734   0.0530
 IEE  C2    C   CR6   0   0.190  -3.2973  -0.5700   0.2415
 IEE  CL1   CL  CL    0  -0.113  -4.3305  -1.9607   0.3632
 IEE  N3    N   N     0  -0.476  -3.8964   0.5926   0.3375
 IEE  C4    C   CR6   0   0.552  -3.0800   1.6541   0.2320
 IEE  N17   N   NH2   0  -0.820  -3.6532   2.8654   0.3487
 IEE  N5    N   N     0  -0.515  -1.7655   1.6128   0.0506
 IEE  C6    C   CR6   0   0.550  -1.1908   0.4108  -0.0326
 IEE  N7    N   NH1   0  -0.648   0.1405   0.3926  -0.1942
 IEE  C8    C   CH2   0  -0.340   0.9274  -0.8037  -0.4073
 IEE  C9    C   CR6   0   0.059   2.3909  -0.4967  -0.2529
 IEE  C10   C   CR16  0  -0.267   2.9126  -0.1647   0.9962
 IEE  C11   C   CR16  0  -0.282   4.2573   0.1299   1.1450
 IEE  C12   C   CR6   0   0.088   5.1257   0.1032   0.0524
 IEE  C15   C   CH3   0  -0.722   6.5875   0.3947   0.2270
 IEE  C13   C   CR16  0  -0.288   4.5986  -0.2238  -1.1925
 IEE  C14   C   CR16  0  -0.287   3.2487  -0.5187  -1.3443
 IEE  H16   H   HCR6  0   0.290  -1.5283  -1.7606  -0.0347
 IEE  H171  H   HNH2  0   0.398  -4.6546   2.9374   0.3049
 IEE  H172  H   HNH2  0   0.397  -3.1206   3.6819   0.1045
 IEE  H7    H   HNH1  0   0.393   0.5797   1.2835  -0.3672
 IEE  H81C  H   HCH2  0   0.259   0.6374  -1.5590   0.3275
 IEE  H82C  H   HCH2  0   0.255   0.7357  -1.2310  -1.3969
 IEE  H10   H   HCR6  0   0.252   2.2594  -0.1388   1.8608
 IEE  H14   H   HCR6  0   0.252   2.8641  -0.7679  -2.3263
 IEE  H11   H   HCR6  0   0.248   4.6411   0.3848   2.1260
 IEE  H151  H   HCH3  0   0.249   7.1159  -0.4788   0.6147
 IEE  H152  H   HCH3  0   0.244   7.0573   0.6664  -0.7175
 IEE  H153  H   HCH3  0   0.244   6.7518   1.2087   0.9332
 IEE  H13   H   HCR6  0   0.248   5.2483  -0.2456  -2.0595

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
 IEE  C16  C2    aromatic  1.373  0.020  1.373
 IEE  C16  C6    aromatic  1.411  0.020  1.411
 IEE  C2   CL1   single    1.737  0.020  1.737
 IEE  C2   N3    aromatic  1.311  0.020  1.311
 IEE  N3   C4    aromatic  1.343  0.020  1.343
 IEE  C4   N17   single    1.345  0.020  1.345
 IEE  C4   N5    aromatic  1.328  0.020  1.328
 IEE  N5   C6    aromatic  1.335  0.020  1.335
 IEE  C6   N7    single    1.341  0.020  1.341
 IEE  N7   C8    single    1.448  0.020  1.448
 IEE  C8   C9    single    1.503  0.020  1.503
 IEE  C9   C10   aromatic  1.394  0.020  1.394
 IEE  C9   C14   aromatic  1.388  0.020  1.388
 IEE  C10  C11   aromatic  1.385  0.020  1.385
 IEE  C11  C12   aromatic  1.396  0.020  1.396
 IEE  C12  C15   single    1.501  0.020  1.501
 IEE  C12  C13   aromatic  1.391  0.020  1.391
 IEE  C13  C14   aromatic  1.390  0.020  1.390
 IEE  C16  H16   single    0.930  0.020  1.080
 IEE  N17  H171  single    0.890  0.020  1.040
 IEE  N17  H172  single    0.890  0.020  1.040
 IEE  N7   H7    single    0.860  0.020  1.020
 IEE  C8   H81C  single    0.970  0.020  1.090
 IEE  C8   H82C  single    0.970  0.020  1.090
 IEE  C10  H10   single    0.930  0.020  1.080
 IEE  C14  H14   single    0.930  0.020  1.080
 IEE  C11  H11   single    0.930  0.020  1.080
 IEE  C15  H151  single    0.970  0.020  1.090
 IEE  C15  H152  single    0.970  0.020  1.090
 IEE  C15  H153  single    0.970  0.020  1.090
 IEE  C13  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
 IEE  H16   C16  C6    123.46  3.000
 IEE  H16   C16  C2    122.16  3.000
 IEE  C6    C16  C2    114.38  3.000
 IEE  N3    C2   CL1   115.66  3.000
 IEE  N3    C2   C16   126.07  3.000
 IEE  CL1   C2   C16   118.27  3.000
 IEE  C4    N3   C2    114.66  3.000
 IEE  N5    C4   N17   117.50  3.000
 IEE  N5    C4   N3    126.01  3.000
 IEE  N17   C4   N3    116.48  3.000
 IEE  H172  N17  H171  117.35  3.000
 IEE  H172  N17  C4    119.00  3.000
 IEE  H171  N17  C4    119.03  3.000
 IEE  C6    N5   C4    117.57  3.000
 IEE  N7    C6   N5    116.55  3.000
 IEE  N7    C6   C16   122.14  3.000
 IEE  N5    C6   C16   121.31  3.000
 IEE  H7    N7   C8    117.91  3.000
 IEE  H7    N7   C6    116.18  3.000
 IEE  C8    N7   C6    124.65  3.000
 IEE  H82C  C8   H81C  106.95  3.000
 IEE  H82C  C8   C9    110.06  3.000
 IEE  H81C  C8   C9    109.30  3.000
 IEE  H82C  C8   N7    111.12  3.000
 IEE  H81C  C8   N7    109.14  3.000
 IEE  C9    C8   N7    110.20  3.000
 IEE  C14   C9   C10   118.49  3.000
 IEE  C14   C9   C8    121.17  3.000
 IEE  C10   C9   C8    120.33  3.000
 IEE  H10   C10  C11   119.63  3.000
 IEE  H10   C10  C9    119.67  3.000
 IEE  C11   C10  C9    120.70  3.000
 IEE  H11   C11  C12   119.52  3.000
 IEE  H11   C11  C10   119.42  3.000
 IEE  C12   C11  C10   121.06  3.000
 IEE  C13   C12  C15   121.26  3.000
 IEE  C13   C12  C11   117.99  3.000
 IEE  C15   C12  C11   120.74  3.000
 IEE  H153  C15  H152  108.09  3.000
 IEE  H153  C15  H151  107.12  3.000
 IEE  H152  C15  H151  107.38  3.000
 IEE  H153  C15  C12   111.54  3.000
 IEE  H152  C15  C12   111.57  3.000
 IEE  H151  C15  C12   110.93  3.000
 IEE  H13   C13  C14   119.38  3.000
 IEE  H13   C13  C12   119.58  3.000
 IEE  C14   C13  C12   121.04  3.000
 IEE  H14   C14  C13   119.50  3.000
 IEE  H14   C14  C9    119.78  3.000
 IEE  C13   C14  C9    120.72  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
 IEE  CONST_01  C4    N3   C2   C16     0.00   0.0  0
 IEE  CONST_02  C4    N5   C6   C16     0.00   0.0  0
 IEE  CONST_03  N5    C6   C16  C2      0.00   0.0  0
 IEE  CONST_04  N5    C4   N3   C2      0.00   0.0  0
 IEE  CONST_05  C6    C16  C2   N3      0.00   0.0  0
 IEE  CONST_06  C6    N5   C4   N3      0.00   0.0  0
 IEE  CONST_07  C12   C11  C10  C9      0.00   0.0  0
 IEE  CONST_08  C12   C13  C14  C9      0.00   0.0  0
 IEE  CONST_09  C13   C14  C9   C10     0.00   0.0  0
 IEE  CONST_10  C13   C12  C11  C10     0.00   0.0  0
 IEE  CONST_11  C14   C9   C10  C11     0.00   0.0  0
 IEE  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 IEE  CONST_13  N7    C6   C16  C2    180.00   0.0  0
 IEE  CONST_14  N17   C4   N3   C2    180.00   0.0  0
 IEE  CONST_15  C6    C16  C2   CL1   180.00   0.0  0
 IEE  CONST_16  C4    N3   C2   CL1   180.00   0.0  0
 IEE  CONST_17  N7    C6   N5   C4    180.00   0.0  0
 IEE  CONST_18  C6    N5   C4   N17   180.00   0.0  0
 IEE  CONST_19  C11   C10  C9   C8    180.00   0.0  0
 IEE  CONST_20  C13   C14  C9   C8    180.00   0.0  0
 IEE  CONST_21  C15   C12  C11  C10   180.00   0.0  0
 IEE  CONST_22  C14   C13  C12  C15   180.00   0.0  0
 IEE  CONST_23  H16   C16  C2   N3    180.00   0.0  0
 IEE  CONST_24  H11   C11  C10  C9    180.00   0.0  0
 IEE  CONST_25  H13   C13  C14  C9    180.00   0.0  0
 IEE  CONST_26  H14   C14  C9   C10   180.00   0.0  0
 IEE  CONST_27  H10   C10  C11  C12   180.00   0.0  0
 IEE  CONST_28  C8    N7   C6   C16     0.00   0.0  0
 IEE  CONST_29  C8    N7   C6   N5    180.00   0.0  0
 IEE  CONST_30  H7    N7   C6   C16   180.00   0.0  0
 IEE  CONST_31  H171  N17  C4   N3      0.00   0.0  0
 IEE  CONST_32  H172  N17  C4   N3    180.00   0.0  0
 IEE  Var_01    C9    C8   N7   C6   -167.89  30.0  3
 IEE  Var_02    C10   C9   C8   N7     68.29  30.0  2
 IEE  Var_03    H151  C15  C12  C11    79.66  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
 IEE  plan-1  C16   0.020
 IEE  plan-1  C2    0.020
 IEE  plan-1  CL1   0.020
 IEE  plan-1  N3    0.020
 IEE  plan-1  C4    0.020
 IEE  plan-1  N17   0.020
 IEE  plan-1  N5    0.020
 IEE  plan-1  C6    0.020
 IEE  plan-1  N7    0.020
 IEE  plan-1  H16   0.020
 IEE  plan-2  C8    0.020
 IEE  plan-2  C9    0.020
 IEE  plan-2  C10   0.020
 IEE  plan-2  C11   0.020
 IEE  plan-2  C12   0.020
 IEE  plan-2  C15   0.020
 IEE  plan-2  C13   0.020
 IEE  plan-2  C14   0.020
 IEE  plan-2  H10   0.020
 IEE  plan-2  H14   0.020
 IEE  plan-2  H11   0.020
 IEE  plan-2  H13   0.020
 IEE  plan-3  C4    0.020
 IEE  plan-3  N17   0.020
 IEE  plan-3  H171  0.020
 IEE  plan-3  H172  0.020
 IEE  plan-4  C6    0.020
 IEE  plan-4  N7    0.020
 IEE  plan-4  C8    0.020
 IEE  plan-4  H7    0.020

