# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 15:07:38 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 6-(4-methoxyphenyl)-N~4~-octylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCNc1cc(nc(N)n1)c2ccc(OC)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
 KK1  KK1  6-(4-methoxyphenyl)-N~4~-octylpyrimidine-2,4-diamine  ligand  52  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KK1
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
 KK1  C01  C  CH3   0  -0.663  10.2699  -1.5156  -0.2218
 KK1  C02  C  CH2   0  -0.418   8.8192  -1.7968   0.1439
 KK1  C03  C  CH2   0  -0.407   7.8981  -0.6168  -0.1413
 KK1  C04  C  CH2   0  -0.412   6.4431  -0.8853   0.2198
 KK1  C05  C  CH2   0  -0.412   5.5259   0.2986  -0.0604
 KK1  C06  C  CH2   0  -0.418   4.0688   0.0192   0.2829
 KK1  C07  C  CH2   0  -0.458   3.1561   1.2085   0.0136
 KK1  C08  C  CH2   0  -0.249   1.7010   0.8840   0.3079
 KK1  N09  N  NH1   0  -0.661   0.8604   2.0367   0.0801
 KK1  C10  C  CR6   0   0.541  -0.4827   2.0130   0.0312
 KK1  C11  C  CR16  0  -0.498  -1.2169   0.8137   0.0777
 KK1  C12  C  CR6   0   0.294  -2.5924   0.9229  -0.0297
 KK1  N13  N  N     0  -0.519  -3.2045   2.1040  -0.1404
 KK1  C14  C  CR6   0   0.523  -2.4198   3.1823  -0.1481
 KK1  N15  N  NH2   0  -0.827  -3.0362   4.3803  -0.2850
 KK1  N16  N  N     0  -0.517  -1.0925   3.1960  -0.0743
 KK1  C17  C  CR6   0   0.030  -3.4677  -0.2667  -0.0169
 KK1  C18  C  CR16  0  -0.266  -4.8322  -0.1366   0.2609
 KK1  C19  C  CR16  0  -0.328  -5.6693  -1.2328   0.2764
 KK1  C20  C  CR6   0   0.379  -5.1680  -2.5076  -0.0013
 KK1  O21  O  O2    0  -0.466  -6.0533  -3.5165   0.0272
 KK1  C22  C  CH3   0  -0.438  -5.6030  -4.8238  -0.2731
 KK1  C23  C  CR16  0  -0.367  -3.8126  -2.6552  -0.2891
 KK1  C24  C  CR16  0  -0.305  -2.9836  -1.5427  -0.2912
 KK1  H1   H  HCH3  0   0.215  10.3721  -1.2847  -1.2839
 KK1  H2   H  HCH3  0   0.216  10.6574  -0.6620   0.3378
 KK1  H3   H  HCH3  0   0.226  10.9122  -2.3702  -0.0058
 KK1  H4   H  HCH2  0   0.210   8.4640  -2.6741  -0.4061
 KK1  H5   H  HCH2  0   0.210   8.7528  -2.0584   1.2045
 KK1  H6   H  HCH2  0   0.206   8.2542   0.2610   0.4099
 KK1  H7   H  HCH2  0   0.206   7.9663  -0.3536  -1.2027
 KK1  H8   H  HCH2  0   0.207   6.0867  -1.7600  -0.3359
 KK1  H9   H  HCH2  0   0.207   6.3747  -1.1531   1.2800
 KK1  H10  H  HCH2  0   0.210   5.8739   1.1699   0.5055
 KK1  H11  H  HCH2  0   0.210   5.6024   0.5743  -1.1178
 KK1  H12  H  HCH2  0   0.215   3.7206  -0.8448  -0.2939
 KK1  H13  H  HCH2  0   0.215   3.9902  -0.2675   1.3368
 KK1  H14  H  HCH2  0   0.227   3.4758   2.0591   0.6249
 KK1  H15  H  HCH2  0   0.229   3.2512   1.5193  -1.0310
 KK1  H16  H  HCH2  0   0.232   1.3830   0.0676  -0.3457
 KK1  H17  H  HCH2  0   0.226   1.6014   0.5214   1.3384
 KK1  H18  H  HNH1  0   0.383   1.2798   2.9495   0.1661
 KK1  H19  H  HCR6  0   0.263  -0.7298  -0.1385   0.2178
 KK1  H20  H  HNH2  0   0.387  -4.0271   4.4197  -0.1202
 KK1  H21  H  HNH2  0   0.388  -2.5140   5.2104  -0.0638
 KK1  H22  H  HCR6  0   0.254  -5.2391   0.8427   0.4733
 KK1  H23  H  HCR6  0   0.264  -6.7219  -1.1115   0.5001
 KK1  H24  H  HCH3  0   0.231  -4.8393  -5.1645   0.4304
 KK1  H25  H  HCH3  0   0.262  -6.4696  -5.4748  -0.1911
 KK1  H26  H  HCH3  0   0.231  -5.2041  -4.8933  -1.2880
 KK1  H27  H  HCR6  0   0.282  -3.3852  -3.6208  -0.5218
 KK1  H28  H  HCR6  0   0.254  -1.9401  -1.6927  -0.5356

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
 KK1  C22  O21  single    1.415  0.020  1.415
 KK1  O21  C20  single    1.343  0.020  1.343
 KK1  C20  C19  aromatic  1.398  0.020  1.398
 KK1  C20  C23  aromatic  1.393  0.020  1.393
 KK1  C19  C18  aromatic  1.379  0.020  1.379
 KK1  C23  C24  aromatic  1.387  0.020  1.387
 KK1  C18  C17  aromatic  1.399  0.020  1.399
 KK1  C24  C17  aromatic  1.392  0.020  1.392
 KK1  C17  C12  single    1.477  0.020  1.477
 KK1  C12  N13  aromatic  1.335  0.020  1.335
 KK1  C12  C11  aromatic  1.384  0.020  1.384
 KK1  N13  C14  aromatic  1.334  0.020  1.334
 KK1  C11  C10  aromatic  1.407  0.020  1.407
 KK1  C14  N15  single    1.354  0.020  1.354
 KK1  C14  N16  aromatic  1.330  0.020  1.330
 KK1  C10  N16  aromatic  1.335  0.020  1.335
 KK1  C10  N09  single    1.344  0.020  1.344
 KK1  N09  C08  single    1.445  0.020  1.445
 KK1  C08  C07  single    1.520  0.020  1.520
 KK1  C07  C06  single    1.523  0.020  1.523
 KK1  C06  C05  single    1.523  0.020  1.523
 KK1  C05  C04  single    1.524  0.020  1.524
 KK1  C04  C03  single    1.523  0.020  1.523
 KK1  C03  C02  single    1.524  0.020  1.524
 KK1  C02  C01  single    1.522  0.020  1.522
 KK1  C01  H1   single    0.970  0.020  1.090
 KK1  C01  H2   single    0.970  0.020  1.090
 KK1  C01  H3   single    0.970  0.020  1.090
 KK1  C02  H4   single    0.970  0.020  1.090
 KK1  C02  H5   single    0.970  0.020  1.090
 KK1  C03  H6   single    0.970  0.020  1.090
 KK1  C03  H7   single    0.970  0.020  1.090
 KK1  C04  H8   single    0.970  0.020  1.090
 KK1  C04  H9   single    0.970  0.020  1.090
 KK1  C05  H10  single    0.970  0.020  1.090
 KK1  C05  H11  single    0.970  0.020  1.090
 KK1  C06  H12  single    0.970  0.020  1.090
 KK1  C06  H13  single    0.970  0.020  1.090
 KK1  C07  H14  single    0.970  0.020  1.090
 KK1  C07  H15  single    0.970  0.020  1.090
 KK1  C08  H16  single    0.970  0.020  1.090
 KK1  C08  H17  single    0.970  0.020  1.090
 KK1  N09  H18  single    0.860  0.020  1.020
 KK1  C11  H19  single    0.930  0.020  1.080
 KK1  N15  H20  single    0.890  0.020  1.040
 KK1  N15  H21  single    0.890  0.020  1.040
 KK1  C18  H22  single    0.930  0.020  1.080
 KK1  C19  H23  single    0.930  0.020  1.080
 KK1  C22  H24  single    0.970  0.020  1.090
 KK1  C22  H25  single    0.970  0.020  1.090
 KK1  C22  H26  single    0.970  0.020  1.090
 KK1  C23  H27  single    0.930  0.020  1.080
 KK1  C24  H28  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
 KK1  H3   C01  H2   107.58  3.000
 KK1  H3   C01  H1   107.65  3.000
 KK1  H2   C01  H1   107.46  3.000
 KK1  H3   C01  C02  111.65  3.000
 KK1  H2   C01  C02  111.08  3.000
 KK1  H1   C01  C02  111.22  3.000
 KK1  H5   C02  H4   106.00  3.000
 KK1  H5   C02  C03  109.26  3.000
 KK1  H4   C02  C03  109.30  3.000
 KK1  H5   C02  C01  109.55  3.000
 KK1  H4   C02  C01  109.67  3.000
 KK1  C03  C02  C01  112.83  3.000
 KK1  H7   C03  H6   105.94  3.000
 KK1  H7   C03  C04  109.36  3.000
 KK1  H6   C03  C04  109.42  3.000
 KK1  H7   C03  C02  109.25  3.000
 KK1  H6   C03  C02  109.25  3.000
 KK1  C04  C03  C02  113.36  3.000
 KK1  H9   C04  H8   105.98  3.000
 KK1  H9   C04  C05  109.29  3.000
 KK1  H8   C04  C05  109.34  3.000
 KK1  H9   C04  C03  109.40  3.000
 KK1  H8   C04  C03  109.34  3.000
 KK1  C05  C04  C03  113.24  3.000
 KK1  H11  C05  H10  106.03  3.000
 KK1  H11  C05  C06  109.31  3.000
 KK1  H10  C05  C06  109.48  3.000
 KK1  H11  C05  C04  109.33  3.000
 KK1  H10  C05  C04  109.37  3.000
 KK1  C06  C05  C04  113.08  3.000
 KK1  H13  C06  H12  106.11  3.000
 KK1  H13  C06  C07  109.37  3.000
 KK1  H12  C06  C07  109.41  3.000
 KK1  H13  C06  C05  109.49  3.000
 KK1  H12  C06  C05  109.28  3.000
 KK1  C07  C06  C05  112.97  3.000
 KK1  H15  C07  H14  106.68  3.000
 KK1  H15  C07  C08  109.19  3.000
 KK1  H14  C07  C08  109.71  3.000
 KK1  H15  C07  C06  109.79  3.000
 KK1  H14  C07  C06  109.44  3.000
 KK1  C08  C07  C06  111.89  3.000
 KK1  H17  C08  H16  106.76  3.000
 KK1  H17  C08  N09  111.04  3.000
 KK1  H16  C08  N09  109.41  3.000
 KK1  H17  C08  C07  109.84  3.000
 KK1  H16  C08  C07  108.80  3.000
 KK1  N09  C08  C07  110.87  3.000
 KK1  H18  N09  C10  115.76  3.000
 KK1  H18  N09  C08  117.83  3.000
 KK1  C10  N09  C08  124.96  3.000
 KK1  N16  C10  C11  121.30  3.000
 KK1  N16  C10  N09  116.33  3.000
 KK1  C11  C10  N09  122.36  3.000
 KK1  H19  C11  C12  121.90  3.000
 KK1  H19  C11  C10  121.40  3.000
 KK1  C12  C11  C10  116.67  3.000
 KK1  C17  C12  N13  116.21  3.000
 KK1  N13  C12  C11  122.14  3.000
 KK1  C17  C12  C11  121.65  3.000
 KK1  C14  N13  C12  116.49  3.000
 KK1  N16  C14  N15  116.80  3.000
 KK1  N16  C14  N13  126.55  3.000
 KK1  N15  C14  N13  116.62  3.000
 KK1  H21  N15  H20  116.33  3.000
 KK1  H21  N15  C14  118.15  3.000
 KK1  H20  N15  C14  117.82  3.000
 KK1  C14  N16  C10  116.82  3.000
 KK1  C24  C17  C18  117.63  3.000
 KK1  C24  C17  C12  122.04  3.000
 KK1  C18  C17  C12  120.33  3.000
 KK1  H22  C18  C19  119.28  3.000
 KK1  H22  C18  C17  119.36  3.000
 KK1  C19  C18  C17  121.36  3.000
 KK1  H23  C19  C20  119.46  3.000
 KK1  H23  C19  C18  120.21  3.000
 KK1  C20  C19  C18  120.33  3.000
 KK1  C23  C20  O21  124.49  3.000
 KK1  C23  C20  C19  119.11  3.000
 KK1  O21  C20  C19  116.40  3.000
 KK1  C22  O21  C20  118.68  3.000
 KK1  H26  C22  H25  108.85  3.000
 KK1  H26  C22  H24  108.84  3.000
 KK1  H25  C22  H24  108.78  3.000
 KK1  H26  C22  O21  111.84  3.000
 KK1  H25  C22  O21  106.48  3.000
 KK1  H24  C22  O21  111.95  3.000
 KK1  H27  C23  C24  118.66  3.000
 KK1  H27  C23  C20  121.57  3.000
 KK1  C24  C23  C20  119.77  3.000
 KK1  H28  C24  C23  117.73  3.000
 KK1  H28  C24  C17  120.46  3.000
 KK1  C23  C24  C17  121.80  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
 KK1  CONST_01  C17  C12  C11  C10  180.00   0.0  0
 KK1  CONST_02  N13  C12  C11  C10    0.00   0.0  0
 KK1  CONST_03  N13  C14  N16  C10    0.00   0.0  0
 KK1  CONST_06  C14  N13  C12  C11    0.00   0.0  0
 KK1  CONST_07  C14  N16  C10  C11    0.00   0.0  0
 KK1  CONST_08  C19  C18  C17  C12  180.00   0.0  0
 KK1  CONST_09  C23  C24  C17  C12  180.00   0.0  0
 KK1  CONST_10  N16  C14  N13  C12    0.00   0.0  0
 KK1  CONST_11  N16  C10  C11  C12    0.00   0.0  0
 KK1  CONST_14  C17  C12  N13  C14  180.00   0.0  0
 KK1  CONST_15  C20  C19  C18  C17    0.00   0.0  0
 KK1  CONST_16  C20  C23  C24  C17    0.00   0.0  0
 KK1  CONST_17  C23  C20  C19  C18    0.00   0.0  0
 KK1  CONST_18  C23  C24  C17  C18    0.00   0.0  0
 KK1  CONST_19  C24  C23  C20  C19    0.00   0.0  0
 KK1  CONST_20  C24  C17  C18  C19    0.00   0.0  0
 KK1  CONST_21  C12  C11  C10  N09  180.00   0.0  0
 KK1  CONST_22  C14  N16  C10  N09  180.00   0.0  0
 KK1  CONST_23  N15  C14  N16  C10  180.00   0.0  0
 KK1  CONST_24  N15  C14  N13  C12  180.00   0.0  0
 KK1  CONST_25  O21  C20  C19  C18  180.00   0.0  0
 KK1  CONST_26  C24  C23  C20  O21  180.00   0.0  0
 KK1  CONST_27  H22  C18  C17  C12    0.00   0.0  0
 KK1  CONST_28  H28  C24  C17  C12    0.00   0.0  0
 KK1  CONST_29  H19  C11  C12  N13  180.00   0.0  0
 KK1  CONST_30  H23  C19  C18  C17  180.00   0.0  0
 KK1  CONST_31  H27  C23  C24  C17  180.00   0.0  0
 KK1  CONST_32  C11  C10  N09  C08    0.00   0.0  0
 KK1  CONST_33  N16  C10  N09  C08  180.00   0.0  0
 KK1  CONST_34  H18  N09  C10  C11  180.00   0.0  0
 KK1  Var_01    C23  C20  O21  C22   -1.04  30.0  2
 KK1  Var_02    C10  N09  C08  C07  168.12  30.0  1
 KK1  Var_03    H24  C22  O21  C20   61.17  30.0  3
 KK1  Var_04    C04  C03  C02  C01  179.98  30.0  1
 KK1  Var_05    C05  C04  C03  C02  179.73  30.0  2
 KK1  Var_06    C06  C05  C04  C03  179.16  30.0  1
 KK1  Var_07    C07  C06  C05  C04  179.48  30.0  2
 KK1  Var_08    C08  C07  C06  C05  177.56  30.0  1
 KK1  Var_09    N09  C08  C07  C06  178.44  30.0  1
 KK1  Var_10    H1   C01  C02  C03  -59.99  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
 KK1  plan-1  N09  0.020
 KK1  plan-1  C10  0.020
 KK1  plan-1  C11  0.020
 KK1  plan-1  C12  0.020
 KK1  plan-1  N13  0.020
 KK1  plan-1  C14  0.020
 KK1  plan-1  N15  0.020
 KK1  plan-1  N16  0.020
 KK1  plan-1  C17  0.020
 KK1  plan-1  H19  0.020
 KK1  plan-2  C12  0.020
 KK1  plan-2  C17  0.020
 KK1  plan-2  C18  0.020
 KK1  plan-2  C19  0.020
 KK1  plan-2  C20  0.020
 KK1  plan-2  O21  0.020
 KK1  plan-2  C23  0.020
 KK1  plan-2  C24  0.020
 KK1  plan-2  H22  0.020
 KK1  plan-2  H23  0.020
 KK1  plan-2  H27  0.020
 KK1  plan-2  H28  0.020
 KK1  plan-3  C08  0.020
 KK1  plan-3  N09  0.020
 KK1  plan-3  C10  0.020
 KK1  plan-3  H18  0.020
 KK1  plan-4  C14  0.020
 KK1  plan-4  N15  0.020
 KK1  plan-4  H20  0.020
 KK1  plan-4  H21  0.020

