# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:15:07 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2nccc(n2)N(C)c3ccc4c([nH]nc4C)c3)cc(OC)c1OC
#
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
 KIM  KIM  N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine  ligand  55  31  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KIM
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
 KIM  N1    N  NH1   0  -0.778  -1.7923   0.6651  -0.5488
 KIM  N3    N  N     0  -0.533   0.4523   0.6470  -0.7834
 KIM  C4    C  CR6   0   0.419  -3.0976   0.4410  -0.1290
 KIM  C5    C  CR6   0   0.599  -0.5993   0.1523  -0.1273
 KIM  C6    C  CR16  0  -0.004   0.6517  -1.1824   1.1743
 KIM  C7    C  CR16  0  -0.432   1.8091  -0.7561   0.5802
 KIM  C8    C  CR6   0   0.537   1.6585   0.2119  -0.4401
 KIM  C10   C  CR6   0   0.233   4.0421   0.4284  -0.7288
 KIM  C13   C  CR56  0  -0.105   6.6452  -0.0570   0.0826
 KIM  C17   C  CR16  0  -0.322   4.8397  -0.3299  -1.5580
 KIM  C21   C  CR6   0   0.146  -5.7876   0.1404   0.5787
 KIM  C2    C  CR6   0   0.348  -5.4229   1.0049  -0.4573
 KIM  C3    C  CR16  0  -0.546  -4.0874   1.1592  -0.8076
 KIM  N2    N  N     0  -0.496  -0.5674  -0.7449   0.8466
 KIM  N4    N  NT    0  -0.560   2.7111   0.7201  -1.1224
 KIM  C9    C  CH3   0  -0.529   2.4888   1.6540  -2.2146
 KIM  C11   C  CR16  0  -0.269   4.5239   0.9490   0.4939
 KIM  C12   C  CR16  0  -0.334   5.8119   0.7060   0.9090
 KIM  C14   C  CR5   0   0.215   7.9952  -0.5127   0.1407
 KIM  N5    N  N     0  -0.253   8.2774  -1.2105  -0.9315
 KIM  N6    N  NR15  0  -0.558   7.1770  -1.2359  -1.6939
 KIM  C16   C  CR56  0   0.438   6.1532  -0.5550  -1.1349
 KIM  C18   C  CR16  0  -0.523  -3.4480  -0.4304   0.9000
 KIM  C19   C  CR6   0   0.381  -4.7918  -0.5765   1.2410
 KIM  O2    O  O2    0  -0.468  -5.2212  -1.3955   2.2179
 KIM  O3    O  O2    0  -0.482  -7.0947   0.0141   0.9384
 KIM  HN1   H  HNH1  0   0.405  -1.6897   1.3319  -1.2985
 KIM  H6    H  HCR6  0   0.265   0.6925  -1.9257   1.9626
 KIM  H7    H  HCR6  0   0.276   2.7669  -1.1523   0.8779
 KIM  H15   H  HCH3  0   0.249   8.6488  -0.6960   2.1686
 KIM  H15A  H  HCH3  0   0.253   9.9477  -0.7238   0.9739
 KIM  H15B  H  HCH3  0   0.249   9.1458   0.7937   1.3832
 KIM  H17   H  HCR6  0   0.278   4.4599  -0.7310  -2.4888
 KIM  H20   H  HCH3  0   0.261  -4.8224  -2.7219   3.6772
 KIM  H20A  H  HCH3  0   0.227  -3.7148  -2.8363   2.2998
 KIM  H20B  H  HCH3  0   0.227  -3.5528  -1.5035   3.4642
 KIM  H22   H  HCH3  0   0.234  -8.8250  -0.9871   0.5837
 KIM  H22A  H  HCH3  0   0.218  -7.7548  -0.8927  -0.8246
 KIM  H22B  H  HCH3  0   0.219  -7.3802  -2.0095   0.5046
 KIM  H1    H  HCH3  0   0.229  -5.4979   3.3769  -1.7581
 KIM  H1A   H  HCH3  0   0.228  -5.6572   2.0643  -2.9462
 KIM  H1B   H  HCH3  0   0.261  -7.0877   2.9723  -2.4280
 KIM  H3    H  HCR6  0   0.287  -3.7986   1.8289  -1.6075
 KIM  H9    H  HCH3  0   0.247   2.0055   2.5685  -1.8683
 KIM  H9A   H  HCH3  0   0.253   3.4510   1.9154  -2.6450
 KIM  H9B   H  HCH3  0   0.245   1.8679   1.2141  -2.9944
 KIM  H11   H  HCR6  0   0.267   3.8592   1.5489   1.1019
 KIM  H12   H  HCR6  0   0.259   6.1715   1.1063   1.8483
 KIM  HN6   H  HNR5  0   0.415   7.1891  -1.7311  -2.5701
 KIM  H18   H  HCR6  0   0.310  -2.6743  -0.9776   1.4114
 KIM  O1    O  O2    0  -0.464  -6.4369   1.6525  -1.0560
 KIM  C15   C  CH3   0  -0.740   8.9882  -0.2736   1.2217
 KIM  C20   C  CH3   0  -0.438  -4.2667  -2.1453   2.9420
 KIM  C22   C  CH3   0  -0.406  -7.7859  -1.0246   0.2599
 KIM  C1    C  CH3   0  -0.439  -6.1380   2.5587  -2.0983

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
 KIM  N1   C4    single    1.389  0.020  1.389
 KIM  N1   C5    single    1.365  0.020  1.365
 KIM  N3   C5    aromatic  1.335  0.020  1.335
 KIM  N3   C8    aromatic  1.327  0.020  1.327
 KIM  C4   C3    aromatic  1.399  0.020  1.399
 KIM  C4   C18   aromatic  1.393  0.020  1.393
 KIM  C5   N2    aromatic  1.325  0.020  1.325
 KIM  C6   C7    aromatic  1.369  0.020  1.369
 KIM  C6   N2    aromatic  1.336  0.020  1.336
 KIM  C7   C8    aromatic  1.414  0.020  1.414
 KIM  C8   N4    single    1.353  0.020  1.353
 KIM  C10  C17   aromatic  1.378  0.020  1.378
 KIM  C10  N4    single    1.418  0.020  1.418
 KIM  C10  C11   aromatic  1.414  0.020  1.414
 KIM  C13  C12   aromatic  1.400  0.020  1.400
 KIM  C13  C14   aromatic  1.426  0.020  1.426
 KIM  C13  C16   aromatic  1.404  0.020  1.404
 KIM  C15  C14   single    1.487  0.020  1.487
 KIM  C17  C16   aromatic  1.398  0.020  1.398
 KIM  C20  O2    single    1.413  0.020  1.413
 KIM  C21  C2    aromatic  1.398  0.020  1.398
 KIM  C21  C19   aromatic  1.394  0.020  1.394
 KIM  C21  O3    single    1.362  0.020  1.362
 KIM  C22  O3    single    1.420  0.020  1.420
 KIM  C1   O1    single    1.413  0.020  1.413
 KIM  O1   C2    single    1.344  0.020  1.344
 KIM  C2   C3    aromatic  1.389  0.020  1.389
 KIM  N4   C9    single    1.454  0.020  1.454
 KIM  C11  C12   aromatic  1.375  0.020  1.375
 KIM  C14  N5    aromatic  1.310  0.020  1.310
 KIM  N5   N6    aromatic  1.339  0.020  1.339
 KIM  N6   C16   aromatic  1.351  0.020  1.351
 KIM  C18  C19   aromatic  1.394  0.020  1.394
 KIM  C19  O2    single    1.345  0.020  1.345
 KIM  N1   HN1   single    0.860  0.020  1.020
 KIM  C6   H6    single    0.930  0.020  1.080
 KIM  C7   H7    single    0.930  0.020  1.080
 KIM  C15  H15   single    0.970  0.020  1.090
 KIM  C15  H15A  single    0.970  0.020  1.090
 KIM  C15  H15B  single    0.970  0.020  1.090
 KIM  C17  H17   single    0.930  0.020  1.080
 KIM  C20  H20   single    0.970  0.020  1.090
 KIM  C20  H20A  single    0.970  0.020  1.090
 KIM  C20  H20B  single    0.970  0.020  1.090
 KIM  C22  H22   single    0.970  0.020  1.090
 KIM  C22  H22A  single    0.970  0.020  1.090
 KIM  C22  H22B  single    0.970  0.020  1.090
 KIM  C1   H1    single    0.970  0.020  1.090
 KIM  C1   H1A   single    0.970  0.020  1.090
 KIM  C1   H1B   single    0.970  0.020  1.090
 KIM  C3   H3    single    0.930  0.020  1.080
 KIM  C9   H9    single    0.970  0.020  1.090
 KIM  C9   H9A   single    0.970  0.020  1.090
 KIM  C9   H9B   single    0.970  0.020  1.090
 KIM  C11  H11   single    0.930  0.020  1.080
 KIM  C12  H12   single    0.930  0.020  1.080
 KIM  N6   HN6   single    0.860  0.020  1.020
 KIM  C18  H18   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
 KIM  HN1   N1   C5    112.89  3.000
 KIM  HN1   N1   C4    115.27  3.000
 KIM  C5    N1   C4    131.84  3.000
 KIM  C8    N3   C5    117.87  3.000
 KIM  C18   C4   C3    120.10  3.000
 KIM  C18   C4   N1    124.08  3.000
 KIM  C3    C4   N1    115.81  3.000
 KIM  N2    C5   N3    126.41  3.000
 KIM  N2    C5   N1    120.17  3.000
 KIM  N3    C5   N1    113.43  3.000
 KIM  H6    C6   N2    115.92  3.000
 KIM  H6    C6   C7    119.82  3.000
 KIM  N2    C6   C7    124.26  3.000
 KIM  H7    C7   C8    123.03  3.000
 KIM  H7    C7   C6    121.11  3.000
 KIM  C8    C7   C6    115.86  3.000
 KIM  N4    C8   C7    122.54  3.000
 KIM  N4    C8   N3    116.95  3.000
 KIM  C7    C8   N3    120.50  3.000
 KIM  C11   C10  N4    118.96  3.000
 KIM  C11   C10  C17   121.73  3.000
 KIM  N4    C10  C17   119.30  3.000
 KIM  C16   C13  C14   104.69  3.000
 KIM  C16   C13  C12   119.77  3.000
 KIM  C14   C13  C12   135.53  3.000
 KIM  H17   C17  C16   122.02  3.000
 KIM  H17   C17  C10   121.22  3.000
 KIM  C16   C17  C10   116.76  3.000
 KIM  O3    C21  C19   120.83  3.000
 KIM  O3    C21  C2    120.24  3.000
 KIM  C19   C21  C2    118.92  3.000
 KIM  C3    C2   O1    124.03  3.000
 KIM  C3    C2   C21   120.42  3.000
 KIM  O1    C2   C21   115.55  3.000
 KIM  H3    C3   C2    120.76  3.000
 KIM  H3    C3   C4    119.18  3.000
 KIM  C2    C3   C4    120.06  3.000
 KIM  C6    N2   C5    115.10  3.000
 KIM  C9    N4   C10   118.95  3.000
 KIM  C9    N4   C8    120.06  3.000
 KIM  C10   N4   C8    120.84  3.000
 KIM  H9B   C9   H9A   108.57  3.000
 KIM  H9B   C9   H9    108.25  3.000
 KIM  H9A   C9   H9    108.46  3.000
 KIM  H9B   C9   N4    111.43  3.000
 KIM  H9A   C9   N4    108.47  3.000
 KIM  H9    C9   N4    111.58  3.000
 KIM  H11   C11  C12   120.25  3.000
 KIM  H11   C11  C10   118.73  3.000
 KIM  C12   C11  C10   121.02  3.000
 KIM  H12   C12  C11   120.51  3.000
 KIM  H12   C12  C13   121.07  3.000
 KIM  C11   C12  C13   118.41  3.000
 KIM  N5    C14  C15   122.46  3.000
 KIM  N5    C14  C13   109.93  3.000
 KIM  C15   C14  C13   127.61  3.000
 KIM  N6    N5   C14   107.41  3.000
 KIM  HN6   N6   C16   128.13  3.000
 KIM  HN6   N6   N5    119.68  3.000
 KIM  C16   N6   N5    112.19  3.000
 KIM  N6    C16  C17   131.91  3.000
 KIM  N6    C16  C13   105.78  3.000
 KIM  C17   C16  C13   122.30  3.000
 KIM  H18   C18  C19   121.55  3.000
 KIM  H18   C18  C4    119.20  3.000
 KIM  C19   C18  C4    119.25  3.000
 KIM  O2    C19  C18   123.31  3.000
 KIM  O2    C19  C21   115.47  3.000
 KIM  C18   C19  C21   121.23  3.000
 KIM  C19   O2   C20   118.65  3.000
 KIM  C22   O3   C21   114.13  3.000
 KIM  C2    O1   C1    118.55  3.000
 KIM  H15B  C15  H15A  108.12  3.000
 KIM  H15B  C15  H15   107.17  3.000
 KIM  H15A  C15  H15   108.16  3.000
 KIM  H15B  C15  C14   111.19  3.000
 KIM  H15A  C15  C14   110.89  3.000
 KIM  H15   C15  C14   111.16  3.000
 KIM  H20B  C20  H20A  108.80  3.000
 KIM  H20B  C20  H20   108.80  3.000
 KIM  H20A  C20  H20   108.67  3.000
 KIM  H20B  C20  O2    111.99  3.000
 KIM  H20A  C20  O2    112.05  3.000
 KIM  H20   C20  O2    106.42  3.000
 KIM  H22B  C22  H22A  108.68  3.000
 KIM  H22B  C22  H22   108.57  3.000
 KIM  H22A  C22  H22   108.54  3.000
 KIM  H22B  C22  O3    111.81  3.000
 KIM  H22A  C22  O3    111.84  3.000
 KIM  H22   C22  O3    107.28  3.000
 KIM  H1B   C1   H1A   108.73  3.000
 KIM  H1B   C1   H1    108.73  3.000
 KIM  H1A   C1   H1    108.81  3.000
 KIM  H1B   C1   O1    106.43  3.000
 KIM  H1A   C1   O1    112.04  3.000
 KIM  H1    C1   O1    111.98  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
 KIM  CONST_01  C6   N2   C5   N3      0.00   0.0  0
 KIM  CONST_02  C6   C7   C8   N3      0.00   0.0  0
 KIM  CONST_03  C21  C2   C3   C4      0.00   0.0  0
 KIM  CONST_04  C21  C19  C18  C4      0.00   0.0  0
 KIM  CONST_05  C7   C8   N3   C5      0.00   0.0  0
 KIM  CONST_06  C7   C6   N2   C5      0.00   0.0  0
 KIM  CONST_07  N2   C5   N3   C8      0.00   0.0  0
 KIM  CONST_08  N2   C6   C7   C8      0.00   0.0  0
 KIM  CONST_09  C13  C16  C17  C10     0.00   0.0  0
 KIM  CONST_10  N6   C16  C17  C10   180.00   0.0  0
 KIM  CONST_11  C13  C12  C11  C10     0.00   0.0  0
 KIM  CONST_12  N6   N5   C14  C13     0.00   0.0  0
 KIM  CONST_13  N5   N6   C16  C13     0.00   0.0  0
 KIM  CONST_14  C12  C11  C10  C17     0.00   0.0  0
 KIM  CONST_15  C12  C13  C16  C17     0.00   0.0  0
 KIM  CONST_16  C14  C13  C16  C17   180.00   0.0  0
 KIM  CONST_17  N5   N6   C16  C17   180.00   0.0  0
 KIM  CONST_18  C18  C19  C21  C2      0.00   0.0  0
 KIM  CONST_19  C18  C4   C3   C2      0.00   0.0  0
 KIM  CONST_20  C19  C18  C4   C3      0.00   0.0  0
 KIM  CONST_21  C19  C21  C2   C3      0.00   0.0  0
 KIM  CONST_22  C16  C17  C10  C11     0.00   0.0  0
 KIM  CONST_23  C14  C13  C12  C11   180.00   0.0  0
 KIM  CONST_24  C16  C13  C12  C11     0.00   0.0  0
 KIM  CONST_25  N5   C14  C13  C12   180.00   0.0  0
 KIM  CONST_26  N6   C16  C13  C12   180.00   0.0  0
 KIM  CONST_27  N6   C16  C13  C14     0.00   0.0  0
 KIM  CONST_28  C16  N6   N5   C14     0.00   0.0  0
 KIM  CONST_29  C16  C13  C14  N5      0.00   0.0  0
 KIM  CONST_30  C2   C3   C4   N1    180.00   0.0  0
 KIM  CONST_31  C19  C18  C4   N1    180.00   0.0  0
 KIM  CONST_32  C8   N3   C5   N1    180.00   0.0  0
 KIM  CONST_33  C6   N2   C5   N1    180.00   0.0  0
 KIM  CONST_34  O1   C2   C3   C4    180.00   0.0  0
 KIM  CONST_35  O2   C19  C18  C4    180.00   0.0  0
 KIM  CONST_36  N4   C8   N3   C5    180.00   0.0  0
 KIM  CONST_37  N4   C8   C7   C6    180.00   0.0  0
 KIM  CONST_38  C12  C13  C14  C15     0.00   0.0  0
 KIM  CONST_39  C16  C13  C14  C15   180.00   0.0  0
 KIM  CONST_40  N6   N5   C14  C15   180.00   0.0  0
 KIM  CONST_41  C19  C21  C2   O1    180.00   0.0  0
 KIM  CONST_42  O2   C19  C21  C2    180.00   0.0  0
 KIM  CONST_43  O3   C21  C2   C3    180.00   0.0  0
 KIM  CONST_44  C16  C17  C10  N4    180.00   0.0  0
 KIM  CONST_45  C12  C11  C10  N4    180.00   0.0  0
 KIM  CONST_46  O3   C21  C19  C18   180.00   0.0  0
 KIM  CONST_47  H7   C7   C8   N3    180.00   0.0  0
 KIM  CONST_48  H6   C6   N2   C5    180.00   0.0  0
 KIM  CONST_49  H12  C12  C11  C10   180.00   0.0  0
 KIM  CONST_50  H11  C11  C12  C13   180.00   0.0  0
 KIM  CONST_51  H17  C17  C16  C13   180.00   0.0  0
 KIM  CONST_52  HN6  N6   C16  C13   180.00   0.0  0
 KIM  CONST_53  H3   C3   C2   C21   180.00   0.0  0
 KIM  CONST_54  H18  C18  C19  C21   180.00   0.0  0
 KIM  Var_01    C4   N1   C5   N3   -178.92  30.0  2
 KIM  Var_02    C10  N4   C8   N3    172.96  30.0  2
 KIM  Var_03    C3   C4   N1   C5   -179.99  30.0  2
 KIM  Var_04    C17  C10  N4   C8    113.28  30.0  2
 KIM  Var_05    C21  C19  O2   C20  -179.42  30.0  3
 KIM  Var_06    C2   C21  O3   C22    91.40  30.0  2
 KIM  Var_07    C3   C2   O1   C1     -0.66  30.0  2
 KIM  Var_08    H15  C15  C14  C13    61.22  30.0  2
 KIM  Var_09    H9   C9   N4   C8     62.30  30.0  3
 KIM  Var_10    H22  C22  O3   C21  -176.61  30.0  3
 KIM  Var_11    H1   C1   O1   C2    -60.70  30.0  3
 KIM  Var_12    H20  C20  O2   C19   179.44  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
 KIM  plan-1  N1   0.020
 KIM  plan-1  N3   0.020
 KIM  plan-1  C5   0.020
 KIM  plan-1  C6   0.020
 KIM  plan-1  C7   0.020
 KIM  plan-1  C8   0.020
 KIM  plan-1  N2   0.020
 KIM  plan-1  N4   0.020
 KIM  plan-1  H6   0.020
 KIM  plan-1  H7   0.020
 KIM  plan-2  N1   0.020
 KIM  plan-2  C4   0.020
 KIM  plan-2  C21  0.020
 KIM  plan-2  C2   0.020
 KIM  plan-2  C3   0.020
 KIM  plan-2  C18  0.020
 KIM  plan-2  C19  0.020
 KIM  plan-2  O2   0.020
 KIM  plan-2  O3   0.020
 KIM  plan-2  H3   0.020
 KIM  plan-2  H18  0.020
 KIM  plan-2  O1   0.020
 KIM  plan-3  C10  0.020
 KIM  plan-3  C13  0.020
 KIM  plan-3  C17  0.020
 KIM  plan-3  N4   0.020
 KIM  plan-3  C11  0.020
 KIM  plan-3  C12  0.020
 KIM  plan-3  C14  0.020
 KIM  plan-3  N5   0.020
 KIM  plan-3  N6   0.020
 KIM  plan-3  C16  0.020
 KIM  plan-3  H17  0.020
 KIM  plan-3  H11  0.020
 KIM  plan-3  H12  0.020
 KIM  plan-3  HN6  0.020
 KIM  plan-3  C15  0.020

