# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:41:01 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 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(Nc3ccc4c([nH]nc4C)c3)n2)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
 SAV  SAV  N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine  ligand  52  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SAV
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
 SAV  N1    N  NH1   0  -0.780  -1.0081   0.3344   0.0842
 SAV  N3    N  NH1   0  -0.780   3.1740   2.1977   0.0369
 SAV  C4    C  CR6   0   0.422  -2.3750   0.0930   0.1649
 SAV  C5    C  CR6   0   0.624  -0.2799   1.4838   0.1607
 SAV  C6    C  CR16  0   0.006  -0.0699   3.7088   0.4062
 SAV  C7    C  CR16  0  -0.469   1.2932   3.6313   0.3175
 SAV  C8    C  CR6   0   0.576   1.8271   2.3378   0.1308
 SAV  C10   C  CR16  0  -0.373   5.3741   1.3243  -0.0916
 SAV  C13   C  CR5   0   0.212   6.4335  -2.2484  -0.7422
 SAV  C15   C  CR56  0   0.473   4.4561  -1.2061  -0.5694
 SAV  C17   C  CR16  0  -0.545  -2.7540  -1.2527   0.1707
 SAV  C20   C  CR6   0   0.148  -5.0786  -0.6018   0.3058
 SAV  C21   C  CH3   0  -0.406  -7.0483  -1.0868  -0.8514
 SAV  C1    C  CH3   0  -0.439  -5.3670   3.0080   0.3319
 SAV  C2    C  CR6   0   0.377  -4.6869   0.7364   0.2889
 SAV  C3    C  CR16  0  -0.519  -3.3409   1.0944   0.2262
 SAV  N2    N  N     0  -0.497  -0.8822   2.6499   0.3300
 SAV  C9    C  CR6   0   0.357   3.9741   1.0740  -0.1524
 SAV  C11   C  CR16  0  -0.318   6.2963   0.3258  -0.2673
 SAV  C12   C  CR56  0  -0.133   5.8380  -0.9746  -0.5119
 SAV  N4    N  N     0  -0.262   5.5022  -3.1523  -0.9210
 SAV  N5    N  NR15  0  -0.564   4.3191  -2.5275  -0.8158
 SAV  C16   C  CR16  0  -0.393   3.4965  -0.2030  -0.3939
 SAV  N6    N  N     0  -0.538   1.0386   1.2811   0.0525
 SAV  C18   C  CR6   0   0.349  -4.0985  -1.5959   0.2368
 SAV  O2    O  O2    0  -0.466  -4.5532  -2.8604   0.2497
 SAV  C19   C  CH3   0  -0.439  -3.6160  -3.9183   0.2148
 SAV  O3    O  O2    0  -0.482  -6.3949  -0.9357   0.4007
 SAV  HN1   H  HNH1  0   0.410  -0.4326  -0.4869  -0.0211
 SAV  HN3   H  HNH1  0   0.419   3.6878   3.0584   0.1451
 SAV  H6    H  HCR6  0   0.270  -0.5517   4.6696   0.5482
 SAV  H7    H  HCR6  0   0.280   1.9201   4.5090   0.3850
 SAV  H10   H  HCR6  0   0.268   5.7139   2.3346   0.1031
 SAV  H17   H  HCR6  0   0.289  -1.9879  -2.0153   0.1274
 SAV  H21   H  HCH3  0   0.219  -7.0143  -0.1671  -1.4407
 SAV  H21A  H  HCH3  0   0.218  -6.6121  -1.8965  -1.4421
 SAV  H21B  H  HCH3  0   0.234  -8.0897  -1.3295  -0.6456
 SAV  H1    H  HCH3  0   0.227  -4.7634   3.2954   1.1969
 SAV  H1A   H  HCH3  0   0.228  -4.8376   3.2983  -0.5794
 SAV  H1B   H  HCH3  0   0.261  -6.3120   3.5443   0.3728
 SAV  H3    H  HCR6  0   0.308  -3.0320   2.1263   0.2244
 SAV  H11   H  HCR6  0   0.257   7.3544   0.5485  -0.2133
 SAV  H14   H  HCH3  0   0.247   8.3703  -2.3414   0.1603
 SAV  H14A  H  HCH3  0   0.251   8.0367  -3.6360  -0.9926
 SAV  H14B  H  HCH3  0   0.247   8.3927  -2.0035  -1.5619
 SAV  HN5   H  HNR5  0   0.411   3.4681  -3.0513  -0.9331
 SAV  H16   H  HCR6  0   0.298   2.4417  -0.4153  -0.4456
 SAV  H19   H  HCH3  0   0.229  -3.0172  -3.9061  -0.6993
 SAV  H19A  H  HCH3  0   0.229  -2.9462  -3.9000   1.0783
 SAV  H19B  H  HCH3  0   0.262  -4.1921  -4.8400   0.2402
 SAV  O1    O  O2    0  -0.466  -5.6882   1.6320   0.3428
 SAV  C14   C  CH3   0  -0.741   7.8833  -2.5782  -0.7869

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
 SAV  N1   C4    single    1.390  0.020  1.390
 SAV  N1   C5    single    1.363  0.020  1.363
 SAV  N3   C8    single    1.357  0.020  1.357
 SAV  N3   C9    single    1.392  0.020  1.392
 SAV  C4   C17   aromatic  1.398  0.020  1.398
 SAV  C4   C3    aromatic  1.393  0.020  1.393
 SAV  C5   N2    aromatic  1.323  0.020  1.323
 SAV  C5   N6    aromatic  1.338  0.020  1.338
 SAV  C6   C7    aromatic  1.368  0.020  1.368
 SAV  C6   N2    aromatic  1.337  0.020  1.337
 SAV  C7   C8    aromatic  1.412  0.020  1.412
 SAV  C8   N6    aromatic  1.321  0.020  1.321
 SAV  C10  C9    aromatic  1.424  0.020  1.424
 SAV  C10  C11   aromatic  1.371  0.020  1.371
 SAV  C13  C12   aromatic  1.425  0.020  1.425
 SAV  C13  C14   single    1.488  0.020  1.488
 SAV  C13  N4    aromatic  1.310  0.020  1.310
 SAV  C15  C12   aromatic  1.402  0.020  1.402
 SAV  C15  N5    aromatic  1.351  0.020  1.351
 SAV  C15  C16   aromatic  1.399  0.020  1.399
 SAV  C17  C18   aromatic  1.389  0.020  1.389
 SAV  C20  C2    aromatic  1.395  0.020  1.395
 SAV  C20  C18   aromatic  1.398  0.020  1.398
 SAV  C20  O3    single    1.361  0.020  1.361
 SAV  C21  O3    single    1.420  0.020  1.420
 SAV  C1   O1    single    1.413  0.020  1.413
 SAV  O1   C2    single    1.344  0.020  1.344
 SAV  C2   C3    aromatic  1.394  0.020  1.394
 SAV  C9   C16   aromatic  1.385  0.020  1.385
 SAV  C11  C12   aromatic  1.400  0.020  1.400
 SAV  N4   N5    aromatic  1.342  0.020  1.342
 SAV  C18  O2    single    1.344  0.020  1.344
 SAV  O2   C19   single    1.414  0.020  1.414
 SAV  N1   HN1   single    0.860  0.020  1.020
 SAV  N3   HN3   single    0.860  0.020  1.020
 SAV  C6   H6    single    0.930  0.020  1.080
 SAV  C7   H7    single    0.930  0.020  1.080
 SAV  C10  H10   single    0.930  0.020  1.080
 SAV  C17  H17   single    0.930  0.020  1.080
 SAV  C21  H21   single    0.970  0.020  1.090
 SAV  C21  H21A  single    0.970  0.020  1.090
 SAV  C21  H21B  single    0.970  0.020  1.090
 SAV  C1   H1    single    0.970  0.020  1.090
 SAV  C1   H1A   single    0.970  0.020  1.090
 SAV  C1   H1B   single    0.970  0.020  1.090
 SAV  C3   H3    single    0.930  0.020  1.080
 SAV  C11  H11   single    0.930  0.020  1.080
 SAV  C14  H14   single    0.970  0.020  1.090
 SAV  C14  H14A  single    0.970  0.020  1.090
 SAV  C14  H14B  single    0.970  0.020  1.090
 SAV  N5   HN5   single    0.860  0.020  1.020
 SAV  C16  H16   single    0.930  0.020  1.080
 SAV  C19  H19   single    0.970  0.020  1.090
 SAV  C19  H19A  single    0.970  0.020  1.090
 SAV  C19  H19B  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
 SAV  HN1   N1   C5    112.82  3.000
 SAV  HN1   N1   C4    115.20  3.000
 SAV  C5    N1   C4    131.95  3.000
 SAV  HN3   N3   C9    114.25  3.000
 SAV  HN3   N3   C8    114.21  3.000
 SAV  C9    N3   C8    131.52  3.000
 SAV  C3    C4   C17   120.26  3.000
 SAV  C3    C4   N1    124.02  3.000
 SAV  C17   C4   N1    115.71  3.000
 SAV  N6    C5   N2    126.31  3.000
 SAV  N6    C5   N1    113.21  3.000
 SAV  N2    C5   N1    120.47  3.000
 SAV  H6    C6   N2    116.07  3.000
 SAV  H6    C6   C7    120.10  3.000
 SAV  N2    C6   C7    123.83  3.000
 SAV  H7    C7   C8    122.21  3.000
 SAV  H7    C7   C6    121.86  3.000
 SAV  C8    C7   C6    115.93  3.000
 SAV  N6    C8   C7    121.00  3.000
 SAV  N6    C8   N3    120.38  3.000
 SAV  C7    C8   N3    118.62  3.000
 SAV  H10   C10  C11   119.42  3.000
 SAV  H10   C10  C9    118.69  3.000
 SAV  C11   C10  C9    121.89  3.000
 SAV  N4    C13  C14   122.40  3.000
 SAV  N4    C13  C12   109.99  3.000
 SAV  C14   C13  C12   127.62  3.000
 SAV  C16   C15  N5    130.87  3.000
 SAV  C16   C15  C12   123.53  3.000
 SAV  N5    C15  C12   105.59  3.000
 SAV  H17   C17  C18   120.88  3.000
 SAV  H17   C17  C4    119.10  3.000
 SAV  C18   C17  C4    120.02  3.000
 SAV  O3    C20  C18   120.47  3.000
 SAV  O3    C20  C2    120.52  3.000
 SAV  C18   C20  C2    119.01  3.000
 SAV  H21B  C21  H21A  108.58  3.000
 SAV  H21B  C21  H21   108.61  3.000
 SAV  H21A  C21  H21   108.64  3.000
 SAV  H21B  C21  O3    107.28  3.000
 SAV  H21A  C21  O3    111.82  3.000
 SAV  H21   C21  O3    111.80  3.000
 SAV  H1B   C1   H1A   108.74  3.000
 SAV  H1B   C1   H1    108.68  3.000
 SAV  H1A   C1   H1    108.81  3.000
 SAV  H1B   C1   O1    106.41  3.000
 SAV  H1A   C1   O1    112.03  3.000
 SAV  H1    C1   O1    112.05  3.000
 SAV  C3    C2   O1    123.35  3.000
 SAV  C3    C2   C20   121.20  3.000
 SAV  O1    C2   C20   115.44  3.000
 SAV  H3    C3   C2    121.53  3.000
 SAV  H3    C3   C4    119.33  3.000
 SAV  C2    C3   C4    119.14  3.000
 SAV  C6    N2   C5    115.39  3.000
 SAV  C16   C9   C10   120.58  3.000
 SAV  C16   C9   N3    124.74  3.000
 SAV  C10   C9   N3    114.67  3.000
 SAV  H11   C11  C12   121.30  3.000
 SAV  H11   C11  C10   120.09  3.000
 SAV  C12   C11  C10   118.60  3.000
 SAV  C11   C12  C15   118.88  3.000
 SAV  C11   C12  C13   136.19  3.000
 SAV  C15   C12  C13   104.93  3.000
 SAV  N5    N4   C13   107.14  3.000
 SAV  HN5   N5   N4    119.61  3.000
 SAV  HN5   N5   C15   128.04  3.000
 SAV  N4    N5   C15   112.34  3.000
 SAV  H16   C16  C9    121.86  3.000
 SAV  H16   C16  C15   121.62  3.000
 SAV  C9    C16  C15   116.52  3.000
 SAV  C8    N6   C5    117.53  3.000
 SAV  O2    C18  C20   115.56  3.000
 SAV  O2    C18  C17   124.08  3.000
 SAV  C20   C18  C17   120.35  3.000
 SAV  C19   O2   C18   118.66  3.000
 SAV  H19B  C19  H19A  108.69  3.000
 SAV  H19B  C19  H19   108.62  3.000
 SAV  H19A  C19  H19   108.95  3.000
 SAV  H19B  C19  O2    106.41  3.000
 SAV  H19A  C19  O2    111.98  3.000
 SAV  H19   C19  O2    112.06  3.000
 SAV  C21   O3   C20   114.17  3.000
 SAV  C2    O1   C1    118.63  3.000
 SAV  H14B  C14  H14A  108.17  3.000
 SAV  H14B  C14  H14   107.10  3.000
 SAV  H14A  C14  H14   108.18  3.000
 SAV  H14B  C14  C13   111.08  3.000
 SAV  H14A  C14  C13   111.01  3.000
 SAV  H14   C14  C13   111.15  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
 SAV  CONST_01  C20  C18  C17  C4      0.00   0.0  0
 SAV  CONST_02  C20  C2   C3   C4      0.00   0.0  0
 SAV  CONST_03  C7   C6   N2   C5      0.00   0.0  0
 SAV  CONST_04  C7   C8   N6   C5      0.00   0.0  0
 SAV  CONST_05  N6   C8   C7   C6      0.00   0.0  0
 SAV  CONST_06  N6   C5   N2   C6      0.00   0.0  0
 SAV  CONST_07  N2   C6   C7   C8      0.00   0.0  0
 SAV  CONST_08  N2   C5   N6   C8      0.00   0.0  0
 SAV  CONST_09  C15  C16  C9   C10     0.00   0.0  0
 SAV  CONST_10  C13  C12  C11  C10   180.00   0.0  0
 SAV  CONST_11  C15  C12  C11  C10     0.00   0.0  0
 SAV  CONST_12  N5   C15  C12  C13     0.00   0.0  0
 SAV  CONST_13  C16  C15  C12  C13   180.00   0.0  0
 SAV  CONST_14  C15  N5   N4   C13     0.00   0.0  0
 SAV  CONST_15  N4   C13  C12  C15     0.00   0.0  0
 SAV  CONST_16  C2   C3   C4   C17     0.00   0.0  0
 SAV  CONST_17  C2   C20  C18  C17     0.00   0.0  0
 SAV  CONST_18  C18  C17  C4   C3      0.00   0.0  0
 SAV  CONST_19  C18  C20  C2   C3      0.00   0.0  0
 SAV  CONST_20  C12  C11  C10  C9      0.00   0.0  0
 SAV  CONST_21  C12  C15  C16  C9      0.00   0.0  0
 SAV  CONST_22  N5   C15  C16  C9    180.00   0.0  0
 SAV  CONST_23  C16  C9   C10  C11     0.00   0.0  0
 SAV  CONST_24  N4   C13  C12  C11   180.00   0.0  0
 SAV  CONST_25  N5   C15  C12  C11   180.00   0.0  0
 SAV  CONST_26  C16  C15  C12  C11     0.00   0.0  0
 SAV  CONST_27  N5   N4   C13  C12     0.00   0.0  0
 SAV  CONST_28  N4   N5   C15  C12     0.00   0.0  0
 SAV  CONST_29  C16  C15  N5   N4    180.00   0.0  0
 SAV  CONST_30  C18  C17  C4   N1    180.00   0.0  0
 SAV  CONST_31  C2   C3   C4   N1    180.00   0.0  0
 SAV  CONST_32  C6   N2   C5   N1    180.00   0.0  0
 SAV  CONST_33  C8   N6   C5   N1    180.00   0.0  0
 SAV  CONST_34  C6   C7   C8   N3    180.00   0.0  0
 SAV  CONST_35  C5   N6   C8   N3    180.00   0.0  0
 SAV  CONST_36  C11  C10  C9   N3    180.00   0.0  0
 SAV  CONST_37  C15  C16  C9   N3    180.00   0.0  0
 SAV  CONST_38  O2   C18  C17  C4    180.00   0.0  0
 SAV  CONST_39  O1   C2   C3   C4    180.00   0.0  0
 SAV  CONST_40  C14  C13  C12  C15   180.00   0.0  0
 SAV  CONST_41  O3   C20  C18  C17   180.00   0.0  0
 SAV  CONST_42  C18  C20  C2   O1    180.00   0.0  0
 SAV  CONST_43  O2   C18  C20  C2    180.00   0.0  0
 SAV  CONST_44  O3   C20  C2   C3    180.00   0.0  0
 SAV  CONST_45  C14  C13  C12  C11     0.00   0.0  0
 SAV  CONST_46  N5   N4   C13  C14   180.00   0.0  0
 SAV  CONST_47  H6   C6   N2   C5    180.00   0.0  0
 SAV  CONST_48  H16  C16  C9   C10   180.00   0.0  0
 SAV  CONST_49  H11  C11  C12  C13     0.00   0.0  0
 SAV  CONST_50  HN5  N5   N4   C13   180.00   0.0  0
 SAV  CONST_51  H3   C3   C4   C17   180.00   0.0  0
 SAV  CONST_52  H17  C17  C18  C20   180.00   0.0  0
 SAV  CONST_53  H7   C7   C6   N2    180.00   0.0  0
 SAV  CONST_54  H10  C10  C11  C12   180.00   0.0  0
 SAV  Var_01    N2   C5   N1   C4     -0.75  30.0  2
 SAV  Var_02    C17  C4   N1   C5   -174.00  30.0  2
 SAV  Var_03    C9   N3   C8   C7   -179.57  30.0  3
 SAV  Var_04    C10  C9   N3   C8   -175.28  30.0  2
 SAV  Var_05    C2   C20  O3   C21    90.93  30.0  2
 SAV  Var_06    C3   C2   O1   C1      0.18  30.0  2
 SAV  Var_07    H14  C14  C13  C12    60.13  30.0  2
 SAV  Var_08    H21  C21  O3   C20   -59.80  30.0  3
 SAV  Var_09    H1   C1   O1   C2    -61.82  30.0  3
 SAV  Var_10    H19  C19  O2   C18   -61.82  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
 SAV  plan-1  N1   0.020
 SAV  plan-1  C4   0.020
 SAV  plan-1  C17  0.020
 SAV  plan-1  C20  0.020
 SAV  plan-1  C2   0.020
 SAV  plan-1  C3   0.020
 SAV  plan-1  C18  0.020
 SAV  plan-1  O2   0.020
 SAV  plan-1  O3   0.020
 SAV  plan-1  H17  0.020
 SAV  plan-1  H3   0.020
 SAV  plan-1  O1   0.020
 SAV  plan-2  N1   0.020
 SAV  plan-2  N3   0.020
 SAV  plan-2  C5   0.020
 SAV  plan-2  C6   0.020
 SAV  plan-2  C7   0.020
 SAV  plan-2  C8   0.020
 SAV  plan-2  N2   0.020
 SAV  plan-2  N6   0.020
 SAV  plan-2  H6   0.020
 SAV  plan-2  H7   0.020
 SAV  plan-3  N3   0.020
 SAV  plan-3  C10  0.020
 SAV  plan-3  C13  0.020
 SAV  plan-3  C15  0.020
 SAV  plan-3  C9   0.020
 SAV  plan-3  C11  0.020
 SAV  plan-3  C12  0.020
 SAV  plan-3  N4   0.020
 SAV  plan-3  N5   0.020
 SAV  plan-3  C16  0.020
 SAV  plan-3  H10  0.020
 SAV  plan-3  H11  0.020
 SAV  plan-3  HN5  0.020
 SAV  plan-3  H16  0.020
 SAV  plan-3  C14  0.020

