# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 00:56:26 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-chloro-N~2~-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-N~4~-(3-methyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncc(Cl)c(Nc2[nH]nc(C)c2)n1)c3ncc(F)cn3
#
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
 AZ5  AZ5  5-chloro-N~2~-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-N~4~-(3-methyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine  ligand  38  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AZ5
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
 AZ5  C3    C   CR15  0  -0.521   2.1604  -2.4951  -0.0988
 AZ5  C19   C   CR16  0  -0.154  -5.6968   0.8056   0.4433
 AZ5  C21   C   CR16  0  -0.145  -4.5500  -1.2376   0.0756
 AZ5  C10   C   CR16  0   0.020   1.5790   2.9004   0.1052
 AZ5  C20   C   CR6   0   0.399  -5.7137  -0.5753   0.4004
 AZ5  C9    C   CR6   0  -0.259   2.6407   2.0340   0.1864
 AZ5  C2    C   CR5   0   0.253   2.7583  -3.7727  -0.1501
 AZ5  C4    C   CR5   0   0.632   3.2260  -1.6268   0.0232
 AZ5  C8    C   CR6   0   0.638   2.3514   0.6572   0.0680
 AZ5  C17   C   CR6   0   0.390  -3.5028   0.7669  -0.1266
 AZ5  C12   C   CR6   0   0.627   0.1463   1.1806  -0.1691
 AZ5  C1    C   CH3   0  -0.736   2.0644  -5.0842  -0.2857
 AZ5  C16   C   CH3   0  -0.657  -2.4039   2.1297  -1.8902
 AZ5  C15   C   CH1   0  -0.133  -2.2653   1.5576  -0.4760
 AZ5  N18   N   N     0  -0.390  -4.5851   1.4720   0.1782
 AZ5  N22   N   N     0  -0.412  -3.4452  -0.5538  -0.1895
 AZ5  N11   N   N     0  -0.489   0.3269   2.4991  -0.0737
 AZ5  N13   N   N     0  -0.514   1.1101   0.2531  -0.1079
 AZ5  N5    N   NR15  0  -0.523   4.3378  -2.3878   0.0357
 AZ5  N6    N   N     0  -0.302   4.0710  -3.6949  -0.0666
 AZ5  N7    N   NH1   0  -0.770   3.3485  -0.2578   0.1337
 AZ5  N14   N   NH1   0  -0.668  -1.1035   0.7183  -0.3302
 AZ5  H3    H   HCR5  0   0.269   1.1150  -2.2553  -0.1424
 AZ5  H19   H   HCR6  0   0.304  -6.5858   1.3726   0.6975
 AZ5  H21   H   HCR6  0   0.305  -4.5063  -2.3200   0.0287
 AZ5  H10   H   HCR6  0   0.286   1.7463   3.9691   0.1853
 AZ5  H11C  H   HCH3  0   0.245   1.5325  -5.1530  -1.2358
 AZ5  H12C  H   HCH3  0   0.244   2.7754  -5.9074  -0.2374
 AZ5  H13C  H   HCH3  0   0.244   1.3276  -5.2250   0.5059
 AZ5  H5    H   HNR5  0   0.418   5.2934  -2.0761   0.1094
 AZ5  H7    H   HNH1  0   0.414   4.2809   0.0986   0.2810
 AZ5  H15   H   HCH1  0   0.274  -2.1935   2.3878   0.2295
 AZ5  H14   H   HNH1  0   0.399  -1.2232  -0.2764  -0.4457
 AZ5  H161  H   HCH3  0   0.232  -2.5010   1.3281  -2.6234
 AZ5  H162  H   HCH3  0   0.239  -3.2812   2.7724  -1.9611
 AZ5  H163  H   HCH3  0   0.247  -1.5266   2.7254  -2.1388
 AZ5  CL2   CL  CL    0  -0.119   4.2556   2.6065   0.4130
 AZ5  F23   F   F     0  -0.287  -6.8310  -1.2499   0.6681

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
 AZ5  C3   C2    aromatic  1.411  0.020  1.411
 AZ5  C3   C4    aromatic  1.380  0.020  1.380
 AZ5  C19  C20   aromatic  1.382  0.020  1.382
 AZ5  C19  N18   aromatic  1.323  0.020  1.323
 AZ5  C21  C20   aromatic  1.378  0.020  1.378
 AZ5  C21  N22   aromatic  1.326  0.020  1.326
 AZ5  C10  C9    aromatic  1.373  0.020  1.373
 AZ5  C10  N11   aromatic  1.327  0.020  1.327
 AZ5  C20  F23   single    1.332  0.020  1.332
 AZ5  C9   C8    aromatic  1.412  0.020  1.412
 AZ5  C9   CL2   single    1.728  0.020  1.728
 AZ5  C2   C1    single    1.490  0.020  1.490
 AZ5  C2   N6    aromatic  1.318  0.020  1.318
 AZ5  C4   N5    aromatic  1.347  0.020  1.347
 AZ5  C4   N7    single    1.379  0.020  1.379
 AZ5  C8   N13   aromatic  1.317  0.020  1.317
 AZ5  C8   N7    single    1.355  0.020  1.355
 AZ5  C17  C15   single    1.510  0.020  1.510
 AZ5  C17  N18   aromatic  1.327  0.020  1.327
 AZ5  C17  N22   aromatic  1.323  0.020  1.323
 AZ5  C12  N11   aromatic  1.334  0.020  1.334
 AZ5  C12  N13   aromatic  1.339  0.020  1.339
 AZ5  C12  N14   single    1.342  0.020  1.342
 AZ5  C16  C15   single    1.532  0.020  1.532
 AZ5  C15  N14   single    1.441  0.020  1.441
 AZ5  N5   N6    aromatic  1.338  0.020  1.338
 AZ5  C3   H3    single    0.930  0.020  1.080
 AZ5  C19  H19   single    0.930  0.020  1.080
 AZ5  C21  H21   single    0.930  0.020  1.080
 AZ5  C10  H10   single    0.930  0.020  1.080
 AZ5  C1   H11C  single    0.970  0.020  1.090
 AZ5  C1   H12C  single    0.970  0.020  1.090
 AZ5  C1   H13C  single    0.970  0.020  1.090
 AZ5  N5   H5    single    0.860  0.020  1.020
 AZ5  N7   H7    single    0.860  0.020  1.020
 AZ5  C15  H15   single    0.970  0.020  1.090
 AZ5  N14  H14   single    0.860  0.020  1.020
 AZ5  C16  H161  single    0.970  0.020  1.090
 AZ5  C16  H162  single    0.970  0.020  1.090
 AZ5  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
 AZ5  H3    C3   C4    127.95  3.000
 AZ5  H3    C3   C2    127.83  3.000
 AZ5  C4    C3   C2    104.22  3.000
 AZ5  H19   C19  N18   118.19  3.000
 AZ5  H19   C19  C20   121.31  3.000
 AZ5  N18   C19  C20   120.50  3.000
 AZ5  H21   C21  N22   118.20  3.000
 AZ5  H21   C21  C20   121.60  3.000
 AZ5  N22   C21  C20   120.19  3.000
 AZ5  H10   C10  N11   116.97  3.000
 AZ5  H10   C10  C9    119.88  3.000
 AZ5  N11   C10  C9    123.15  3.000
 AZ5  F23   C20  C21   120.82  3.000
 AZ5  F23   C20  C19   120.67  3.000
 AZ5  C21   C20  C19   118.52  3.000
 AZ5  CL2   C9   C8    121.70  3.000
 AZ5  CL2   C9   C10   121.43  3.000
 AZ5  C8    C9   C10   116.87  3.000
 AZ5  N6    C2   C1    121.44  3.000
 AZ5  N6    C2   C3    111.49  3.000
 AZ5  C1    C2   C3    127.07  3.000
 AZ5  N7    C4   N5    119.12  3.000
 AZ5  N7    C4   C3    134.46  3.000
 AZ5  N5    C4   C3    106.42  3.000
 AZ5  N7    C8   N13   119.53  3.000
 AZ5  N7    C8   C9    120.24  3.000
 AZ5  N13   C8   C9    120.23  3.000
 AZ5  N22   C17  N18   125.21  3.000
 AZ5  N22   C17  C15   118.43  3.000
 AZ5  N18   C17  C15   116.32  3.000
 AZ5  N14   C12  N13   115.91  3.000
 AZ5  N14   C12  N11   118.36  3.000
 AZ5  N13   C12  N11   125.72  3.000
 AZ5  H13C  C1   H12C  108.14  3.000
 AZ5  H13C  C1   H11C  107.13  3.000
 AZ5  H12C  C1   H11C  108.02  3.000
 AZ5  H13C  C1   C2    111.24  3.000
 AZ5  H12C  C1   C2    110.94  3.000
 AZ5  H11C  C1   C2    111.21  3.000
 AZ5  H163  C16  H162  108.12  3.000
 AZ5  H163  C16  H161  108.68  3.000
 AZ5  H162  C16  H161  108.55  3.000
 AZ5  H163  C16  C15   110.00  3.000
 AZ5  H162  C16  C15   110.68  3.000
 AZ5  H161  C16  C15   110.74  3.000
 AZ5  H15   C15  N14   108.94  3.000
 AZ5  H15   C15  C16   108.57  3.000
 AZ5  N14   C15  C16   112.58  3.000
 AZ5  H15   C15  C17   107.62  3.000
 AZ5  N14   C15  C17   109.42  3.000
 AZ5  C16   C15  C17   109.58  3.000
 AZ5  C17   N18  C19   117.62  3.000
 AZ5  C17   N22  C21   117.96  3.000
 AZ5  C12   N11  C10   115.86  3.000
 AZ5  C12   N13  C8    118.16  3.000
 AZ5  H5    N5   N6    119.79  3.000
 AZ5  H5    N5   C4    127.47  3.000
 AZ5  N6    N5   C4    112.74  3.000
 AZ5  N5    N6   C2    105.14  3.000
 AZ5  H7    N7   C8    116.65  3.000
 AZ5  H7    N7   C4    116.39  3.000
 AZ5  C8    N7   C4    126.96  3.000
 AZ5  H14   N14  C15   117.86  3.000
 AZ5  H14   N14  C12   117.65  3.000
 AZ5  C15   N14  C12   124.22  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
 AZ5  CONST_01  N5    N6   C2   C3      0.00   0.0  0
 AZ5  CONST_02  N6    N5   C4   C3      0.00   0.0  0
 AZ5  CONST_03  N22   C21  C20  C19     0.00   0.0  0
 AZ5  CONST_04  N22   C17  N18  C19     0.00   0.0  0
 AZ5  CONST_05  N18   C19  C20  C21     0.00   0.0  0
 AZ5  CONST_06  N18   C17  N22  C21     0.00   0.0  0
 AZ5  CONST_07  N13   C8   C9   C10     0.00   0.0  0
 AZ5  CONST_08  N13   C12  N11  C10     0.00   0.0  0
 AZ5  CONST_09  C17   N18  C19  C20     0.00   0.0  0
 AZ5  CONST_10  C17   N22  C21  C20     0.00   0.0  0
 AZ5  CONST_11  C12   N11  C10  C9      0.00   0.0  0
 AZ5  CONST_12  C12   N13  C8   C9      0.00   0.0  0
 AZ5  CONST_13  N5    C4   C3   C2      0.00   0.0  0
 AZ5  CONST_14  C4    N5   N6   C2      0.00   0.0  0
 AZ5  CONST_15  N6    C2   C3   C4      0.00   0.0  0
 AZ5  CONST_16  N11   C10  C9   C8      0.00   0.0  0
 AZ5  CONST_17  N11   C12  N13  C8      0.00   0.0  0
 AZ5  CONST_18  C15   C17  N18  C19   180.00   0.0  0
 AZ5  CONST_19  C15   C17  N22  C21   180.00   0.0  0
 AZ5  CONST_20  N7    C8   C9   C10   180.00   0.0  0
 AZ5  CONST_21  N14   C12  N11  C10   180.00   0.0  0
 AZ5  CONST_22  N7    C4   C3   C2    180.00   0.0  0
 AZ5  CONST_23  C1    C2   C3   C4    180.00   0.0  0
 AZ5  CONST_24  N14   C12  N13  C8    180.00   0.0  0
 AZ5  CONST_25  N7    C8   N13  C12   180.00   0.0  0
 AZ5  CONST_26  N5    N6   C2   C1    180.00   0.0  0
 AZ5  CONST_27  F23   C20  C19  N18   180.00   0.0  0
 AZ5  CONST_28  F23   C20  C21  N22   180.00   0.0  0
 AZ5  CONST_29  CL2   C9   C10  N11   180.00   0.0  0
 AZ5  CONST_30  CL2   C9   C8   N13   180.00   0.0  0
 AZ5  CONST_31  N7    C4   N5   N6    180.00   0.0  0
 AZ5  CONST_32  H5    N5   C4   C3    180.00   0.0  0
 AZ5  CONST_33  H21   C21  C20  C19   180.00   0.0  0
 AZ5  CONST_34  H19   C19  C20  C21   180.00   0.0  0
 AZ5  CONST_35  H10   C10  C9   C8    180.00   0.0  0
 AZ5  CONST_36  H3    C3   C4   N5    180.00   0.0  0
 AZ5  CONST_37  N11   C12  N14  C15     0.00   0.0  0
 AZ5  CONST_38  N13   C12  N14  C15   180.00   0.0  0
 AZ5  CONST_39  H14   N14  C12  N11   180.00   0.0  0
 AZ5  Var_01    C8    N7   C4   C3     -4.36  30.0  2
 AZ5  Var_02    C4    N7   C8   C9   -179.34  30.0  2
 AZ5  Var_03    H11C  C1   C2   C3     63.15  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AZ5  chir_01  C15  C17  C16  N14  positiv

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
 AZ5  plan-1  C3   0.020
 AZ5  plan-1  C2   0.020
 AZ5  plan-1  C4   0.020
 AZ5  plan-1  C1   0.020
 AZ5  plan-1  N5   0.020
 AZ5  plan-1  N6   0.020
 AZ5  plan-1  N7   0.020
 AZ5  plan-1  H3   0.020
 AZ5  plan-1  H5   0.020
 AZ5  plan-2  C19  0.020
 AZ5  plan-2  C21  0.020
 AZ5  plan-2  C20  0.020
 AZ5  plan-2  C17  0.020
 AZ5  plan-2  C15  0.020
 AZ5  plan-2  N18  0.020
 AZ5  plan-2  N22  0.020
 AZ5  plan-2  H19  0.020
 AZ5  plan-2  H21  0.020
 AZ5  plan-2  F23  0.020
 AZ5  plan-3  C10  0.020
 AZ5  plan-3  C9   0.020
 AZ5  plan-3  C8   0.020
 AZ5  plan-3  C12  0.020
 AZ5  plan-3  N11  0.020
 AZ5  plan-3  N13  0.020
 AZ5  plan-3  N7   0.020
 AZ5  plan-3  N14  0.020
 AZ5  plan-3  H10  0.020
 AZ5  plan-3  CL2  0.020
 AZ5  plan-4  C12  0.020
 AZ5  plan-4  C15  0.020
 AZ5  plan-4  N14  0.020
 AZ5  plan-4  H14  0.020

