# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 07:35:21 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 5-chloro-N~2~-[(1S)-1-(5-fluoropyridin-2-yl)ethyl]-N~4~-[3-(propan-2-yloxy)-1H-pyrazol-5-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1cc([nH]n1)Nc2nc(N[C@@H](C)c3ccc(F)cn3)ncc2Cl
#
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
 V4Z  V4Z  5-chloro-N~2~-[(1S)-1-(5-fluoropyridin-2-yl)ethyl]-N~4~-[3-(propan-2-yloxy)-1H-pyrazol-5-yl]pyrimidine-2,4-diamine  ligand  46  27  .  2022-07-22  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_V4Z
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
 V4Z  C1    C   CH3   0  -0.670   2.9607   5.9155  -0.6984
 V4Z  C2    C   CH1   0   0.010   3.6218   4.6832  -0.1166
 V4Z  C3    C   CH3   0  -0.676   4.1111   4.9107   1.3031
 V4Z  O1    O   O2    0  -0.491   2.6360   3.6399  -0.1504
 V4Z  C4    C   CR5   0   0.512   3.0539   2.3726  -0.1282
 V4Z  C5    C   CR15  0  -0.585   2.1733   1.2699  -0.1122
 V4Z  C6    C   CR5   0   0.661   3.0273   0.1847  -0.1199
 V4Z  N1    N   NH1   0  -0.767   2.8390  -1.1793  -0.1327
 V4Z  C7    C   CR6   0   0.640   1.6583  -1.8408  -0.0442
 V4Z  N2    N   N     0  -0.514   0.5412  -1.1581   0.0957
 V4Z  C8    C   CR6   0   0.627  -0.6097  -1.8383   0.1810
 V4Z  N3    N   NH1   0  -0.667  -1.7210  -1.0992   0.3163
 V4Z  C9    C   CH1   0  -0.117  -3.0433  -1.6428   0.5068
 V4Z  C10   C   CH3   0  -0.655  -3.2683  -2.1383   1.9381
 V4Z  C11   C   CR6   0   0.256  -4.0649  -0.5825   0.1638
 V4Z  C12   C   CR16  0  -0.309  -5.3444  -0.9441  -0.2467
 V4Z  C13   C   CR16  0  -0.297  -6.2794   0.0446  -0.4959
 V4Z  C14   C   CR6   0   0.429  -5.8805   1.3548  -0.3212
 V4Z  F1    F   F     0  -0.301  -6.7407   2.3542  -0.5484
 V4Z  C15   C   CR16  0  -0.204  -4.5927   1.6458   0.0822
 V4Z  N4    N   N     0  -0.428  -3.7101   0.6849   0.3202
 V4Z  N5    N   N     0  -0.489  -0.7330  -3.1666   0.1310
 V4Z  C16   C   CR16  0   0.020   0.3954  -3.8484  -0.0120
 V4Z  C17   C   CR6   0  -0.259   1.6282  -3.2505  -0.1024
 V4Z  CL1   CL  CL    0  -0.119   3.0701  -4.1859  -0.2819
 V4Z  N6    N   NR15  0  -0.539   4.2807   0.6713  -0.1357
 V4Z  N7    N   N     0  -0.330   4.3167   2.0178  -0.1374
 V4Z  H11C  H   HCH3  0   0.233   3.6709   6.7421  -0.7127
 V4Z  H12C  H   HCH3  0   0.238   2.6282   5.7451  -1.7227
 V4Z  H13C  H   HCH3  0   0.228   2.1007   6.2242  -0.1013
 V4Z  H2    H   HCH1  0   0.227   4.4660   4.3949  -0.7502
 V4Z  H31C  H   HCH3  0   0.233   4.8729   5.6908   1.3115
 V4Z  H32C  H   HCH3  0   0.225   3.2931   5.2337   1.9499
 V4Z  H33C  H   HCH3  0   0.240   4.5557   4.0106   1.7262
 V4Z  H5    H   HCR5  0   0.276   1.1001   1.2730  -0.1016
 V4Z  H1    H   HNH1  0   0.416   3.6703  -1.7437  -0.2281
 V4Z  H6    H   HNR5  0   0.418   5.1431   0.1516  -0.1152
 V4Z  H3    H   HNH1  0   0.396  -1.6135  -0.1011   0.4188
 V4Z  H9    H   HCH1  0   0.265  -3.1752  -2.4844  -0.1767
 V4Z  H101  H   HCH3  0   0.230  -3.1594  -1.3190   2.6497
 V4Z  H102  H   HCH3  0   0.237  -4.2683  -2.5586   2.0495
 V4Z  H103  H   HCH3  0   0.245  -2.5465  -2.9154   2.1864
 V4Z  H12   H   HCR6  0   0.282  -5.6064  -1.9860  -0.3737
 V4Z  H13   H   HCR6  0   0.301  -7.2826  -0.1968  -0.8215
 V4Z  H15   H   HCR6  0   0.287  -4.2704   2.6728   0.2140
 V4Z  H16   H   HCR6  0   0.286   0.3149  -4.9293  -0.0560

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
 V4Z  C1   C2    single    1.515  0.020  1.515
 V4Z  C2   C3    single    1.519  0.020  1.519
 V4Z  C2   O1    single    1.436  0.020  1.436
 V4Z  O1   C4    single    1.335  0.020  1.335
 V4Z  C4   C5    aromatic  1.411  0.020  1.411
 V4Z  C4   N7    aromatic  1.312  0.020  1.312
 V4Z  C5   C6    aromatic  1.381  0.020  1.381
 V4Z  C6   N1    single    1.377  0.020  1.377
 V4Z  C6   N6    aromatic  1.345  0.020  1.345
 V4Z  N1   C7    single    1.356  0.020  1.356
 V4Z  C7   N2    aromatic  1.317  0.020  1.317
 V4Z  C7   C17   aromatic  1.411  0.020  1.411
 V4Z  N2   C8    aromatic  1.340  0.020  1.340
 V4Z  C8   N3    single    1.341  0.020  1.341
 V4Z  C8   N5    aromatic  1.335  0.020  1.335
 V4Z  N3   C9    single    1.442  0.020  1.442
 V4Z  C9   C10   single    1.531  0.020  1.531
 V4Z  C9   C11   single    1.512  0.020  1.512
 V4Z  C11  C12   aromatic  1.392  0.020  1.392
 V4Z  C11  N4    aromatic  1.325  0.020  1.325
 V4Z  C12  C13   aromatic  1.383  0.020  1.383
 V4Z  C13  C14   aromatic  1.381  0.020  1.381
 V4Z  C14  F1    single    1.338  0.020  1.338
 V4Z  C14  C15   aromatic  1.381  0.020  1.381
 V4Z  C15  N4    aromatic  1.326  0.020  1.326
 V4Z  N5   C16   aromatic  1.326  0.020  1.326
 V4Z  C16  C17   aromatic  1.373  0.020  1.373
 V4Z  C17  CL1   single    1.728  0.020  1.728
 V4Z  N6   N7    aromatic  1.347  0.020  1.347
 V4Z  C1   H11C  single    0.970  0.020  1.090
 V4Z  C1   H12C  single    0.970  0.020  1.090
 V4Z  C1   H13C  single    0.970  0.020  1.090
 V4Z  C2   H2    single    0.970  0.020  1.090
 V4Z  C3   H31C  single    0.970  0.020  1.090
 V4Z  C3   H32C  single    0.970  0.020  1.090
 V4Z  C3   H33C  single    0.970  0.020  1.090
 V4Z  C5   H5    single    0.930  0.020  1.080
 V4Z  N1   H1    single    0.860  0.020  1.020
 V4Z  N6   H6    single    0.860  0.020  1.020
 V4Z  N3   H3    single    0.860  0.020  1.020
 V4Z  C9   H9    single    0.970  0.020  1.090
 V4Z  C10  H101  single    0.970  0.020  1.090
 V4Z  C10  H102  single    0.970  0.020  1.090
 V4Z  C10  H103  single    0.970  0.020  1.090
 V4Z  C12  H12   single    0.930  0.020  1.080
 V4Z  C13  H13   single    0.930  0.020  1.080
 V4Z  C15  H15   single    0.930  0.020  1.080
 V4Z  C16  H16   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
 V4Z  H13C  C1   H12C  108.53  3.000
 V4Z  H13C  C1   H11C  107.83  3.000
 V4Z  H12C  C1   H11C  107.75  3.000
 V4Z  H13C  C1   C2    111.34  3.000
 V4Z  H12C  C1   C2    111.52  3.000
 V4Z  H11C  C1   C2    109.73  3.000
 V4Z  H2    C2   O1    108.95  3.000
 V4Z  H2    C2   C3    109.40  3.000
 V4Z  O1    C2   C3    110.61  3.000
 V4Z  H2    C2   C1    109.19  3.000
 V4Z  O1    C2   C1    106.41  3.000
 V4Z  C3    C2   C1    112.20  3.000
 V4Z  H33C  C3   H32C  108.68  3.000
 V4Z  H33C  C3   H31C  107.64  3.000
 V4Z  H32C  C3   H31C  107.89  3.000
 V4Z  H33C  C3   C2    111.76  3.000
 V4Z  H32C  C3   C2    110.90  3.000
 V4Z  H31C  C3   C2    109.84  3.000
 V4Z  C4    O1   C2    118.33  3.000
 V4Z  N7    C4   C5    112.92  3.000
 V4Z  N7    C4   O1    123.93  3.000
 V4Z  C5    C4   O1    123.15  3.000
 V4Z  H5    C5   C6    128.37  3.000
 V4Z  H5    C5   C4    128.44  3.000
 V4Z  C6    C5   C4    103.18  3.000
 V4Z  N6    C6   N1    119.07  3.000
 V4Z  N6    C6   C5    106.99  3.000
 V4Z  N1    C6   C5    133.94  3.000
 V4Z  H1    N1   C7    116.77  3.000
 V4Z  H1    N1   C6    116.24  3.000
 V4Z  C7    N1   C6    126.98  3.000
 V4Z  C17   C7   N2    120.28  3.000
 V4Z  C17   C7   N1    120.21  3.000
 V4Z  N2    C7   N1    119.51  3.000
 V4Z  C8    N2   C7    118.19  3.000
 V4Z  N5    C8   N3    118.39  3.000
 V4Z  N5    C8   N2    125.61  3.000
 V4Z  N3    C8   N2    116.00  3.000
 V4Z  H3    N3   C9    117.19  3.000
 V4Z  H3    N3   C8    117.84  3.000
 V4Z  C9    N3   C8    124.41  3.000
 V4Z  H9    C9   C11   108.47  3.000
 V4Z  H9    C9   C10   108.53  3.000
 V4Z  C11   C9   C10   109.86  3.000
 V4Z  H9    C9   N3    108.57  3.000
 V4Z  C11   C9   N3    108.98  3.000
 V4Z  C10   C9   N3    112.34  3.000
 V4Z  H103  C10  H102  108.02  3.000
 V4Z  H103  C10  H101  108.72  3.000
 V4Z  H102  C10  H101  108.33  3.000
 V4Z  H103  C10  C9    110.28  3.000
 V4Z  H102  C10  C9    110.79  3.000
 V4Z  H101  C10  C9    110.61  3.000
 V4Z  N4    C11  C12   121.97  3.000
 V4Z  N4    C11  C9    117.58  3.000
 V4Z  C12   C11  C9    120.40  3.000
 V4Z  H12   C12  C13   120.23  3.000
 V4Z  H12   C12  C11   120.51  3.000
 V4Z  C13   C12  C11   119.26  3.000
 V4Z  H13   C13  C14   121.18  3.000
 V4Z  H13   C13  C12   121.42  3.000
 V4Z  C14   C13  C12   117.40  3.000
 V4Z  C15   C14  F1    119.46  3.000
 V4Z  C15   C14  C13   120.44  3.000
 V4Z  F1    C14  C13   120.10  3.000
 V4Z  H15   C15  N4    117.81  3.000
 V4Z  H15   C15  C14   120.83  3.000
 V4Z  N4    C15  C14   121.36  3.000
 V4Z  C15   N4   C11   119.57  3.000
 V4Z  C16   N5   C8    115.91  3.000
 V4Z  H16   C16  C17   119.86  3.000
 V4Z  H16   C16  N5    116.97  3.000
 V4Z  C17   C16  N5    123.17  3.000
 V4Z  CL1   C17  C16   121.35  3.000
 V4Z  CL1   C17  C7    121.82  3.000
 V4Z  C16   C17  C7    116.83  3.000
 V4Z  H6    N6   N7    119.54  3.000
 V4Z  H6    N6   C6    127.68  3.000
 V4Z  N7    N6   C6    112.75  3.000
 V4Z  N6    N7   C4    104.16  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
 V4Z  CONST_01  N6    C6   C5   C4     0.00   0.0  0
 V4Z  CONST_02  C6    N6   N7   C4     0.00   0.0  0
 V4Z  CONST_03  N6    N7   C4   C5     0.00   0.0  0
 V4Z  CONST_04  N7    N6   C6   C5     0.00   0.0  0
 V4Z  CONST_05  N7    C4   C5   C6     0.00   0.0  0
 V4Z  CONST_06  N5    C8   N2   C7     0.00   0.0  0
 V4Z  CONST_07  N5    C16  C17  C7     0.00   0.0  0
 V4Z  CONST_08  C16   C17  C7   N2     0.00   0.0  0
 V4Z  CONST_09  C16   N5   C8   N2     0.00   0.0  0
 V4Z  CONST_10  C17   C7   N2   C8     0.00   0.0  0
 V4Z  CONST_11  C17   C16  N5   C8     0.00   0.0  0
 V4Z  CONST_12  C14   C13  C12  C11    0.00   0.0  0
 V4Z  CONST_13  C14   C15  N4   C11    0.00   0.0  0
 V4Z  CONST_14  C15   N4   C11  C12    0.00   0.0  0
 V4Z  CONST_15  C15   C14  C13  C12    0.00   0.0  0
 V4Z  CONST_16  N4    C11  C12  C13    0.00   0.0  0
 V4Z  CONST_17  N4    C15  C14  C13    0.00   0.0  0
 V4Z  CONST_18  C6    C5   C4   O1   180.00   0.0  0
 V4Z  CONST_19  N6    N7   C4   O1   180.00   0.0  0
 V4Z  CONST_20  N1    C6   C5   C4   180.00   0.0  0
 V4Z  CONST_21  N7    N6   C6   N1   180.00   0.0  0
 V4Z  CONST_22  C8    N2   C7   N1   180.00   0.0  0
 V4Z  CONST_23  C16   C17  C7   N1   180.00   0.0  0
 V4Z  CONST_24  N3    C8   N2   C7   180.00   0.0  0
 V4Z  CONST_25  CL1   C17  C7   N2   180.00   0.0  0
 V4Z  CONST_26  C16   N5   C8   N3   180.00   0.0  0
 V4Z  CONST_27  C13   C12  C11  C9   180.00   0.0  0
 V4Z  CONST_28  C15   N4   C11  C9   180.00   0.0  0
 V4Z  CONST_29  F1    C14  C13  C12  180.00   0.0  0
 V4Z  CONST_30  N4    C15  C14  F1   180.00   0.0  0
 V4Z  CONST_31  CL1   C17  C16  N5   180.00   0.0  0
 V4Z  CONST_32  H6    N6   N7   C4   180.00   0.0  0
 V4Z  CONST_33  H16   C16  C17  C7   180.00   0.0  0
 V4Z  CONST_34  H13   C13  C12  C11  180.00   0.0  0
 V4Z  CONST_35  H15   C15  N4   C11  180.00   0.0  0
 V4Z  CONST_36  H12   C12  C13  C14  180.00   0.0  0
 V4Z  CONST_37  H5    C5   C6   N6   180.00   0.0  0
 V4Z  CONST_38  C9    N3   C8   N2   180.00   0.0  0
 V4Z  CONST_39  N5    C8   N3   C9     0.00   0.0  0
 V4Z  CONST_40  H3    N3   C8   N2     0.00   0.0  0
 V4Z  Var_01    C7    N1   C6   C5    -5.15  30.0  2
 V4Z  Var_02    N2    C7   N1   C6    -1.42  30.0  2
 V4Z  Var_03    C5    C4   O1   C2   177.80  30.0  2
 V4Z  Var_04    H2    C2   O1   C4    40.16  30.0  2
 V4Z  Var_05    H31C  C3   C2   C1   -62.48  30.0  3
 V4Z  Var_06    H11C  C1   C2   C3    59.77  30.0  3

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
 V4Z  chir_01  C9  N3  C10  C11  negativ

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
 V4Z  plan-1  O1   0.020
 V4Z  plan-1  C4   0.020
 V4Z  plan-1  C5   0.020
 V4Z  plan-1  C6   0.020
 V4Z  plan-1  N1   0.020
 V4Z  plan-1  N6   0.020
 V4Z  plan-1  N7   0.020
 V4Z  plan-1  H5   0.020
 V4Z  plan-1  H6   0.020
 V4Z  plan-2  N1   0.020
 V4Z  plan-2  C7   0.020
 V4Z  plan-2  N2   0.020
 V4Z  plan-2  C8   0.020
 V4Z  plan-2  N3   0.020
 V4Z  plan-2  N5   0.020
 V4Z  plan-2  C16  0.020
 V4Z  plan-2  C17  0.020
 V4Z  plan-2  CL1  0.020
 V4Z  plan-2  H16  0.020
 V4Z  plan-3  C9   0.020
 V4Z  plan-3  C11  0.020
 V4Z  plan-3  C12  0.020
 V4Z  plan-3  C13  0.020
 V4Z  plan-3  C14  0.020
 V4Z  plan-3  F1   0.020
 V4Z  plan-3  C15  0.020
 V4Z  plan-3  N4   0.020
 V4Z  plan-3  H12  0.020
 V4Z  plan-3  H13  0.020
 V4Z  plan-3  H15  0.020
 V4Z  plan-4  C8   0.020
 V4Z  plan-4  N3   0.020
 V4Z  plan-4  C9   0.020
 V4Z  plan-4  H3   0.020

