# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:45:55 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CCc1ccc(Nc2nccc(Nc3cc([nH]n3)C4CC4)n2)cc1
#
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
 REB  REB  '[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile'  ligand  42  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_REB
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
 REB  C10   C  CR15  0  -0.545   3.3384   0.4424  -0.0242
 REB  N12   N  NR15  0  -0.522   5.4976   0.1761  -0.1167
 REB  C15   C  CH2   0  -0.476   5.8957   3.0981  -1.1091
 REB  C20   C  CR16  0  -0.269  -4.1951   1.9615   0.3677
 REB  C21   C  CR6   0   0.089  -5.2157   1.0162   0.4056
 REB  C22   C  CR16  0  -0.279  -4.8654  -0.3259   0.4006
 REB  C24   C  CH2   0  -0.628  -6.6638   1.4411   0.4350
 REB  C02   C  CR16  0  -0.459   1.0143  -3.4588   0.3605
 REB  C03   C  CR16  0   0.001  -0.3514  -3.4880   0.4380
 REB  N04   N  N     0  -0.496  -1.1234  -2.3961   0.4126
 REB  C05   C  CR6   0   0.616  -0.4745  -1.2479   0.3064
 REB  N06   N  N     0  -0.528   0.8496  -1.0880   0.2237
 REB  C07   C  CR6   0   0.565   1.5973  -2.1779   0.2493
 REB  N08   N  NH1   0  -0.755   2.9423  -2.0642   0.1683
 REB  C09   C  CR5   0   0.452   3.7090  -0.9156   0.0507
 REB  C11   C  CR5   0   0.494   4.5390   1.1164  -0.1325
 REB  N13   N  N     0  -0.327   5.0185  -1.0676  -0.0063
 REB  C14   C  CH1   0  -0.370   4.7844   2.5596  -0.2475
 REB  C16   C  CH2   0  -0.476   5.9957   3.2012   0.3755
 REB  C18   C  CR6   0   0.360  -2.5179   0.2147   0.3234
 REB  C19   C  CR16  0  -0.344  -2.8713   1.5710   0.3274
 REB  C23   C  CR16  0  -0.300  -3.5399  -0.7365   0.3627
 REB  C25   C  CSP   0   0.138  -7.1488   1.7711  -0.8990
 REB  N26   N  NS    0  -0.277  -7.5177   2.0208  -1.9599
 REB  H10   H  HCR5  0   0.273   2.3533   0.8684  -0.0032
 REB  H15   H  HCH2  0   0.257   6.5320   2.3869  -1.6212
 REB  H15A  H  HCH2  0   0.266   5.6901   3.9965  -1.6757
 REB  H20   H  HCR6  0   0.261  -4.4299   3.0193   0.3737
 REB  H22   H  HCR6  0   0.259  -5.6395  -1.0833   0.4282
 REB  H24   H  HCH2  0   0.328  -7.2989   0.6487   0.8350
 REB  H24A  H  HCH2  0   0.328  -6.8102   2.3149   1.0731
 REB  H02   H  HCR6  0   0.279   1.6078  -4.3616   0.3835
 REB  H03   H  HCR6  0   0.269  -0.8701  -4.4359   0.5272
 REB  HN08  H  HNH1  0   0.411   3.4709  -2.9230   0.1929
 REB  H14   H  HCH1  0   0.276   3.8730   3.1436  -0.2274
 REB  H16   H  HCH2  0   0.257   6.7020   2.5615   0.8901
 REB  H16A  H  HCH2  0   0.266   5.8590   4.1710   0.8354
 REB  HN17  H  HNH1  0   0.409  -0.5553   0.7348   0.2092
 REB  H19   H  HCR6  0   0.271  -2.0964   2.3281   0.3034
 REB  H23   H  HCR6  0   0.286  -3.3060  -1.7880   0.3659
 REB  HN12  H  HNR5  0   0.417   6.4944   0.3065  -0.1774
 REB  N17   N  NH1   0  -0.772  -1.1613  -0.0687   0.2757

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
 REB  C10  C11   aromatic  1.381  0.020  1.381
 REB  C10  C09   aromatic  1.410  0.020  1.410
 REB  C10  H10   single    0.930  0.020  1.080
 REB  C11  N12   aromatic  1.343  0.020  1.343
 REB  N12  N13   aromatic  1.337  0.020  1.337
 REB  C15  C16   single    1.491  0.020  1.491
 REB  C15  C14   single    1.506  0.020  1.506
 REB  C15  H15   single    0.970  0.020  1.090
 REB  C15  H15A  single    0.970  0.020  1.090
 REB  C20  C21   aromatic  1.392  0.020  1.392
 REB  C20  C19   aromatic  1.381  0.020  1.381
 REB  C20  H20   single    0.930  0.020  1.080
 REB  C24  C21   single    1.509  0.020  1.509
 REB  C21  C22   aromatic  1.387  0.020  1.387
 REB  C22  C23   aromatic  1.388  0.020  1.388
 REB  C22  H22   single    0.930  0.020  1.080
 REB  C24  C25   single    1.457  0.020  1.457
 REB  C24  H24   single    0.970  0.020  1.090
 REB  C24  H24A  single    0.970  0.020  1.090
 REB  C03  C02   aromatic  1.368  0.020  1.368
 REB  C07  C02   aromatic  1.412  0.020  1.412
 REB  C02  H02   single    0.930  0.020  1.080
 REB  N04  C03   aromatic  1.337  0.020  1.337
 REB  C03  H03   single    0.930  0.020  1.080
 REB  C05  N04   aromatic  1.323  0.020  1.323
 REB  N17  C05   single    1.365  0.020  1.365
 REB  C05  N06   aromatic  1.336  0.020  1.336
 REB  N06  C07   aromatic  1.322  0.020  1.322
 REB  C07  N08   single    1.352  0.020  1.352
 REB  C09  N08   single    1.386  0.020  1.386
 REB  N08  HN08  single    0.860  0.020  1.020
 REB  C09  N13   aromatic  1.320  0.020  1.320
 REB  C14  C11   single    1.468  0.020  1.468
 REB  C16  C14   single    1.506  0.020  1.506
 REB  C14  H14   single    0.970  0.020  1.090
 REB  C16  H16   single    0.970  0.020  1.090
 REB  C16  H16A  single    0.970  0.020  1.090
 REB  C18  N17   single    1.387  0.020  1.387
 REB  N17  HN17  single    0.860  0.020  1.020
 REB  C19  C18   aromatic  1.402  0.020  1.402
 REB  C18  C23   aromatic  1.397  0.020  1.397
 REB  C19  H19   single    0.930  0.020  1.080
 REB  C23  H23   single    0.930  0.020  1.080
 REB  C25  N26   triple    1.151  0.020  1.151
 REB  N12  HN12  single    0.860  0.020  1.020

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
 REB  H10   C10  C11  127.27  3.000
 REB  H10   C10  C09  128.50  3.000
 REB  C11   C10  C09  104.23  3.000
 REB  HN12  N12  N13  118.69  3.000
 REB  HN12  N12  C11  127.96  3.000
 REB  N13   N12  C11  113.35  3.000
 REB  H15A  C15  H15  114.16  3.000
 REB  H15A  C15  C16  118.47  3.000
 REB  H15   C15  C16  118.46  3.000
 REB  H15A  C15  C14  117.15  3.000
 REB  H15   C15  C14  117.99  3.000
 REB  C16   C15  C14   60.31  3.000
 REB  H20   C20  C19  118.95  3.000
 REB  H20   C20  C21  120.28  3.000
 REB  C19   C20  C21  120.78  3.000
 REB  C24   C21  C22  120.98  3.000
 REB  C22   C21  C20  118.16  3.000
 REB  C24   C21  C20  120.85  3.000
 REB  H22   C22  C23  118.44  3.000
 REB  H22   C22  C21  119.73  3.000
 REB  C23   C22  C21  121.83  3.000
 REB  H24A  C24  H24  106.79  3.000
 REB  H24A  C24  C25  108.00  3.000
 REB  H24   C24  C25  107.83  3.000
 REB  H24A  C24  C21  111.43  3.000
 REB  H24   C24  C21  111.16  3.000
 REB  C25   C24  C21  111.42  3.000
 REB  H02   C02  C07  122.19  3.000
 REB  H02   C02  C03  121.95  3.000
 REB  C07   C02  C03  115.86  3.000
 REB  H03   C03  N04  116.05  3.000
 REB  H03   C03  C02  120.06  3.000
 REB  N04   C03  C02  123.89  3.000
 REB  C05   N04  C03  115.27  3.000
 REB  N17   C05  N06  113.19  3.000
 REB  N06   C05  N04  126.50  3.000
 REB  N17   C05  N04  120.31  3.000
 REB  C07   N06  C05  117.42  3.000
 REB  N08   C07  N06  119.48  3.000
 REB  N08   C07  C02  119.46  3.000
 REB  N06   C07  C02  121.06  3.000
 REB  HN08  N08  C09  114.69  3.000
 REB  HN08  N08  C07  116.63  3.000
 REB  C09   N08  C07  128.68  3.000
 REB  N13   C09  N08  117.21  3.000
 REB  N13   C09  C10  111.69  3.000
 REB  N08   C09  C10  131.11  3.000
 REB  C14   C11  N12  124.74  3.000
 REB  C14   C11  C10  129.13  3.000
 REB  N12   C11  C10  106.13  3.000
 REB  C09   N13  N12  104.59  3.000
 REB  H14   C14  C16  116.08  3.000
 REB  H14   C14  C11  112.83  3.000
 REB  C16   C14  C11  121.39  3.000
 REB  H14   C14  C15  116.04  3.000
 REB  C16   C14  C15   59.38  3.000
 REB  C11   C14  C15  121.31  3.000
 REB  H16A  C16  H16  114.20  3.000
 REB  H16A  C16  C14  117.14  3.000
 REB  H16   C16  C14  118.01  3.000
 REB  H16A  C16  C15  118.46  3.000
 REB  H16   C16  C15  118.42  3.000
 REB  C14   C16  C15   60.31  3.000
 REB  C23   C18  C19  118.32  3.000
 REB  C23   C18  N17  125.28  3.000
 REB  C19   C18  N17  116.39  3.000
 REB  H19   C19  C18  119.71  3.000
 REB  H19   C19  C20  119.25  3.000
 REB  C18   C19  C20  121.03  3.000
 REB  H23   C23  C18  120.40  3.000
 REB  H23   C23  C22  119.73  3.000
 REB  C18   C23  C22  119.87  3.000
 REB  N26   C25  C24  180.00  3.000
 REB  HN17  N17  C18  115.29  3.000
 REB  HN17  N17  C05  112.79  3.000
 REB  C18   N17  C05  131.92  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
 REB  CONST_01  N13   N12  C11  C10     0.00   0.0  0
 REB  CONST_02  N12   N13  C09  C10     0.00   0.0  0
 REB  CONST_03  C09   C10  C11  N12     0.00   0.0  0
 REB  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 REB  CONST_05  C23   C18  C19  C20     0.00   0.0  0
 REB  CONST_06  C18   C19  C20  C21     0.00   0.0  0
 REB  CONST_07  C18   C23  C22  C21     0.00   0.0  0
 REB  CONST_08  C19   C20  C21  C22     0.00   0.0  0
 REB  CONST_09  C19   C18  C23  C22     0.00   0.0  0
 REB  CONST_10  C05   N04  C03  C02     0.00   0.0  0
 REB  CONST_11  C05   N06  C07  C02     0.00   0.0  0
 REB  CONST_12  N06   C07  C02  C03     0.00   0.0  0
 REB  CONST_13  N06   C05  N04  C03     0.00   0.0  0
 REB  CONST_14  C07   C02  C03  N04     0.00   0.0  0
 REB  CONST_15  C07   N06  C05  N04     0.00   0.0  0
 REB  CONST_16  C11   N12  N13  C09     0.00   0.0  0
 REB  CONST_17  N13   C09  C10  C11     0.00   0.0  0
 REB  CONST_18  C14   C11  C10  C09   180.00   0.0  0
 REB  CONST_19  C14   C11  N12  N13   180.00   0.0  0
 REB  CONST_20  N08   C09  N13  N12   180.00   0.0  0
 REB  CONST_21  N17   C18  C19  C20   180.00   0.0  0
 REB  CONST_22  N17   C18  C23  C22   180.00   0.0  0
 REB  CONST_23  C19   C20  C21  C24   180.00   0.0  0
 REB  CONST_24  C23   C22  C21  C24   180.00   0.0  0
 REB  CONST_25  N08   C07  C02  C03   180.00   0.0  0
 REB  CONST_26  N17   C05  N04  C03   180.00   0.0  0
 REB  CONST_27  N08   C07  N06  C05   180.00   0.0  0
 REB  CONST_28  N17   C05  N06  C07   180.00   0.0  0
 REB  CONST_29  C11   C10  C09  N08   180.00   0.0  0
 REB  CONST_30  HN12  N12  C11  C10   180.00   0.0  0
 REB  CONST_31  H10   C10  C11  N12   180.00   0.0  0
 REB  CONST_32  H22   C22  C21  C20   180.00   0.0  0
 REB  CONST_33  H19   C19  C20  C21   180.00   0.0  0
 REB  CONST_34  H23   C23  C22  C21   180.00   0.0  0
 REB  CONST_35  H20   C20  C21  C22   180.00   0.0  0
 REB  CONST_36  H02   C02  C03  N04   180.00   0.0  0
 REB  CONST_37  H03   C03  N04  C05   180.00   0.0  0
 REB  Var_01    C15   C14  C11  C10  -143.54  30.0  1
 REB  Var_02    C11   C14  C16  C15   110.26  30.0  1
 REB  Var_03    C07   N08  C09  C10    -0.29  30.0  2
 REB  Var_04    C09   N08  C07  C02   179.76  30.0  2
 REB  Var_05    C18   N17  C05  N04    -0.77  30.0  1
 REB  Var_06    C19   C18  N17  C05   177.29  30.0  3
 REB  Var_07    C25   C24  C21  C20    81.22  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
 REB  chir_01  C14  C15  C11  C16  both

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
 REB  plan-1  C10   0.020
 REB  plan-1  N12   0.020
 REB  plan-1  N08   0.020
 REB  plan-1  C09   0.020
 REB  plan-1  C11   0.020
 REB  plan-1  N13   0.020
 REB  plan-1  C14   0.020
 REB  plan-1  H10   0.020
 REB  plan-1  HN12  0.020
 REB  plan-2  C20   0.020
 REB  plan-2  C21   0.020
 REB  plan-2  C22   0.020
 REB  plan-2  C24   0.020
 REB  plan-2  C18   0.020
 REB  plan-2  C19   0.020
 REB  plan-2  C23   0.020
 REB  plan-2  H20   0.020
 REB  plan-2  H22   0.020
 REB  plan-2  H19   0.020
 REB  plan-2  H23   0.020
 REB  plan-2  N17   0.020
 REB  plan-3  C02   0.020
 REB  plan-3  C03   0.020
 REB  plan-3  N04   0.020
 REB  plan-3  C05   0.020
 REB  plan-3  N06   0.020
 REB  plan-3  C07   0.020
 REB  plan-3  N08   0.020
 REB  plan-3  H02   0.020
 REB  plan-3  H03   0.020
 REB  plan-3  N17   0.020

