# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:42:22 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N~2~-(4-aminophenyl)-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(Nc2nc(Nc3cc([nH]n3)C4CC4)c5ccccc5n2)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
 3RF  3RF  N~2~-(4-aminophenyl)-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)quinazoline-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_3RF
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
 3RF  C13   C  CR16  0  -0.309   0.6016   4.0220   0.1221
 3RF  C15   C  CR16  0  -0.245  -1.6101   4.9570   0.1600
 3RF  C17   C  CR6   0   0.543   0.8179   1.5024   0.0592
 3RF  C22   C  CR5   0   0.492   4.1755  -1.3893   0.0042
 3RF  C24   C  CH2   0  -0.477   5.9648  -3.1706   0.5946
 3RF  C26   C  CR15  0  -0.539   2.8946  -0.8783   0.0861
 3RF  C02   C  CR6   0   0.276  -5.4915  -2.6442   0.0517
 3RF  C03   C  CR16  0  -0.312  -5.3292  -1.2585   0.0432
 3RF  C04   C  CR16  0  -0.310  -4.0747  -0.6647   0.0459
 3RF  C05   C  CR16  0  -0.311  -4.3309  -3.4243   0.0598
 3RF  C06   C  CR16  0  -0.347  -3.0795  -2.8379   0.0626
 3RF  C07   C  CR6   0   0.329  -2.9208  -1.4490   0.0564
 3RF  C09   C  CR6   0   0.588  -1.1235   0.3023   0.0672
 3RF  N10   N  N     0  -0.536  -1.9299   1.3325   0.0902
 3RF  C11   C  CR66  0   0.286  -1.3449   2.5555   0.1063
 3RF  C12   C  CR66  0  -0.060   0.0548   2.7284   0.0952
 3RF  C14   C  CR16  0  -0.266  -0.2166   5.1251   0.1538
 3RF  C16   C  CR16  0  -0.322  -2.1650   3.7021   0.1373
 3RF  N18   N  NH1   0  -0.757   2.1643   1.5634   0.0326
 3RF  C19   C  CR5   0   0.456   3.0736   0.5159  -0.0051
 3RF  N20   N  N     0  -0.325   4.3466   0.8382  -0.1327
 3RF  N21   N  NR15  0  -0.520   4.9922  -0.3309  -0.1236
 3RF  C23   C  CH1   0  -0.370   4.6197  -2.7884   0.0384
 3RF  C25   C  CH2   0  -0.474   5.7133  -3.2847  -0.8711
 3RF  N27   N  N     0  -0.530   0.2304   0.3357   0.0508
 3RF  H131  H  HCR6  0   0.254   1.6732   4.1795   0.1224
 3RF  H151  H  HCR6  0   0.264  -2.2540   5.8266   0.1848
 3RF  H241  H  HCH2  0   0.255   6.6162  -2.3785   0.9440
 3RF  H242  H  HCH2  0   0.268   6.0194  -4.0768   1.1833
 3RF  H261  H  HCR5  0   0.275   1.9819  -1.4328   0.1959
 3RF  H011  H  HNH2  0   0.373  -7.4910  -2.6574  -0.2721
 3RF  H012  H  HNH2  0   0.373  -6.7972  -4.1627  -0.2573
 3RF  H031  H  HCR6  0   0.253  -6.2039  -0.6183   0.0339
 3RF  H041  H  HCR6  0   0.283  -3.9989   0.4104   0.0380
 3RF  H051  H  HCR6  0   0.256  -4.4067  -4.5054   0.0645
 3RF  H061  H  HCR6  0   0.262  -2.2045  -3.4783   0.0678
 3RF  H081  H  HNH1  0   0.405  -0.8903  -1.6695   0.0394
 3RF  H141  H  HCR6  0   0.263   0.2113   6.1180   0.1750
 3RF  H161  H  HCR6  0   0.258  -3.2389   3.5670   0.1445
 3RF  H181  H  HNH1  0   0.417   2.5949   2.4734   0.0029
 3RF  H211  H  HNR5  0   0.417   5.9957  -0.3289  -0.2082
 3RF  H231  H  HCH1  0   0.277   3.8088  -3.4814   0.2254
 3RF  H251  H  HCH2  0   0.258   6.1888  -2.5708  -1.5323
 3RF  H252  H  HCH2  0   0.266   5.5887  -4.2711  -1.2978
 3RF  N08   N  NH1   0  -0.773  -1.6109  -0.9646   0.0543
 3RF  N01   N  NH2   0  -0.861  -6.7495  -3.2246   0.1082

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
 3RF  C14  C15   aromatic  1.404  0.020  1.404
 3RF  C14  C13   aromatic  1.374  0.020  1.374
 3RF  C15  C16   aromatic  1.372  0.020  1.372
 3RF  C13  C12   aromatic  1.405  0.020  1.405
 3RF  C16  C11   aromatic  1.410  0.020  1.410
 3RF  C12  C11   aromatic  1.410  0.020  1.410
 3RF  C12  C17   aromatic  1.445  0.020  1.445
 3RF  C11  N10   aromatic  1.356  0.020  1.356
 3RF  N18  C17   single    1.348  0.020  1.348
 3RF  N18  C19   single    1.388  0.020  1.388
 3RF  C17  N27   aromatic  1.306  0.020  1.306
 3RF  N20  C19   aromatic  1.319  0.020  1.319
 3RF  N20  N21   aromatic  1.335  0.020  1.335
 3RF  N10  C09   aromatic  1.308  0.020  1.308
 3RF  C19  C26   aromatic  1.409  0.020  1.409
 3RF  N27  C09   aromatic  1.354  0.020  1.354
 3RF  N21  C22   aromatic  1.343  0.020  1.343
 3RF  C09  N08   single    1.357  0.020  1.357
 3RF  C26  C22   aromatic  1.381  0.020  1.381
 3RF  C22  C23   single    1.468  0.020  1.468
 3RF  N08  C07   single    1.397  0.020  1.397
 3RF  C06  C07   aromatic  1.398  0.020  1.398
 3RF  C06  C05   aromatic  1.382  0.020  1.382
 3RF  C23  C24   single    1.505  0.020  1.505
 3RF  C23  C25   single    1.506  0.020  1.506
 3RF  C07  C04   aromatic  1.395  0.020  1.395
 3RF  C24  C25   single    1.491  0.020  1.491
 3RF  C05  C02   aromatic  1.398  0.020  1.398
 3RF  C04  C03   aromatic  1.388  0.020  1.388
 3RF  C02  C03   aromatic  1.395  0.020  1.395
 3RF  C02  N01   single    1.387  0.020  1.387
 3RF  C13  H131  single    0.930  0.020  1.080
 3RF  C15  H151  single    0.930  0.020  1.080
 3RF  C24  H241  single    0.970  0.020  1.090
 3RF  C24  H242  single    0.970  0.020  1.090
 3RF  C26  H261  single    0.930  0.020  1.080
 3RF  N01  H011  single    0.890  0.020  1.040
 3RF  N01  H012  single    0.890  0.020  1.040
 3RF  C03  H031  single    0.930  0.020  1.080
 3RF  C04  H041  single    0.930  0.020  1.080
 3RF  C05  H051  single    0.930  0.020  1.080
 3RF  C06  H061  single    0.930  0.020  1.080
 3RF  N08  H081  single    0.860  0.020  1.020
 3RF  C14  H141  single    0.930  0.020  1.080
 3RF  C16  H161  single    0.930  0.020  1.080
 3RF  N18  H181  single    0.860  0.020  1.020
 3RF  N21  H211  single    0.860  0.020  1.020
 3RF  C23  H231  single    0.970  0.020  1.090
 3RF  C25  H251  single    0.970  0.020  1.090
 3RF  C25  H252  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
 3RF  H131  C13  C14   118.20  3.000
 3RF  H131  C13  C12   121.27  3.000
 3RF  C14   C13  C12   120.53  3.000
 3RF  H151  C15  C16   119.64  3.000
 3RF  H151  C15  C14   119.64  3.000
 3RF  C16   C15  C14   120.72  3.000
 3RF  N27   C17  N18   119.31  3.000
 3RF  N27   C17  C12   121.37  3.000
 3RF  N18   C17  C12   119.32  3.000
 3RF  C23   C22  N21   124.70  3.000
 3RF  C23   C22  C26   129.17  3.000
 3RF  N21   C22  C26   106.13  3.000
 3RF  H242  C24  H241  113.99  3.000
 3RF  H242  C24  C25   118.63  3.000
 3RF  H241  C24  C25   118.31  3.000
 3RF  H242  C24  C23   117.31  3.000
 3RF  H241  C24  C23   118.09  3.000
 3RF  C25   C24  C23    60.36  3.000
 3RF  H261  C26  C19   128.75  3.000
 3RF  H261  C26  C22   127.10  3.000
 3RF  C19   C26  C22   104.15  3.000
 3RF  C05   C02  C03   117.23  3.000
 3RF  C03   C02  N01   121.44  3.000
 3RF  C05   C02  N01   121.28  3.000
 3RF  H031  C03  C04   118.48  3.000
 3RF  H031  C03  C02   119.52  3.000
 3RF  C04   C03  C02   122.01  3.000
 3RF  H041  C04  C07   120.17  3.000
 3RF  H041  C04  C03   119.36  3.000
 3RF  C07   C04  C03   120.47  3.000
 3RF  H051  C05  C06   119.11  3.000
 3RF  H051  C05  C02   119.90  3.000
 3RF  C06   C05  C02   120.99  3.000
 3RF  H061  C06  C07   119.68  3.000
 3RF  H061  C06  C05   118.69  3.000
 3RF  C07   C06  C05   121.62  3.000
 3RF  N08   C07  C06   116.81  3.000
 3RF  C06   C07  C04   117.69  3.000
 3RF  N08   C07  C04   125.50  3.000
 3RF  N27   C09  N10   126.65  3.000
 3RF  N27   C09  N08   112.44  3.000
 3RF  N10   C09  N08   120.91  3.000
 3RF  C11   N10  C09   116.39  3.000
 3RF  C16   C11  C12   118.54  3.000
 3RF  C12   C11  N10   122.59  3.000
 3RF  C16   C11  N10   118.87  3.000
 3RF  C11   C12  C17   114.86  3.000
 3RF  C17   C12  C13   125.20  3.000
 3RF  C11   C12  C13   119.94  3.000
 3RF  H141  C14  C15   120.19  3.000
 3RF  H141  C14  C13   120.13  3.000
 3RF  C15   C14  C13   119.69  3.000
 3RF  H161  C16  C11   118.40  3.000
 3RF  H161  C16  C15   121.01  3.000
 3RF  C11   C16  C15   120.59  3.000
 3RF  H181  N18  C19   113.64  3.000
 3RF  H181  N18  C17   117.94  3.000
 3RF  C19   N18  C17   128.38  3.000
 3RF  N20   C19  N18   116.78  3.000
 3RF  N20   C19  C26   111.76  3.000
 3RF  N18   C19  C26   131.46  3.000
 3RF  N21   N20  C19   104.59  3.000
 3RF  H211  N21  N20   118.64  3.000
 3RF  H211  N21  C22   127.99  3.000
 3RF  N20   N21  C22   113.37  3.000
 3RF  H231  C23  C25   115.91  3.000
 3RF  H231  C23  C24   116.29  3.000
 3RF  C25   C23  C24    59.38  3.000
 3RF  H231  C23  C22   112.78  3.000
 3RF  C25   C23  C22   121.30  3.000
 3RF  C24   C23  C22   121.40  3.000
 3RF  H252  C25  H251  114.25  3.000
 3RF  H252  C25  C23   117.05  3.000
 3RF  H251  C25  C23   118.05  3.000
 3RF  H252  C25  C24   118.47  3.000
 3RF  H251  C25  C24   118.39  3.000
 3RF  C23   C25  C24    60.26  3.000
 3RF  C09   N27  C17   118.13  3.000
 3RF  H081  N08  C09   113.33  3.000
 3RF  H081  N08  C07   115.33  3.000
 3RF  C09   N08  C07   131.33  3.000
 3RF  H012  N01  H011  110.61  3.000
 3RF  H012  N01  C02   114.69  3.000
 3RF  H011  N01  C02   114.61  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
 3RF  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 3RF  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 3RF  CONST_03  N10   C11  C12  C13   180.00   0.0  0
 3RF  CONST_04  N27   C17  C12  C13   180.00   0.0  0
 3RF  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 3RF  CONST_06  C12   C11  C16  C15     0.00   0.0  0
 3RF  CONST_07  N10   C11  C16  C15   180.00   0.0  0
 3RF  CONST_08  C14   C13  C12  C17   180.00   0.0  0
 3RF  CONST_09  C16   C11  C12  C17   180.00   0.0  0
 3RF  CONST_10  N10   C11  C12  C17     0.00   0.0  0
 3RF  CONST_11  N10   C09  N27  C17     0.00   0.0  0
 3RF  CONST_12  C19   N20  N21  C22     0.00   0.0  0
 3RF  CONST_13  N20   C19  C26  C22     0.00   0.0  0
 3RF  CONST_14  N21   N20  C19  C26     0.00   0.0  0
 3RF  CONST_15  N20   N21  C22  C26     0.00   0.0  0
 3RF  CONST_16  C07   C06  C05  C02     0.00   0.0  0
 3RF  CONST_17  C07   C04  C03  C02     0.00   0.0  0
 3RF  CONST_18  C06   C07  C04  C03     0.00   0.0  0
 3RF  CONST_19  C06   C05  C02  C03     0.00   0.0  0
 3RF  CONST_20  C05   C06  C07  C04     0.00   0.0  0
 3RF  CONST_21  C05   C02  C03  C04     0.00   0.0  0
 3RF  CONST_22  C16   C11  N10  C09   180.00   0.0  0
 3RF  CONST_23  C12   C11  N10  C09     0.00   0.0  0
 3RF  CONST_24  C12   C17  N27  C09     0.00   0.0  0
 3RF  CONST_25  C14   C15  C16  C11     0.00   0.0  0
 3RF  CONST_26  C14   C13  C12  C11     0.00   0.0  0
 3RF  CONST_27  N27   C17  C12  C11     0.00   0.0  0
 3RF  CONST_28  N27   C09  N10  C11     0.00   0.0  0
 3RF  CONST_29  N21   C22  C26  C19     0.00   0.0  0
 3RF  CONST_30  C23   C22  C26  C19   180.00   0.0  0
 3RF  CONST_31  C23   C22  N21  N20   180.00   0.0  0
 3RF  CONST_32  N18   C17  C12  C13     0.00   0.0  0
 3RF  CONST_33  N08   C09  N27  C17   180.00   0.0  0
 3RF  CONST_34  N18   C19  C26  C22   180.00   0.0  0
 3RF  CONST_35  C06   C05  C02  N01   180.00   0.0  0
 3RF  CONST_36  C04   C03  C02  N01   180.00   0.0  0
 3RF  CONST_37  N08   C07  C04  C03   180.00   0.0  0
 3RF  CONST_38  N08   C07  C06  C05   180.00   0.0  0
 3RF  CONST_39  C11   N10  C09  N08   180.00   0.0  0
 3RF  CONST_40  N18   C17  N27  C09   180.00   0.0  0
 3RF  CONST_41  N18   C17  C12  C11   180.00   0.0  0
 3RF  CONST_42  N21   N20  C19  N18   180.00   0.0  0
 3RF  CONST_43  H151  C15  C14  C13   180.00   0.0  0
 3RF  CONST_44  H131  C13  C14  C15   180.00   0.0  0
 3RF  CONST_45  H211  N21  C22  C26   180.00   0.0  0
 3RF  CONST_46  H061  C06  C05  C02   180.00   0.0  0
 3RF  CONST_47  H041  C04  C03  C02   180.00   0.0  0
 3RF  CONST_48  H051  C05  C02  C03   180.00   0.0  0
 3RF  CONST_49  H031  C03  C02  C05   180.00   0.0  0
 3RF  CONST_50  H161  C16  C11  N10     0.00   0.0  0
 3RF  CONST_51  H141  C14  C13  C12   180.00   0.0  0
 3RF  CONST_52  H261  C26  C19  N20   180.00   0.0  0
 3RF  Var_01    C25   C24  C23  C22  -110.24  30.0  1
 3RF  Var_02    N21   C22  C23  C24    30.48  30.0  1
 3RF  Var_03    N20   C19  N18  C17   174.77  30.0  2
 3RF  Var_04    C09   N08  C07  C04     1.39  30.0  3
 3RF  Var_05    N10   C09  N08  C07     0.26  30.0  1
 3RF  Var_06    C19   N18  C17  C12  -179.91  30.0  1

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
 3RF  chir_01  C23  C22  C24  C25  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
 3RF  plan-1  C22   0.020
 3RF  plan-1  C26   0.020
 3RF  plan-1  N18   0.020
 3RF  plan-1  C19   0.020
 3RF  plan-1  N20   0.020
 3RF  plan-1  N21   0.020
 3RF  plan-1  C23   0.020
 3RF  plan-1  H261  0.020
 3RF  plan-1  H211  0.020
 3RF  plan-2  C02   0.020
 3RF  plan-2  C03   0.020
 3RF  plan-2  C04   0.020
 3RF  plan-2  C05   0.020
 3RF  plan-2  C06   0.020
 3RF  plan-2  C07   0.020
 3RF  plan-2  H031  0.020
 3RF  plan-2  H041  0.020
 3RF  plan-2  H051  0.020
 3RF  plan-2  H061  0.020
 3RF  plan-2  N08   0.020
 3RF  plan-2  N01   0.020
 3RF  plan-3  C13   0.020
 3RF  plan-3  C15   0.020
 3RF  plan-3  C17   0.020
 3RF  plan-3  C09   0.020
 3RF  plan-3  N10   0.020
 3RF  plan-3  C11   0.020
 3RF  plan-3  C12   0.020
 3RF  plan-3  C14   0.020
 3RF  plan-3  C16   0.020
 3RF  plan-3  N18   0.020
 3RF  plan-3  N27   0.020
 3RF  plan-3  H131  0.020
 3RF  plan-3  H151  0.020
 3RF  plan-3  H141  0.020
 3RF  plan-3  H161  0.020
 3RF  plan-3  N08   0.020
 3RF  plan-4  C02   0.020
 3RF  plan-4  H011  0.020
 3RF  plan-4  H012  0.020
 3RF  plan-4  N01   0.020

