# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:18:42 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(C1)c2[nH]nc(Nc3nc(Nc4ccc5nc[nH]c5c4)nc6ccccc36)c2
#
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
 3RJ  3RJ  N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine  ligand  50  30  .  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_3RJ
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
 3RJ  C13   C  C     0  -0.366  -4.9825  -2.3233  -0.0389
 3RJ  C15   C  C     0  -0.466  -6.7343  -3.5697   0.0548
 3RJ  C17   C  CR15  0  -0.543  -3.1192  -0.5091  -0.0119
 3RJ  C21   C  CR6   0   0.349   2.6544  -1.3750  -0.0331
 3RJ  C22   C  CR16  0  -0.398   3.8291  -0.6319   0.0001
 3RJ  C28   C  CR16  0  -0.314   3.8970  -3.4814  -0.0819
 3RJ  C01   C  CR66  0   0.292   1.2924   2.7033   0.0938
 3RJ  C02   C  CR16  0  -0.320   2.1716   3.8038   0.1432
 3RJ  C03   C  CR16  0  -0.245   1.6827   5.0848   0.1990
 3RJ  C04   C  CR16  0  -0.264   0.2999   5.3245   0.2093
 3RJ  C05   C  CR16  0  -0.310  -0.5752   4.2667   0.1590
 3RJ  C06   C  CR66  0  -0.062  -0.0962   2.9476   0.0976
 3RJ  C07   C  CR6   0   0.546  -0.9229   1.7645   0.0393
 3RJ  C09   C  CR5   0   0.456  -3.2262   0.8953  -0.0139
 3RJ  N10   N  N     0  -0.322  -4.4864   1.2875  -0.0492
 3RJ  N11   N  NR15  0  -0.506  -5.1902   0.1563  -0.0676
 3RJ  C12   C  CR5   0   0.483  -4.4279  -0.9494  -0.0459
 3RJ  C14   C  C     0  -0.420  -5.9501  -2.7484   1.0938
 3RJ  C16   C  C     0  -0.421  -6.0828  -2.7213  -1.0518
 3RJ  N18   N  N     0  -0.531  -0.3953   0.5688   0.0021
 3RJ  C19   C  CR6   0   0.595   0.9534   0.4677   0.0098
 3RJ  N20   N  NH1   0  -0.778   1.3758  -0.8263  -0.0305
 3RJ  C23   C  CR56  0   0.376   5.0190  -1.3534  -0.0087
 3RJ  N24   N  NR15  0  -0.667   6.3255  -0.9489   0.0157
 3RJ  C25   C  CR15  0   0.093   7.0925  -2.0677  -0.0096
 3RJ  N26   N  N     0  -0.460   6.3986  -3.1686  -0.0482
 3RJ  C27   C  CR56  0   0.106   5.0863  -2.7529  -0.0488
 3RJ  C29   C  CR16  0  -0.371   2.7065  -2.7899  -0.0736
 3RJ  N30   N  N     0  -0.536   1.8125   1.4511   0.0477
 3RJ  H131  H  H     0   0.266  -4.1516  -3.0285  -0.0978
 3RJ  H152  H  H     0   0.233  -6.3935  -4.6051   0.0203
 3RJ  H151  H  H     0   0.235  -7.8215  -3.5633   0.1226
 3RJ  H171  H  HCR5  0   0.274  -2.2340  -1.1161   0.0130
 3RJ  H221  H  HCR6  0   0.297   3.8135   0.4454   0.0304
 3RJ  H281  H  HCR6  0   0.257   3.9026  -4.5631  -0.1130
 3RJ  H021  H  HCR6  0   0.260   3.2373   3.6139   0.1387
 3RJ  H031  H  HCR6  0   0.265   2.3704   5.9195   0.2383
 3RJ  H041  H  HCR6  0   0.264  -0.0755   6.3375   0.2590
 3RJ  H051  H  HCR6  0   0.257  -1.6372   4.4778   0.1737
 3RJ  H081  H  HNH1  0   0.420  -2.6475   2.8260   0.0308
 3RJ  H111  H  HNR5  0   0.414  -6.1957   0.2091  -0.0951
 3RJ  H142  H  H     0   0.243  -5.5142  -3.2698   1.9456
 3RJ  H141  H  H     0   0.229  -6.5327  -1.9032   1.4645
 3RJ  H161  H  H     0   0.227  -6.7095  -1.8720  -1.3316
 3RJ  H162  H  H     0   0.244  -5.7571  -3.2223  -1.9631
 3RJ  H201  H  HNH1  0   0.408   0.6185  -1.4911  -0.0582
 3RJ  H241  H  HNR5  0   0.420   6.6661  -0.0010   0.0454
 3RJ  H251  H  HCR5  0   0.283   8.1706  -2.0083   0.0020
 3RJ  H291  H  HCR6  0   0.264   1.7763  -3.3451  -0.0999
 3RJ  N08   N  NH1   0  -0.758  -2.2633   1.8946   0.0220

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
 3RJ  C04  C03   aromatic  1.404  0.020  1.404
 3RJ  C04  C05   aromatic  1.374  0.020  1.374
 3RJ  C03  C02   aromatic  1.372  0.020  1.372
 3RJ  C05  C06   aromatic  1.405  0.020  1.405
 3RJ  C02  C01   aromatic  1.409  0.020  1.409
 3RJ  C06  C01   aromatic  1.410  0.020  1.410
 3RJ  C06  C07   aromatic  1.445  0.020  1.445
 3RJ  N08  C07   single    1.347  0.020  1.347
 3RJ  N08  C09   single    1.388  0.020  1.388
 3RJ  C01  N30   aromatic  1.357  0.020  1.357
 3RJ  N10  C09   aromatic  1.320  0.020  1.320
 3RJ  N10  N11   aromatic  1.332  0.020  1.332
 3RJ  C07  N18   aromatic  1.307  0.020  1.307
 3RJ  C09  C17   aromatic  1.408  0.020  1.408
 3RJ  N11  C12   aromatic  1.343  0.020  1.343
 3RJ  N30  C19   aromatic  1.306  0.020  1.306
 3RJ  N18  C19   aromatic  1.353  0.020  1.353
 3RJ  C19  N20   single    1.362  0.020  1.362
 3RJ  C17  C12   aromatic  1.381  0.020  1.381
 3RJ  C12  C13   single    1.482  0.020  1.482
 3RJ  N20  C21   single    1.391  0.020  1.391
 3RJ  C13  C16   single    1.548  0.020  1.548
 3RJ  C13  C14   single    1.549  0.020  1.549
 3RJ  C22  C21   aromatic  1.390  0.020  1.390
 3RJ  C22  C23   aromatic  1.392  0.020  1.392
 3RJ  C16  C15   single    1.539  0.020  1.539
 3RJ  C21  C29   aromatic  1.416  0.020  1.416
 3RJ  N24  C23   aromatic  1.368  0.020  1.368
 3RJ  N24  C25   aromatic  1.357  0.020  1.357
 3RJ  C23  C27   aromatic  1.402  0.020  1.402
 3RJ  C29  C28   aromatic  1.377  0.020  1.377
 3RJ  C14  C15   single    1.539  0.020  1.539
 3RJ  C25  N26   aromatic  1.302  0.020  1.302
 3RJ  C27  C28   aromatic  1.395  0.020  1.395
 3RJ  C27  N26   aromatic  1.377  0.020  1.377
 3RJ  C13  H131  single    0.970  0.020  1.090
 3RJ  C15  H152  single    0.970  0.020  1.090
 3RJ  C15  H151  single    0.970  0.020  1.090
 3RJ  C17  H171  single    0.930  0.020  1.080
 3RJ  C22  H221  single    0.930  0.020  1.080
 3RJ  C28  H281  single    0.930  0.020  1.080
 3RJ  C02  H021  single    0.930  0.020  1.080
 3RJ  C03  H031  single    0.930  0.020  1.080
 3RJ  C04  H041  single    0.930  0.020  1.080
 3RJ  C05  H051  single    0.930  0.020  1.080
 3RJ  N08  H081  single    0.860  0.020  1.020
 3RJ  N11  H111  single    0.860  0.020  1.020
 3RJ  C14  H142  single    0.970  0.020  1.090
 3RJ  C14  H141  single    0.970  0.020  1.090
 3RJ  C16  H161  single    0.970  0.020  1.090
 3RJ  C16  H162  single    0.970  0.020  1.090
 3RJ  N20  H201  single    0.860  0.020  1.020
 3RJ  N24  H241  single    0.860  0.020  1.020
 3RJ  C25  H251  single    0.930  0.020  1.080
 3RJ  C29  H291  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
 3RJ  H131  C13  C16   109.86  3.000
 3RJ  H131  C13  C14   109.74  3.000
 3RJ  C16   C13  C14    87.93  3.000
 3RJ  H131  C13  C12   108.29  3.000
 3RJ  C14   C13  C12   119.45  3.000
 3RJ  C16   C13  C12   120.10  3.000
 3RJ  H151  C15  H152  108.63  3.000
 3RJ  H151  C15  C16   117.65  3.000
 3RJ  H152  C15  C16   111.61  3.000
 3RJ  H151  C15  C14   117.61  3.000
 3RJ  H152  C15  C14   111.63  3.000
 3RJ  C16   C15  C14    88.60  3.000
 3RJ  H171  C17  C12   126.98  3.000
 3RJ  H171  C17  C09   128.78  3.000
 3RJ  C12   C17  C09   104.23  3.000
 3RJ  C29   C21  N20   115.33  3.000
 3RJ  C29   C21  C22   120.23  3.000
 3RJ  N20   C21  C22   124.44  3.000
 3RJ  H221  C22  C23   122.06  3.000
 3RJ  H221  C22  C21   121.51  3.000
 3RJ  C23   C22  C21   116.43  3.000
 3RJ  H281  C28  C29   120.44  3.000
 3RJ  H281  C28  C27   121.21  3.000
 3RJ  C29   C28  C27   118.34  3.000
 3RJ  N30   C01  C06   122.52  3.000
 3RJ  N30   C01  C02   118.86  3.000
 3RJ  C06   C01  C02   118.62  3.000
 3RJ  H021  C02  C03   120.97  3.000
 3RJ  H021  C02  C01   118.49  3.000
 3RJ  C03   C02  C01   120.53  3.000
 3RJ  H031  C03  C04   119.61  3.000
 3RJ  H031  C03  C02   119.68  3.000
 3RJ  C04   C03  C02   120.71  3.000
 3RJ  H041  C04  C05   120.12  3.000
 3RJ  H041  C04  C03   120.16  3.000
 3RJ  C05   C04  C03   119.72  3.000
 3RJ  H051  C05  C06   121.21  3.000
 3RJ  H051  C05  C04   118.30  3.000
 3RJ  C06   C05  C04   120.49  3.000
 3RJ  C07   C06  C05   125.15  3.000
 3RJ  C07   C06  C01   114.94  3.000
 3RJ  C05   C06  C01   119.91  3.000
 3RJ  N18   C07  N08   119.31  3.000
 3RJ  N18   C07  C06   121.28  3.000
 3RJ  N08   C07  C06   119.40  3.000
 3RJ  N10   C09  N08   116.68  3.000
 3RJ  N10   C09  C17   111.64  3.000
 3RJ  N08   C09  C17   131.68  3.000
 3RJ  N11   N10  C09   104.62  3.000
 3RJ  H111  N11  C12   127.60  3.000
 3RJ  H111  N11  N10   118.89  3.000
 3RJ  C12   N11  N10   113.51  3.000
 3RJ  N11   C12  C17   106.00  3.000
 3RJ  C17   C12  C13   130.56  3.000
 3RJ  N11   C12  C13   123.43  3.000
 3RJ  H141  C14  H142  108.58  3.000
 3RJ  H141  C14  C15   111.74  3.000
 3RJ  H142  C14  C15   118.43  3.000
 3RJ  H141  C14  C13   111.67  3.000
 3RJ  H142  C14  C13   116.94  3.000
 3RJ  C15   C14  C13    88.35  3.000
 3RJ  H162  C16  H161  108.35  3.000
 3RJ  H162  C16  C15   118.32  3.000
 3RJ  H161  C16  C15   111.72  3.000
 3RJ  H162  C16  C13   116.94  3.000
 3RJ  H161  C16  C13   112.07  3.000
 3RJ  C15   C16  C13    88.40  3.000
 3RJ  C19   N18  C07   118.07  3.000
 3RJ  N30   C19  N20   120.81  3.000
 3RJ  N20   C19  N18   112.35  3.000
 3RJ  N30   C19  N18   126.85  3.000
 3RJ  H201  N20  C19   113.23  3.000
 3RJ  H201  N20  C21   115.48  3.000
 3RJ  C19   N20  C21   131.29  3.000
 3RJ  C27   C23  N24   104.47  3.000
 3RJ  C27   C23  C22   123.98  3.000
 3RJ  N24   C23  C22   131.55  3.000
 3RJ  H241  N24  C25   125.81  3.000
 3RJ  H241  N24  C23   126.98  3.000
 3RJ  C25   N24  C23   107.21  3.000
 3RJ  H251  C25  N26   125.38  3.000
 3RJ  H251  C25  N24   121.26  3.000
 3RJ  N26   C25  N24   113.36  3.000
 3RJ  C27   N26  C25   104.64  3.000
 3RJ  N26   C27  C23   110.32  3.000
 3RJ  N26   C27  C28   130.92  3.000
 3RJ  C23   C27  C28   118.75  3.000
 3RJ  H291  C29  C28   119.00  3.000
 3RJ  H291  C29  C21   118.75  3.000
 3RJ  C28   C29  C21   122.25  3.000
 3RJ  C19   N30  C01   116.34  3.000
 3RJ  H081  N08  C09   113.65  3.000
 3RJ  H081  N08  C07   117.95  3.000
 3RJ  C09   N08  C07   128.40  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
 3RJ  CONST_01  N11   N10  C09  C17     0.00   0.0  0
 3RJ  CONST_02  N10   N11  C12  C17     0.00   0.0  0
 3RJ  CONST_03  N24   C23  C22  C21   180.00   0.0  0
 3RJ  CONST_04  C27   C23  C22  C21     0.00   0.0  0
 3RJ  CONST_05  C27   C28  C29  C21     0.00   0.0  0
 3RJ  CONST_06  C28   C29  C21  C22     0.00   0.0  0
 3RJ  CONST_07  C25   N24  C23  C22   180.00   0.0  0
 3RJ  CONST_08  C28   C27  C23  C22     0.00   0.0  0
 3RJ  CONST_09  N26   C27  C23  C22   180.00   0.0  0
 3RJ  CONST_10  N24   C23  C27  C28   180.00   0.0  0
 3RJ  CONST_11  C25   N26  C27  C28   180.00   0.0  0
 3RJ  CONST_12  C04   C03  C02  C01     0.00   0.0  0
 3RJ  CONST_13  C04   C05  C06  C01     0.00   0.0  0
 3RJ  CONST_14  N18   C07  C06  C01     0.00   0.0  0
 3RJ  CONST_15  N18   C19  N30  C01     0.00   0.0  0
 3RJ  CONST_16  C05   C04  C03  C02     0.00   0.0  0
 3RJ  CONST_17  C05   C06  C01  C02     0.00   0.0  0
 3RJ  CONST_18  C07   C06  C01  C02   180.00   0.0  0
 3RJ  CONST_19  C19   N30  C01  C02   180.00   0.0  0
 3RJ  CONST_20  C06   C05  C04  C03     0.00   0.0  0
 3RJ  CONST_21  C06   C01  C02  C03     0.00   0.0  0
 3RJ  CONST_22  N30   C01  C02  C03   180.00   0.0  0
 3RJ  CONST_23  C07   C06  C05  C04   180.00   0.0  0
 3RJ  CONST_24  N30   C01  C06  C05   180.00   0.0  0
 3RJ  CONST_25  N18   C07  C06  C05   180.00   0.0  0
 3RJ  CONST_26  C19   N30  C01  C06     0.00   0.0  0
 3RJ  CONST_27  C19   N18  C07  C06     0.00   0.0  0
 3RJ  CONST_28  N30   C01  C06  C07     0.00   0.0  0
 3RJ  CONST_29  N30   C19  N18  C07     0.00   0.0  0
 3RJ  CONST_30  C12   N11  N10  C09     0.00   0.0  0
 3RJ  CONST_31  N11   C12  C17  C09     0.00   0.0  0
 3RJ  CONST_32  C12   C17  C09  N10     0.00   0.0  0
 3RJ  CONST_33  C29   C21  C22  C23     0.00   0.0  0
 3RJ  CONST_34  N26   C25  N24  C23     0.00   0.0  0
 3RJ  CONST_35  C29   C28  C27  C23     0.00   0.0  0
 3RJ  CONST_36  C25   N26  C27  C23     0.00   0.0  0
 3RJ  CONST_37  N26   C27  C23  N24     0.00   0.0  0
 3RJ  CONST_38  C27   N26  C25  N24     0.00   0.0  0
 3RJ  CONST_39  C27   C23  N24  C25     0.00   0.0  0
 3RJ  CONST_40  C29   C28  C27  N26   180.00   0.0  0
 3RJ  CONST_41  N10   N11  C12  C13   180.00   0.0  0
 3RJ  CONST_42  C09   C17  C12  C13   180.00   0.0  0
 3RJ  CONST_43  N20   C21  C29  C28   180.00   0.0  0
 3RJ  CONST_44  N08   C07  C06  C01   180.00   0.0  0
 3RJ  CONST_45  N20   C19  N30  C01   180.00   0.0  0
 3RJ  CONST_46  N08   C07  C06  C05     0.00   0.0  0
 3RJ  CONST_47  N20   C19  N18  C07   180.00   0.0  0
 3RJ  CONST_48  C19   N18  C07  N08   180.00   0.0  0
 3RJ  CONST_49  N11   N10  C09  N08   180.00   0.0  0
 3RJ  CONST_50  C12   C17  C09  N08   180.00   0.0  0
 3RJ  CONST_51  C23   C22  C21  N20   180.00   0.0  0
 3RJ  CONST_52  H111  N11  C12  C13     0.00   0.0  0
 3RJ  CONST_53  H171  C17  C12  C13     0.00   0.0  0
 3RJ  CONST_54  H281  C28  C29  C21   180.00   0.0  0
 3RJ  CONST_55  H291  C29  C21  C22   180.00   0.0  0
 3RJ  CONST_56  H241  N24  C23  C22     0.00   0.0  0
 3RJ  CONST_57  H031  C03  C02  C01   180.00   0.0  0
 3RJ  CONST_58  H051  C05  C06  C01   180.00   0.0  0
 3RJ  CONST_59  H041  C04  C03  C02   180.00   0.0  0
 3RJ  CONST_60  H021  C02  C03  C04   180.00   0.0  0
 3RJ  CONST_61  H251  C25  N24  C23   180.00   0.0  0
 3RJ  CONST_62  H221  C22  C23  N24     0.00   0.0  0
 3RJ  Var_01    C14   C15  C16  C13    19.50  30.0  1
 3RJ  Var_02    C07   N08  C09  C17     1.67  30.0  2
 3RJ  Var_03    N30   C19  N20  C21     0.42  30.0  1
 3RJ  Var_04    C19   N20  C21  C22    -0.43  30.0  1
 3RJ  Var_05    C09   N08  C07  C06  -179.07  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
 3RJ  chir_01  C13  C12  C16  C14  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
 3RJ  plan-1  C13   0.020
 3RJ  plan-1  C17   0.020
 3RJ  plan-1  C09   0.020
 3RJ  plan-1  N10   0.020
 3RJ  plan-1  N11   0.020
 3RJ  plan-1  C12   0.020
 3RJ  plan-1  H171  0.020
 3RJ  plan-1  H111  0.020
 3RJ  plan-1  N08   0.020
 3RJ  plan-2  C21   0.020
 3RJ  plan-2  C22   0.020
 3RJ  plan-2  C28   0.020
 3RJ  plan-2  N20   0.020
 3RJ  plan-2  C23   0.020
 3RJ  plan-2  N24   0.020
 3RJ  plan-2  C25   0.020
 3RJ  plan-2  N26   0.020
 3RJ  plan-2  C27   0.020
 3RJ  plan-2  C29   0.020
 3RJ  plan-2  H221  0.020
 3RJ  plan-2  H281  0.020
 3RJ  plan-2  H241  0.020
 3RJ  plan-2  H251  0.020
 3RJ  plan-2  H291  0.020
 3RJ  plan-3  C01   0.020
 3RJ  plan-3  C02   0.020
 3RJ  plan-3  C03   0.020
 3RJ  plan-3  C04   0.020
 3RJ  plan-3  C05   0.020
 3RJ  plan-3  C06   0.020
 3RJ  plan-3  C07   0.020
 3RJ  plan-3  N18   0.020
 3RJ  plan-3  C19   0.020
 3RJ  plan-3  N20   0.020
 3RJ  plan-3  N30   0.020
 3RJ  plan-3  H021  0.020
 3RJ  plan-3  H031  0.020
 3RJ  plan-3  H041  0.020
 3RJ  plan-3  H051  0.020
 3RJ  plan-3  N08   0.020

