# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:42:35 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 1-(trans-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl)-3-propan-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)N[C@@H]1CC[C@H](CC1)Nc2ncc3C=CC(=O)N(C(C)C)c3n2
#
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
 519  519  1-(trans-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl)-3-propan-2-ylurea  ligand  58  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_519
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
 519  C01   C  CH3   0  -0.649   -8.5693   0.9456  -1.2569
 519  C02   C  CH1   0  -0.082   -8.3866   0.3560   0.1388
 519  C03   C  CH3   0  -0.668   -9.5220  -0.5947   0.4896
 519  N04   N  NH1   0  -0.677   -7.1247  -0.3491   0.2745
 519  C05   C  C     0   0.739   -5.9409   0.2950   0.4554
 519  O06   O  O     0  -0.553   -5.8709   1.4999   0.6832
 519  N07   N  NH1   0  -0.692   -4.8437  -0.5099   0.4186
 519  C08   C  CH1   0  -0.040   -3.4937   0.0089   0.4397
 519  C09   C  CH2   0  -0.437   -3.0160   0.4475  -0.9455
 519  C10   C  CH2   0  -0.457   -1.5825   0.9652  -0.9080
 519  C11   C  CH1   0  -0.043   -0.6400  -0.0812  -0.3232
 519  C12   C  CH2   0  -0.438   -1.1133  -0.5154   1.0645
 519  C13   C  CH2   0  -0.454   -2.5464  -1.0337   1.0249
 519  N14   N  NH1   0  -0.660    0.7098   0.4441  -0.2966
 519  C15   C  CR6   0   0.622    1.8262  -0.2945  -0.2845
 519  N16   N  N     0  -0.469    1.7007  -1.6270  -0.4335
 519  C17   C  CR16  0  -0.035    2.8210  -2.3091  -0.4417
 519  C18   C  CR66  0  -0.134    4.0819  -1.7338  -0.3018
 519  C19   C  CR16  0  -0.140    5.3022  -2.4572  -0.3059
 519  C20   C  CR16  0  -0.448    6.4656  -1.7986  -0.1585
 519  C21   C  CR6   0   0.582    6.5105  -0.3589   0.0148
 519  O22   O  O     0  -0.486    7.5653   0.2416   0.1584
 519  N23   N  NR6   0  -0.606    5.2945   0.3244   0.0139
 519  C24   C  CH1   0  -0.125    5.2904   1.7950   0.1948
 519  C25   C  CH3   0  -0.659    5.7898   2.2103   1.5725
 519  C26   C  CH3   0  -0.660    5.9852   2.5239  -0.9479
 519  C27   C  CR66  0   0.577    4.0973  -0.3327  -0.1419
 519  N28   N  N     0  -0.519    2.9769   0.3661  -0.1373
 519  H011  H  HCH3  0   0.232   -7.7674   1.6434  -1.4977
 519  H012  H  HCH3  0   0.216   -8.5760   0.1572  -2.0123
 519  H013  H  HCH3  0   0.223   -9.5152   1.4854  -1.3262
 519  H021  H  HCH1  0   0.235   -8.3832   1.1713   0.8643
 519  H033  H  HCH3  0   0.222   -9.5669  -1.4307  -0.2127
 519  H032  H  HCH3  0   0.236   -9.4053  -1.0010   1.4948
 519  H031  H  HCH3  0   0.235  -10.4790  -0.0754   0.4439
 519  H041  H  HNH1  0   0.381   -7.1076  -1.3025  -0.0525
 519  H071  H  HNH1  0   0.381   -4.9567  -1.4632   0.1099
 519  H081  H  HCH1  0   0.234   -3.4861   0.8809   1.0993
 519  H091  H  HCH2  0   0.218   -3.0837  -0.4047  -1.6304
 519  H092  H  HCH2  0   0.242   -3.6795   1.2222  -1.3356
 519  H102  H  HCH2  0   0.248   -1.2542   1.2421  -1.9123
 519  H101  H  HCH2  0   0.225   -1.5414   1.8744  -0.2962
 519  H111  H  HCH1  0   0.242   -0.6447  -0.9551  -0.9798
 519  H122  H  HCH2  0   0.243   -0.4488  -1.2883   1.4568
 519  H121  H  HCH2  0   0.220   -1.0461   0.3398   1.7452
 519  H132  H  HCH2  0   0.245   -2.8738  -1.3103   2.0295
 519  H131  H  HCH2  0   0.221   -2.5843  -1.9450   0.4159
 519  H141  H  HNH1  0   0.393    0.8316   1.4283  -0.1133
 519  H171  H  HCR6  0   0.278    2.7404  -3.3857  -0.5622
 519  H191  H  HCR6  0   0.277    5.2811  -3.5335  -0.4279
 519  H201  H  HCR6  0   0.273    7.4166  -2.3125  -0.1575
 519  H241  H  HCH1  0   0.280    4.2392   2.0629   0.1470
 519  H251  H  HCH3  0   0.237    6.8600   2.0655   1.6949
 519  H253  H  HCH3  0   0.234    5.5759   3.2701   1.7149
 519  H252  H  HCH3  0   0.234    5.2704   1.6622   2.3593
 519  H261  H  HCH3  0   0.234    5.6109   2.1842  -1.9141
 519  H262  H  HCH3  0   0.234    5.7646   3.5889  -0.8664
 519  H263  H  HCH3  0   0.238    7.0651   2.4034  -0.9304

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
 519  C19  C20   double    1.345  0.020  1.345
 519  C19  C18   single    1.419  0.020  1.419
 519  C17  C18   aromatic  1.393  0.020  1.393
 519  C17  N16   aromatic  1.312  0.020  1.312
 519  C20  C21   single    1.451  0.020  1.451
 519  C18  C27   aromatic  1.410  0.020  1.410
 519  N16  C15   aromatic  1.347  0.020  1.347
 519  C21  O22   double    1.222  0.020  1.222
 519  C21  N23   single    1.395  0.020  1.395
 519  C27  N23   single    1.375  0.020  1.375
 519  C27  N28   aromatic  1.320  0.020  1.320
 519  C15  N28   aromatic  1.335  0.020  1.335
 519  C15  N14   single    1.339  0.020  1.339
 519  C26  C24   single    1.523  0.020  1.523
 519  N23  C24   single    1.482  0.020  1.482
 519  N14  C11   single    1.449  0.020  1.449
 519  C10  C11   single    1.525  0.020  1.525
 519  C10  C09   single    1.525  0.020  1.525
 519  C24  C25   single    1.523  0.020  1.523
 519  C11  C12   single    1.529  0.020  1.529
 519  C09  C08   single    1.530  0.020  1.530
 519  C12  C13   single    1.525  0.020  1.525
 519  C08  C13   single    1.525  0.020  1.525
 519  C08  N07   single    1.446  0.020  1.446
 519  O06  C05   double    1.228  0.020  1.228
 519  N07  C05   single    1.361  0.020  1.361
 519  C05  N04   single    1.360  0.020  1.360
 519  C01  C02   single    1.526  0.020  1.526
 519  N04  C02   single    1.452  0.020  1.452
 519  C02  C03   single    1.522  0.020  1.522
 519  C01  H011  single    0.970  0.020  1.090
 519  C01  H012  single    0.970  0.020  1.090
 519  C01  H013  single    0.970  0.020  1.090
 519  C02  H021  single    0.970  0.020  1.090
 519  C03  H033  single    0.970  0.020  1.090
 519  C03  H032  single    0.970  0.020  1.090
 519  C03  H031  single    0.970  0.020  1.090
 519  N04  H041  single    0.860  0.020  1.020
 519  N07  H071  single    0.860  0.020  1.020
 519  C08  H081  single    0.970  0.020  1.090
 519  C09  H091  single    0.970  0.020  1.090
 519  C09  H092  single    0.970  0.020  1.090
 519  C10  H102  single    0.970  0.020  1.090
 519  C10  H101  single    0.970  0.020  1.090
 519  C11  H111  single    0.970  0.020  1.090
 519  C12  H122  single    0.970  0.020  1.090
 519  C12  H121  single    0.970  0.020  1.090
 519  C13  H132  single    0.970  0.020  1.090
 519  C13  H131  single    0.970  0.020  1.090
 519  N14  H141  single    0.860  0.020  1.020
 519  C17  H171  single    0.930  0.020  1.080
 519  C19  H191  single    0.930  0.020  1.080
 519  C20  H201  single    0.930  0.020  1.080
 519  C24  H241  single    0.970  0.020  1.090
 519  C25  H251  single    0.970  0.020  1.090
 519  C25  H253  single    0.970  0.020  1.090
 519  C25  H252  single    0.970  0.020  1.090
 519  C26  H261  single    0.970  0.020  1.090
 519  C26  H262  single    0.970  0.020  1.090
 519  C26  H263  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
 519  H013  C01  H012  107.93  3.000
 519  H013  C01  H011  107.88  3.000
 519  H012  C01  H011  108.30  3.000
 519  H013  C01  C02   110.67  3.000
 519  H012  C01  C02   110.76  3.000
 519  H011  C01  C02   111.18  3.000
 519  H021  C02  N04   107.33  3.000
 519  H021  C02  C03   108.40  3.000
 519  N04   C02  C03   108.88  3.000
 519  H021  C02  C01   108.64  3.000
 519  C03   C02  C01   111.28  3.000
 519  N04   C02  C01   112.16  3.000
 519  H031  C03  H032  108.07  3.000
 519  H031  C03  H033  107.55  3.000
 519  H032  C03  H033  108.17  3.000
 519  H031  C03  C02   110.35  3.000
 519  H032  C03  C02   111.43  3.000
 519  H033  C03  C02   111.12  3.000
 519  H041  N04  C05   118.45  3.000
 519  H041  N04  C02   116.34  3.000
 519  C05   N04  C02   122.62  3.000
 519  N07   C05  O06   122.62  3.000
 519  N07   C05  N04   114.71  3.000
 519  O06   C05  N04   122.61  3.000
 519  H071  N07  C08   116.63  3.000
 519  H071  N07  C05   118.48  3.000
 519  C08   N07  C05   122.67  3.000
 519  H081  C08  C13   108.02  3.000
 519  H081  C08  C09   108.39  3.000
 519  C13   C08  C09   110.46  3.000
 519  H081  C08  N07   107.54  3.000
 519  C13   C08  N07   109.88  3.000
 519  C09   C08  N07   112.40  3.000
 519  H092  C09  H091  106.92  3.000
 519  H092  C09  C10   109.82  3.000
 519  H091  C09  C10   109.74  3.000
 519  H092  C09  C08   109.71  3.000
 519  H091  C09  C08   108.90  3.000
 519  C10   C09  C08   111.63  3.000
 519  H101  C10  H102  106.95  3.000
 519  H101  C10  C11   109.38  3.000
 519  H102  C10  C11   109.93  3.000
 519  H101  C10  C09   109.30  3.000
 519  H102  C10  C09   110.25  3.000
 519  C11   C10  C09   110.95  3.000
 519  H111  C11  N14   107.75  3.000
 519  H111  C11  C12   108.47  3.000
 519  N14   C11  C12   112.00  3.000
 519  H111  C11  C10   108.40  3.000
 519  C12   C11  C10   110.59  3.000
 519  N14   C11  C10   109.52  3.000
 519  H121  C12  H122  106.99  3.000
 519  H121  C12  C13   109.84  3.000
 519  H122  C12  C13   109.92  3.000
 519  H121  C12  C11   108.87  3.000
 519  H122  C12  C11   109.79  3.000
 519  C13   C12  C11   111.34  3.000
 519  H131  C13  H132  106.86  3.000
 519  H131  C13  C12   109.23  3.000
 519  H132  C13  C12   110.12  3.000
 519  H131  C13  C08   109.48  3.000
 519  H132  C13  C08   109.87  3.000
 519  C12   C13  C08   111.18  3.000
 519  H141  N14  C15   115.85  3.000
 519  H141  N14  C11   118.02  3.000
 519  C15   N14  C11   125.25  3.000
 519  N28   C15  N16   125.60  3.000
 519  N28   C15  N14   116.54  3.000
 519  N16   C15  N14   117.86  3.000
 519  C17   N16  C15   115.83  3.000
 519  H171  C17  C18   119.18  3.000
 519  H171  C17  N16   116.92  3.000
 519  C18   C17  N16   123.89  3.000
 519  C27   C18  C19   119.84  3.000
 519  C27   C18  C17   115.57  3.000
 519  C19   C18  C17   124.59  3.000
 519  H191  C19  C20   121.04  3.000
 519  H191  C19  C18   119.35  3.000
 519  C20   C19  C18   119.60  3.000
 519  H201  C20  C21   116.40  3.000
 519  H201  C20  C19   121.88  3.000
 519  C21   C20  C19   121.72  3.000
 519  N23   C21  O22   120.78  3.000
 519  N23   C21  C20   117.33  3.000
 519  O22   C21  C20   121.89  3.000
 519  C27   N23  C24   119.07  3.000
 519  C24   N23  C21   119.25  3.000
 519  C27   N23  C21   121.68  3.000
 519  H241  C24  C26   106.89  3.000
 519  H241  C24  C25   106.85  3.000
 519  C26   C24  C25   113.49  3.000
 519  H241  C24  N23   104.01  3.000
 519  C25   C24  N23   112.34  3.000
 519  C26   C24  N23   112.47  3.000
 519  H252  C25  H253  107.51  3.000
 519  H252  C25  H251  108.70  3.000
 519  H253  C25  H251  107.93  3.000
 519  H252  C25  C24   111.06  3.000
 519  H253  C25  C24   108.59  3.000
 519  H251  C25  C24   112.85  3.000
 519  H263  C26  H262  107.94  3.000
 519  H263  C26  H261  108.71  3.000
 519  H262  C26  H261  107.51  3.000
 519  H263  C26  C24   112.85  3.000
 519  H262  C26  C24   108.60  3.000
 519  H261  C26  C24   111.04  3.000
 519  N28   C27  N23   119.05  3.000
 519  N28   C27  C18   121.13  3.000
 519  N23   C27  C18   119.82  3.000
 519  C27   N28  C15   117.98  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
 519  CONST_01  C18   C17  N16  C15    0.00   0.0  0
 519  CONST_02  C18   C27  N28  C15    0.00   0.0  0
 519  CONST_03  C27   C18  C17  N16    0.00   0.0  0
 519  CONST_04  C27   N28  C15  N16    0.00   0.0  0
 519  CONST_05  N28   C27  C18  C17    0.00   0.0  0
 519  CONST_06  N28   C15  N16  C17    0.00   0.0  0
 519  CONST_07  C27   N23  C21  C20    0.00   0.0  0
 519  CONST_08  C17   N16  C15  N14  180.00   0.0  0
 519  CONST_09  C27   N28  C15  N14  180.00   0.0  0
 519  CONST_10  N16   C15  N14  C11    0.00   0.0  0
 519  CONST_11  N28   C15  N14  C11  180.00   0.0  0
 519  CONST_12  C24   N23  C21  C20  180.00   0.0  0
 519  CONST_13  C27   N23  C21  O22  180.00   0.0  0
 519  CONST_14  H171  C17  N16  C15  180.00   0.0  0
 519  CONST_15  C24   N23  C21  O22    0.00   0.0  0
 519  CONST_16  H141  N14  C15  N16  180.00   0.0  0
 519  CONST_17  C08   N07  C05  O06    0.00   0.0  0
 519  CONST_18  C08   N07  C05  N04  180.00   0.0  0
 519  CONST_19  O06   C05  N04  C02    0.00   0.0  0
 519  CONST_20  N07   C05  N04  C02  180.00   0.0  0
 519  CONST_21  H071  N07  C05  O06  180.00   0.0  0
 519  CONST_22  H041  N04  C05  O06  180.00   0.0  0
 519  Var_01    C11   C10  C09  C08   56.20  30.0  1
 519  Var_02    C11   C12  C13  C08  -56.33  30.0  1
 519  Var_03    C26   C24  N23  C21   64.31  30.0  3
 519  Var_04    H261  C26  C24  N23   50.07  30.0  3
 519  Var_05    H251  C25  C24  N23   71.61  30.0  3
 519  Var_06    C05   N04  C02  C01   78.13  30.0  2
 519  Var_07    H033  C03  C02  C01   60.51  30.0  3
 519  Var_08    H011  C01  C02  C03  178.71  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
 519  chir_01  C08  C09  C13  N07  positiv
 519  chir_02  C11  N14  C10  C12  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
 519  plan-1  N14   0.020
 519  plan-1  C15   0.020
 519  plan-1  N16   0.020
 519  plan-1  C17   0.020
 519  plan-1  C18   0.020
 519  plan-1  C19   0.020
 519  plan-1  C20   0.020
 519  plan-1  C21   0.020
 519  plan-1  O22   0.020
 519  plan-1  N23   0.020
 519  plan-1  C24   0.020
 519  plan-1  C27   0.020
 519  plan-1  N28   0.020
 519  plan-1  H171  0.020
 519  plan-1  H191  0.020
 519  plan-1  H201  0.020
 519  plan-2  C02   0.020
 519  plan-2  N04   0.020
 519  plan-2  C05   0.020
 519  plan-2  O06   0.020
 519  plan-2  N07   0.020
 519  plan-2  C08   0.020
 519  plan-2  H041  0.020
 519  plan-2  H071  0.020
 519  plan-3  C11   0.020
 519  plan-3  N14   0.020
 519  plan-3  C15   0.020
 519  plan-3  H141  0.020

