# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:10:44 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-{trans-4-[(8-cyclopentyl-7-oxo-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(C4CCCC4)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
 4F2  4F2  1-{trans-4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]cyclohexyl}-3-propan-2-ylurea  ligand  62  30  .  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_4F2
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
 4F2  C10   C  CH2   0  -0.458   -1.9514   0.7612  -0.9295
 4F2  C11   C  CH1   0  -0.043   -1.0904  -0.3514  -0.3404
 4F2  C12   C  CH2   0  -0.439   -1.5934  -0.7468   1.0484
 4F2  C13   C  CH2   0  -0.452   -3.0637  -1.1489   1.0157
 4F2  C18   C  CR66  0  -0.139    3.5218  -2.2973  -0.1501
 4F2  C19   C  CR16  0  -0.140    4.6965  -3.0907  -0.0869
 4F2  C20   C  CR16  0  -0.451    5.8954  -2.4960   0.0536
 4F2  C21   C  CR6   0   0.570    6.0251  -1.0543   0.1418
 4F2  C24   C  CR15  0  -0.097    4.9431   1.1621   0.1603
 4F2  C25   C  CH2   0  -0.445    5.6268   1.8164  -1.0507
 4F2  C26   C  CH2   0  -0.453    6.1616   3.1246  -0.4747
 4F2  C28   C  CH2   0  -0.447    5.6359   1.7301   1.4245
 4F2  C29   C  CR66  0   0.578    3.6194  -0.8938  -0.0611
 4F2  C15   C  CR6   0   0.623    1.3590  -0.7239  -0.2536
 4F2  C01   C  CH3   0  -0.648   -8.8929   1.3964  -1.2551
 4F2  C02   C  CH1   0  -0.079   -8.7619   0.7655   0.1282
 4F2  C03   C  CH3   0  -0.670   -9.9769  -0.0878   0.4634
 4F2  N04   N  NH1   0  -0.677   -7.5677  -0.0515   0.2458
 4F2  O06   O  O     0  -0.554   -6.1518   1.6678   0.6826
 4F2  N07   N  NH1   0  -0.692   -5.3147  -0.4300   0.4265
 4F2  C08   C  CH1   0  -0.042   -3.9238  -0.0310   0.4357
 4F2  C09   C  CH2   0  -0.436   -3.4224   0.3632  -0.9540
 4F2  N14   N  NH1   0  -0.660    0.2921   0.0821  -0.3147
 4F2  N16   N  N     0  -0.469    1.1547  -2.0516  -0.3493
 4F2  C17   C  CR16  0  -0.036    2.2307  -2.8007  -0.2977
 4F2  O22   O  O     0  -0.482    7.1089  -0.5024   0.2622
 4F2  N23   N  NR6   0  -0.614    4.8511  -0.3031   0.0864
 4F2  C27   C  CH2   0  -0.437    6.6886   2.7122   0.9004
 4F2  N30   N  N     0  -0.518    2.5456  -0.1281  -0.1156
 4F2  H101  H  HCH2  0   0.225   -1.8311   1.6697  -0.3274
 4F2  H102  H  HCH2  0   0.248   -1.6088   1.0013  -1.9385
 4F2  H111  H  HCH1  0   0.242   -1.1567  -1.2245  -0.9950
 4F2  H121  H  HCH2  0   0.243   -0.9888  -1.5685   1.4376
 4F2  H122  H  HCH2  0   0.220   -1.4573   0.1001   1.7295
 4F2  H131  H  HCH2  0   0.221   -3.1805  -2.0545   0.4083
 4F2  H132  H  HCH2  0   0.245   -3.4061  -1.3966   2.0228
 4F2  H191  H  HCR6  0   0.277    4.6124  -4.1688  -0.1520
 4F2  H201  H  HCR6  0   0.273    6.8120  -3.0667   0.1045
 4F2  H241  H  HCR5  0   0.292    3.9117   1.4972   0.1719
 4F2  H252  H  HCH2  0   0.238    6.4547   1.2127  -1.4203
 4F2  H251  H  HCH2  0   0.235    4.9257   1.9575  -1.8745
 4F2  H262  H  HCH2  0   0.234    6.9217   3.5861  -1.1063
 4F2  H261  H  HCH2  0   0.220    5.3487   3.8482  -0.3625
 4F2  H281  H  HCH2  0   0.233    4.8896   2.2596   2.0198
 4F2  H282  H  HCH2  0   0.243    6.0630   0.9638   2.0682
 4F2  H013  H  HCH3  0   0.216   -8.9846   0.6276  -2.0251
 4F2  H012  H  HCH3  0   0.223   -9.7797   2.0302  -1.3068
 4F2  H011  H  HCH3  0   0.232   -8.0263   2.0146  -1.4901
 4F2  H021  H  HCH1  0   0.235   -8.6868   1.5634   0.8694
 4F2  H033  H  HCH3  0   0.222  -10.0923  -0.9055  -0.2521
 4F2  H031  H  HCH3  0   0.237   -9.8982  -0.5181   1.4623
 4F2  H032  H  HCH3  0   0.236  -10.8853   0.5132   0.4257
 4F2  H041  H  HNH1  0   0.382   -7.6421  -1.0100  -0.0575
 4F2  H071  H  HNH1  0   0.380   -5.5125  -1.3624   0.0977
 4F2  H081  H  HCH1  0   0.234   -3.8364   0.8376   1.0932
 4F2  H091  H  HCH2  0   0.241   -4.0238   1.1886  -1.3407
 4F2  H092  H  HCH2  0   0.217   -3.5650  -0.4812  -1.6374
 4F2  H141  H  HNH1  0   0.393    0.4741   1.0615  -0.1570
 4F2  H171  H  HCR6  0   0.278    2.0868  -3.8747  -0.3726
 4F2  H271  H  HCH2  0   0.225    7.6492   2.2062   0.7876
 4F2  H272  H  HCH2  0   0.227    6.8399   3.5598   1.5700
 4F2  C05   C  C     0   0.739   -6.3326   0.4753   0.4496

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
 4F2  C19  C20   double    1.346  0.020  1.346
 4F2  C19  C18   single    1.419  0.020  1.419
 4F2  C20  C21   single    1.450  0.020  1.450
 4F2  C17  C18   aromatic  1.394  0.020  1.394
 4F2  C17  N16   aromatic  1.312  0.020  1.312
 4F2  C18  C29   aromatic  1.410  0.020  1.410
 4F2  N16  C15   aromatic  1.347  0.020  1.347
 4F2  C21  O22   double    1.222  0.020  1.222
 4F2  C21  N23   single    1.395  0.020  1.395
 4F2  C29  N23   single    1.374  0.020  1.374
 4F2  C29  N30   aromatic  1.320  0.020  1.320
 4F2  N23  C24   single    1.470  0.020  1.470
 4F2  C15  N30   aromatic  1.335  0.020  1.335
 4F2  C15  N14   single    1.339  0.020  1.339
 4F2  C28  C24   single    1.549  0.020  1.549
 4F2  C28  C27   single    1.532  0.020  1.532
 4F2  N14  C11   single    1.449  0.020  1.449
 4F2  C12  C11   single    1.529  0.020  1.529
 4F2  C12  C13   single    1.525  0.020  1.525
 4F2  C24  C25   single    1.537  0.020  1.537
 4F2  C11  C10   single    1.525  0.020  1.525
 4F2  C13  C08   single    1.525  0.020  1.525
 4F2  C27  C26   single    1.529  0.020  1.529
 4F2  C25  C26   single    1.526  0.020  1.526
 4F2  C01  C02   single    1.526  0.020  1.526
 4F2  C10  C09   single    1.524  0.020  1.524
 4F2  C08  C09   single    1.529  0.020  1.529
 4F2  C08  N07   single    1.447  0.020  1.447
 4F2  C03  C02   single    1.522  0.020  1.522
 4F2  N04  C02   single    1.452  0.020  1.452
 4F2  N04  C05   single    1.358  0.020  1.358
 4F2  N07  C05   single    1.362  0.020  1.362
 4F2  C05  O06   double    1.228  0.020  1.228
 4F2  C10  H101  single    0.970  0.020  1.090
 4F2  C10  H102  single    0.970  0.020  1.090
 4F2  C11  H111  single    0.970  0.020  1.090
 4F2  C12  H121  single    0.970  0.020  1.090
 4F2  C12  H122  single    0.970  0.020  1.090
 4F2  C13  H131  single    0.970  0.020  1.090
 4F2  C13  H132  single    0.970  0.020  1.090
 4F2  C19  H191  single    0.930  0.020  1.080
 4F2  C20  H201  single    0.930  0.020  1.080
 4F2  C24  H241  single    0.970  0.020  1.090
 4F2  C25  H252  single    0.970  0.020  1.090
 4F2  C25  H251  single    0.970  0.020  1.090
 4F2  C26  H262  single    0.970  0.020  1.090
 4F2  C26  H261  single    0.970  0.020  1.090
 4F2  C28  H281  single    0.970  0.020  1.090
 4F2  C28  H282  single    0.970  0.020  1.090
 4F2  C01  H013  single    0.970  0.020  1.090
 4F2  C01  H012  single    0.970  0.020  1.090
 4F2  C01  H011  single    0.970  0.020  1.090
 4F2  C02  H021  single    0.970  0.020  1.090
 4F2  C03  H033  single    0.970  0.020  1.090
 4F2  C03  H031  single    0.970  0.020  1.090
 4F2  C03  H032  single    0.970  0.020  1.090
 4F2  N04  H041  single    0.860  0.020  1.020
 4F2  N07  H071  single    0.890  0.020  1.040
 4F2  C08  H081  single    0.970  0.020  1.090
 4F2  C09  H091  single    0.970  0.020  1.090
 4F2  C09  H092  single    0.970  0.020  1.090
 4F2  N14  H141  single    0.860  0.020  1.020
 4F2  C17  H171  single    0.930  0.020  1.080
 4F2  C27  H271  single    0.970  0.020  1.090
 4F2  C27  H272  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
 4F2  H102  C10  H101  106.90  3.000
 4F2  H102  C10  C09   110.20  3.000
 4F2  H101  C10  C09   109.33  3.000
 4F2  H102  C10  C11   109.88  3.000
 4F2  H101  C10  C11   109.29  3.000
 4F2  C09   C10  C11   111.13  3.000
 4F2  H111  C11  N14   107.90  3.000
 4F2  H111  C11  C12   108.50  3.000
 4F2  N14   C11  C12   112.03  3.000
 4F2  H111  C11  C10   108.49  3.000
 4F2  C12   C11  C10   110.72  3.000
 4F2  N14   C11  C10   109.10  3.000
 4F2  H122  C12  H121  106.94  3.000
 4F2  H122  C12  C13   109.70  3.000
 4F2  H121  C12  C13   110.07  3.000
 4F2  H122  C12  C11   108.90  3.000
 4F2  H121  C12  C11   109.65  3.000
 4F2  C13   C12  C11   111.47  3.000
 4F2  H132  C13  H131  106.86  3.000
 4F2  H132  C13  C08   109.89  3.000
 4F2  H131  C13  C08   109.55  3.000
 4F2  H132  C13  C12   110.02  3.000
 4F2  H131  C13  C12   109.41  3.000
 4F2  C08   C13  C12   111.02  3.000
 4F2  C17   C18  C29   115.49  3.000
 4F2  C29   C18  C19   119.78  3.000
 4F2  C17   C18  C19   124.73  3.000
 4F2  H191  C19  C20   121.01  3.000
 4F2  H191  C19  C18   119.31  3.000
 4F2  C20   C19  C18   119.68  3.000
 4F2  H201  C20  C21   116.50  3.000
 4F2  H201  C20  C19   121.80  3.000
 4F2  C21   C20  C19   121.69  3.000
 4F2  N23   C21  O22   120.47  3.000
 4F2  N23   C21  C20   117.24  3.000
 4F2  O22   C21  C20   122.29  3.000
 4F2  H241  C24  N23   104.42  3.000
 4F2  H241  C24  C28   107.65  3.000
 4F2  N23   C24  C28   115.75  3.000
 4F2  H241  C24  C25   107.46  3.000
 4F2  C28   C24  C25   106.73  3.000
 4F2  N23   C24  C25   114.37  3.000
 4F2  H251  C25  H252  107.69  3.000
 4F2  H251  C25  C26   113.53  3.000
 4F2  H252  C25  C26   109.69  3.000
 4F2  H251  C25  C24   111.36  3.000
 4F2  H252  C25  C24   111.69  3.000
 4F2  C26   C25  C24   102.91  3.000
 4F2  H261  C26  H262  107.30  3.000
 4F2  H261  C26  C27   110.01  3.000
 4F2  H262  C26  C27   113.24  3.000
 4F2  H261  C26  C25   110.20  3.000
 4F2  H262  C26  C25   112.85  3.000
 4F2  C27   C26  C25   103.23  3.000
 4F2  H282  C28  H281  106.69  3.000
 4F2  H282  C28  C27   112.59  3.000
 4F2  H281  C28  C27   110.20  3.000
 4F2  H282  C28  C24   113.58  3.000
 4F2  H281  C28  C24   108.48  3.000
 4F2  C27   C28  C24   105.26  3.000
 4F2  N30   C29  N23   118.97  3.000
 4F2  N30   C29  C18   121.24  3.000
 4F2  N23   C29  C18   119.79  3.000
 4F2  N30   C15  N16   125.61  3.000
 4F2  N30   C15  N14   116.39  3.000
 4F2  N16   C15  N14   118.00  3.000
 4F2  H011  C01  H012  107.85  3.000
 4F2  H011  C01  H013  108.29  3.000
 4F2  H012  C01  H013  107.89  3.000
 4F2  H011  C01  C02   111.20  3.000
 4F2  H012  C01  C02   110.66  3.000
 4F2  H013  C01  C02   110.81  3.000
 4F2  H021  C02  N04   107.44  3.000
 4F2  H021  C02  C03   108.37  3.000
 4F2  N04   C02  C03   108.86  3.000
 4F2  H021  C02  C01   108.61  3.000
 4F2  N04   C02  C01   112.13  3.000
 4F2  C03   C02  C01   111.28  3.000
 4F2  H032  C03  H031  108.03  3.000
 4F2  H032  C03  H033  107.58  3.000
 4F2  H031  C03  H033  108.19  3.000
 4F2  H032  C03  C02   110.40  3.000
 4F2  H031  C03  C02   111.43  3.000
 4F2  H033  C03  C02   111.08  3.000
 4F2  H041  N04  C05   118.76  3.000
 4F2  H041  N04  C02   116.75  3.000
 4F2  C05   N04  C02   122.81  3.000
 4F2  H071  N07  C08   116.46  3.000
 4F2  H071  N07  C05   118.26  3.000
 4F2  C08   N07  C05   122.33  3.000
 4F2  H081  C08  C09   108.40  3.000
 4F2  H081  C08  N07   107.45  3.000
 4F2  C09   C08  N07   112.37  3.000
 4F2  H081  C08  C13   107.98  3.000
 4F2  N07   C08  C13   110.02  3.000
 4F2  C09   C08  C13   110.47  3.000
 4F2  H092  C09  H091  106.86  3.000
 4F2  H092  C09  C08   109.00  3.000
 4F2  H091  C09  C08   109.64  3.000
 4F2  H092  C09  C10   109.69  3.000
 4F2  H091  C09  C10   109.87  3.000
 4F2  C08   C09  C10   111.67  3.000
 4F2  H141  N14  C15   115.71  3.000
 4F2  H141  N14  C11   117.73  3.000
 4F2  C15   N14  C11   125.53  3.000
 4F2  C17   N16  C15   115.82  3.000
 4F2  H171  C17  N16   116.95  3.000
 4F2  H171  C17  C18   119.16  3.000
 4F2  N16   C17  C18   123.90  3.000
 4F2  C29   N23  C24   119.34  3.000
 4F2  C24   N23  C21   118.83  3.000
 4F2  C29   N23  C21   121.82  3.000
 4F2  H272  C27  H271  107.56  3.000
 4F2  H272  C27  C28   112.55  3.000
 4F2  H271  C27  C28   110.05  3.000
 4F2  H272  C27  C26   112.97  3.000
 4F2  H271  C27  C26   109.60  3.000
 4F2  C28   C27  C26   104.10  3.000
 4F2  C15   N30  C29   117.94  3.000
 4F2  N07   C05  O06   122.57  3.000
 4F2  O06   C05  N04   122.61  3.000
 4F2  N07   C05  N04   114.78  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
 4F2  CONST_01  C15   N16  C17  C18    0.00   0.0  0
 4F2  CONST_02  C15   N30  C29  C18    0.00   0.0  0
 4F2  CONST_03  N16   C17  C18  C29    0.00   0.0  0
 4F2  CONST_04  N16   C15  N30  C29    0.00   0.0  0
 4F2  CONST_05  N30   C29  C18  C17    0.00   0.0  0
 4F2  CONST_06  N30   C15  N16  C17    0.00   0.0  0
 4F2  CONST_07  C29   N23  C21  C20    0.00   0.0  0
 4F2  CONST_08  C24   N23  C21  C20  180.00   0.0  0
 4F2  CONST_09  N14   C15  N30  C29  180.00   0.0  0
 4F2  CONST_10  C17   N16  C15  N14  180.00   0.0  0
 4F2  CONST_11  N16   C15  N14  C11    0.00   0.0  0
 4F2  CONST_12  N30   C15  N14  C11  180.00   0.0  0
 4F2  CONST_13  O22   C21  N23  C24    0.00   0.0  0
 4F2  CONST_14  O22   C21  N23  C29  180.00   0.0  0
 4F2  CONST_15  H171  C17  C18  C19    0.00   0.0  0
 4F2  CONST_16  H141  N14  C15  N16  180.00   0.0  0
 4F2  CONST_17  C08   N07  C05  O06    0.00   0.0  0
 4F2  CONST_18  C08   N07  C05  N04  180.00   0.0  0
 4F2  CONST_19  O06   C05  N04  C02    0.00   0.0  0
 4F2  CONST_20  N07   C05  N04  C02  180.00   0.0  0
 4F2  CONST_21  H041  N04  C05  O06  180.00   0.0  0
 4F2  CONST_22  H071  N07  C05  O06  180.00   0.0  0
 4F2  Var_01    C08   C13  C12  C11  -56.40  30.0  1
 4F2  Var_02    C08   C09  C10  C11   55.81  30.0  1
 4F2  Var_03    C26   C27  C28  C24   24.27  30.0  1
 4F2  Var_04    C27   C26  C25  C24   40.53  30.0  1
 4F2  Var_05    C28   C27  C26  C25  -40.59  30.0  1
 4F2  Var_06    C05   N04  C02  C01   78.85  30.0  2
 4F2  Var_07    H033  C03  C02  C01   60.83  30.0  3
 4F2  Var_08    H013  C01  C02  C03  -60.01  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
 4F2  chir_01  C11  N14  C12  C10  negativ
 4F2  chir_02  C24  N23  C28  C25  negativ
 4F2  chir_03  C08  C13  C09  N07  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
 4F2  plan-1  C02   0.020
 4F2  plan-1  N04   0.020
 4F2  plan-1  O06   0.020
 4F2  plan-1  N07   0.020
 4F2  plan-1  C08   0.020
 4F2  plan-1  H041  0.020
 4F2  plan-1  H071  0.020
 4F2  plan-1  C05   0.020
 4F2  plan-2  C18   0.020
 4F2  plan-2  C19   0.020
 4F2  plan-2  C20   0.020
 4F2  plan-2  C21   0.020
 4F2  plan-2  C24   0.020
 4F2  plan-2  C29   0.020
 4F2  plan-2  C15   0.020
 4F2  plan-2  N14   0.020
 4F2  plan-2  N16   0.020
 4F2  plan-2  C17   0.020
 4F2  plan-2  O22   0.020
 4F2  plan-2  N23   0.020
 4F2  plan-2  N30   0.020
 4F2  plan-2  H191  0.020
 4F2  plan-2  H201  0.020
 4F2  plan-2  H171  0.020
 4F2  plan-3  C11   0.020
 4F2  plan-3  C15   0.020
 4F2  plan-3  N14   0.020
 4F2  plan-3  H141  0.020

