# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:40:38 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S,3S)-3-amino-4-(3,3-difluoropyrrolidin-1-yl)-N,N-dimethyl-4-oxo-2-(trans-4-[1,2,4]triazolo[1,5-a]pyridin-6-ylcyclohexyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H]([C@H](N)C(=O)N1CCC(F)(F)C1)[C@H]2CC[C@@H](CC2)c3ccc4ncnn4c3
#
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
 474  474  (2S,3S)-3-amino-4-(3,3-difluoropyrrolidin-1-yl)-N,N-dimethyl-4-oxo-2-(trans-4-[1,2,4]triazolo[1,5-a]pyridin-6-ylcyclohexyl)butanamide  ligand  62  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_474
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
 474  C1    C  CH1   0  -0.368  -1.3437   1.1811   0.0685
 474  C2    C  CH1   0  -0.205  -2.1927   0.8969  -1.1885
 474  C3    C  C     0   0.569  -3.6637   1.1606  -0.8444
 474  N4    N  NT    0  -0.489  -4.5241   0.1330  -0.7954
 474  C5    C  C     0   0.581  -1.8133   0.2636   1.1875
 474  N6    N  NH2   0  -0.776  -1.7510   1.7322  -2.2864
 474  O7    O  O     0  -0.503  -4.0368   2.3091  -0.6264
 474  O8    O  O     0  -0.506  -1.7168  -0.9561   1.0645
 474  N9    N  NT    0  -0.444  -2.3639   0.8022   2.2913
 474  C10   C  CH3   0  -0.520  -2.8661  -0.1186   3.2976
 474  C14   C  CH3   0  -0.548  -2.4394   2.2327   2.5460
 474  C18   C  CH2   0  -0.385  -4.2345  -1.2700  -1.0466
 474  C19   C  CT    0   0.723  -5.4625  -1.9507  -0.4716
 474  C20   C  CH2   0  -0.602  -6.5957  -0.9851  -0.7151
 474  C21   C  CH2   0  -0.271  -5.9348   0.3674  -0.4757
 474  F28   F  F     0  -0.345  -5.2957  -2.1454   0.8737
 474  C29   C  CH1   0  -0.350   2.9568   0.1191   0.1790
 474  C30   C  CH2   0  -0.407   2.4706   1.4331   0.7958
 474  C31   C  CH2   0  -0.440   0.9721   1.3877   1.0774
 474  C32   C  CH1   0  -0.191   0.1719   1.0696  -0.1872
 474  C33   C  CH2   0  -0.439   0.6550  -0.2489  -0.7885
 474  C34   C  CH2   0  -0.410   2.1511  -0.1962  -1.0852
 474  C48   C  CR56  0   0.545   7.1704   0.1245  -0.6184
 474  C49   C  CR16  0  -0.399   6.3634   1.1096  -1.2155
 474  C50   C  CR16  0  -0.182   5.0245   1.1000  -0.9515
 474  C51   C  CR6   0   0.039   4.4361   0.1297  -0.0938
 474  C52   C  CR16  0  -0.012   5.2425  -0.8111   0.4712
 474  N53   N  N     0  -0.363   6.5721  -0.7931   0.1990
 474  N54   N  N     0  -0.287   7.4852  -1.6487   0.6744
 474  C55   C  CR15  0   0.011   8.5974  -1.2062   0.1190
 474  N56   N  N     0  -0.491   8.4729  -0.1354  -0.6740
 474  F62   F  F     0  -0.334  -5.6629  -3.1829  -1.0022
 474  HN61  H  HNH2  0   0.357  -2.2209   1.4584  -3.1400
 474  HN62  H  HNH2  0   0.344  -2.0108   2.6958  -2.1115
 474  H2    H  HCH1  0   0.267  -2.0411  -0.1392  -1.4912
 474  H211  H  HCH2  0   0.254  -6.0393   0.6892   0.5625
 474  H212  H  HCH2  0   0.263  -6.3567   1.1464  -1.1086
 474  H201  H  HCH2  0   0.278  -6.9219  -1.0765  -1.7521
 474  H202  H  HCH2  0   0.291  -7.4521  -1.1635  -0.0662
 474  H181  H  HCH2  0   0.273  -4.1634  -1.4854  -2.1163
 474  H182  H  HCH2  0   0.292  -3.3233  -1.6051  -0.5555
 474  H1    H  HCH1  0   0.265  -1.5273   2.2237   0.3380
 474  H101  H  HCH3  0   0.238  -2.0594  -0.6378   3.8177
 474  H102  H  HCH3  0   0.243  -3.4420   0.4361   4.0320
 474  H103  H  HCH3  0   0.242  -3.5181  -0.8658   2.8480
 474  H141  H  HCH3  0   0.253  -3.0430   2.7490   1.8011
 474  H142  H  HCH3  0   0.262  -2.9046   2.3913   3.5144
 474  H143  H  HCH3  0   0.248  -1.4537   2.6967   2.5809
 474  H32   H  HCH1  0   0.229   0.3920   1.8521  -0.9210
 474  H311  H  HCH2  0   0.220   0.7794   0.6296   1.8457
 474  H312  H  HCH2  0   0.234   0.6577   2.3487   1.4952
 474  H302  H  HCH2  0   0.218   2.6790   2.2618   0.1106
 474  H29   H  HCH1  0   0.242   2.7617  -0.6800   0.9041
 474  H52   H  HCR6  0   0.309   4.8978  -1.5939   1.1316
 474  H55   H  HCR5  0   0.274   9.5421  -1.6950   0.3059
 474  H49   H  HCR6  0   0.284   6.8152   1.8457  -1.8650
 474  H50   H  HCR6  0   0.270   4.3950   1.8522  -1.4092
 474  H341  H  HCH2  0   0.217   2.3497   0.5664  -1.8470
 474  H342  H  HCH2  0   0.237   2.4804  -1.1503  -1.5043
 474  H331  H  HCH2  0   0.224   0.4579  -1.0725  -0.0998
 474  H332  H  HCH2  0   0.232   0.1164  -0.4730  -1.7121
 474  H301  H  HCH2  0   0.239   3.0193   1.6415   1.7176

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
 474  C1   C2    single    1.543  0.020  1.543
 474  C1   H1    single    0.970  0.020  1.090
 474  C1   C5    single    1.521  0.020  1.521
 474  C1   C32   single    1.541  0.020  1.541
 474  C2   N6    single    1.449  0.020  1.449
 474  C2   H2    single    0.970  0.020  1.090
 474  C2   C3    single    1.534  0.020  1.534
 474  C3   O7    double    1.227  0.020  1.227
 474  C3   N4    single    1.341  0.020  1.341
 474  N4   C21   single    1.465  0.020  1.465
 474  N4   C18   single    1.454  0.020  1.454
 474  C5   O8    double    1.230  0.020  1.230
 474  C5   N9    single    1.346  0.020  1.346
 474  N6   HN61  single    0.890  0.020  1.040
 474  N6   HN62  single    0.890  0.020  1.040
 474  N9   C10   single    1.454  0.020  1.454
 474  N9   C14   single    1.455  0.020  1.455
 474  C10  H101  single    0.970  0.020  1.090
 474  C10  H102  single    0.970  0.020  1.090
 474  C10  H103  single    0.970  0.020  1.090
 474  C14  H141  single    0.970  0.020  1.090
 474  C14  H142  single    0.970  0.020  1.090
 474  C14  H143  single    0.970  0.020  1.090
 474  C18  C19   single    1.517  0.020  1.517
 474  C18  H181  single    0.970  0.020  1.090
 474  C18  H182  single    0.970  0.020  1.090
 474  C19  C20   single    1.509  0.020  1.509
 474  C19  F62   single    1.356  0.020  1.356
 474  C19  F28   single    1.369  0.020  1.369
 474  C20  C21   single    1.524  0.020  1.524
 474  C20  H201  single    0.970  0.020  1.090
 474  C20  H202  single    0.970  0.020  1.090
 474  C21  H211  single    0.970  0.020  1.090
 474  C21  H212  single    0.970  0.020  1.090
 474  C29  C30   single    1.531  0.020  1.531
 474  C29  H29   single    0.970  0.020  1.090
 474  C29  C51   single    1.504  0.020  1.504
 474  C29  C34   single    1.532  0.020  1.532
 474  C30  C31   single    1.525  0.020  1.525
 474  C30  H301  single    0.970  0.020  1.090
 474  C30  H302  single    0.970  0.020  1.090
 474  C31  C32   single    1.530  0.020  1.530
 474  C31  H311  single    0.970  0.020  1.090
 474  C31  H312  single    0.970  0.020  1.090
 474  C32  H32   single    0.970  0.020  1.090
 474  C32  C33   single    1.528  0.020  1.528
 474  C33  C34   single    1.526  0.020  1.526
 474  C33  H331  single    0.970  0.020  1.090
 474  C33  H332  single    0.970  0.020  1.090
 474  C34  H341  single    0.970  0.020  1.090
 474  C34  H342  single    0.970  0.020  1.090
 474  C48  N53   aromatic  1.367  0.020  1.367
 474  C48  N56   aromatic  1.329  0.020  1.329
 474  C48  C49   aromatic  1.406  0.020  1.406
 474  C49  H49   single    0.930  0.020  1.080
 474  C49  C50   aromatic  1.365  0.020  1.365
 474  C50  C51   aromatic  1.422  0.020  1.422
 474  C50  H50   single    0.930  0.020  1.080
 474  C51  C52   aromatic  1.362  0.020  1.362
 474  C52  H52   single    0.930  0.020  1.080
 474  C52  N53   aromatic  1.357  0.020  1.357
 474  N53  N54   aromatic  1.339  0.020  1.339
 474  N54  C55   aromatic  1.320  0.020  1.320
 474  C55  N56   aromatic  1.338  0.020  1.338
 474  C55  H55   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
 474  H1    C1   C32   105.98  3.000
 474  C32   C1   C5    112.46  3.000
 474  H1    C1   C5    110.01  3.000
 474  C32   C1   C2    113.11  3.000
 474  C5    C1   C2    108.56  3.000
 474  H1    C1   C2    106.52  3.000
 474  H2    C2   N6    107.17  3.000
 474  H2    C2   C3    111.05  3.000
 474  N6    C2   C3    111.31  3.000
 474  C3    C2   C1    108.25  3.000
 474  H2    C2   C1    108.95  3.000
 474  N6    C2   C1    110.09  3.000
 474  O7    C3   N4    121.03  3.000
 474  N4    C3   C2    119.46  3.000
 474  O7    C3   C2    119.50  3.000
 474  C21   N4   C18   112.56  3.000
 474  C18   N4   C3    127.23  3.000
 474  C21   N4   C3    120.20  3.000
 474  N9    C5   O8    120.73  3.000
 474  N9    C5   C1    119.22  3.000
 474  O8    C5   C1    120.03  3.000
 474  HN62  N6   HN61  106.49  3.000
 474  HN62  N6   C2    109.84  3.000
 474  HN61  N6   C2    109.97  3.000
 474  C14   N9   C10   118.93  3.000
 474  C14   N9   C5    123.93  3.000
 474  C10   N9   C5    117.11  3.000
 474  H103  C10  H102  108.19  3.000
 474  H103  C10  H101  108.24  3.000
 474  H102  C10  H101  108.23  3.000
 474  H103  C10  N9    110.83  3.000
 474  H102  C10  N9    109.15  3.000
 474  H101  C10  N9    112.08  3.000
 474  H143  C14  H142  107.26  3.000
 474  H143  C14  H141  108.74  3.000
 474  H142  C14  H141  107.65  3.000
 474  H143  C14  N9    112.16  3.000
 474  H142  C14  N9    108.78  3.000
 474  H141  C14  N9    112.04  3.000
 474  H182  C18  H181  109.05  3.000
 474  H182  C18  C19   111.63  3.000
 474  H181  C18  C19   109.57  3.000
 474  H182  C18  N4    112.70  3.000
 474  H181  C18  N4    111.83  3.000
 474  C19   C18  N4    101.90  3.000
 474  F62   C19  F28   105.85  3.000
 474  F28   C19  C20   109.94  3.000
 474  F62   C19  C20   114.04  3.000
 474  F28   C19  C18   109.72  3.000
 474  F62   C19  C18   112.27  3.000
 474  C20   C19  C18   105.05  3.000
 474  H202  C20  H201  108.51  3.000
 474  H202  C20  C21   113.12  3.000
 474  H201  C20  C21   110.69  3.000
 474  H202  C20  C19   112.93  3.000
 474  H201  C20  C19   108.93  3.000
 474  C21   C20  C19   102.53  3.000
 474  H212  C21  H211  107.74  3.000
 474  H212  C21  C20   112.06  3.000
 474  H211  C21  C20   111.67  3.000
 474  H212  C21  N4    111.14  3.000
 474  H211  C21  N4    110.29  3.000
 474  C20   C21  N4    103.96  3.000
 474  H29   C29  C51   107.46  3.000
 474  C51   C29  C34   111.66  3.000
 474  H29   C29  C34   107.59  3.000
 474  C34   C29  C30   110.01  3.000
 474  C51   C29  C30   112.29  3.000
 474  H29   C29  C30   107.61  3.000
 474  H302  C30  H301  106.74  3.000
 474  H302  C30  C31   108.96  3.000
 474  H301  C30  C31   110.07  3.000
 474  H302  C30  C29   109.69  3.000
 474  H301  C30  C29   110.13  3.000
 474  C31   C30  C29   111.15  3.000
 474  H312  C31  H311  106.81  3.000
 474  H312  C31  C32   110.37  3.000
 474  H311  C31  C32   110.09  3.000
 474  H312  C31  C30   109.07  3.000
 474  H311  C31  C30   108.82  3.000
 474  C32   C31  C30   111.56  3.000
 474  H32   C32  C33   106.82  3.000
 474  C33   C32  C31   109.84  3.000
 474  H32   C32  C31   107.47  3.000
 474  C33   C32  C1    116.03  3.000
 474  H32   C32  C1    104.91  3.000
 474  C31   C32  C1    111.23  3.000
 474  H332  C33  H331  106.83  3.000
 474  H332  C33  C34   109.03  3.000
 474  H331  C33  C34   109.01  3.000
 474  H332  C33  C32   110.73  3.000
 474  H331  C33  C32   110.23  3.000
 474  C34   C33  C32   110.90  3.000
 474  H342  C34  H341  106.64  3.000
 474  H342  C34  C33   109.86  3.000
 474  H341  C34  C33   109.68  3.000
 474  H342  C34  C29   109.73  3.000
 474  H341  C34  C29   109.57  3.000
 474  C33   C34  C29   111.24  3.000
 474  N56   C48  N53   108.82  3.000
 474  N56   C48  C49   132.95  3.000
 474  N53   C48  C49   118.23  3.000
 474  H49   C49  C50   122.09  3.000
 474  C50   C49  C48   118.41  3.000
 474  H49   C49  C48   119.50  3.000
 474  H50   C50  C51   119.24  3.000
 474  H50   C50  C49   118.93  3.000
 474  C51   C50  C49   121.82  3.000
 474  C52   C51  C50   118.46  3.000
 474  C52   C51  C29   120.14  3.000
 474  C50   C51  C29   121.40  3.000
 474  H52   C52  N53   116.40  3.000
 474  N53   C52  C51   119.19  3.000
 474  H52   C52  C51   124.41  3.000
 474  N54   N53  C52   126.05  3.000
 474  N54   N53  C48   110.06  3.000
 474  C52   N53  C48   123.89  3.000
 474  C55   N54  N53   102.19  3.000
 474  H55   C55  N56   123.10  3.000
 474  H55   C55  N54   120.84  3.000
 474  N56   C55  N54   116.06  3.000
 474  C55   N56  C48   102.87  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
 474  CONST_01  C51   C52  N53  C48    0.00   0.0  0
 474  CONST_02  C55   N54  N53  C48    0.00   0.0  0
 474  CONST_03  N54   C55  N56  C48    0.00   0.0  0
 474  CONST_04  C51   C50  C49  C48    0.00   0.0  0
 474  CONST_05  C52   N53  C48  C49    0.00   0.0  0
 474  CONST_06  N54   N53  C48  C49  180.00   0.0  0
 474  CONST_07  C55   N56  C48  C49  180.00   0.0  0
 474  CONST_08  C52   C51  C50  C49    0.00   0.0  0
 474  CONST_09  N53   C48  C49  C50    0.00   0.0  0
 474  CONST_10  N56   C48  C49  C50  180.00   0.0  0
 474  CONST_11  N53   C52  C51  C50    0.00   0.0  0
 474  CONST_12  N54   N53  C52  C51  180.00   0.0  0
 474  CONST_13  N56   C48  N53  C52  180.00   0.0  0
 474  CONST_14  C55   N54  N53  C52  180.00   0.0  0
 474  CONST_15  C55   N56  C48  N53    0.00   0.0  0
 474  CONST_16  N56   C55  N54  N53    0.00   0.0  0
 474  CONST_17  N56   C48  N53  N54    0.00   0.0  0
 474  CONST_18  C49   C50  C51  C29  180.00   0.0  0
 474  CONST_19  N53   C52  C51  C29  180.00   0.0  0
 474  CONST_20  H50   C50  C51  C29    0.00   0.0  0
 474  CONST_21  H52   C52  C51  C29    0.00   0.0  0
 474  CONST_22  H55   C55  N56  C48  180.00   0.0  0
 474  CONST_23  H49   C49  C50  C51  180.00   0.0  0
 474  CONST_24  C21   N4   C3   C2   180.00   0.0  0
 474  CONST_25  C18   N4   C3   C2     0.00   0.0  0
 474  CONST_26  C21   N4   C3   O7     0.00   0.0  0
 474  CONST_27  C18   N4   C3   O7   180.00   0.0  0
 474  CONST_28  C10   N9   C5   C1   180.00   0.0  0
 474  CONST_29  C14   N9   C5   C1     0.00   0.0  0
 474  CONST_30  C10   N9   C5   O8     0.00   0.0  0
 474  CONST_31  C14   N9   C5   O8   180.00   0.0  0
 474  Var_01    C19   C20  C21  N4    27.20  30.0  1
 474  Var_02    C20   C19  C18  N4    32.98  30.0  1
 474  Var_03    C20   C21  N4   C18   -7.13  30.0  1
 474  Var_04    C21   C20  C19  C18  -37.71  30.0  1
 474  Var_05    C21   N4   C18  C19  -15.86  30.0  1
 474  Var_06    C32   C31  C30  C29  -56.56  30.0  1
 474  Var_07    C32   C33  C34  C29   57.69  30.0  1
 474  Var_08    H101  C10  N9   C5    70.66  30.0  3
 474  Var_09    H141  C14  N9   C5    62.60  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
 474  chir_01  C1   C2   C5   C32  negativ
 474  chir_02  C2   N6   C1   C3   negativ
 474  chir_03  C29  C30  C51  C34  positiv
 474  chir_04  C32  C33  C31  C1   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
 474  plan-1  C2   0.020
 474  plan-1  C3   0.020
 474  plan-1  N4   0.020
 474  plan-1  O7   0.020
 474  plan-1  C18  0.020
 474  plan-1  C21  0.020
 474  plan-2  C29  0.020
 474  plan-2  C48  0.020
 474  plan-2  C49  0.020
 474  plan-2  C50  0.020
 474  plan-2  C51  0.020
 474  plan-2  C52  0.020
 474  plan-2  N53  0.020
 474  plan-2  N54  0.020
 474  plan-2  C55  0.020
 474  plan-2  N56  0.020
 474  plan-2  H52  0.020
 474  plan-2  H55  0.020
 474  plan-2  H49  0.020
 474  plan-2  H50  0.020
 474  plan-3  C1   0.020
 474  plan-3  C5   0.020
 474  plan-3  O8   0.020
 474  plan-3  N9   0.020
 474  plan-3  C10  0.020
 474  plan-3  C14  0.020

