# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:28:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-(trans-4-{(1S,2S)-2-amino-3-[(3S)-3-fluoropyrrolidin-1-yl]-1-methyl-3-oxopropyl}cyclohexyl)-N-methylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]([C@H](N)C(=O)N1CC[C@H](F)C1)[C@@H]2CC[C@H](CC2)N(C)C(C)=O
#
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
 277  277  N-(trans-4-{(1S,2S)-2-amino-3-[(3S)-3-fluoropyrrolidin-1-yl]-1-methyl-3-oxopropyl}cyclohexyl)-N-methylacetamide  ligand  53  23  .  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_277
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
 277  C1    C  CH2   0  -0.421  -0.7754  -3.7601  -1.2805
 277  C2    C  CH2   0  -0.446   0.7031  -3.3898  -1.1883
 277  C3    C  CH1   0  -0.202   0.9175  -2.1341  -0.3436
 277  C4    C  CH2   0  -0.427   0.0877  -0.9795  -0.9071
 277  C5    C  CH2   0  -0.424  -1.3932  -1.3382  -0.9870
 277  C6    C  CH1   0  -0.089  -1.5943  -2.5950  -1.8314
 277  C15   C  CH1   0  -0.225   2.3944  -1.7414  -0.1667
 277  C17   C  CH1   0  -0.203   3.1910  -2.8121   0.6036
 277  C18   C  C     0   0.547   4.6013  -2.2842   0.8887
 277  N19   N  NT    0  -0.480   5.6480  -2.8639   0.2825
 277  N20   N  NT    0  -0.445  -3.0063  -2.9338  -1.9847
 277  C22   C  C     0   0.512  -3.5875  -2.9023  -3.2051
 277  C23   C  CH3   0  -0.546  -3.7752  -3.2543  -0.7956
 277  C27   C  CH3   0  -0.795  -5.0594  -3.2376  -3.2540
 277  O31   O  O     0  -0.516  -2.9733  -2.6233  -4.2301
 277  O32   O  O     0  -0.512   4.7563  -1.3652   1.6885
 277  N33   N  NH2   0  -0.776   2.5226  -3.1747   1.8415
 277  C35   C  CH3   0  -0.695   3.0831  -1.4036  -1.4887
 277  C42   C  CH2   0  -0.324   5.6008  -3.9125  -0.7323
 277  C43   C  CH1   0   0.150   7.0178  -3.9545  -1.2664
 277  C44   C  CH2   0  -0.535   7.8581  -3.5376  -0.0798
 277  C45   C  CH2   0  -0.265   7.0172  -2.4564   0.5878
 277  F52   F  F     0  -0.383   7.1503  -2.9970  -2.2778
 277  H11   H  HCH2  0   0.234  -0.9039  -4.6347  -1.9233
 277  H12   H  HCH2  0   0.216  -1.1330  -4.0392  -0.2840
 277  H21   H  HCH2  0   0.235   1.2519  -4.2362  -0.7685
 277  H22   H  HCH2  0   0.214   1.0949  -3.2361  -2.1995
 277  H3    H  HCH1  0   0.223   0.5283  -2.3497   0.6576
 277  H41   H  HCH2  0   0.214   0.4386  -0.7119  -1.9092
 277  H42   H  HCH2  0   0.227   0.2151  -0.0904  -0.2826
 277  H51   H  HCH2  0   0.216  -1.7806  -1.4915   0.0263
 277  H52   H  HCH2  0   0.234  -1.9595  -0.5104  -1.4216
 277  H6    H  HCH1  0   0.248  -1.2259  -2.3791  -2.8353
 277  H15   H  HCH1  0   0.223   2.4054  -0.8359   0.4538
 277  H17   H  HCH1  0   0.252   3.2379  -3.7166  -0.0064
 277  H231  H  HCH3  0   0.252  -4.2421  -4.2372  -0.8641
 277  H232  H  HCH3  0   0.249  -4.5540  -2.5167  -0.5960
 277  H233  H  HCH3  0   0.264  -3.1193  -3.2742   0.0697
 277  H271  H  HCH3  0   0.264  -5.4165  -3.1449  -4.2765
 277  H272  H  HCH3  0   0.263  -5.2477  -4.2567  -2.9130
 277  H273  H  HCH3  0   0.261  -5.6471  -2.5737  -2.6189
 277  H331  H  HNH2  0   0.352   3.0172  -3.9355   2.2909
 277  H332  H  HNH2  0   0.340   2.5577  -2.3936   2.4855
 277  H351  H  HCH3  0   0.239   4.1121  -1.0711  -1.3436
 277  H352  H  HCH3  0   0.246   2.5693  -0.5967  -2.0100
 277  H353  H  HCH3  0   0.224   3.1106  -2.2607  -2.1629
 277  H421  H  HCH2  0   0.271   4.8888  -3.6952  -1.5281
 277  H422  H  HCH2  0   0.263   5.3377  -4.8815  -0.3002
 277  H43   H  HCH1  0   0.247   7.2805  -4.9237  -1.6899
 277  H441  H  HCH2  0   0.273   8.8537  -3.1982  -0.3623
 277  H442  H  HCH2  0   0.258   7.9728  -4.3958   0.5853
 277  H451  H  HCH2  0   0.254   7.1791  -2.4084   1.6639
 277  H452  H  HCH2  0   0.244   7.2290  -1.4662   0.1766

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
 277  C1   C2    single  1.527  0.020  1.527
 277  C1   C6    single  1.527  0.020  1.527
 277  C1   H11   single  0.970  0.020  1.090
 277  C1   H12   single  0.970  0.020  1.090
 277  C2   C3    single  1.529  0.020  1.529
 277  C2   H21   single  0.970  0.020  1.090
 277  C2   H22   single  0.970  0.020  1.090
 277  C3   C15   single  1.538  0.020  1.538
 277  C3   C4    single  1.530  0.020  1.530
 277  C3   H3    single  0.970  0.020  1.090
 277  C4   C5    single  1.526  0.020  1.526
 277  C4   H41   single  0.970  0.020  1.090
 277  C4   H42   single  0.970  0.020  1.090
 277  C5   C6    single  1.527  0.020  1.527
 277  C5   H51   single  0.970  0.020  1.090
 277  C5   H52   single  0.970  0.020  1.090
 277  C6   N20   single  1.460  0.020  1.460
 277  C6   H6    single  0.970  0.020  1.090
 277  C15  C17   single  1.541  0.020  1.541
 277  C15  C35   single  1.528  0.020  1.528
 277  C15  H15   single  0.970  0.020  1.090
 277  C17  N33   single  1.453  0.020  1.453
 277  C17  C18   single  1.533  0.020  1.533
 277  C17  H17   single  0.970  0.020  1.090
 277  C18  N19   single  1.341  0.020  1.341
 277  C18  O32   double  1.228  0.020  1.228
 277  N19  C42   single  1.460  0.020  1.460
 277  N19  C45   single  1.461  0.020  1.461
 277  N20  C23   single  1.452  0.020  1.452
 277  N20  C22   single  1.352  0.020  1.352
 277  C22  O31   double  1.227  0.020  1.227
 277  C22  C27   single  1.510  0.020  1.510
 277  C23  H231  single  0.970  0.020  1.090
 277  C23  H232  single  0.970  0.020  1.090
 277  C23  H233  single  0.970  0.020  1.090
 277  C27  H271  single  0.970  0.020  1.090
 277  C27  H272  single  0.970  0.020  1.090
 277  C27  H273  single  0.970  0.020  1.090
 277  N33  H331  single  0.890  0.020  1.040
 277  N33  H332  single  0.890  0.020  1.040
 277  C35  H351  single  0.970  0.020  1.090
 277  C35  H352  single  0.970  0.020  1.090
 277  C35  H353  single  0.970  0.020  1.090
 277  C42  C43   single  1.515  0.020  1.515
 277  C42  H421  single  0.970  0.020  1.090
 277  C42  H422  single  0.970  0.020  1.090
 277  C43  C44   single  1.513  0.020  1.513
 277  C43  F52   single  1.399  0.020  1.399
 277  C43  H43   single  0.970  0.020  1.090
 277  C44  C45   single  1.524  0.020  1.524
 277  C44  H441  single  0.970  0.020  1.090
 277  C44  H442  single  0.970  0.020  1.090
 277  C45  H451  single  0.970  0.020  1.090
 277  C45  H452  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
 277  H12   C1   H11   107.03  3.000
 277  H12   C1   C6    110.35  3.000
 277  H11   C1   C6    109.60  3.000
 277  H12   C1   C2    108.85  3.000
 277  H11   C1   C2    110.08  3.000
 277  C6    C1   C2    110.86  3.000
 277  H22   C2   H21   106.49  3.000
 277  H22   C2   C3    110.17  3.000
 277  H21   C2   C3    110.70  3.000
 277  H22   C2   C1    108.94  3.000
 277  H21   C2   C1    108.77  3.000
 277  C3    C2   C1    111.62  3.000
 277  H3    C3   C15   106.63  3.000
 277  H3    C3   C4    107.01  3.000
 277  C15   C3   C4    111.75  3.000
 277  H3    C3   C2    107.07  3.000
 277  C4    C3   C2    109.90  3.000
 277  C15   C3   C2    114.07  3.000
 277  H42   C4   H41   106.65  3.000
 277  H42   C4   C5    109.51  3.000
 277  H41   C4   C5    108.70  3.000
 277  H42   C4   C3    109.88  3.000
 277  H41   C4   C3    110.35  3.000
 277  C5    C4   C3    111.62  3.000
 277  H52   C5   H51   106.88  3.000
 277  H52   C5   C6    109.58  3.000
 277  H51   C5   C6    110.46  3.000
 277  H52   C5   C4    110.22  3.000
 277  H51   C5   C4    109.12  3.000
 277  C6    C5   C4    110.50  3.000
 277  H6    C6   N20   106.01  3.000
 277  H6    C6   C5    107.54  3.000
 277  N20   C6   C5    112.11  3.000
 277  H6    C6   C1    107.57  3.000
 277  N20   C6   C1    112.30  3.000
 277  C5    C6   C1    110.97  3.000
 277  H15   C15  C35   107.58  3.000
 277  H15   C15  C17   106.58  3.000
 277  C35   C15  C17   110.67  3.000
 277  H15   C15  C3    106.57  3.000
 277  C35   C15  C3    112.93  3.000
 277  C17   C15  C3    112.11  3.000
 277  H17   C17  N33   106.80  3.000
 277  H17   C17  C18   110.47  3.000
 277  N33   C17  C18   110.54  3.000
 277  H17   C17  C15   108.57  3.000
 277  C18   C17  C15   109.23  3.000
 277  N33   C17  C15   111.19  3.000
 277  O32   C18  N19   121.28  3.000
 277  O32   C18  C17   119.67  3.000
 277  N19   C18  C17   119.02  3.000
 277  C45   N19  C42   112.08  3.000
 277  C45   N19  C18   121.10  3.000
 277  C42   N19  C18   126.82  3.000
 277  C23   N20  C22   121.11  3.000
 277  C22   N20  C6    120.33  3.000
 277  C23   N20  C6    118.52  3.000
 277  O31   C22  C27   120.75  3.000
 277  C27   C22  N20   116.29  3.000
 277  O31   C22  N20   122.96  3.000
 277  H233  C23  H232  107.32  3.000
 277  H233  C23  H231  106.99  3.000
 277  H232  C23  H231  108.38  3.000
 277  H233  C23  N20   109.68  3.000
 277  H232  C23  N20   112.25  3.000
 277  H231  C23  N20   111.98  3.000
 277  H273  C27  H272  107.08  3.000
 277  H273  C27  H271  108.58  3.000
 277  H272  C27  H271  108.48  3.000
 277  H273  C27  C22   111.79  3.000
 277  H272  C27  C22   111.44  3.000
 277  H271  C27  C22   109.37  3.000
 277  H332  N33  H331  106.28  3.000
 277  H332  N33  C17   109.47  3.000
 277  H331  N33  C17   109.93  3.000
 277  H353  C35  H352  107.34  3.000
 277  H353  C35  H351  107.33  3.000
 277  H352  C35  H351  106.42  3.000
 277  H353  C35  C15   111.86  3.000
 277  H352  C35  C15   111.42  3.000
 277  H351  C35  C15   112.17  3.000
 277  H422  C42  H421  107.95  3.000
 277  H422  C42  C43   109.87  3.000
 277  H421  C42  C43   111.05  3.000
 277  H422  C42  N19   111.70  3.000
 277  H421  C42  N19   112.68  3.000
 277  C43   C42  N19   103.58  3.000
 277  H43   C43  F52   107.75  3.000
 277  H43   C43  C44   114.58  3.000
 277  F52   C43  C44   109.02  3.000
 277  H43   C43  C42   112.78  3.000
 277  F52   C43  C42   108.93  3.000
 277  C44   C43  C42   103.62  3.000
 277  H442  C44  H441  107.87  3.000
 277  H442  C44  C45   110.42  3.000
 277  H441  C44  C45   113.39  3.000
 277  H442  C44  C43   108.64  3.000
 277  H441  C44  C43   112.97  3.000
 277  C45   C44  C43   103.46  3.000
 277  H452  C45  H451  107.64  3.000
 277  H452  C45  C44   111.78  3.000
 277  H451  C45  C44   112.46  3.000
 277  H452  C45  N19   110.84  3.000
 277  H451  C45  N19   110.98  3.000
 277  C44   C45  N19   103.16  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
 277  CONST_01  C42   N19  C18  C17     0.00   0.0  0
 277  CONST_02  C45   N19  C18  C17   180.00   0.0  0
 277  CONST_03  C42   N19  C18  O32   180.00   0.0  0
 277  CONST_04  C45   N19  C18  O32     0.00   0.0  0
 277  CONST_05  O31   C22  N20  C6      0.00   0.0  0
 277  CONST_06  C27   C22  N20  C6    180.00   0.0  0
 277  CONST_07  O31   C22  N20  C23   180.00   0.0  0
 277  CONST_08  C27   C22  N20  C23     0.00   0.0  0
 277  Var_01    C6    C1   C2   C3     56.19  30.0  1
 277  Var_02    C6    C5   C4   C3    -56.94  30.0  1
 277  Var_03    C43   C44  C45  N19    30.67  30.0  1
 277  Var_04    C44   C45  N19  C42   -12.20  30.0  1
 277  Var_05    C45   N19  C42  C43   -11.22  30.0  1
 277  Var_06    H231  C23  N20  C6   -123.62  30.0  3
 277  Var_07    H271  C27  C22  N20   178.05  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
 277  chir_01  C3   C2   C15  C4   negativ
 277  chir_02  C6   N20  C5   C1   negativ
 277  chir_03  C15  C3   C17  C35  negativ
 277  chir_04  C17  N33  C15  C18  negativ
 277  chir_05  C43  F52  C42  C44  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
 277  plan-1  C17  0.020
 277  plan-1  C18  0.020
 277  plan-1  N19  0.020
 277  plan-1  O32  0.020
 277  plan-1  C42  0.020
 277  plan-1  C45  0.020
 277  plan-2  C6   0.020
 277  plan-2  N20  0.020
 277  plan-2  C22  0.020
 277  plan-2  C23  0.020
 277  plan-2  C27  0.020
 277  plan-2  O31  0.020

