# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 11:05:30 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: ~{N}-[(2~{S})-3-(3-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(C[C@H](NC(=O)c2[nH]c3ccccc3c2)C(=O)N[C@@H](C[C@@H]4CCNC4=O)C=O)c1
#
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
 FJC  FJC  ~{N}-[(2~{S})-3-(3-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide  peptide  59  34  .  2022-03-18  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FJC
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
 FJC  C02  C  C     0   0.508  -11.7938  11.0357  69.0298
 FJC  C07  C  CR16  0  -0.270   -9.1587   5.9995  71.0550
 FJC  C08  C  CR16  0  -0.277   -9.6725   5.5190  69.8344
 FJC  C09  C  CR16  0  -0.307  -10.3781   6.3358  68.9772
 FJC  C10  C  CR56  0   0.354  -10.5651   7.6638  69.3680
 FJC  C05  C  CR56  0   0.070  -10.0577   8.1664  70.5884
 FJC  C06  C  CR16  0  -0.336   -9.3443   7.3091  71.4390
 FJC  C04  C  CR15  0  -0.424  -10.4362   9.5362  70.6572
 FJC  C03  C  CR5   0   0.264  -11.1370   9.8101  69.5110
 FJC  N11  N  NR15  0  -0.723  -11.2107   8.6816  68.7416
 FJC  O01  O  O     0  -0.480  -12.4988  11.0164  68.0294
 FJC  N12  N  NH1   0  -0.652  -11.5887  12.1489  69.7589
 FJC  C13  C  CH1   0  -0.199  -12.1425  13.4146  69.3553
 FJC  C22  C  C     0   0.574  -11.3687  13.9630  68.1543
 FJC  O34  O  O     0  -0.476  -10.1507  13.9397  68.1327
 FJC  C14  C  CH2   0  -0.559  -12.0739  14.4167  70.5134
 FJC  C15  C  CR6   0   0.170  -12.8580  13.9412  71.7043
 FJC  C21  C  CR16  0  -0.486  -12.2076  13.3881  72.8028
 FJC  C16  C  CR16  0  -0.313  -14.2492  14.0179  71.7082
 FJC  C19  C  CR6   0   0.544  -12.9575  12.9263  73.8682
 FJC  C18  C  CR16  0  -0.424  -14.3359  12.9906  73.8888
 FJC  C17  C  CR16  0  -0.223  -14.9781  13.5471  72.7898
 FJC  F20  F  F     0  -0.316  -12.3158  12.3938  74.9213
 FJC  C30  C  C     0   0.572  -12.3569  11.8343  63.7133
 FJC  N29  N  NH1   0  -0.629  -11.4836  10.8351  63.5089
 FJC  C28  C  CH2   0  -0.259  -10.3784  10.8053  64.4437
 FJC  C27  C  CH2   0  -0.470  -10.3751  12.2355  64.9839
 FJC  C26  C  CH1   0  -0.431  -11.8411  12.6556  64.8849
 FJC  C25  C  CH2   0  -0.433  -12.1090  14.1433  64.7272
 FJC  C24  C  CH1   0  -0.218  -11.6109  14.9581  65.9167
 FJC  N23  N  NH1   0  -0.638  -12.1330  14.4815  67.1767
 FJC  C32  C  C1    0   0.198  -11.9046  16.4383  65.7970
 FJC  O33  O  O     0  -0.365  -12.2563  16.9843  64.7852
 FJC  H12  H  HCR6  0   0.252   -8.6099   5.3237  71.6976
 FJC  H13  H  HCR6  0   0.256   -9.5092   4.4835  69.5653
 FJC  H14  H  HCR6  0   0.265  -10.7744   5.9634  68.0416
 FJC  H11  H  HCR6  0   0.253   -8.9475   7.6720  72.3788
 FJC  H10  H  HCR5  0   0.259  -10.2239  10.2173  71.4669
 FJC  H25  H  HNR5  0   0.409  -11.6962   8.6260  67.8606
 FJC  H1   H  HNH1  0   0.410  -10.8618  12.1512  70.4564
 FJC  H2   H  HCH1  0   0.290  -13.1904  13.2611  69.0858
 FJC  H15  H  HCH2  0   0.279  -11.0302  14.5891  70.7864
 FJC  H16  H  HCH2  0   0.288  -12.4692  15.3715  70.1606
 FJC  H4   H  HCR6  0   0.275  -11.1262  13.3270  72.8400
 FJC  H17  H  HCR6  0   0.256  -14.7664  14.4534  70.8619
 FJC  H18  H  HCR6  0   0.280  -14.8935  12.6205  74.7390
 FJC  H3   H  HCR6  0   0.269  -16.0578  13.6146  72.7837
 FJC  H7   H  HCH2  0   0.232  -10.5526  10.0762  65.2411
 FJC  H8   H  HCH2  0   0.252   -9.4473  10.5397  63.9445
 FJC  H21  H  HCH2  0   0.244   -9.7608  12.8728  64.3421
 FJC  H22  H  HCH2  0   0.258   -9.9771  12.2916  65.9944
 FJC  H6   H  HCH1  0   0.295  -12.3763  12.2811  65.7666
 FJC  H19  H  HCH2  0   0.251  -13.1807  14.3071  64.5893
 FJC  H20  H  HCH2  0   0.254  -11.6149  14.5132  63.8259
 FJC  H5   H  HCH1  0   0.307  -10.5187  14.8874  65.9841
 FJC  H26  H  HNH1  0   0.410  -13.1355  14.4013  67.2596
 FJC  H24  H  H     0   0.212  -11.7554  17.0005  66.7365
 FJC  H27  H  HNH1  0   0.396  -11.6748  10.0791  62.8697
 FJC  O31  O  O     0  -0.496  -13.3860  12.0328  63.0869

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
 FJC  C10  C05  aromatic  1.414  0.020  1.414
 FJC  C10  C09  aromatic  1.397  0.020  1.397
 FJC  C10  N11  aromatic  1.358  0.020  1.358
 FJC  N12  C13  single    1.439  0.020  1.439
 FJC  N12  C02  single    1.346  0.020  1.346
 FJC  C13  C22  single    1.530  0.020  1.530
 FJC  C13  C14  single    1.533  0.020  1.533
 FJC  C15  C21  aromatic  1.391  0.020  1.391
 FJC  C15  C14  single    1.503  0.020  1.503
 FJC  C15  C16  aromatic  1.393  0.020  1.393
 FJC  C17  C16  aromatic  1.387  0.020  1.387
 FJC  C17  C18  aromatic  1.389  0.020  1.389
 FJC  C21  C19  aromatic  1.382  0.020  1.382
 FJC  C22  N23  single    1.345  0.020  1.345
 FJC  C22  O34  double    1.218  0.020  1.218
 FJC  C24  C25  single    1.525  0.020  1.525
 FJC  C24  C32  single    1.514  0.020  1.514
 FJC  C24  N23  single    1.445  0.020  1.445
 FJC  C26  C25  single    1.520  0.020  1.520
 FJC  C26  C27  single    1.528  0.020  1.528
 FJC  C26  C30  single    1.521  0.020  1.521
 FJC  C28  N29  single    1.448  0.020  1.448
 FJC  C02  C03  single    1.471  0.020  1.471
 FJC  C02  O01  double    1.224  0.020  1.224
 FJC  C03  C04  aromatic  1.371  0.020  1.371
 FJC  C03  N11  aromatic  1.368  0.020  1.368
 FJC  C04  C05  aromatic  1.423  0.020  1.423
 FJC  C05  C06  aromatic  1.403  0.020  1.403
 FJC  C06  C07  aromatic  1.377  0.020  1.377
 FJC  C07  C08  aromatic  1.409  0.020  1.409
 FJC  C08  C09  aromatic  1.378  0.020  1.378
 FJC  C18  C19  aromatic  1.380  0.020  1.380
 FJC  C19  F20  single    1.343  0.020  1.343
 FJC  C30  N29  single    1.343  0.020  1.343
 FJC  C30  O31  double    1.221  0.020  1.221
 FJC  C32  O33  double    1.202  0.020  1.202
 FJC  N12  H1   single    0.860  0.020  1.020
 FJC  C13  H2   single    0.970  0.020  1.090
 FJC  C17  H3   single    0.930  0.020  1.080
 FJC  C21  H4   single    0.930  0.020  1.080
 FJC  C24  H5   single    0.970  0.020  1.090
 FJC  C26  H6   single    0.970  0.020  1.090
 FJC  C28  H7   single    0.970  0.020  1.090
 FJC  C28  H8   single    0.970  0.020  1.090
 FJC  C04  H10  single    0.930  0.020  1.080
 FJC  C06  H11  single    0.930  0.020  1.080
 FJC  C07  H12  single    0.930  0.020  1.080
 FJC  C08  H13  single    0.930  0.020  1.080
 FJC  C09  H14  single    0.930  0.020  1.080
 FJC  C14  H15  single    0.970  0.020  1.090
 FJC  C14  H16  single    0.970  0.020  1.090
 FJC  C16  H17  single    0.930  0.020  1.080
 FJC  C18  H18  single    0.930  0.020  1.080
 FJC  C25  H19  single    0.970  0.020  1.090
 FJC  C25  H20  single    0.970  0.020  1.090
 FJC  C27  H21  single    0.970  0.020  1.090
 FJC  C27  H22  single    0.970  0.020  1.090
 FJC  C32  H24  single    0.930  0.020  1.080
 FJC  N11  H25  single    0.860  0.020  1.020
 FJC  N23  H26  single    0.860  0.020  1.020
 FJC  N29  H27  single    0.860  0.020  1.020
 FJC  C28  C27  single    1.529  0.020  1.529

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
 FJC  N12  C02  O01  122.91  3.000
 FJC  O01  C02  C03  120.75  3.000
 FJC  N12  C02  C03  116.33  3.000
 FJC  H12  C07  C06  119.77  3.000
 FJC  H12  C07  C08  119.11  3.000
 FJC  C06  C07  C08  121.11  3.000
 FJC  H13  C08  C09  119.31  3.000
 FJC  H13  C08  C07  119.13  3.000
 FJC  C09  C08  C07  121.56  3.000
 FJC  H14  C09  C10  121.33  3.000
 FJC  H14  C09  C08  121.41  3.000
 FJC  C10  C09  C08  117.26  3.000
 FJC  N11  C10  C05  107.59  3.000
 FJC  N11  C10  C09  130.32  3.000
 FJC  C05  C10  C09  122.09  3.000
 FJC  C04  C05  C06  133.98  3.000
 FJC  C06  C05  C10  119.26  3.000
 FJC  C04  C05  C10  106.77  3.000
 FJC  H11  C06  C05  120.53  3.000
 FJC  H11  C06  C07  120.75  3.000
 FJC  C05  C06  C07  118.72  3.000
 FJC  H10  C04  C03  126.99  3.000
 FJC  H10  C04  C05  126.27  3.000
 FJC  C03  C04  C05  106.73  3.000
 FJC  N11  C03  C04  109.45  3.000
 FJC  N11  C03  C02  118.64  3.000
 FJC  C04  C03  C02  131.91  3.000
 FJC  H25  N11  C03  124.29  3.000
 FJC  H25  N11  C10  126.22  3.000
 FJC  C03  N11  C10  109.47  3.000
 FJC  H1   N12  C13  118.02  3.000
 FJC  H1   N12  C02  119.12  3.000
 FJC  C13  N12  C02  121.11  3.000
 FJC  H2   C13  C14  108.73  3.000
 FJC  H2   C13  C22  109.97  3.000
 FJC  C14  C13  C22  109.63  3.000
 FJC  H2   C13  N12  108.33  3.000
 FJC  C14  C13  N12  110.23  3.000
 FJC  C22  C13  N12  109.92  3.000
 FJC  N23  C22  O34  124.24  3.000
 FJC  O34  C22  C13  120.83  3.000
 FJC  N23  C22  C13  114.91  3.000
 FJC  H16  C14  H15  106.78  3.000
 FJC  H16  C14  C15  110.10  3.000
 FJC  H15  C14  C15  110.51  3.000
 FJC  H16  C14  C13  108.14  3.000
 FJC  H15  C14  C13  109.55  3.000
 FJC  C15  C14  C13  111.61  3.000
 FJC  C16  C15  C21  119.11  3.000
 FJC  C16  C15  C14  120.38  3.000
 FJC  C21  C15  C14  120.49  3.000
 FJC  H4   C21  C19  119.74  3.000
 FJC  H4   C21  C15  121.07  3.000
 FJC  C19  C21  C15  119.19  3.000
 FJC  H17  C16  C17  119.67  3.000
 FJC  H17  C16  C15  119.78  3.000
 FJC  C17  C16  C15  120.55  3.000
 FJC  F20  C19  C18  118.94  3.000
 FJC  F20  C19  C21  118.52  3.000
 FJC  C18  C19  C21  122.53  3.000
 FJC  H18  C18  C17  121.36  3.000
 FJC  H18  C18  C19  120.70  3.000
 FJC  C17  C18  C19  117.94  3.000
 FJC  H3   C17  C18  119.40  3.000
 FJC  H3   C17  C16  119.94  3.000
 FJC  C18  C17  C16  120.67  3.000
 FJC  C26  C30  N29  107.37  3.000
 FJC  N29  C30  O31  126.23  3.000
 FJC  C26  C30  O31  126.39  3.000
 FJC  H27  N29  C28  122.60  3.000
 FJC  H27  N29  C30  122.08  3.000
 FJC  C28  N29  C30  114.42  3.000
 FJC  H8   C28  H7   107.90  3.000
 FJC  H8   C28  C27  112.84  3.000
 FJC  H7   C28  C27  111.48  3.000
 FJC  C27  C28  N29  102.16  3.000
 FJC  H8   C28  N29  111.20  3.000
 FJC  H7   C28  N29  111.26  3.000
 FJC  H22  C27  H21  108.05  3.000
 FJC  H22  C27  C26  113.40  3.000
 FJC  H21  C27  C26  109.92  3.000
 FJC  H22  C27  C28  112.17  3.000
 FJC  H21  C27  C28  109.82  3.000
 FJC  C26  C27  C28  103.42  3.000
 FJC  H6   C26  C25  109.36  3.000
 FJC  H6   C26  C27  108.78  3.000
 FJC  C25  C26  C27  116.41  3.000
 FJC  H6   C26  C30  105.62  3.000
 FJC  C27  C26  C30  103.11  3.000
 FJC  C25  C26  C30  112.89  3.000
 FJC  H20  C25  H19  106.78  3.000
 FJC  H20  C25  C24  108.35  3.000
 FJC  H19  C25  C24  109.79  3.000
 FJC  H20  C25  C26  109.71  3.000
 FJC  H19  C25  C26  109.43  3.000
 FJC  C24  C25  C26  112.61  3.000
 FJC  H5   C24  C32  105.15  3.000
 FJC  H5   C24  N23  106.56  3.000
 FJC  C32  C24  N23  108.75  3.000
 FJC  H5   C24  C25  109.80  3.000
 FJC  N23  C24  C25  112.69  3.000
 FJC  C32  C24  C25  113.41  3.000
 FJC  H26  N23  C24  117.19  3.000
 FJC  H26  N23  C22  118.31  3.000
 FJC  C24  N23  C22  123.76  3.000
 FJC  H24  C32  O33  121.60  3.000
 FJC  H24  C32  C24  113.83  3.000
 FJC  O33  C32  C24  124.57  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
 FJC  CONST_01  C10  C05  C06  C07    0.00   0.0  0
 FJC  CONST_02  C04  C05  C06  C07  180.00   0.0  0
 FJC  CONST_03  C10  C09  C08  C07    0.00   0.0  0
 FJC  CONST_04  C05  C06  C07  C08    0.00   0.0  0
 FJC  CONST_05  C05  C10  C09  C08    0.00   0.0  0
 FJC  CONST_06  N11  C10  C09  C08  180.00   0.0  0
 FJC  CONST_07  C04  C05  C10  C09  180.00   0.0  0
 FJC  CONST_08  C06  C05  C10  C09    0.00   0.0  0
 FJC  CONST_09  C03  N11  C10  C09  180.00   0.0  0
 FJC  CONST_10  C06  C07  C08  C09    0.00   0.0  0
 FJC  CONST_11  C03  C04  C05  C10    0.00   0.0  0
 FJC  CONST_12  C04  C03  N11  C10    0.00   0.0  0
 FJC  CONST_13  C03  N11  C10  C05    0.00   0.0  0
 FJC  CONST_14  N11  C03  C04  C05    0.00   0.0  0
 FJC  CONST_15  N11  C10  C05  C06  180.00   0.0  0
 FJC  CONST_16  C03  C04  C05  C06  180.00   0.0  0
 FJC  CONST_17  N11  C10  C05  C04    0.00   0.0  0
 FJC  CONST_18  C18  C19  C21  C15    0.00   0.0  0
 FJC  CONST_19  C18  C17  C16  C15    0.00   0.0  0
 FJC  CONST_20  C17  C16  C15  C21    0.00   0.0  0
 FJC  CONST_21  C17  C18  C19  C21    0.00   0.0  0
 FJC  CONST_22  C19  C21  C15  C16    0.00   0.0  0
 FJC  CONST_23  C19  C18  C17  C16    0.00   0.0  0
 FJC  CONST_24  C26  C30  N29  C28    0.00   0.0  0
 FJC  CONST_25  C05  C04  C03  C02  180.00   0.0  0
 FJC  CONST_26  C10  N11  C03  C02  180.00   0.0  0
 FJC  CONST_27  C19  C21  C15  C14  180.00   0.0  0
 FJC  CONST_28  C17  C16  C15  C14  180.00   0.0  0
 FJC  CONST_29  F20  C19  C21  C15  180.00   0.0  0
 FJC  CONST_30  F20  C19  C18  C17  180.00   0.0  0
 FJC  CONST_31  C28  N29  C30  O31  180.00   0.0  0
 FJC  CONST_32  H14  C09  C08  C07  180.00   0.0  0
 FJC  CONST_33  H11  C06  C07  C08  180.00   0.0  0
 FJC  CONST_34  H25  N11  C10  C09    0.00   0.0  0
 FJC  CONST_35  H12  C07  C08  C09  180.00   0.0  0
 FJC  CONST_36  H10  C04  C05  C10  180.00   0.0  0
 FJC  CONST_37  H13  C08  C09  C10  180.00   0.0  0
 FJC  CONST_38  H3   C17  C16  C15  180.00   0.0  0
 FJC  CONST_39  H17  C16  C15  C21  180.00   0.0  0
 FJC  CONST_40  H18  C18  C19  C21  180.00   0.0  0
 FJC  CONST_41  H4   C21  C15  C16  180.00   0.0  0
 FJC  CONST_42  H27  N29  C30  C26  180.00   0.0  0
 FJC  CONST_43  C13  N12  C02  C03  180.00   0.0  0
 FJC  CONST_44  H1   N12  C02  C03    0.00   0.0  0
 FJC  CONST_45  C13  N12  C02  O01    0.00   0.0  0
 FJC  CONST_46  C24  N23  C22  C13  180.00   0.0  0
 FJC  CONST_47  C24  N23  C22  O34    0.00   0.0  0
 FJC  CONST_48  H26  N23  C22  C13    0.00   0.0  0
 FJC  Var_01    C27  C28  N29  C30  -20.15  30.0  1
 FJC  Var_02    C26  C27  C28  N29   29.37  30.0  1
 FJC  Var_03    N12  C02  C03  C04    7.26  30.0  2
 FJC  Var_04    C21  C15  C14  C13  102.30  30.0  2

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
 FJC  chir_01  C13  N12  C22  C14  positiv
 FJC  chir_02  C26  C25  C27  C30  positiv
 FJC  chir_03  C24  N23  C32  C25  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
 FJC  plan-1  C24  0.020
 FJC  plan-1  C32  0.020
 FJC  plan-1  O33  0.020
 FJC  plan-1  H24  0.020
 FJC  plan-2  C14  0.020
 FJC  plan-2  C15  0.020
 FJC  plan-2  C21  0.020
 FJC  plan-2  C16  0.020
 FJC  plan-2  C19  0.020
 FJC  plan-2  C18  0.020
 FJC  plan-2  C17  0.020
 FJC  plan-2  F20  0.020
 FJC  plan-2  H4   0.020
 FJC  plan-2  H17  0.020
 FJC  plan-2  H18  0.020
 FJC  plan-2  H3   0.020
 FJC  plan-3  C02  0.020
 FJC  plan-3  C07  0.020
 FJC  plan-3  C08  0.020
 FJC  plan-3  C09  0.020
 FJC  plan-3  C10  0.020
 FJC  plan-3  C05  0.020
 FJC  plan-3  C06  0.020
 FJC  plan-3  C04  0.020
 FJC  plan-3  C03  0.020
 FJC  plan-3  N11  0.020
 FJC  plan-3  H12  0.020
 FJC  plan-3  H13  0.020
 FJC  plan-3  H14  0.020
 FJC  plan-3  H11  0.020
 FJC  plan-3  H10  0.020
 FJC  plan-3  H25  0.020
 FJC  plan-4  C13  0.020
 FJC  plan-4  C22  0.020
 FJC  plan-4  O34  0.020
 FJC  plan-4  C24  0.020
 FJC  plan-4  N23  0.020
 FJC  plan-4  H26  0.020
 FJC  plan-5  C02  0.020
 FJC  plan-5  C03  0.020
 FJC  plan-5  O01  0.020
 FJC  plan-5  N12  0.020
 FJC  plan-5  C13  0.020
 FJC  plan-5  H1   0.020
 FJC  plan-6  C30  0.020
 FJC  plan-6  N29  0.020
 FJC  plan-6  C28  0.020
 FJC  plan-6  C26  0.020
 FJC  plan-6  H27  0.020
 FJC  plan-6  O31  0.020

