# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 17:30:02 2021
#   Inital geometry file: a 168 line input string
#   Ligand name: N-acetyl-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccc(cc1)C(F)(F)[P](O)(O)=O)C(=O)N[C@@H](CCCNC(=O)c2cccc(I)c2)C(N)=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
 75A  75A  N-acetyl-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithinamide  peptide  67  39  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_75A
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
 75A  C23  C  C     0   0.525  19.2875  -0.0941   -3.5970
 75A  O7   O  O     0  -0.490  19.6041  -1.1034   -2.9820
 75A  C24  C  CH3   0  -0.776  20.2437   0.6745   -4.4685
 75A  N1   N  NH1   0  -0.651  18.0239   0.3778   -3.5706
 75A  C9   C  CH1   0  -0.143  17.0061  -0.2122   -2.7342
 75A  C10  C  C     0   0.548  16.7683  -1.6859   -3.0481
 75A  O4   O  O     0  -0.469  16.4640  -2.4804   -2.1756
 75A  C8   C  CH2   0  -0.571  15.6965   0.5690   -2.9341
 75A  C5   C  CR6   0   0.139  14.5742   0.0447   -2.0871
 75A  C6   C  CR16  0  -0.284  13.5854  -0.7665   -2.6334
 75A  C4   C  CR16  0  -0.292  14.5114   0.3485   -0.7308
 75A  C7   C  CR16  0  -0.256  12.5599  -1.2684   -1.8485
 75A  C3   C  CR16  0  -0.269  13.4929  -0.1492    0.0646
 75A  C2   C  CR6   0  -0.140  12.5163  -0.9715   -0.4904
 75A  C1   C  CT    0   0.545  11.3925  -1.4835    0.3518
 75A  F1   F  F     0  -0.329  11.7728  -1.5925    1.6523
 75A  F2   F  F     0  -0.335  11.0083  -2.7283   -0.0520
 75A  P1   P  P     0   1.309   9.8922  -0.3930    0.2543
 75A  O2   O  O     0  -0.678   9.3496  -0.3608   -1.1185
 75A  O1   O  OH1   0  -0.732  10.3941   0.9722    0.9065
 75A  O3   O  OH1   0  -0.731   8.9418  -0.8802    1.4370
 75A  N2   N  NH1   0  -0.664  16.8409  -2.0245   -4.3465
 75A  N4   N  NH1   0  -0.642  15.6981  -3.4992   -9.1991
 75A  C11  C  CH1   0  -0.123  16.4823  -3.3437   -4.8132
 75A  C12  C  C     0   0.502  17.3316  -4.4444   -4.1773
 75A  C13  C  CH2   0  -0.487  16.6306  -3.3751   -6.3386
 75A  C14  C  CH2   0  -0.432  16.0317  -4.6094   -6.9968
 75A  C15  C  CH2   0  -0.306  16.2557  -4.6410   -8.5053
 75A  C16  C  C     0   0.534  16.4277  -2.4620   -9.6379
 75A  C17  C  CR6   0  -0.020  15.6593  -1.3530  -10.2916
 75A  C18  C  CR16  0  -0.292  14.3387  -1.0558   -9.9686
 75A  C19  C  CR16  0  -0.233  13.6895  -0.0005  -10.5915
 75A  C20  C  CR16  0  -0.224  14.3433   0.7670  -11.5447
 75A  C21  C  CR6   0  -0.207  15.6634   0.4682  -11.8536
 75A  C22  C  CR16  0  -0.241  16.3305  -0.5730  -11.2311
 75A  O5   O  O     0  -0.489  16.8561  -5.5530   -3.9795
 75A  O6   O  O     0  -0.485  17.6456  -2.3995   -9.5393
 75A  I    I  I     0   0.064  16.6745   1.6259  -13.2899
 75A  N3   N  NH2   0  -0.802  18.6179  -4.1419   -3.9590
 75A  H24  H  HCH3  0   0.267  21.2700   0.4404   -4.1986
 75A  H25  H  HCH3  0   0.276  20.0928   0.3936   -5.5124
 75A  H26  H  HCH3  0   0.261  20.0912   1.7504   -4.3927
 75A  H1   H  HNH1  0   0.415  17.8188   1.2529   -4.0277
 75A  H12  H  HCH1  0   0.286  17.2960  -0.1575   -1.6805
 75A  H10  H  HCH2  0   0.288  15.8908   1.6149   -2.6830
 75A  H11  H  HCH2  0   0.275  15.4146   0.5399   -3.9898
 75A  H8   H  HCR6  0   0.259  13.6131  -1.0117   -3.6882
 75A  H7   H  HCR6  0   0.260  15.2663   0.9850   -0.2851
 75A  H9   H  HCR6  0   0.268  11.8033  -1.8910   -2.3062
 75A  H6   H  HCR6  0   0.270  13.4728   0.1090    1.1146
 75A  H27  H  HOH1  0   0.508  10.6741   1.6421    0.2682
 75A  H28  H  HOH1  0   0.508   8.3417  -1.6018    1.2052
 75A  H2   H  HNH1  0   0.404  17.0497  -1.3116   -5.0295
 75A  H5   H  HNH1  0   0.408  14.7103  -3.5205   -9.3935
 75A  H13  H  HCH1  0   0.270  15.4423  -3.5630   -4.5504
 75A  H14  H  HCH2  0   0.245  17.6872  -3.2785   -6.6055
 75A  H15  H  HCH2  0   0.251  16.1270  -2.4865   -6.7307
 75A  H16  H  HCH2  0   0.232  14.9605  -4.6581   -6.7804
 75A  H17  H  HCH2  0   0.245  16.4700  -5.5217   -6.5887
 75A  H18  H  HCH2  0   0.262  15.8020  -5.5423   -8.9187
 75A  H19  H  HCH2  0   0.250  17.3216  -4.6896   -8.7240
 75A  H20  H  HCR6  0   0.267  13.8072  -1.6230   -9.2152
 75A  H21  H  HCR6  0   0.278  12.6656   0.2320  -10.3319
 75A  H22  H  HCR6  0   0.286  13.8242   1.5833  -12.0278
 75A  H23  H  HCR6  0   0.282  17.3621  -0.7943  -11.4679
 75A  H3   H  HNH2  0   0.400  19.2197  -4.8244   -3.5267
 75A  H4   H  HNH2  0   0.406  18.9542  -3.1928   -3.9854

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
 75A  I    C21  single    2.104  0.020  2.104
 75A  C20  C21  aromatic  1.388  0.020  1.388
 75A  C20  C19  aromatic  1.387  0.020  1.387
 75A  C21  C22  aromatic  1.384  0.020  1.384
 75A  C19  C18  aromatic  1.387  0.020  1.387
 75A  C22  C17  aromatic  1.393  0.020  1.393
 75A  C18  C17  aromatic  1.392  0.020  1.392
 75A  C17  C16  single    1.499  0.020  1.499
 75A  C16  O6   double    1.224  0.020  1.224
 75A  C16  N4   single    1.342  0.020  1.342
 75A  N4   C15  single    1.448  0.020  1.448
 75A  C15  C14  single    1.525  0.020  1.525
 75A  C14  C13  single    1.522  0.020  1.522
 75A  C13  C11  single    1.533  0.020  1.533
 75A  N3   C12  single    1.339  0.020  1.339
 75A  C11  C12  single    1.529  0.020  1.529
 75A  C11  N2   single    1.445  0.020  1.445
 75A  C12  O5   double    1.222  0.020  1.222
 75A  N2   C10  single    1.344  0.020  1.344
 75A  N1   C23  single    1.349  0.020  1.349
 75A  N1   C9   single    1.443  0.020  1.443
 75A  C24  C23  single    1.505  0.020  1.505
 75A  C10  C9   single    1.525  0.020  1.525
 75A  C10  O4   double    1.219  0.020  1.219
 75A  C23  O7   double    1.224  0.020  1.224
 75A  C8   C9   single    1.538  0.020  1.538
 75A  C8   C5   single    1.501  0.020  1.501
 75A  C6   C5   aromatic  1.391  0.020  1.391
 75A  C6   C7   aromatic  1.386  0.020  1.386
 75A  C5   C4   aromatic  1.391  0.020  1.391
 75A  C7   C2   aromatic  1.391  0.020  1.391
 75A  O2   P1   double    1.477  0.020  1.477
 75A  C4   C3   aromatic  1.385  0.020  1.385
 75A  C2   C3   aromatic  1.392  0.020  1.392
 75A  C2   C1   single    1.495  0.020  1.495
 75A  P1   C1   single    1.857  0.020  1.857
 75A  P1   O1   single    1.594  0.020  1.594
 75A  P1   O3   single    1.594  0.020  1.594
 75A  C1   F2   single    1.364  0.020  1.364
 75A  C1   F1   single    1.359  0.020  1.359
 75A  N1   H1   single    0.860  0.020  1.020
 75A  N2   H2   single    0.860  0.020  1.020
 75A  N3   H3   single    0.860  0.020  1.020
 75A  N3   H4   single    0.860  0.020  1.020
 75A  N4   H5   single    0.860  0.020  1.020
 75A  C3   H6   single    0.930  0.020  1.080
 75A  C4   H7   single    0.930  0.020  1.080
 75A  C6   H8   single    0.930  0.020  1.080
 75A  C7   H9   single    0.930  0.020  1.080
 75A  C8   H10  single    0.970  0.020  1.090
 75A  C8   H11  single    0.970  0.020  1.090
 75A  C9   H12  single    0.970  0.020  1.090
 75A  C11  H13  single    0.970  0.020  1.090
 75A  C13  H14  single    0.970  0.020  1.090
 75A  C13  H15  single    0.970  0.020  1.090
 75A  C14  H16  single    0.970  0.020  1.090
 75A  C14  H17  single    0.970  0.020  1.090
 75A  C15  H18  single    0.970  0.020  1.090
 75A  C15  H19  single    0.970  0.020  1.090
 75A  C18  H20  single    0.930  0.020  1.080
 75A  C19  H21  single    0.930  0.020  1.080
 75A  C20  H22  single    0.930  0.020  1.080
 75A  C22  H23  single    0.930  0.020  1.080
 75A  C24  H24  single    0.970  0.020  1.090
 75A  C24  H25  single    0.970  0.020  1.090
 75A  C24  H26  single    0.970  0.020  1.090
 75A  O1   H27  single    0.850  0.020  0.980
 75A  O3   H28  single    0.850  0.020  0.980

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
 75A  N1   C23  C24  115.33  3.000
 75A  C24  C23  O7   123.23  3.000
 75A  N1   C23  O7   121.40  3.000
 75A  H26  C24  H25  107.54  3.000
 75A  H26  C24  H24  109.13  3.000
 75A  H25  C24  H24  108.22  3.000
 75A  H26  C24  C23  112.04  3.000
 75A  H25  C24  C23  109.55  3.000
 75A  H24  C24  C23  110.25  3.000
 75A  H1   N1   C9   118.29  3.000
 75A  H1   N1   C23  119.02  3.000
 75A  C9   N1   C23  121.92  3.000
 75A  H12  C9   C8   108.99  3.000
 75A  H12  C9   C10  106.72  3.000
 75A  C8   C9   C10  109.35  3.000
 75A  H12  C9   N1   110.53  3.000
 75A  C8   C9   N1   108.51  3.000
 75A  C10  C9   N1   112.68  3.000
 75A  N2   C10  O4   122.75  3.000
 75A  O4   C10  C9   121.43  3.000
 75A  N2   C10  C9   115.71  3.000
 75A  H11  C8   H10  107.06  3.000
 75A  H11  C8   C5   110.05  3.000
 75A  H10  C8   C5   109.73  3.000
 75A  H11  C8   C9   109.37  3.000
 75A  H10  C8   C9   107.75  3.000
 75A  C5   C8   C9   112.70  3.000
 75A  C4   C5   C6   118.56  3.000
 75A  C4   C5   C8   120.51  3.000
 75A  C6   C5   C8   120.92  3.000
 75A  H8   C6   C7   119.24  3.000
 75A  H8   C6   C5   119.76  3.000
 75A  C7   C6   C5   121.00  3.000
 75A  H7   C4   C3   119.16  3.000
 75A  H7   C4   C5   119.86  3.000
 75A  C3   C4   C5   120.97  3.000
 75A  H9   C7   C2   120.95  3.000
 75A  H9   C7   C6   119.12  3.000
 75A  C2   C7   C6   119.93  3.000
 75A  H6   C3   C2   121.00  3.000
 75A  H6   C3   C4   119.05  3.000
 75A  C2   C3   C4   119.95  3.000
 75A  C1   C2   C3   120.34  3.000
 75A  C1   C2   C7   120.04  3.000
 75A  C3   C2   C7   119.56  3.000
 75A  P1   C1   F2   107.03  3.000
 75A  F2   C1   F1   106.79  3.000
 75A  P1   C1   F1   108.86  3.000
 75A  F1   C1   C2   110.86  3.000
 75A  F2   C1   C2   110.95  3.000
 75A  P1   C1   C2   112.13  3.000
 75A  O3   P1   O1    98.40  3.000
 75A  O3   P1   O2   118.53  3.000
 75A  O1   P1   O2   118.51  3.000
 75A  O3   P1   C1   105.27  3.000
 75A  O1   P1   C1   103.12  3.000
 75A  O2   P1   C1   111.01  3.000
 75A  H27  O1   P1   114.49  3.000
 75A  H28  O3   P1   114.86  3.000
 75A  H2   N2   C11  118.55  3.000
 75A  H2   N2   C10  119.15  3.000
 75A  C11  N2   C10  121.93  3.000
 75A  H5   N4   C16  119.12  3.000
 75A  H5   N4   C15  116.98  3.000
 75A  C16  N4   C15  123.84  3.000
 75A  H13  C11  C13  109.06  3.000
 75A  H13  C11  C12  106.48  3.000
 75A  C13  C11  C12  110.21  3.000
 75A  H13  C11  N2   109.95  3.000
 75A  C12  C11  N2   112.66  3.000
 75A  C13  C11  N2   108.43  3.000
 75A  N3   C12  O5   123.51  3.000
 75A  O5   C12  C11  120.27  3.000
 75A  N3   C12  C11  116.03  3.000
 75A  H15  C13  H14  106.58  3.000
 75A  H15  C13  C14  108.82  3.000
 75A  H14  C13  C14  110.26  3.000
 75A  H15  C13  C11  107.19  3.000
 75A  H14  C13  C11  109.53  3.000
 75A  C14  C13  C11  114.14  3.000
 75A  H17  C14  H16  106.39  3.000
 75A  H17  C14  C15  107.07  3.000
 75A  H16  C14  C15  109.78  3.000
 75A  H17  C14  C13  111.00  3.000
 75A  H16  C14  C13  109.63  3.000
 75A  C15  C14  C13  112.75  3.000
 75A  H19  C15  H18  107.11  3.000
 75A  H19  C15  C14  110.08  3.000
 75A  H18  C15  C14  109.32  3.000
 75A  H19  C15  N4   108.41  3.000
 75A  H18  C15  N4   108.05  3.000
 75A  C14  C15  N4   113.65  3.000
 75A  O6   C16  C17  120.50  3.000
 75A  O6   C16  N4   123.67  3.000
 75A  C17  C16  N4   115.83  3.000
 75A  C22  C17  C18  119.61  3.000
 75A  C18  C17  C16  122.89  3.000
 75A  C22  C17  C16  117.46  3.000
 75A  H20  C18  C19  118.79  3.000
 75A  H20  C18  C17  121.04  3.000
 75A  C19  C18  C17  120.16  3.000
 75A  H21  C19  C20  119.48  3.000
 75A  H21  C19  C18  119.93  3.000
 75A  C20  C19  C18  120.59  3.000
 75A  H22  C20  C21  121.30  3.000
 75A  H22  C20  C19  119.89  3.000
 75A  C21  C20  C19  118.81  3.000
 75A  I    C21  C22  119.29  3.000
 75A  C22  C21  C20  121.34  3.000
 75A  I    C21  C20  119.37  3.000
 75A  H23  C22  C21  121.01  3.000
 75A  H23  C22  C17  119.52  3.000
 75A  C21  C22  C17  119.47  3.000
 75A  H4   N3   H3   116.76  3.000
 75A  H4   N3   C12  121.94  3.000
 75A  H3   N3   C12  119.39  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
 75A  CONST_01  C2   C7   C6   C5      0.00   0.0  0
 75A  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 75A  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 75A  CONST_04  C3   C2   C7   C6      0.00   0.0  0
 75A  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 75A  CONST_06  C7   C2   C3   C4      0.00   0.0  0
 75A  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 75A  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 75A  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 75A  CONST_10  C21  C22  C17  C18     0.00   0.0  0
 75A  CONST_11  C22  C21  C20  C19     0.00   0.0  0
 75A  CONST_12  C22  C17  C18  C19     0.00   0.0  0
 75A  CONST_13  C7   C6   C5   C8    180.00   0.0  0
 75A  CONST_14  C3   C4   C5   C8    180.00   0.0  0
 75A  CONST_15  C1   C2   C7   C6    180.00   0.0  0
 75A  CONST_16  C1   C2   C3   C4    180.00   0.0  0
 75A  CONST_17  C21  C22  C17  C16   180.00   0.0  0
 75A  CONST_18  C19  C18  C17  C16   180.00   0.0  0
 75A  CONST_19  I    C21  C22  C17   180.00   0.0  0
 75A  CONST_20  I    C21  C20  C19   180.00   0.0  0
 75A  CONST_21  H9   C7   C6   C5    180.00   0.0  0
 75A  CONST_22  H6   C3   C4   C5    180.00   0.0  0
 75A  CONST_23  H7   C4   C5   C6    180.00   0.0  0
 75A  CONST_24  H8   C6   C5   C4    180.00   0.0  0
 75A  CONST_25  H21  C19  C18  C17   180.00   0.0  0
 75A  CONST_26  H22  C20  C19  C18   180.00   0.0  0
 75A  CONST_27  H23  C22  C17  C18   180.00   0.0  0
 75A  CONST_28  H20  C18  C19  C20   180.00   0.0  0
 75A  CONST_29  C17  C16  N4   C15   180.00   0.0  0
 75A  CONST_30  H5   N4   C16  C17     0.00   0.0  0
 75A  CONST_31  C9   N1   C23  O7      0.00   0.0  0
 75A  CONST_32  C9   N1   C23  C24   180.00   0.0  0
 75A  CONST_33  C11  N2   C10  C9    180.00   0.0  0
 75A  CONST_34  C11  N2   C10  O4      0.00   0.0  0
 75A  CONST_35  O6   C16  N4   C15     0.00   0.0  0
 75A  CONST_36  H1   N1   C23  O7    180.00   0.0  0
 75A  CONST_37  H2   N2   C10  C9      0.00   0.0  0
 75A  CONST_38  H3   N3   C12  C11   180.00   0.0  0
 75A  Var_01    C6   C5   C8   C9   -101.80  30.0  2
 75A  Var_02    P1   C1   C2   C7    -83.62  30.0  2
 75A  Var_03    C22  C17  C16  N4   -153.40  30.0  2
 75A  Var_04    O2   P1   C1   C2     63.19  30.0  1
 75A  Var_05    C13  C14  C15  N4    -58.93  30.0  3
 75A  Var_06    C15  C14  C13  C11  -177.23  30.0  2
 75A  Var_07    C16  N4   C15  C14   102.44  30.0  1
 75A  Var_08    H24  C24  C23  O7    -20.18  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
 75A  chir_01  C9   N1  C10  C8   positiv
 75A  chir_02  C11  N2  C12  C13  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
 75A  plan-1  C8   0.020
 75A  plan-1  C5   0.020
 75A  plan-1  C6   0.020
 75A  plan-1  C4   0.020
 75A  plan-1  C7   0.020
 75A  plan-1  C3   0.020
 75A  plan-1  C2   0.020
 75A  plan-1  C1   0.020
 75A  plan-1  H8   0.020
 75A  plan-1  H7   0.020
 75A  plan-1  H9   0.020
 75A  plan-1  H6   0.020
 75A  plan-2  C16  0.020
 75A  plan-2  C17  0.020
 75A  plan-2  C18  0.020
 75A  plan-2  C19  0.020
 75A  plan-2  C20  0.020
 75A  plan-2  C21  0.020
 75A  plan-2  C22  0.020
 75A  plan-2  I    0.020
 75A  plan-2  H20  0.020
 75A  plan-2  H21  0.020
 75A  plan-2  H22  0.020
 75A  plan-2  H23  0.020
 75A  plan-3  C23  0.020
 75A  plan-3  O7   0.020
 75A  plan-3  C24  0.020
 75A  plan-3  N1   0.020
 75A  plan-3  C9   0.020
 75A  plan-3  H1   0.020
 75A  plan-4  C9   0.020
 75A  plan-4  C10  0.020
 75A  plan-4  O4   0.020
 75A  plan-4  N2   0.020
 75A  plan-4  C11  0.020
 75A  plan-4  H2   0.020
 75A  plan-5  C11  0.020
 75A  plan-5  C12  0.020
 75A  plan-5  O5   0.020
 75A  plan-5  N3   0.020
 75A  plan-5  H3   0.020
 75A  plan-5  H4   0.020
 75A  plan-6  N4   0.020
 75A  plan-6  C15  0.020
 75A  plan-6  C16  0.020
 75A  plan-6  C17  0.020
 75A  plan-6  O6   0.020
 75A  plan-6  H5   0.020

