# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 02:17:25 2020
#   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  65  39  .  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_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   0.537  -3.4388  -2.2673  -2.9675
 75A  O7   O  O      0  -0.500  -3.6062  -3.3507  -2.4247
 75A  C24  C  CH3    0  -0.773  -4.1321  -1.9012  -4.2554
 75A  N1   N  NH1    0  -0.621  -2.6258  -1.3247  -2.4618
 75A  C9   C  CH1    0  -0.195  -1.8851  -1.4985  -1.2435
 75A  C10  C  C      0   0.585  -0.8805  -2.6492  -1.4015
 75A  O4   O  O      0  -0.481  -0.5290  -3.0437  -2.4987
 75A  C8   C  CH2    0  -0.575  -2.7900  -1.6006   0.0038
 75A  C5   C  CR6    0   0.152  -3.8146  -0.5029   0.0270
 75A  C6   C  CR16   0  -0.300  -3.4817   0.7749   0.4670
 75A  C4   C  CR16   0  -0.303  -5.1119  -0.7195  -0.4267
 75A  C7   C  CR16   0  -0.287  -4.4074   1.8073   0.4409
 75A  C3   C  CR16   0  -0.277  -6.0421   0.3087  -0.4549
 75A  C2   C  CR6    0  -0.053  -5.6956   1.5905  -0.0381
 75A  C1   C  CT     0   0.453  -6.7107   2.6872  -0.0521
 75A  F1   F  F      0  -0.378  -6.0554   3.8946  -0.2100
 75A  F2   F  F      0  -0.381  -7.4763   2.5613  -1.1986
 75A  P1   P  P      0   1.101  -7.8201   2.7431   1.4724
 75A  O2   O  O      0  -0.889  -8.7043   3.9655   1.2360
 75A  O1   O  OP    -1  -0.877  -8.5464   1.4032   1.4091
 75A  O3   O  OP    -1  -0.878  -6.8127   2.8870   2.6081
 75A  N2   N  NH1    0  -0.642  -0.3519  -3.1211  -0.2582
 75A  N4   N  NH1    0  -0.649   4.2381  -1.6516   1.9670
 75A  C11  C  CH1    0  -0.211   0.5790  -4.2180  -0.2338
 75A  C12  C  C      0   0.520  -0.1704  -5.5518  -0.1733
 75A  C13  C  CH2    0  -0.449   1.5217  -4.1041   0.9665
 75A  C14  C  CH2    0  -0.447   2.4114  -2.8706   0.8915
 75A  C15  C  CH2    0  -0.256   3.4084  -2.8347   2.0405
 75A  C16  C  C      0   0.529   5.5560  -1.6382   2.2156
 75A  C17  C  CR6    0  -0.027   6.2431  -0.3198   2.0237
 75A  C18  C  CR16   0  -0.267   7.3749  -0.0467   2.7859
 75A  C19  C  CR16   0  -0.234   8.0507   1.1514   2.6237
 75A  C20  C  CR16   0  -0.224   7.6229   2.0833   1.6870
 75A  C21  C  CR6    0  -0.207   6.5081   1.7927   0.9149
 75A  C22  C  CR16   0  -0.262   5.8117   0.6041   1.0741
 75A  O5   O  O      0  -0.476  -1.2507  -5.6515   0.3829
 75A  O6   O  O      0  -0.485   6.1899  -2.6215   2.5727
 75A  I    I  I      0   0.066   5.8632   3.1778  -0.5308
 75A  N3   N  NH2    0  -0.799   0.4805  -6.5796  -0.7330
 75A  H24  H  HCH3   0   0.263  -5.2050  -2.0531  -4.1438
 75A  H25  H  HCH3   0   0.248  -3.9583  -0.8732  -4.5678
 75A  H26  H  HCH3   0   0.266  -3.7900  -2.5642  -5.0508
 75A  H1   H  HNH1   0   0.403  -2.5413  -0.4447  -2.9393
 75A  H12  H  HCH1   0   0.307  -1.2776  -0.5945  -1.1341
 75A  H10  H  HCH2   0   0.272  -3.2750  -2.5757   0.0325
 75A  H11  H  HCH2   0   0.256  -2.1728  -1.5169   0.9013
 75A  H8   H  HCR6   0   0.242  -2.4815   0.9710   0.8376
 75A  H7   H  HCR6   0   0.241  -5.4018  -1.7080  -0.7619
 75A  H9   H  HCR6   0   0.244  -4.1108   2.7849   0.7949
 75A  H6   H  HCR6   0   0.243  -7.0440   0.1028  -0.8049
 75A  H2   H  HNH1   0   0.405  -0.7313  -2.8232   0.6255
 75A  H5   H  HNH1   0   0.406   3.7625  -0.7743   1.8260
 75A  H13  H  HCH1   0   0.275   1.1786  -4.1751  -1.1462
 75A  H14  H  HCH2   0   0.246   0.9407  -4.1009   1.8944
 75A  H15  H  HCH2   0   0.255   2.1460  -5.0008   0.9954
 75A  H16  H  HCH2   0   0.238   2.9570  -2.8677  -0.0565
 75A  H17  H  HCH2   0   0.238   1.7989  -1.9651   0.9095
 75A  H18  H  HCH2   0   0.249   4.0554  -3.7097   2.0015
 75A  H19  H  HCH2   0   0.240   2.8804  -2.8669   2.9988
 75A  H20  H  HCR6   0   0.269   7.7251  -0.7671   3.5125
 75A  H21  H  HCR6   0   0.275   8.9216   1.3680   3.2277
 75A  H22  H  HCR6   0   0.286   8.1603   3.0142   1.5687
 75A  H23  H  HCR6   0   0.280   4.9589   0.3881   0.4443
 75A  H3   H  HNH2   0   0.409   1.3547  -6.4585  -1.2143
 75A  H4   H  HNH2   0   0.404   0.1015  -7.5123  -0.6911

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    2.103  0.020  2.103
 75A  C20  C21  aromatic  1.387  0.020  1.387
 75A  C20  C19  aromatic  1.389  0.020  1.389
 75A  C21  C22  aromatic  1.387  0.020  1.387
 75A  C19  C18  aromatic  1.385  0.020  1.385
 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    1.223  0.020  1.223
 75A  C16  N4   single    1.341  0.020  1.341
 75A  N4   C15  single    1.447  0.020  1.447
 75A  C15  C14  single    1.522  0.020  1.522
 75A  C14  C13  single    1.523  0.020  1.523
 75A  C13  C11  single    1.531  0.020  1.531
 75A  N3   C12  single    1.339  0.020  1.339
 75A  C11  C12  single    1.531  0.020  1.531
 75A  C11  N2   single    1.439  0.020  1.439
 75A  C12  O5   double    1.219  0.020  1.219
 75A  N2   C10  single    1.345  0.020  1.345
 75A  N1   C23  single    1.344  0.020  1.344
 75A  N1   C9   single    1.436  0.020  1.436
 75A  C24  C23  single    1.508  0.020  1.508
 75A  C10  C9   single    1.536  0.020  1.536
 75A  C10  O4   double    1.218  0.020  1.218
 75A  C23  O7   double    1.223  0.020  1.223
 75A  C8   C9   single    1.544  0.020  1.544
 75A  C8   C5   single    1.502  0.020  1.502
 75A  C6   C5   aromatic  1.392  0.020  1.392
 75A  C6   C7   aromatic  1.387  0.020  1.387
 75A  C5   C4   aromatic  1.391  0.020  1.391
 75A  C7   C2   aromatic  1.391  0.020  1.391
 75A  O2   P1   deloc     1.527  0.020  1.527
 75A  C4   C3   aromatic  1.387  0.020  1.387
 75A  C2   C3   aromatic  1.392  0.020  1.392
 75A  C2   C1   single    1.494  0.020  1.494
 75A  P1   C1   single    1.886  0.020  1.886
 75A  P1   O1   deloc     1.525  0.020  1.525
 75A  P1   O3   deloc     1.525  0.020  1.525
 75A  C1   F2   single    1.384  0.020  1.384
 75A  C1   F1   single    1.383  0.020  1.383
 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

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  115.43  3.000
 75A  C24  C23  O7   122.08  3.000
 75A  N1   C23  O7   122.49  3.000
 75A  H26  C24  H25  108.34  3.000
 75A  H26  C24  H24  107.39  3.000
 75A  H25  C24  H24  108.56  3.000
 75A  H26  C24  C23  109.34  3.000
 75A  H25  C24  C23  113.65  3.000
 75A  H24  C24  C23  109.36  3.000
 75A  H1   N1   C9   117.76  3.000
 75A  H1   N1   C23  119.10  3.000
 75A  C9   N1   C23  123.12  3.000
 75A  H12  C9   C8   107.41  3.000
 75A  H12  C9   C10  105.43  3.000
 75A  C8   C9   C10  114.64  3.000
 75A  H12  C9   N1   105.72  3.000
 75A  C8   C9   N1   113.01  3.000
 75A  C10  C9   N1   109.92  3.000
 75A  N2   C10  O4   122.59  3.000
 75A  O4   C10  C9   121.62  3.000
 75A  N2   C10  C9   115.63  3.000
 75A  H11  C8   H10  107.37  3.000
 75A  H11  C8   C5   108.46  3.000
 75A  H10  C8   C5   110.49  3.000
 75A  H11  C8   C9   109.11  3.000
 75A  H10  C8   C9   109.96  3.000
 75A  C5   C8   C9   111.34  3.000
 75A  C4   C5   C6   117.97  3.000
 75A  C4   C5   C8   121.15  3.000
 75A  C6   C5   C8   120.85  3.000
 75A  H8   C6   C7   119.17  3.000
 75A  H8   C6   C5   119.64  3.000
 75A  C7   C6   C5   121.18  3.000
 75A  H7   C4   C3   119.39  3.000
 75A  H7   C4   C5   119.50  3.000
 75A  C3   C4   C5   121.11  3.000
 75A  H9   C7   C2   120.50  3.000
 75A  H9   C7   C6   118.93  3.000
 75A  C2   C7   C6   120.56  3.000
 75A  H6   C3   C2   120.21  3.000
 75A  H6   C3   C4   119.14  3.000
 75A  C2   C3   C4   120.65  3.000
 75A  C1   C2   C3   120.26  3.000
 75A  C1   C2   C7   121.19  3.000
 75A  C3   C2   C7   118.50  3.000
 75A  P1   C1   F2   110.29  3.000
 75A  F2   C1   F1   104.29  3.000
 75A  P1   C1   F1   110.19  3.000
 75A  F1   C1   C2   108.65  3.000
 75A  F2   C1   C2   108.46  3.000
 75A  P1   C1   C2   114.44  3.000
 75A  O3   P1   O1   115.36  3.000
 75A  O3   P1   O2   114.98  3.000
 75A  O1   P1   O2   114.90  3.000
 75A  O3   P1   C1   102.48  3.000
 75A  O1   P1   C1   102.73  3.000
 75A  O2   P1   C1   103.84  3.000
 75A  H2   N2   C11  117.03  3.000
 75A  H2   N2   C10  119.61  3.000
 75A  C11  N2   C10  122.42  3.000
 75A  H5   N4   C16  118.75  3.000
 75A  H5   N4   C15  116.63  3.000
 75A  C16  N4   C15  124.20  3.000
 75A  H13  C11  C13  108.29  3.000
 75A  H13  C11  C12  109.62  3.000
 75A  C13  C11  C12  109.59  3.000
 75A  H13  C11  N2   108.12  3.000
 75A  C12  C11  N2   110.37  3.000
 75A  C13  C11  N2   110.80  3.000
 75A  N3   C12  O5   123.96  3.000
 75A  O5   C12  C11  121.53  3.000
 75A  N3   C12  C11  114.47  3.000
 75A  H15  C13  H14  106.44  3.000
 75A  H15  C13  C14  109.40  3.000
 75A  H14  C13  C14  110.45  3.000
 75A  H15  C13  C11  108.15  3.000
 75A  H14  C13  C11  109.75  3.000
 75A  C14  C13  C11  112.43  3.000
 75A  H17  C14  H16  106.95  3.000
 75A  H17  C14  C15  109.58  3.000
 75A  H16  C14  C15  109.12  3.000
 75A  H17  C14  C13  110.05  3.000
 75A  H16  C14  C13  109.65  3.000
 75A  C15  C14  C13  111.39  3.000
 75A  H19  C15  H18  107.12  3.000
 75A  H19  C15  C14  110.14  3.000
 75A  H18  C15  C14  110.08  3.000
 75A  H19  C15  N4   110.19  3.000
 75A  H18  C15  N4   108.33  3.000
 75A  C14  C15  N4   110.89  3.000
 75A  O6   C16  C17  120.45  3.000
 75A  O6   C16  N4   123.73  3.000
 75A  C17  C16  N4   115.81  3.000
 75A  C22  C17  C18  119.67  3.000
 75A  C18  C17  C16  118.38  3.000
 75A  C22  C17  C16  121.90  3.000
 75A  H20  C18  C19  119.80  3.000
 75A  H20  C18  C17  120.04  3.000
 75A  C19  C18  C17  120.16  3.000
 75A  H21  C19  C20  119.35  3.000
 75A  H21  C19  C18  120.04  3.000
 75A  C20  C19  C18  120.61  3.000
 75A  H22  C20  C21  121.26  3.000
 75A  H22  C20  C19  119.89  3.000
 75A  C21  C20  C19  118.85  3.000
 75A  I    C21  C22  119.29  3.000
 75A  C22  C21  C20  121.29  3.000
 75A  I    C21  C20  119.42  3.000
 75A  H23  C22  C21  120.01  3.000
 75A  H23  C22  C17  120.56  3.000
 75A  C21  C22  C17  119.41  3.000
 75A  H4   N3   H3   117.29  3.000
 75A  H4   N3   C12  120.68  3.000
 75A  H3   N3   C12  122.03  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     0.00   0.0  0
 75A  CONST_39  H4   N3   C12  C11   180.00   0.0  0
 75A  Var_01    C6   C5   C8   C9    -80.49  30.0  2
 75A  Var_02    P1   C1   C2   C7    -93.49  30.0  2
 75A  Var_03    C22  C17  C16  N4    -31.14  30.0  2
 75A  Var_04    O2   P1   C1   C2    177.62  30.0  3
 75A  Var_05    C13  C14  C15  N4   -179.38  30.0  3
 75A  Var_06    C15  C14  C13  C11  -175.79  30.0  2
 75A  Var_07    C16  N4   C15  C14  -139.05  30.0  1
 75A  Var_08    H24  C24  C23  O7     53.12  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

