# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:21:46 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{R})-~{N}-[2-[[(2~{S})-1-[[4-[bis(oxidanyl)amino]phenyl]amino]-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCC[C@H](NC(=O)CNC(=O)[C@H]1CCC(=O)N1)C(=O)Nc2ccc(cc2)N(O)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
 7YR  7YR  (2~{R})-~{N}-[2-[[(2~{S})-1-[[4-[bis(oxidanyl)amino]phenyl]amino]-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-pyrrolidine-2-carboxamide  peptide  61  33  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7YR
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
 7YR  C5   C  C     0   0.545  -4.9406  -1.7553   0.3925
 7YR  O2   O  O     0  -0.483  -5.0950  -2.0722   1.5606
 7YR  C4   C  CH1   0  -0.159  -5.9647  -2.0709  -0.6854
 7YR  N1   N  NH1   0  -0.627  -7.2531  -2.3878  -0.1329
 7YR  C3   C  CH2   0  -0.470  -5.5985  -3.3657  -1.4407
 7YR  C2   C  CH2   0  -0.590  -6.9529  -3.9784  -1.7778
 7YR  C1   C  C     0   0.520  -7.8860  -3.4205  -0.7231
 7YR  O1   O  O     0  -0.488  -9.0117  -3.8085  -0.4649
 7YR  N2   N  NH1   0  -0.646  -3.8447  -1.1415  -0.0688
 7YR  C6   C  CH2   0  -0.374  -2.7159  -0.8495   0.7680
 7YR  C7   C  C     0   0.528  -1.6117  -0.2181  -0.0629
 7YR  O3   O  O     0  -0.481  -1.7118  -0.0819  -1.2719
 7YR  N3   N  NH1   0  -0.626  -0.5451   0.1597   0.6561
 7YR  C8   C  CH1   0  -0.249   0.6417   0.7451   0.0919
 7YR  C9   C  C     0   0.560   1.8507  -0.1268   0.4376
 7YR  O4   O  O     0  -0.458   1.8423  -0.8868   1.3876
 7YR  C10  C  CH2   0  -0.418   0.8639   2.1808   0.5867
 7YR  C11  C  CH2   0  -0.458  -0.3033   3.0969   0.2481
 7YR  C12  C  CH2   0  -0.230  -0.0175   4.5383   0.6391
 7YR  N4   N  NH1   0  -0.647  -1.1665   5.3673   0.3560
 7YR  C13  C  C     0   0.546  -1.0861   6.7314   0.4568
 7YR  N6   N  NH2   0  -0.839  -2.3169   7.3537   0.3981
 7YR  N5   N  N     0  -0.714   0.0452   7.3126   0.6156
 7YR  N7   N  NH1   0  -0.742   2.9030   0.0648  -0.3889
 7YR  C14  C  CR6   0   0.366   4.1804  -0.5085  -0.3456
 7YR  C19  C  CR16  0  -0.342   5.1076  -0.0642  -1.2880
 7YR  C18  C  CR16  0  -0.293   6.3892  -0.5795  -1.3368
 7YR  C17  C  CR6   0   0.284   6.7870  -1.5642  -0.4343
 7YR  N8   N  NT    0  -0.053   8.0636  -2.1716  -0.5477
 7YR  O6   O  OH1   0  -0.552   8.4813  -2.6232   0.6924
 7YR  O5   O  OH1   0  -0.553   8.9851  -1.2430  -1.0028
 7YR  C16  C  CR16  0  -0.298   5.8647  -2.0101   0.5065
 7YR  C15  C  CR16  0  -0.307   4.5777  -1.4938   0.5553
 7YR  H23  H  HCH1  0   0.281  -6.0316  -1.2302  -1.3861
 7YR  H24  H  HNH1  0   0.399  -7.7226  -1.7828   0.5237
 7YR  H25  H  HCH2  0   0.268  -4.9819  -3.1602  -2.3126
 7YR  H26  H  HCH2  0   0.261  -5.0403  -4.0347  -0.7838
 7YR  H27  H  HCH2  0   0.280  -7.3142  -3.6506  -2.7566
 7YR  H28  H  HCH2  0   0.279  -6.9568  -5.0675  -1.7758
 7YR  H22  H  HNH1  0   0.405  -3.7714  -0.8917  -1.0444
 7YR  H20  H  HCH2  0   0.282  -2.9906  -0.1734   1.5830
 7YR  H21  H  HCH2  0   0.285  -2.3258  -1.7595   1.2344
 7YR  H19  H  HNH1  0   0.408  -0.5512  -0.0050   1.6517
 7YR  H12  H  HCH1  0   0.291   0.5140   0.7660  -0.9926
 7YR  H1   H  HCH2  0   0.245   1.0360   2.1717   1.6675
 7YR  H2   H  HCH2  0   0.245   1.7779   2.5701   0.1298
 7YR  H13  H  HCH2  0   0.233  -0.5153   3.0474  -0.8237
 7YR  H14  H  HCH2  0   0.232  -1.2025   2.7491   0.7653
 7YR  H3   H  HCH2  0   0.210   0.2691   4.5883   1.6979
 7YR  H4   H  HCH2  0   0.231   0.8337   4.9149   0.0707
 7YR  H15  H  HNH1  0   0.377  -2.0499   4.9689   0.6365
 7YR  H16  H  HNH2  0   0.382  -3.0197   6.8972  -0.1634
 7YR  H17  H  HNH2  0   0.384  -2.2866   8.3450   0.2216
 7YR  H18  H  H     0   0.316  -0.0649   8.3195   0.5837
 7YR  H5   H  HNH1  0   0.420   2.7612   0.7173  -1.1458
 7YR  H6   H  HCR6  0   0.273   4.8272   0.7015  -2.0018
 7YR  H7   H  HCR6  0   0.268   7.0687  -0.2032  -2.0871
 7YR  H8   H  HCR6  0   0.266   6.1304  -2.7766   1.2195
 7YR  H9   H  HCR6  0   0.282   3.8996  -1.8757   1.3000
 7YR  H10  H  HOH1  0   0.473   8.8195  -3.5111   0.5249
 7YR  H11  H  HOH1  0   0.473   9.4833  -1.7100  -1.6846

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
 7YR  O1   C1   double    1.218  0.020  1.218
 7YR  C1   C2   single    1.515  0.020  1.515
 7YR  C1   N1   single    1.347  0.020  1.347
 7YR  C2   C3   single    1.524  0.020  1.524
 7YR  N1   C4   single    1.437  0.020  1.437
 7YR  C3   C4   single    1.543  0.020  1.543
 7YR  C4   C5   single    1.520  0.020  1.520
 7YR  C5   O2   double    1.220  0.020  1.220
 7YR  C5   N2   single    1.338  0.020  1.338
 7YR  N5   C13  double    1.282  0.020  1.282
 7YR  N2   C6   single    1.435  0.020  1.435
 7YR  C13  N4   single    1.370  0.020  1.370
 7YR  C13  N6   single    1.380  0.020  1.380
 7YR  N4   C12  single    1.445  0.020  1.445
 7YR  N3   C8   single    1.439  0.020  1.439
 7YR  N3   C7   single    1.341  0.020  1.341
 7YR  C6   C7   single    1.519  0.020  1.519
 7YR  C11  C12  single    1.521  0.020  1.521
 7YR  C11  C10  single    1.522  0.020  1.522
 7YR  C8   C10  single    1.535  0.020  1.535
 7YR  C8   C9   single    1.530  0.020  1.530
 7YR  C7   O3   double    1.221  0.020  1.221
 7YR  C9   N7   single    1.352  0.020  1.352
 7YR  C9   O4   double    1.217  0.020  1.217
 7YR  N7   C14  single    1.401  0.020  1.401
 7YR  C19  C14  aromatic  1.395  0.020  1.395
 7YR  C19  C18  aromatic  1.382  0.020  1.382
 7YR  C14  C15  aromatic  1.393  0.020  1.393
 7YR  C18  C17  aromatic  1.394  0.020  1.394
 7YR  C15  C16  aromatic  1.388  0.020  1.388
 7YR  C17  C16  aromatic  1.391  0.020  1.391
 7YR  C17  N8   single    1.418  0.020  1.418
 7YR  N8   O5   single    1.385  0.020  1.385
 7YR  N8   O6   single    1.384  0.020  1.384
 7YR  C10  H1   single    0.970  0.020  1.090
 7YR  C10  H2   single    0.970  0.020  1.090
 7YR  C12  H3   single    0.970  0.020  1.090
 7YR  C12  H4   single    0.970  0.020  1.090
 7YR  N7   H5   single    0.860  0.020  1.020
 7YR  C19  H6   single    0.930  0.020  1.080
 7YR  C18  H7   single    0.930  0.020  1.080
 7YR  C16  H8   single    0.930  0.020  1.080
 7YR  C15  H9   single    0.930  0.020  1.080
 7YR  O6   H10  single    0.850  0.020  0.980
 7YR  O5   H11  single    0.850  0.020  0.980
 7YR  C8   H12  single    0.970  0.020  1.090
 7YR  C11  H13  single    0.970  0.020  1.090
 7YR  C11  H14  single    0.970  0.020  1.090
 7YR  N4   H15  single    0.890  0.020  1.040
 7YR  N6   H16  single    0.890  0.020  1.040
 7YR  N6   H17  single    0.890  0.020  1.040
 7YR  N5   H18  single    0.890  0.020  1.040
 7YR  N3   H19  single    0.860  0.020  1.020
 7YR  C6   H20  single    0.970  0.020  1.090
 7YR  C6   H21  single    0.970  0.020  1.090
 7YR  N2   H22  single    0.860  0.020  1.020
 7YR  C4   H23  single    0.970  0.020  1.090
 7YR  N1   H24  single    0.860  0.020  1.020
 7YR  C3   H25  single    0.970  0.020  1.090
 7YR  C3   H26  single    0.970  0.020  1.090
 7YR  C2   H27  single    0.970  0.020  1.090
 7YR  C2   H28  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
 7YR  N2   C5   C4   113.74  3.000
 7YR  N2   C5   O2   123.56  3.000
 7YR  C4   C5   O2   122.66  3.000
 7YR  H23  C4   C3   110.18  3.000
 7YR  H23  C4   N1   111.10  3.000
 7YR  C3   C4   N1   102.47  3.000
 7YR  H23  C4   C5   109.57  3.000
 7YR  C3   C4   C5   111.19  3.000
 7YR  N1   C4   C5   112.16  3.000
 7YR  H24  N1   C1   121.75  3.000
 7YR  H24  N1   C4   122.36  3.000
 7YR  C1   N1   C4   114.94  3.000
 7YR  H26  C3   H25  107.97  3.000
 7YR  H26  C3   C2   109.95  3.000
 7YR  H25  C3   C2   113.74  3.000
 7YR  H26  C3   C4   109.95  3.000
 7YR  H25  C3   C4   111.62  3.000
 7YR  C2   C3   C4   103.57  3.000
 7YR  H28  C2   H27  107.47  3.000
 7YR  H28  C2   C1   111.40  3.000
 7YR  H27  C2   C1   108.02  3.000
 7YR  H28  C2   C3   113.87  3.000
 7YR  H27  C2   C3   111.77  3.000
 7YR  C1   C2   C3   104.20  3.000
 7YR  O1   C1   C2   126.83  3.000
 7YR  C2   C1   N1   107.34  3.000
 7YR  O1   C1   N1   125.82  3.000
 7YR  H22  N2   C6   117.12  3.000
 7YR  H22  N2   C5   120.40  3.000
 7YR  C6   N2   C5   122.45  3.000
 7YR  H21  C6   H20  106.61  3.000
 7YR  H21  C6   C7   108.64  3.000
 7YR  H20  C6   C7   109.45  3.000
 7YR  H21  C6   N2   111.08  3.000
 7YR  H20  C6   N2   111.26  3.000
 7YR  C7   C6   N2   109.72  3.000
 7YR  N3   C7   O3   124.40  3.000
 7YR  O3   C7   C6   121.89  3.000
 7YR  N3   C7   C6   113.71  3.000
 7YR  H19  N3   C8   117.28  3.000
 7YR  H19  N3   C7   118.58  3.000
 7YR  C8   N3   C7   124.11  3.000
 7YR  H12  C8   C10  108.61  3.000
 7YR  H12  C8   C9   109.13  3.000
 7YR  C10  C8   C9   110.23  3.000
 7YR  H12  C8   N3   107.50  3.000
 7YR  C9   C8   N3   109.35  3.000
 7YR  C10  C8   N3   111.94  3.000
 7YR  N7   C9   O4   124.85  3.000
 7YR  O4   C9   C8   121.79  3.000
 7YR  N7   C9   C8   113.34  3.000
 7YR  H2   C10  H1   106.51  3.000
 7YR  H2   C10  C11  109.50  3.000
 7YR  H1   C10  C11  110.20  3.000
 7YR  H2   C10  C8   108.62  3.000
 7YR  H1   C10  C8   109.48  3.000
 7YR  C11  C10  C8   112.35  3.000
 7YR  H14  C11  H13  106.84  3.000
 7YR  H14  C11  C12  109.53  3.000
 7YR  H13  C11  C12  109.35  3.000
 7YR  H14  C11  C10  109.50  3.000
 7YR  H13  C11  C10  109.84  3.000
 7YR  C12  C11  C10  111.67  3.000
 7YR  H4   C12  H3   106.45  3.000
 7YR  H4   C12  N4   108.69  3.000
 7YR  H3   C12  N4   111.74  3.000
 7YR  H4   C12  C11  109.88  3.000
 7YR  H3   C12  C11  109.88  3.000
 7YR  N4   C12  C11  110.12  3.000
 7YR  H15  N4   C13  115.09  3.000
 7YR  H15  N4   C12  114.54  3.000
 7YR  C13  N4   C12  120.67  3.000
 7YR  N5   C13  N6   126.01  3.000
 7YR  N6   C13  N4   113.17  3.000
 7YR  N5   C13  N4   120.81  3.000
 7YR  H17  N6   H16  111.64  3.000
 7YR  H17  N6   C13  115.10  3.000
 7YR  H16  N6   C13  116.16  3.000
 7YR  H18  N5   C13  110.53  3.000
 7YR  H5   N7   C14  114.57  3.000
 7YR  H5   N7   C9   116.16  3.000
 7YR  C14  N7   C9   129.27  3.000
 7YR  C15  C14  C19  118.21  3.000
 7YR  C15  C14  N7   124.72  3.000
 7YR  C19  C14  N7   117.06  3.000
 7YR  H6   C19  C18  118.69  3.000
 7YR  H6   C19  C14  119.88  3.000
 7YR  C18  C19  C14  121.44  3.000
 7YR  H7   C18  C17  121.09  3.000
 7YR  H7   C18  C19  118.56  3.000
 7YR  C17  C18  C19  120.34  3.000
 7YR  C16  C17  N8   120.91  3.000
 7YR  N8   C17  C18  120.51  3.000
 7YR  C16  C17  C18  118.37  3.000
 7YR  O5   N8   O6   108.20  3.000
 7YR  O6   N8   C17  109.86  3.000
 7YR  O5   N8   C17  109.75  3.000
 7YR  H10  O6   N8   104.50  3.000
 7YR  H11  O5   N8   104.55  3.000
 7YR  H8   C16  C15  117.97  3.000
 7YR  H8   C16  C17  120.73  3.000
 7YR  C15  C16  C17  121.30  3.000
 7YR  H9   C15  C16  118.44  3.000
 7YR  H9   C15  C14  121.22  3.000
 7YR  C16  C15  C14  120.33  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
 7YR  CONST_01  C17  C18  C19  C14     0.00   0.0  0
 7YR  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 7YR  CONST_03  C16  C15  C14  C19     0.00   0.0  0
 7YR  CONST_04  C16  C17  C18  C19     0.00   0.0  0
 7YR  CONST_05  C15  C14  C19  C18     0.00   0.0  0
 7YR  CONST_06  C15  C16  C17  C18     0.00   0.0  0
 7YR  CONST_07  C2   C1   N1   C4      0.00   0.0  0
 7YR  CONST_08  C18  C19  C14  N7    180.00   0.0  0
 7YR  CONST_09  C16  C15  C14  N7    180.00   0.0  0
 7YR  CONST_10  N8   C17  C18  C19   180.00   0.0  0
 7YR  CONST_11  C15  C16  C17  N8    180.00   0.0  0
 7YR  CONST_12  O1   C1   N1   C4    180.00   0.0  0
 7YR  CONST_13  H7   C18  C19  C14   180.00   0.0  0
 7YR  CONST_14  H8   C16  C15  C14   180.00   0.0  0
 7YR  CONST_15  H9   C15  C14  C19   180.00   0.0  0
 7YR  CONST_16  H6   C19  C18  C17   180.00   0.0  0
 7YR  CONST_17  H24  N1   C1   C2    180.00   0.0  0
 7YR  CONST_18  C19  C14  N7   C9    180.00   0.0  0
 7YR  CONST_19  C15  C14  N7   C9      0.00   0.0  0
 7YR  CONST_24  H5   N7   C14  C19     0.00   0.0  0
 7YR  CONST_25  C6   N2   C5   C4    180.00   0.0  0
 7YR  CONST_26  C14  N7   C9   C8    180.00   0.0  0
 7YR  CONST_27  C14  N7   C9   O4      0.00   0.0  0
 7YR  CONST_28  H22  N2   C5   C4      0.00   0.0  0
 7YR  CONST_31  C6   N2   C5   O2      0.00   0.0  0
 7YR  CONST_32  C8   N3   C7   C6    180.00   0.0  0
 7YR  CONST_33  C8   N3   C7   O3      0.00   0.0  0
 7YR  CONST_34  N5   C13  N4   C12     0.00   0.0  0
 7YR  CONST_35  N6   C13  N4   C12   180.00   0.0  0
 7YR  CONST_36  H19  N3   C7   C6      0.00   0.0  0
 7YR  CONST_37  H18  N5   C13  N4    180.00   0.0  0
 7YR  Var_01    C1   C2   C3   C4    -25.06  30.0  1
 7YR  Var_02    C3   C2   C1   N1     14.62  30.0  1
 7YR  Var_03    C7   C6   N2   C5    177.09  30.0  3
 7YR  Var_04    N3   C7   C6   N2    176.32  30.0  3
 7YR  Var_05    C12  C11  C10  C8   -175.15  30.0  1
 7YR  Var_06    N4   C12  C11  C10  -177.57  30.0  3
 7YR  Var_07    C13  N4   C12  C11  -171.23  30.0  1

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
 7YR  chir_01  C4  N1  C3   C5  positiv
 7YR  chir_02  C8  N3  C10  C9  negativ

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
 7YR  plan-1  C12  0.020
 7YR  plan-1  N4   0.020
 7YR  plan-1  C13  0.020
 7YR  plan-1  N6   0.020
 7YR  plan-1  N5   0.020
 7YR  plan-1  H15  0.020
 7YR  plan-1  H16  0.020
 7YR  plan-1  H17  0.020
 7YR  plan-1  H18  0.020
 7YR  plan-2  C4   0.020
 7YR  plan-2  N1   0.020
 7YR  plan-2  C2   0.020
 7YR  plan-2  C1   0.020
 7YR  plan-2  O1   0.020
 7YR  plan-2  H24  0.020
 7YR  plan-3  N7   0.020
 7YR  plan-3  C14  0.020
 7YR  plan-3  C19  0.020
 7YR  plan-3  C18  0.020
 7YR  plan-3  C17  0.020
 7YR  plan-3  N8   0.020
 7YR  plan-3  C16  0.020
 7YR  plan-3  C15  0.020
 7YR  plan-3  H6   0.020
 7YR  plan-3  H7   0.020
 7YR  plan-3  H8   0.020
 7YR  plan-3  H9   0.020
 7YR  plan-4  C6   0.020
 7YR  plan-4  C7   0.020
 7YR  plan-4  O3   0.020
 7YR  plan-4  N3   0.020
 7YR  plan-4  C8   0.020
 7YR  plan-4  H19  0.020
 7YR  plan-5  C8   0.020
 7YR  plan-5  C9   0.020
 7YR  plan-5  O4   0.020
 7YR  plan-5  N7   0.020
 7YR  plan-5  C14  0.020
 7YR  plan-5  H5   0.020
 7YR  plan-6  C17  0.020
 7YR  plan-6  N8   0.020
 7YR  plan-6  O6   0.020
 7YR  plan-6  O5   0.020
 7YR  plan-7  C5   0.020
 7YR  plan-7  O2   0.020
 7YR  plan-7  C4   0.020
 7YR  plan-7  N2   0.020
 7YR  plan-7  C6   0.020
 7YR  plan-7  H22  0.020

