# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:39:40 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{R})-~{N}-[2-[[(2~{S})-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCC[C@H](NC(=O)CNC(=O)[C@@H]1NC(=O)C=C1)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
 7YF  7YF  (2~{R})-~{N}-[2-[[(2~{S})-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-2-carboxamide  peptide  43  23  .  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_7YF
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
 7YF  C5   C  C     0   0.564  -3.3644   0.6241   0.1523
 7YF  O2   O  O     0  -0.470  -3.3930   1.1704   1.2398
 7YF  C4   C  CR15  0  -0.249  -4.5762   0.6357  -0.7918
 7YF  N1   N  NR15  0  -0.633  -5.3985   1.7879  -0.6033
 7YF  C3   C  CR15  0  -0.178  -5.5012  -0.4826  -0.4036
 7YF  C2   C  CR15  0  -0.356  -6.6567   0.0143   0.0250
 7YF  C1   C  CR5   0   0.512  -6.6068   1.4950  -0.0622
 7YF  O1   O  O     0  -0.485  -7.4677   2.2920   0.2665
 7YF  N2   N  NH1   0  -0.641  -2.3223  -0.0690  -0.3120
 7YF  C6   C  CH2   0  -0.375  -1.1236  -0.2626   0.4553
 7YF  C7   C  C     0   0.531  -0.1314  -1.0799  -0.3530
 7YF  O3   O  O     0  -0.483  -0.4054  -1.5228  -1.4569
 7YF  N3   N  NH1   0  -0.630   1.0588  -1.2454   0.2408
 7YF  C8   C  CH1   0  -0.197   2.0994  -2.0675  -0.3131
 7YF  C9   C  C1    0   0.191   1.8755  -3.5350  -0.0242
 7YF  O4   O  O     0  -0.363   0.9287  -3.9756   0.5709
 7YF  C10  C  CH2   0  -0.463   3.4801  -1.6370   0.1857
 7YF  C11  C  CH2   0  -0.454   3.8523  -0.2300  -0.2609
 7YF  C12  C  CH2   0  -0.227   5.2490   0.1554   0.2009
 7YF  N4   N  NH1   0  -0.650   5.5635   1.4959  -0.2337
 7YF  C13  C  C     0   0.555   6.8183   2.0113  -0.0579
 7YF  N6   N  NH2   0  -0.841   6.9403   3.3311  -0.4368
 7YF  N5   N  N     0  -0.720   7.7799   1.2620   0.3435
 7YF  H17  H  HCR5  0   0.312  -4.2479   0.5302  -1.8316
 7YF  H18  H  HNR5  0   0.406  -5.0509   2.7292  -0.6932
 7YF  H19  H  HCR5  0   0.297  -5.2089  -1.5201  -0.4708
 7YF  H20  H  HCR5  0   0.281  -7.5160  -0.5308   0.3852
 7YF  H16  H  HNH1  0   0.409  -2.3487  -0.4820  -1.2334
 7YF  H14  H  HCH2  0   0.285  -0.6693   0.6950   0.7248
 7YF  H15  H  HCH2  0   0.287  -1.3365  -0.7857   1.3926
 7YF  H5   H  H     0   0.205   2.6677  -4.1947  -0.4208
 7YF  H13  H  HNH1  0   0.412   1.1763  -0.9217   1.1896
 7YF  H6   H  HCH1  0   0.292   2.0919  -1.9712  -1.4053
 7YF  H1   H  HCH2  0   0.251   3.5155  -1.7141   1.2771
 7YF  H2   H  HCH2  0   0.256   4.2156  -2.3489  -0.1977
 7YF  H7   H  HCH2  0   0.236   3.7997  -0.1669  -1.3516
 7YF  H8   H  HCH2  0   0.233   3.1264   0.4877   0.1322
 7YF  H3   H  HCH2  0   0.211   5.3229   0.0523   1.2914
 7YF  H4   H  HCH2  0   0.229   5.9824  -0.5310  -0.2248
 7YF  H9   H  HNH1  0   0.379   4.8005   2.1524  -0.1819
 7YF  H10  H  HNH2  0   0.382   6.0984   3.8835  -0.4802
 7YF  H11  H  HNH2  0   0.385   7.7022   3.8341  -0.0120
 7YF  H12  H  H     0   0.314   8.6522   1.7780   0.3420

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
 7YF  O1   C1   double  1.218  0.020  1.218
 7YF  C1   C2   single  1.484  0.020  1.484
 7YF  C1   N1   single  1.356  0.020  1.356
 7YF  C2   C3   double  1.329  0.020  1.329
 7YF  N1   C4   single  1.428  0.020  1.428
 7YF  C3   C4   single  1.502  0.020  1.502
 7YF  C4   C5   single  1.536  0.020  1.536
 7YF  C5   O2   double  1.217  0.020  1.217
 7YF  C5   N2   single  1.335  0.020  1.335
 7YF  N5   C13  double  1.283  0.020  1.283
 7YF  N2   C6   single  1.436  0.020  1.436
 7YF  O3   C7   double  1.221  0.020  1.221
 7YF  C13  N4   single  1.368  0.020  1.368
 7YF  C13  N6   single  1.378  0.020  1.378
 7YF  N4   C12  single  1.444  0.020  1.444
 7YF  C6   C7   single  1.519  0.020  1.519
 7YF  C7   N3   single  1.340  0.020  1.340
 7YF  C11  C12  single  1.521  0.020  1.521
 7YF  C11  C10  single  1.522  0.020  1.522
 7YF  N3   C8   single  1.437  0.020  1.437
 7YF  C8   C10  single  1.530  0.020  1.530
 7YF  C8   C9   single  1.512  0.020  1.512
 7YF  O4   C9   double  1.202  0.020  1.202
 7YF  C10  H1   single  0.970  0.020  1.090
 7YF  C10  H2   single  0.970  0.020  1.090
 7YF  C12  H3   single  0.970  0.020  1.090
 7YF  C12  H4   single  0.970  0.020  1.090
 7YF  C9   H5   single  0.930  0.020  1.080
 7YF  C8   H6   single  0.970  0.020  1.090
 7YF  C11  H7   single  0.970  0.020  1.090
 7YF  C11  H8   single  0.970  0.020  1.090
 7YF  N4   H9   single  0.890  0.020  1.040
 7YF  N6   H10  single  0.890  0.020  1.040
 7YF  N6   H11  single  0.890  0.020  1.040
 7YF  N5   H12  single  0.890  0.020  1.040
 7YF  N3   H13  single  0.860  0.020  1.020
 7YF  C6   H14  single  0.970  0.020  1.090
 7YF  C6   H15  single  0.970  0.020  1.090
 7YF  N2   H16  single  0.860  0.020  1.020
 7YF  C4   H17  single  0.970  0.020  1.090
 7YF  N1   H18  single  0.860  0.020  1.020
 7YF  C3   H19  single  0.930  0.020  1.080
 7YF  C2   H20  single  0.930  0.020  1.080

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
 7YF  N2   C5   C4   113.95  3.000
 7YF  N2   C5   O2   124.20  3.000
 7YF  C4   C5   O2   121.81  3.000
 7YF  H17  C4   C3   110.98  3.000
 7YF  H17  C4   N1   112.06  3.000
 7YF  C3   C4   N1   102.23  3.000
 7YF  H17  C4   C5   110.26  3.000
 7YF  C3   C4   C5   108.74  3.000
 7YF  N1   C4   C5   112.28  3.000
 7YF  H18  N1   C1   123.02  3.000
 7YF  H18  N1   C4   122.91  3.000
 7YF  C1   N1   C4   113.05  3.000
 7YF  H19  C3   C2   127.92  3.000
 7YF  H19  C3   C4   122.17  3.000
 7YF  C2   C3   C4   109.90  3.000
 7YF  H20  C2   C1   123.38  3.000
 7YF  H20  C2   C3   127.66  3.000
 7YF  C1   C2   C3   108.96  3.000
 7YF  O1   C1   C2   127.81  3.000
 7YF  C2   C1   N1   105.60  3.000
 7YF  O1   C1   N1   126.58  3.000
 7YF  H16  N2   C6   117.01  3.000
 7YF  H16  N2   C5   120.61  3.000
 7YF  C6   N2   C5   122.38  3.000
 7YF  H15  C6   H14  106.76  3.000
 7YF  H15  C6   C7   109.01  3.000
 7YF  H14  C6   C7   109.33  3.000
 7YF  H15  C6   N2   111.08  3.000
 7YF  H14  C6   N2   111.12  3.000
 7YF  C7   C6   N2   109.48  3.000
 7YF  N3   C7   O3   123.72  3.000
 7YF  N3   C7   C6   114.26  3.000
 7YF  O3   C7   C6   122.01  3.000
 7YF  H13  N3   C8   117.48  3.000
 7YF  H13  N3   C7   118.70  3.000
 7YF  C8   N3   C7   122.88  3.000
 7YF  H6   C8   C10  107.83  3.000
 7YF  H6   C8   C9   105.93  3.000
 7YF  C10  C8   C9   110.15  3.000
 7YF  H6   C8   N3   109.19  3.000
 7YF  C9   C8   N3   111.97  3.000
 7YF  C10  C8   N3   111.52  3.000
 7YF  H5   C9   O4   121.59  3.000
 7YF  H5   C9   C8   113.88  3.000
 7YF  O4   C9   C8   124.53  3.000
 7YF  H2   C10  H1   106.38  3.000
 7YF  H2   C10  C11  109.55  3.000
 7YF  H1   C10  C11  110.47  3.000
 7YF  H2   C10  C8   108.04  3.000
 7YF  H1   C10  C8   109.54  3.000
 7YF  C11  C10  C8   112.65  3.000
 7YF  H8   C11  H7   106.77  3.000
 7YF  H8   C11  C12  109.51  3.000
 7YF  H7   C11  C12  109.41  3.000
 7YF  H8   C11  C10  109.80  3.000
 7YF  H7   C11  C10  109.52  3.000
 7YF  C12  C11  C10  111.70  3.000
 7YF  H4   C12  H3   106.46  3.000
 7YF  H4   C12  N4   108.67  3.000
 7YF  H3   C12  N4   111.81  3.000
 7YF  H4   C12  C11  109.84  3.000
 7YF  H3   C12  C11  109.86  3.000
 7YF  N4   C12  C11  110.12  3.000
 7YF  H9   N4   C13  116.26  3.000
 7YF  H9   N4   C12  115.11  3.000
 7YF  C13  N4   C12  120.73  3.000
 7YF  N5   C13  N6   125.36  3.000
 7YF  N6   C13  N4   113.99  3.000
 7YF  N5   C13  N4   120.49  3.000
 7YF  H11  N6   H10  112.11  3.000
 7YF  H11  N6   C13  115.42  3.000
 7YF  H10  N6   C13  117.56  3.000
 7YF  H12  N5   C13  110.30  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
 7YF  CONST_01  C2   C1   N1   C4      0.00   0.0  0
 7YF  CONST_02  O1   C1   N1   C4    180.00   0.0  0
 7YF  CONST_03  H18  N1   C1   C2    180.00   0.0  0
 7YF  CONST_04  C6   N2   C5   C4    180.00   0.0  0
 7YF  CONST_05  H16  N2   C5   C4      0.00   0.0  0
 7YF  CONST_06  C6   N2   C5   O2      0.00   0.0  0
 7YF  CONST_07  C8   N3   C7   C6    180.00   0.0  0
 7YF  CONST_08  C8   N3   C7   O3      0.00   0.0  0
 7YF  CONST_09  N5   C13  N4   C12     0.00   0.0  0
 7YF  CONST_10  N6   C13  N4   C12   180.00   0.0  0
 7YF  CONST_11  H13  N3   C7   C6      0.00   0.0  0
 7YF  CONST_12  H12  N5   C13  N4    180.00   0.0  0
 7YF  Var_01    C1   C2   C3   C4      0.92  30.0  1
 7YF  Var_02    C3   C2   C1   N1      2.28  30.0  1
 7YF  Var_03    C7   C6   N2   C5   -179.58  30.0  3
 7YF  Var_04    O3   C7   C6   N2     -3.00  30.0  3
 7YF  Var_05    C12  C11  C10  C8   -177.81  30.0  1
 7YF  Var_06    N4   C12  C11  C10  -179.68  30.0  3
 7YF  Var_07    C13  N4   C12  C11  -173.09  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
 7YF  chir_01  C4  N1  C3   C5  positiv
 7YF  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
 7YF  plan-1  C5   0.020
 7YF  plan-1  O2   0.020
 7YF  plan-1  C4   0.020
 7YF  plan-1  N2   0.020
 7YF  plan-1  C6   0.020
 7YF  plan-1  H16  0.020
 7YF  plan-2  C8   0.020
 7YF  plan-2  C9   0.020
 7YF  plan-2  O4   0.020
 7YF  plan-2  H5   0.020
 7YF  plan-3  C6   0.020
 7YF  plan-3  C7   0.020
 7YF  plan-3  O3   0.020
 7YF  plan-3  N3   0.020
 7YF  plan-3  C8   0.020
 7YF  plan-3  H13  0.020
 7YF  plan-4  C12  0.020
 7YF  plan-4  N4   0.020
 7YF  plan-4  C13  0.020
 7YF  plan-4  N6   0.020
 7YF  plan-4  N5   0.020
 7YF  plan-4  H9   0.020
 7YF  plan-4  H10  0.020
 7YF  plan-4  H11  0.020
 7YF  plan-4  H12  0.020
 7YF  plan-5  C4   0.020
 7YF  plan-5  N1   0.020
 7YF  plan-5  C2   0.020
 7YF  plan-5  C1   0.020
 7YF  plan-5  O1   0.020
 7YF  plan-5  H18  0.020

