# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul 10 12:57:26 2020
#   Inital geometry file: a 170 line input string
#   Ligand name: N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C[C@H](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CC(N)=O)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
 YEN  YEN  N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide  peptide  65  38  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YEN
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
 YEN  C1   C  CR16   0  -0.295  -3.7350  -1.0019   0.1508
 YEN  C2   C  CR16   0  -0.356  -5.0123  -0.8956  -0.3727
 YEN  C3   C  CR6    0   0.377  -5.7093   0.3200  -0.3432
 YEN  C4   C  CR16   0  -0.376  -5.0732   1.4194   0.2435
 YEN  C5   C  CR16   0  -0.317  -3.7918   1.2933   0.7649
 YEN  C6   C  CR6    0   0.103  -3.0933   0.0903   0.7332
 YEN  O1   O  O2     0  -0.655  -6.9233   0.3550  -0.8893
 YEN  P1   P  P      0   1.230  -8.1981   1.4481  -0.3748
 YEN  O2   O  OP    -1  -0.874  -9.3509   0.8453  -1.1554
 YEN  O3   O  O      0  -0.883  -8.2397   1.2578   1.1293
 YEN  O4   O  OP    -1  -0.880  -7.7386   2.8183  -0.8469
 YEN  C7   C  CH2    0  -0.499  -1.6995  -0.0383   1.2860
 YEN  C8   C  CH1    0  -0.413  -0.6570  -0.2868   0.1917
 YEN  C9   C  C      0   0.609   0.7158  -0.5827   0.7847
 YEN  O5   O  O      0  -0.493   0.9772  -0.4178   1.9652
 YEN  C10  C  CH2    0  -0.559  -0.6017   0.8566  -0.8326
 YEN  C11  C  C      0   0.549  -0.1311   2.1553  -0.2171
 YEN  N1   N  NH1    0  -0.624  -0.9815   3.1870  -0.3066
 YEN  C12  C  CH3    0  -0.515  -0.6754   4.4934   0.2254
 YEN  O7   O  O      0  -0.488   0.9614   2.2477   0.3275
 YEN  N2   N  NH1    0  -0.625   1.5935  -1.0958  -0.0999
 YEN  C13  C  CH1    0  -0.247   2.9929  -1.2955   0.1679
 YEN  C14  C  C      0   0.599   3.8085  -0.2494  -0.5799
 YEN  O8   O  O      0  -0.488   3.5086   0.1245  -1.7025
 YEN  C15  C  CH2    0  -0.406   3.4569  -2.6923  -0.2641
 YEN  C16  C  CH2    0  -0.587   2.7777  -3.7938   0.5303
 YEN  C17  C  C      0   0.415   3.1990  -5.2276   0.1631
 YEN  O9   O  O      0  -0.608   3.8967  -5.3862  -0.8577
 YEN  O10  O  OC    -1  -0.630   2.7851  -6.1266   0.9244
 YEN  N3   N  NH1    0  -0.639   4.9046   0.1906   0.0608
 YEN  C18  C  CH1    0  -0.181   5.8860   0.9944  -0.6177
 YEN  C19  C  C      0   0.516   6.5102   0.2147  -1.7795
 YEN  O12  O  O      0  -0.476   6.6749  -0.9917  -1.7215
 YEN  C20  C  CH2    0  -0.609   6.9812   1.4003   0.3626
 YEN  C21  C  C      0   0.528   6.4521   2.3472   1.4261
 YEN  O13  O  O      0  -0.485   5.7412   3.2975   1.1364
 YEN  N4   N  NH2    0  -0.799   6.8394   2.0686   2.6765
 YEN  N5   N  NH2    0  -0.799   6.8964   0.9775  -2.8086
 YEN  H1   H  HCR6   0   0.236  -3.2322  -1.9630   0.1122
 YEN  H2   H  HCR6   0   0.238  -5.4879  -1.7642  -0.8131
 YEN  H3   H  HCR6   0   0.250  -5.5728   2.3779   0.2649
 YEN  H4   H  HCR6   0   0.236  -3.3255   2.1637   1.2140
 YEN  H7   H  HCH2   0   0.243  -1.4413   0.8589   1.8532
 YEN  H8   H  HCH2   0   0.253  -1.6618  -0.8667   1.9975
 YEN  H9   H  HCH1   0   0.285  -0.9592  -1.1808  -0.3652
 YEN  H11  H  HCH2   0   0.275   0.0906   0.6079  -1.6405
 YEN  H12  H  HCH2   0   0.266  -1.5859   0.9615  -1.2927
 YEN  H13  H  HNH1   0   0.404  -1.8671   3.0525  -0.7640
 YEN  H14  H  HCH3   0   0.250  -1.5171   5.1509   0.0290
 YEN  H15  H  HCH3   0   0.237  -0.5094   4.4601   1.3026
 YEN  H16  H  HCH3   0   0.237   0.2114   4.9211  -0.2436
 YEN  H17  H  HNH1   0   0.392   1.3082  -1.1793  -1.0634
 YEN  H19  H  HCH1   0   0.269   3.1438  -1.1885   1.2435
 YEN  H20  H  HCH2   0   0.224   3.2676  -2.8163  -1.3333
 YEN  H21  H  HCH2   0   0.233   4.5409  -2.7490  -0.1378
 YEN  H22  H  HCH2   0   0.221   2.9525  -3.6405   1.6006
 YEN  H23  H  HCH2   0   0.233   1.6917  -3.7212   0.4060
 YEN  H26  H  HNH1   0   0.405   5.1512  -0.2347   0.9411
 YEN  H28  H  HCH1   0   0.284   5.4094   1.9012  -0.9984
 YEN  H29  H  HCH2   0   0.277   7.4438   0.5125   0.7999
 YEN  H30  H  HCH2   0   0.305   7.7692   1.9292  -0.1795
 YEN  H31  H  HNH2   0   0.411   7.4295   1.2834   2.8894
 YEN  H32  H  HNH2   0   0.404   6.5797   2.6739   3.4389
 YEN  H34  H  HNH2   0   0.410   6.6949   1.9618  -2.8466
 YEN  H35  H  HNH2   0   0.405   7.3731   0.5729  -3.5980

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
 YEN  C1   C2   aromatic  1.384  0.020  1.384
 YEN  C1   C6   aromatic  1.394  0.020  1.394
 YEN  C1   H1   single    0.930  0.020  1.080
 YEN  C2   C3   aromatic  1.402  0.020  1.402
 YEN  C2   H2   single    0.930  0.020  1.080
 YEN  C3   C4   aromatic  1.399  0.020  1.399
 YEN  C3   O1   single    1.332  0.020  1.332
 YEN  C4   C5   aromatic  1.389  0.020  1.389
 YEN  C4   H3   single    0.930  0.020  1.080
 YEN  C5   C6   aromatic  1.391  0.020  1.391
 YEN  C5   H4   single    0.930  0.020  1.080
 YEN  C6   C7   single    1.505  0.020  1.505
 YEN  O1   P1   single    1.756  0.020  1.756
 YEN  P1   O2   deloc     1.517  0.020  1.517
 YEN  P1   O3   deloc     1.517  0.020  1.517
 YEN  P1   O4   deloc     1.520  0.020  1.520
 YEN  C7   C8   single    1.532  0.020  1.532
 YEN  C7   H7   single    0.970  0.020  1.090
 YEN  C7   H8   single    0.970  0.020  1.090
 YEN  C8   C9   single    1.524  0.020  1.524
 YEN  C8   C10  single    1.536  0.020  1.536
 YEN  C8   H9   single    0.970  0.020  1.090
 YEN  C9   O5   double    1.220  0.020  1.220
 YEN  C9   N2   single    1.348  0.020  1.348
 YEN  C10  C11  single    1.512  0.020  1.512
 YEN  C10  H11  single    0.970  0.020  1.090
 YEN  C10  H12  single    0.970  0.020  1.090
 YEN  C11  N1   single    1.340  0.020  1.340
 YEN  C11  O7   double    1.224  0.020  1.224
 YEN  N1   C12  single    1.443  0.020  1.443
 YEN  N1   H13  single    0.860  0.020  1.020
 YEN  C12  H14  single    0.970  0.020  1.090
 YEN  C12  H15  single    0.970  0.020  1.090
 YEN  C12  H16  single    0.970  0.020  1.090
 YEN  N2   C13  single    1.439  0.020  1.439
 YEN  N2   H17  single    0.860  0.020  1.020
 YEN  C13  C14  single    1.523  0.020  1.523
 YEN  C13  C15  single    1.534  0.020  1.534
 YEN  C13  H19  single    0.970  0.020  1.090
 YEN  C14  O8   double    1.221  0.020  1.221
 YEN  C14  N3   single    1.344  0.020  1.344
 YEN  C15  C16  single    1.518  0.020  1.518
 YEN  C15  H20  single    0.970  0.020  1.090
 YEN  C15  H21  single    0.970  0.020  1.090
 YEN  C16  C17  single    1.539  0.020  1.539
 YEN  C16  H22  single    0.970  0.020  1.090
 YEN  C16  H23  single    0.970  0.020  1.090
 YEN  C17  O9   deloc     1.247  0.020  1.247
 YEN  C17  O10  deloc     1.249  0.020  1.249
 YEN  N3   C18  single    1.439  0.020  1.439
 YEN  N3   H26  single    0.860  0.020  1.020
 YEN  C18  C19  single    1.532  0.020  1.532
 YEN  C18  C20  single    1.525  0.020  1.525
 YEN  C18  H28  single    0.970  0.020  1.090
 YEN  C19  O12  double    1.219  0.020  1.219
 YEN  C19  N5   single    1.338  0.020  1.338
 YEN  C20  C21  single    1.519  0.020  1.519
 YEN  C20  H29  single    0.970  0.020  1.090
 YEN  C20  H30  single    0.970  0.020  1.090
 YEN  C21  O13  double    1.222  0.020  1.222
 YEN  C21  N4   single    1.338  0.020  1.338
 YEN  N4   H31  single    0.860  0.020  1.020
 YEN  N4   H32  single    0.860  0.020  1.020
 YEN  N5   H34  single    0.860  0.020  1.020
 YEN  N5   H35  single    0.860  0.020  1.020

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
 YEN  H1   C1   C6   119.70  3.000
 YEN  H1   C1   C2   118.81  3.000
 YEN  C6   C1   C2   121.49  3.000
 YEN  H2   C2   C3   119.04  3.000
 YEN  H2   C2   C1   119.80  3.000
 YEN  C3   C2   C1   121.16  3.000
 YEN  O1   C3   C4   124.46  3.000
 YEN  O1   C3   C2   117.88  3.000
 YEN  C4   C3   C2   117.66  3.000
 YEN  H3   C4   C5   119.96  3.000
 YEN  H3   C4   C3   119.66  3.000
 YEN  C5   C4   C3   120.36  3.000
 YEN  H4   C5   C6   119.17  3.000
 YEN  H4   C5   C4   118.62  3.000
 YEN  C6   C5   C4   122.21  3.000
 YEN  C7   C6   C5   122.03  3.000
 YEN  C7   C6   C1   120.85  3.000
 YEN  C5   C6   C1   117.12  3.000
 YEN  P1   O1   C3   123.92  3.000
 YEN  O4   P1   O3   115.42  3.000
 YEN  O4   P1   O2   115.34  3.000
 YEN  O3   P1   O2   116.08  3.000
 YEN  O4   P1   O1   104.51  3.000
 YEN  O3   P1   O1   103.43  3.000
 YEN  O2   P1   O1    98.83  3.000
 YEN  H8   C7   H7   106.05  3.000
 YEN  H8   C7   C8   108.58  3.000
 YEN  H7   C7   C8   110.09  3.000
 YEN  H8   C7   C6   109.63  3.000
 YEN  H7   C7   C6   109.84  3.000
 YEN  C8   C7   C6   112.44  3.000
 YEN  H9   C8   C10  106.16  3.000
 YEN  H9   C8   C9   106.72  3.000
 YEN  C10  C8   C9   111.81  3.000
 YEN  H9   C8   C7   107.92  3.000
 YEN  C10  C8   C7   112.34  3.000
 YEN  C9   C8   C7   111.50  3.000
 YEN  N2   C9   O5   123.16  3.000
 YEN  N2   C9   C8   113.89  3.000
 YEN  O5   C9   C8   122.89  3.000
 YEN  H12  C10  H11  106.35  3.000
 YEN  H12  C10  C11  111.70  3.000
 YEN  H11  C10  C11  107.41  3.000
 YEN  H12  C10  C8   108.68  3.000
 YEN  H11  C10  C8   110.27  3.000
 YEN  C11  C10  C8   112.27  3.000
 YEN  O7   C11  N1   122.54  3.000
 YEN  O7   C11  C10  121.57  3.000
 YEN  N1   C11  C10  115.88  3.000
 YEN  H13  N1   C12  118.39  3.000
 YEN  H13  N1   C11  119.09  3.000
 YEN  C12  N1   C11  122.52  3.000
 YEN  H16  C12  H15  108.24  3.000
 YEN  H16  C12  H14  108.36  3.000
 YEN  H15  C12  H14  108.37  3.000
 YEN  H16  C12  N1   111.65  3.000
 YEN  H15  C12  N1   111.64  3.000
 YEN  H14  C12  N1   108.47  3.000
 YEN  H17  N2   C13  116.21  3.000
 YEN  H17  N2   C9   118.32  3.000
 YEN  C13  N2   C9   124.34  3.000
 YEN  H19  C13  C15  108.96  3.000
 YEN  H19  C13  C14  110.03  3.000
 YEN  C15  C13  C14  108.98  3.000
 YEN  H19  C13  N2   107.72  3.000
 YEN  C15  C13  N2   111.61  3.000
 YEN  C14  C13  N2   109.53  3.000
 YEN  N3   C14  O8   122.59  3.000
 YEN  N3   C14  C13  115.32  3.000
 YEN  O8   C14  C13  122.04  3.000
 YEN  H21  C15  H20  106.20  3.000
 YEN  H21  C15  C16  110.22  3.000
 YEN  H20  C15  C16  110.61  3.000
 YEN  H21  C15  C13  108.35  3.000
 YEN  H20  C15  C13  109.05  3.000
 YEN  C16  C15  C13  112.21  3.000
 YEN  H23  C16  H22  105.06  3.000
 YEN  H23  C16  C17  107.82  3.000
 YEN  H22  C16  C17  108.65  3.000
 YEN  H23  C16  C15  109.63  3.000
 YEN  H22  C16  C15  109.77  3.000
 YEN  C17  C16  C15  115.38  3.000
 YEN  O10  C17  O9   126.39  3.000
 YEN  O10  C17  C16  115.76  3.000
 YEN  O9   C17  C16  117.85  3.000
 YEN  H26  N3   C18  118.72  3.000
 YEN  H26  N3   C14  118.54  3.000
 YEN  C18  N3   C14  120.97  3.000
 YEN  H28  C18  C20  108.44  3.000
 YEN  H28  C18  C19  109.62  3.000
 YEN  C20  C18  C19  109.29  3.000
 YEN  H28  C18  N3   109.29  3.000
 YEN  C20  C18  N3   109.60  3.000
 YEN  C19  C18  N3   110.56  3.000
 YEN  N5   C19  O12  124.18  3.000
 YEN  N5   C19  C18  114.25  3.000
 YEN  O12  C19  C18  121.51  3.000
 YEN  H30  C20  H29  106.65  3.000
 YEN  H30  C20  C21  107.26  3.000
 YEN  H29  C20  C21  111.95  3.000
 YEN  H30  C20  C18  109.14  3.000
 YEN  H29  C20  C18  110.19  3.000
 YEN  C21  C20  C18  111.46  3.000
 YEN  N4   C21  O13  123.50  3.000
 YEN  N4   C21  C20  115.06  3.000
 YEN  O13  C21  C20  121.43  3.000
 YEN  H32  N4   H31  117.41  3.000
 YEN  H32  N4   C21  120.49  3.000
 YEN  H31  N4   C21  122.03  3.000
 YEN  H35  N5   H34  117.29  3.000
 YEN  H35  N5   C19  120.70  3.000
 YEN  H34  N5   C19  121.97  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
 YEN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 YEN  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 YEN  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 YEN  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 YEN  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 YEN  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 YEN  CONST_07  O1   C3   C2   C1    180.00   0.0  0
 YEN  CONST_08  C7   C6   C1   C2    180.00   0.0  0
 YEN  CONST_09  C7   C6   C5   C4    180.00   0.0  0
 YEN  CONST_10  O1   C3   C4   C5    180.00   0.0  0
 YEN  CONST_11  H4   C5   C6   C1    180.00   0.0  0
 YEN  CONST_12  H3   C4   C3   C2    180.00   0.0  0
 YEN  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 YEN  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 YEN  CONST_15  C13  N2   C9   C8    180.00   0.0  0
 YEN  CONST_16  C13  N2   C9   O5      0.00   0.0  0
 YEN  CONST_17  C12  N1   C11  C10   180.00   0.0  0
 YEN  CONST_18  O7   C11  N1   C12     0.00   0.0  0
 YEN  CONST_19  C18  N3   C14  C13   180.00   0.0  0
 YEN  CONST_20  C18  N3   C14  O8      0.00   0.0  0
 YEN  CONST_21  H17  N2   C9   C8      0.00   0.0  0
 YEN  CONST_22  H13  N1   C11  C10     0.00   0.0  0
 YEN  CONST_23  H26  N3   C14  C13     0.00   0.0  0
 YEN  CONST_24  H34  N5   C19  C18     0.00   0.0  0
 YEN  CONST_25  H35  N5   C19  C18   180.00   0.0  0
 YEN  CONST_26  H31  N4   C21  C20     0.00   0.0  0
 YEN  CONST_27  H32  N4   C21  C20   180.00   0.0  0
 YEN  Var_01    C8   C7   C6   C1     67.15  30.0  2
 YEN  Var_02    O2   P1   O1   C3   -170.02  30.0  3
 YEN  Var_03    N1   C11  C10  C8   -121.05  30.0  3
 YEN  Var_04    C17  C16  C15  C13  -179.54  30.0  3
 YEN  Var_05    O9   C17  C16  C15   -10.01  30.0  3
 YEN  Var_06    O13  C21  C20  C18   -45.74  30.0  3
 YEN  Var_07    H14  C12  N1   C11  -179.97  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
 YEN  chir_01  C8   C7  C9   C10  positiv
 YEN  chir_02  C13  N2  C14  C15  positiv
 YEN  chir_03  C18  N3  C19  C20  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
 YEN  plan-1  C1   0.020
 YEN  plan-1  C2   0.020
 YEN  plan-1  C3   0.020
 YEN  plan-1  C4   0.020
 YEN  plan-1  C5   0.020
 YEN  plan-1  C6   0.020
 YEN  plan-1  O1   0.020
 YEN  plan-1  C7   0.020
 YEN  plan-1  H1   0.020
 YEN  plan-1  H2   0.020
 YEN  plan-1  H3   0.020
 YEN  plan-1  H4   0.020
 YEN  plan-2  C16  0.020
 YEN  plan-2  C17  0.020
 YEN  plan-2  O9   0.020
 YEN  plan-2  O10  0.020
 YEN  plan-3  C8   0.020
 YEN  plan-3  C9   0.020
 YEN  plan-3  O5   0.020
 YEN  plan-3  N2   0.020
 YEN  plan-3  C13  0.020
 YEN  plan-3  H17  0.020
 YEN  plan-4  C10  0.020
 YEN  plan-4  C11  0.020
 YEN  plan-4  N1   0.020
 YEN  plan-4  C12  0.020
 YEN  plan-4  O7   0.020
 YEN  plan-4  H13  0.020
 YEN  plan-5  C13  0.020
 YEN  plan-5  C14  0.020
 YEN  plan-5  O8   0.020
 YEN  plan-5  N3   0.020
 YEN  plan-5  C18  0.020
 YEN  plan-5  H26  0.020
 YEN  plan-6  C18  0.020
 YEN  plan-6  C19  0.020
 YEN  plan-6  O12  0.020
 YEN  plan-6  N5   0.020
 YEN  plan-6  H34  0.020
 YEN  plan-6  H35  0.020
 YEN  plan-7  C20  0.020
 YEN  plan-7  C21  0.020
 YEN  plan-7  O13  0.020
 YEN  plan-7  N4   0.020
 YEN  plan-7  H31  0.020
 YEN  plan-7  H32  0.020

