# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 13:36:00 2021
#   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  68  38  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.272  -0.1581   2.0333   9.7482
 YEN  C2   C  CR16  0  -0.324   0.4621   2.3029   8.5395
 YEN  C3   C  CR6   0   0.357   0.1880   3.4885   7.8680
 YEN  C4   C  CR16  0  -0.345  -0.7219   4.3931   8.3959
 YEN  C5   C  CR16  0  -0.323  -1.3389   4.0991   9.6066
 YEN  C6   C  CR6   0   0.090  -1.0661   2.9300  10.3105
 YEN  O1   O  O2    0  -0.618   0.8617   3.6737   6.6851
 YEN  P1   P  P     0   1.465   0.5580   4.8052   5.5701
 YEN  O2   O  OH1   0  -0.734  -0.8319   4.2760   5.0093
 YEN  O3   O  O     0  -0.687   0.6133   6.2013   6.0355
 YEN  O4   O  OH1   0  -0.713   1.5849   4.3671   4.4451
 YEN  C7   C  CH2   0  -0.516  -1.7112   2.6691  11.6452
 YEN  C8   C  CH1   0  -0.383  -2.3624   1.2869  11.7770
 YEN  C9   C  C     0   0.558  -3.3172   0.9632  10.6408
 YEN  O5   O  O     0  -0.463  -3.3628  -0.1380  10.1184
 YEN  C10  C  CH2   0  -0.596  -3.1148   1.1442  13.1012
 YEN  C11  C  C     0   0.556  -2.1945   1.0397  14.3028
 YEN  N1   N  NH1   0  -0.621  -2.7908   1.1370  15.5010
 YEN  C12  C  CH3   0  -0.528  -4.2023   1.3350  15.7457
 YEN  O7   O  O     0  -0.497  -0.9897   0.8500  14.1895
 YEN  N2   N  NH1   0  -0.667  -4.1412   1.9595  10.2475
 YEN  C13  C  CH1   0  -0.157  -5.1508   1.7496   9.2375
 YEN  C14  C  C     0   0.547  -4.5556   1.4149   7.8720
 YEN  O8   O  O     0  -0.470  -5.1817   0.7481   7.0669
 YEN  C15  C  CH2   0  -0.481  -6.0432   2.9856   9.1182
 YEN  C16  C  CH2   0  -0.583  -6.9008   3.1830  10.3590
 YEN  C17  C  C     0   0.556  -7.7872   4.3949  10.2705
 YEN  O9   O  O     0  -0.441  -7.8696   5.1243   9.3146
 YEN  O10  O  OH1   0  -0.594  -8.4863   4.5722  11.3855
 YEN  N3   N  NH1   0  -0.650  -3.3579   1.9621   7.5915
 YEN  C18  C  CH1   0  -0.232  -2.6275   1.6300   6.3895
 YEN  C19  C  C     0   0.558  -3.4097   1.9728   5.1195
 YEN  O12  O  O     0  -0.472  -3.3398   1.2604   4.1321
 YEN  C20  C  CH2   0  -0.561  -2.1395   0.1805   6.3942
 YEN  C21  C  C     0   0.515  -1.2246  -0.2263   5.2559
 YEN  O13  O  O     0  -0.490  -1.3844  -1.2734   4.6480
 YEN  N4   N  NH2   0  -0.804  -0.1911   0.5973   5.0037
 YEN  N5   N  NH2   0  -0.800  -4.0781   3.1300   5.1589
 YEN  H1   H  HCR6  0   0.267   0.0874   1.1093  10.2573
 YEN  H2   H  HCR6  0   0.286   1.1694   1.5975   8.1215
 YEN  H3   H  HCR6  0   0.292  -0.9547   5.3278   7.9048
 YEN  H4   H  HCR6  0   0.273  -2.0411   4.8170  10.0133
 YEN  H5   H  HOH1  0   0.508  -1.3922   4.9465   4.5954
 YEN  H6   H  HOH1  0   0.509   2.4401   4.8176   4.4817
 YEN  H7   H  HCH2  0   0.291  -0.9562   2.7602  12.4283
 YEN  H8   H  HCH2  0   0.247  -2.4420   3.4565  11.8527
 YEN  H9   H  HCH1  0   0.282  -1.5869   0.5201  11.7403
 YEN  H11  H  HCH2  0   0.272  -3.8176   1.9723  13.2315
 YEN  H12  H  HCH2  0   0.306  -3.7310   0.2377  13.0877
 YEN  H13  H  HNH1  0   0.397  -2.1899   1.0341  16.3041
 YEN  H14  H  HCH3  0   0.269  -4.3659   1.3055  16.8190
 YEN  H15  H  HCH3  0   0.244  -4.5524   2.3015  15.3804
 YEN  H16  H  HCH3  0   0.244  -4.8130   0.5525  15.2935
 YEN  H17  H  HNH1  0   0.408  -4.1051   2.8533  10.7114
 YEN  H19  H  HCH1  0   0.288  -5.7716   0.8898   9.5060
 YEN  H20  H  HCH2  0   0.255  -5.4244   3.8677   8.9319
 YEN  H21  H  HCH2  0   0.280  -6.6862   2.8612   8.2463
 YEN  H22  H  HCH2  0   0.295  -7.5383   2.3078  10.5192
 YEN  H23  H  HCH2  0   0.281  -6.2944   3.2730  11.2649
 YEN  H24  H  HOH1  0   0.481  -9.0531   5.3539  11.3035
 YEN  H26  H  HNH1  0   0.410  -2.8565   2.4436   8.3228
 YEN  H28  H  HCH1  0   0.279  -1.7749   2.3100   6.3885
 YEN  H29  H  HCH2  0   0.279  -1.5979   0.0167   7.3307
 YEN  H30  H  HCH2  0   0.277  -2.9883  -0.4996   6.3934
 YEN  H31  H  HNH2  0   0.404   0.5001   0.3381   4.3186
 YEN  H32  H  HNH2  0   0.388   0.0209   1.3976   5.5709
 YEN  H34  H  HNH2  0   0.405  -4.6038   3.4405   4.3585
 YEN  H35  H  HNH2  0   0.401  -4.1395   3.6814   5.9969

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  1.385  0.020  1.385
 YEN  C1   C6   aromatic  1.395  0.020  1.395
 YEN  C1   H1   single    0.930  0.020  1.080
 YEN  C2   C3   aromatic  1.390  0.020  1.390
 YEN  C2   H2   single    0.930  0.020  1.080
 YEN  C3   C4   aromatic  1.387  0.020  1.387
 YEN  C3   O1   single    1.374  0.020  1.374
 YEN  C4   C5   aromatic  1.390  0.020  1.390
 YEN  C4   H3   single    0.930  0.020  1.080
 YEN  C5   C6   aromatic  1.392  0.020  1.392
 YEN  C5   H4   single    0.930  0.020  1.080
 YEN  C6   C7   single    1.505  0.020  1.505
 YEN  O1   P1   single    1.617  0.020  1.617
 YEN  P1   O2   single    1.589  0.020  1.589
 YEN  P1   O3   double    1.473  0.020  1.473
 YEN  P1   O4   single    1.585  0.020  1.585
 YEN  O2   H5   single    0.850  0.020  0.980
 YEN  O4   H6   single    0.850  0.020  0.980
 YEN  C7   C8   single    1.534  0.020  1.534
 YEN  C7   H7   single    0.970  0.020  1.090
 YEN  C7   H8   single    0.970  0.020  1.090
 YEN  C8   C9   single    1.519  0.020  1.519
 YEN  C8   C10  single    1.530  0.020  1.530
 YEN  C8   H9   single    0.970  0.020  1.090
 YEN  C9   O5   double    1.220  0.020  1.220
 YEN  C9   N2   single    1.351  0.020  1.351
 YEN  C10  C11  single    1.517  0.020  1.517
 YEN  C10  H11  single    0.970  0.020  1.090
 YEN  C10  H12  single    0.970  0.020  1.090
 YEN  C11  N1   single    1.342  0.020  1.342
 YEN  C11  O7   double    1.225  0.020  1.225
 YEN  N1   C12  single    1.446  0.020  1.446
 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    1.443  0.020  1.443
 YEN  N2   H17  single    0.860  0.020  1.020
 YEN  C13  C14  single    1.527  0.020  1.527
 YEN  C13  C15  single    1.529  0.020  1.529
 YEN  C13  H19  single    0.970  0.020  1.090
 YEN  C14  O8   double    1.219  0.020  1.219
 YEN  C14  N3   single    1.346  0.020  1.346
 YEN  C15  C16  single    1.521  0.020  1.521
 YEN  C15  H20  single    0.970  0.020  1.090
 YEN  C15  H21  single    0.970  0.020  1.090
 YEN  C16  C17  single    1.504  0.020  1.504
 YEN  C16  H22  single    0.970  0.020  1.090
 YEN  C16  H23  single    0.970  0.020  1.090
 YEN  C17  O9   double    1.205  0.020  1.205
 YEN  C17  O10  single    1.328  0.020  1.328
 YEN  O10  H24  single    0.850  0.020  0.980
 YEN  N3   C18  single    1.445  0.020  1.445
 YEN  N3   H26  single    0.860  0.020  1.020
 YEN  C18  C19  single    1.530  0.020  1.530
 YEN  C18  C20  single    1.529  0.020  1.529
 YEN  C18  H28  single    0.970  0.020  1.090
 YEN  C19  O12  double    1.220  0.020  1.220
 YEN  C19  N5   single    1.337  0.020  1.337
 YEN  C20  C21  single    1.516  0.020  1.516
 YEN  C20  H29  single    0.970  0.020  1.090
 YEN  C20  H30  single    0.970  0.020  1.090
 YEN  C21  O13  double    1.221  0.020  1.221
 YEN  C21  N4   single    1.345  0.020  1.345
 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   120.44  3.000
 YEN  H1   C1   C2   118.34  3.000
 YEN  C6   C1   C2   121.21  3.000
 YEN  H2   C2   C3   119.87  3.000
 YEN  H2   C2   C1   120.17  3.000
 YEN  C3   C2   C1   119.96  3.000
 YEN  O1   C3   C4   124.15  3.000
 YEN  O1   C3   C2   115.74  3.000
 YEN  C4   C3   C2   120.11  3.000
 YEN  H3   C4   C5   118.87  3.000
 YEN  H3   C4   C3   122.14  3.000
 YEN  C5   C4   C3   118.99  3.000
 YEN  H4   C5   C6   119.59  3.000
 YEN  H4   C5   C4   118.32  3.000
 YEN  C6   C5   C4   122.08  3.000
 YEN  C7   C6   C5   120.67  3.000
 YEN  C7   C6   C1   121.67  3.000
 YEN  C5   C6   C1   117.64  3.000
 YEN  P1   O1   C3   126.57  3.000
 YEN  O4   P1   O3   117.52  3.000
 YEN  O4   P1   O2   102.95  3.000
 YEN  O3   P1   O2   117.39  3.000
 YEN  O4   P1   O1   100.04  3.000
 YEN  O3   P1   O1   115.99  3.000
 YEN  O2   P1   O1   100.05  3.000
 YEN  H5   O2   P1   115.27  3.000
 YEN  H6   O4   P1   114.66  3.000
 YEN  H8   C7   H7   105.42  3.000
 YEN  H8   C7   C8   110.40  3.000
 YEN  H7   C7   C8   107.89  3.000
 YEN  H8   C7   C6   109.25  3.000
 YEN  H7   C7   C6   108.98  3.000
 YEN  C8   C7   C6   114.48  3.000
 YEN  H9   C8   C10  108.24  3.000
 YEN  H9   C8   C9   105.77  3.000
 YEN  C10  C8   C9   108.57  3.000
 YEN  H9   C8   C7   109.19  3.000
 YEN  C10  C8   C7   111.55  3.000
 YEN  C9   C8   C7   113.25  3.000
 YEN  N2   C9   O5   121.21  3.000
 YEN  N2   C9   C8   116.35  3.000
 YEN  O5   C9   C8   122.43  3.000
 YEN  H12  C10  H11  105.45  3.000
 YEN  H12  C10  C11  107.09  3.000
 YEN  H11  C10  C11  110.34  3.000
 YEN  H12  C10  C8   110.05  3.000
 YEN  H11  C10  C8   110.39  3.000
 YEN  C11  C10  C8   113.19  3.000
 YEN  O7   C11  N1   122.07  3.000
 YEN  O7   C11  C10  122.28  3.000
 YEN  N1   C11  C10  115.63  3.000
 YEN  H13  N1   C12  117.45  3.000
 YEN  H13  N1   C11  116.03  3.000
 YEN  C12  N1   C11  126.49  3.000
 YEN  H16  C12  H15  108.49  3.000
 YEN  H16  C12  H14  107.81  3.000
 YEN  H15  C12  H14  107.86  3.000
 YEN  H16  C12  N1   112.21  3.000
 YEN  H15  C12  N1   112.20  3.000
 YEN  H14  C12  N1   108.09  3.000
 YEN  H17  N2   C13  118.43  3.000
 YEN  H17  N2   C9   119.87  3.000
 YEN  C13  N2   C9   121.53  3.000
 YEN  H19  C13  C15  108.86  3.000
 YEN  H19  C13  C14  105.57  3.000
 YEN  C15  C13  C14  109.57  3.000
 YEN  H19  C13  N2   109.84  3.000
 YEN  C15  C13  N2   110.20  3.000
 YEN  C14  C13  N2   112.64  3.000
 YEN  N3   C14  O8   122.81  3.000
 YEN  N3   C14  C13  116.37  3.000
 YEN  O8   C14  C13  120.70  3.000
 YEN  H21  C15  H20  106.83  3.000
 YEN  H21  C15  C16  109.55  3.000
 YEN  H20  C15  C16  110.69  3.000
 YEN  H21  C15  C13  108.32  3.000
 YEN  H20  C15  C13  109.57  3.000
 YEN  C16  C15  C13  111.73  3.000
 YEN  H23  C16  H22  105.51  3.000
 YEN  H23  C16  C17  108.01  3.000
 YEN  H22  C16  C17  108.03  3.000
 YEN  H23  C16  C15  111.94  3.000
 YEN  H22  C16  C15  110.12  3.000
 YEN  C17  C16  C15  112.88  3.000
 YEN  O10  C17  O9   123.31  3.000
 YEN  O10  C17  C16  111.62  3.000
 YEN  O9   C17  C16  125.07  3.000
 YEN  H24  O10  C17  110.15  3.000
 YEN  H26  N3   C18  117.47  3.000
 YEN  H26  N3   C14  119.01  3.000
 YEN  C18  N3   C14  121.98  3.000
 YEN  H28  C18  C20  109.97  3.000
 YEN  H28  C18  C19  105.02  3.000
 YEN  C20  C18  C19  112.20  3.000
 YEN  H28  C18  N3   104.63  3.000
 YEN  C20  C18  N3   112.11  3.000
 YEN  C19  C18  N3   112.36  3.000
 YEN  N5   C19  O12  123.93  3.000
 YEN  N5   C19  C18  115.15  3.000
 YEN  O12  C19  C18  120.78  3.000
 YEN  H30  C20  H29  107.06  3.000
 YEN  H30  C20  C21  107.62  3.000
 YEN  H29  C20  C21  107.68  3.000
 YEN  H30  C20  C18  110.10  3.000
 YEN  H29  C20  C18  107.60  3.000
 YEN  C21  C20  C18  116.39  3.000
 YEN  N4   C21  O13  122.15  3.000
 YEN  N4   C21  C20  116.11  3.000
 YEN  O13  C21  C20  121.66  3.000
 YEN  H32  N4   H31  116.40  3.000
 YEN  H32  N4   C21  122.99  3.000
 YEN  H31  N4   C21  119.82  3.000
 YEN  H35  N5   H34  117.50  3.000
 YEN  H35  N5   C19  122.01  3.000
 YEN  H34  N5   C19  120.31  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     0.00   0.0  0
 YEN  CONST_18  O7   C11  N1   C12   180.00   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   180.00   0.0  0
 YEN  CONST_23  H26  N3   C14  C13     0.00   0.0  0
 YEN  CONST_24  H34  N5   C19  C18   180.00   0.0  0
 YEN  CONST_25  H35  N5   C19  C18     0.00   0.0  0
 YEN  CONST_26  H31  N4   C21  C20   180.00   0.0  0
 YEN  CONST_27  H32  N4   C21  C20     0.00   0.0  0
 YEN  CONST_28  H24  O10  C17  C16   180.00   0.0  0
 YEN  Var_01    C8   C7   C6   C1    -51.14  30.0  2
 YEN  Var_02    O2   P1   O1   C3    -69.73  30.0  3
 YEN  Var_03    N1   C11  C10  C8    169.33  30.0  3
 YEN  Var_04    C17  C16  C15  C13   179.86  30.0  3
 YEN  Var_05    O9   C17  C16  C15     2.59  30.0  3
 YEN  Var_06    O13  C21  C20  C18  -134.67  30.0  3
 YEN  Var_07    H14  C12  N1   C11   176.39  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-2  H24  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

