# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 12:11:10 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N~2~-{[(1S)-1-carboxybut-3-en-1-yl]carbamoyl}-N~6~-[(4-iodophenyl)carbonyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[C@@H](CC=C)C(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
 YZE  YZE  N~2~-{[(1S)-1-carboxybut-3-en-1-yl]carbamoyl}-N~6~-[(4-iodophenyl)carbonyl]-L-lysine  ligand  53  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YZE
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
 YZE  C2    C  C2    0  -0.534   7.9223   1.4456  -3.8947
 YZE  C4    C  C1    0  -0.147   8.6177   1.2427  -2.7828
 YZE  C5    C  CH2   0  -0.537   8.4571   2.0335  -1.5234
 YZE  C6    C  CH1   0  -0.173   8.0894   1.1333  -0.3335
 YZE  C7    C  C     0   0.540   8.0243   1.9738   0.9337
 YZE  O8    O  O     0  -0.435   7.0088   2.4051   1.4135
 YZE  O9    O  OH1   0  -0.591   9.2346   2.2108   1.4192
 YZE  N10   N  NH1   0  -0.678   6.8390   0.4804  -0.5884
 YZE  C11   C  C     0   0.768   6.3542  -0.4242   0.3032
 YZE  N12   N  NH1   0  -0.683   5.0837  -0.8481   0.0696
 YZE  C13   C  CH1   0  -0.175   4.5288  -1.9205   0.8446
 YZE  C14   C  CH2   0  -0.467   3.0386  -2.0870   0.5298
 YZE  C15   C  CH2   0  -0.420   2.2171  -0.8589   0.9021
 YZE  C16   C  CH2   0  -0.463   0.7357  -1.0537   0.6080
 YZE  C17   C  CH2   0  -0.244  -0.0719   0.1795   0.9805
 YZE  N18   N  NH1   0  -0.652  -1.4794  -0.0186   0.7046
 YZE  C19   C  C     0   0.530  -2.3312   0.9924   0.4782
 YZE  C20   C  CR6   0  -0.033  -3.7492   0.6043   0.1978
 YZE  C21   C  CR16  0  -0.260  -4.7553   1.5157   0.5054
 YZE  C22   C  CR16  0  -0.213  -6.0850   1.2177   0.2532
 YZE  C23   C  CR6   0  -0.223  -6.4052   0.0010  -0.3338
 YZE  I24   I  I     0   0.069  -8.4170  -0.4576  -0.7314
 YZE  C25   C  CR16  0  -0.210  -5.4179  -0.9142  -0.6671
 YZE  C26   C  CR16  0  -0.280  -4.0923  -0.6070  -0.3960
 YZE  O27   O  O     0  -0.488  -1.9944   2.1691   0.4895
 YZE  C28   C  C     0   0.540   5.2640  -3.2258   0.5766
 YZE  O29   O  O     0  -0.436   5.9154  -3.4525  -0.4098
 YZE  O30   O  OH1   0  -0.592   5.0685  -4.1020   1.5525
 YZE  O31   O  O     0  -0.539   7.0176  -0.8266   1.2518
 YZE  H2    H  H     0   0.241   8.0896   0.8495  -4.7822
 YZE  H2A   H  H     0   0.238   7.1624   2.2157  -3.9607
 YZE  H4    H  H     0   0.251   9.3673   0.4568  -2.7556
 YZE  H5    H  HCH2  0   0.279   9.3957   2.5414  -1.2897
 YZE  H5A   H  HCH2  0   0.262   7.6946   2.8068  -1.6508
 YZE  H6    H  HCH1  0   0.287   8.8786   0.3863  -0.2107
 YZE  HO9   H  HOH1  0   0.484   9.1793   2.7908   2.1938
 YZE  HN10  H  HNH1  0   0.396   6.2021   0.9292  -1.2287
 YZE  HN12  H  HNH1  0   0.398   4.6661  -0.6596  -0.8290
 YZE  H13   H  HCH1  0   0.282   4.6278  -1.6883   1.9084
 YZE  H14   H  HCH2  0   0.245   2.9142  -2.3158  -0.5337
 YZE  H15   H  HCH2  0   0.229   2.3551  -0.6411   1.9659
 YZE  H16   H  HCH2  0   0.234   0.5949  -1.2728  -0.4543
 YZE  H16A  H  HCH2  0   0.232   0.3629  -1.9223   1.1610
 YZE  H17   H  HCH2  0   0.234   0.0806   0.4200   2.0382
 YZE  H17A  H  HCH2  0   0.242   0.2773   1.0384   0.4067
 YZE  HN18  H  HNH1  0   0.405  -1.8506  -0.9427   0.8598
 YZE  H21   H  HCR6  0   0.272  -4.5041   2.4665   0.9559
 YZE  H22   H  HCR6  0   0.284  -6.8522   1.9340   0.5129
 YZE  H25   H  HCR6  0   0.286  -5.6616  -1.8556  -1.1395
 YZE  H26   H  HCR6  0   0.270  -3.3324  -1.3228  -0.6829
 YZE  HO30  H  HOH1  0   0.483   5.5037  -4.9416   1.3411
 YZE  H23   H  HCH2  0   0.260   2.6604  -2.9522   1.0783
 YZE  H24   H  HCH2  0   0.231   2.5800   0.0180   0.3591

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
 YZE  C2   H2    single    0.930  0.020  1.080
 YZE  C2   H2A   single    0.930  0.020  1.080
 YZE  C4   C2    double    1.327  0.020  1.327
 YZE  C4   C5    single    1.496  0.020  1.496
 YZE  C4   H4    single    0.930  0.020  1.080
 YZE  C5   C6    single    1.537  0.020  1.537
 YZE  C5   H5    single    0.970  0.020  1.090
 YZE  C5   H5A   single    0.970  0.020  1.090
 YZE  C6   N10   single    1.433  0.020  1.433
 YZE  C6   H6    single    0.970  0.020  1.090
 YZE  C7   C6    single    1.522  0.020  1.522
 YZE  C7   O9    single    1.325  0.020  1.325
 YZE  O8   C7    double    1.203  0.020  1.203
 YZE  O9   HO9   single    0.850  0.020  0.980
 YZE  N10  C11   single    1.360  0.020  1.360
 YZE  N10  HN10  single    0.890  0.020  1.040
 YZE  C11  N12   single    1.360  0.020  1.360
 YZE  N12  C13   single    1.435  0.020  1.435
 YZE  N12  HN12  single    0.890  0.020  1.040
 YZE  C13  C28   single    1.522  0.020  1.522
 YZE  C13  H13   single    0.970  0.020  1.090
 YZE  C14  C13   single    1.532  0.020  1.532
 YZE  C14  C15   single    1.524  0.020  1.524
 YZE  C14  H14   single    0.970  0.020  1.090
 YZE  C15  H15   single    0.970  0.020  1.090
 YZE  C16  C15   single    1.523  0.020  1.523
 YZE  C16  C17   single    1.520  0.020  1.520
 YZE  C16  H16   single    0.970  0.020  1.090
 YZE  C16  H16A  single    0.970  0.020  1.090
 YZE  C17  N18   single    1.448  0.020  1.448
 YZE  C17  H17   single    0.970  0.020  1.090
 YZE  C17  H17A  single    0.970  0.020  1.090
 YZE  N18  C19   single    1.341  0.020  1.341
 YZE  N18  HN18  single    0.860  0.020  1.020
 YZE  C19  C20   single    1.497  0.020  1.497
 YZE  C20  C21   aromatic  1.392  0.020  1.392
 YZE  C20  C26   aromatic  1.392  0.020  1.392
 YZE  C21  C22   aromatic  1.386  0.020  1.386
 YZE  C21  H21   single    0.930  0.020  1.080
 YZE  C22  C23   aromatic  1.388  0.020  1.388
 YZE  C22  H22   single    0.930  0.020  1.080
 YZE  C23  I24   single    2.101  0.020  2.101
 YZE  C25  C23   aromatic  1.387  0.020  1.387
 YZE  C25  H25   single    0.930  0.020  1.080
 YZE  C26  C25   aromatic  1.388  0.020  1.388
 YZE  C26  H26   single    0.930  0.020  1.080
 YZE  O27  C19   double    1.224  0.020  1.224
 YZE  C28  O29   double    1.204  0.020  1.204
 YZE  C28  O30   single    1.326  0.020  1.326
 YZE  O30  HO30  single    0.850  0.020  0.980
 YZE  O31  C11   double    1.226  0.020  1.226
 YZE  C14  H23   single    0.970  0.020  1.090
 YZE  C15  H24   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
 YZE  H2A   C2   H2   116.73  3.000
 YZE  H2A   C2   C4   121.81  3.000
 YZE  H2    C2   C4   121.46  3.000
 YZE  H4    C4   C5   115.82  3.000
 YZE  H4    C4   C2   119.55  3.000
 YZE  C5    C4   C2   124.63  3.000
 YZE  H5A   C5   H5   107.17  3.000
 YZE  H5A   C5   C6   109.73  3.000
 YZE  H5    C5   C6   108.20  3.000
 YZE  H5A   C5   C4   110.53  3.000
 YZE  H5    C5   C4   109.49  3.000
 YZE  C6    C5   C4   111.59  3.000
 YZE  H6    C6   N10  109.78  3.000
 YZE  H6    C6   C7   108.33  3.000
 YZE  N10   C6   C7   111.24  3.000
 YZE  C7    C6   C5   109.36  3.000
 YZE  H6    C6   C5   108.33  3.000
 YZE  N10   C6   C5   109.74  3.000
 YZE  O9    C7   O8   124.10  3.000
 YZE  O8    C7   C6   124.48  3.000
 YZE  O9    C7   C6   111.39  3.000
 YZE  HO9   O9   C7   110.34  3.000
 YZE  HN10  N10  C11  119.16  3.000
 YZE  HN10  N10  C6   117.46  3.000
 YZE  C11   N10  C6   119.83  3.000
 YZE  O31   C11  N12  122.45  3.000
 YZE  O31   C11  N10  122.21  3.000
 YZE  N12   C11  N10  115.34  3.000
 YZE  HN12  N12  C13  117.44  3.000
 YZE  HN12  N12  C11  118.80  3.000
 YZE  C13   N12  C11  120.11  3.000
 YZE  H13   C13  C28  108.05  3.000
 YZE  H13   C13  C14  108.12  3.000
 YZE  C28   C13  C14  109.90  3.000
 YZE  C14   C13  N12  110.27  3.000
 YZE  H13   C13  N12  109.38  3.000
 YZE  C28   C13  N12  111.05  3.000
 YZE  H23   C14  H14  106.43  3.000
 YZE  H23   C14  C15  109.22  3.000
 YZE  H14   C14  C15  110.16  3.000
 YZE  H23   C14  C13  108.65  3.000
 YZE  H14   C14  C13  109.43  3.000
 YZE  C15   C14  C13  112.74  3.000
 YZE  H24   C15  H15  106.34  3.000
 YZE  H24   C15  C16  109.25  3.000
 YZE  H15   C15  C16  109.63  3.000
 YZE  H24   C15  C14  110.25  3.000
 YZE  C16   C15  C14  111.97  3.000
 YZE  H15   C15  C14  109.26  3.000
 YZE  H16A  C16  H16  106.72  3.000
 YZE  H16A  C16  C17  109.81  3.000
 YZE  H16   C16  C17  109.39  3.000
 YZE  H16A  C16  C15  109.58  3.000
 YZE  H16   C16  C15  109.78  3.000
 YZE  C17   C16  C15  111.44  3.000
 YZE  H17A  C17  H17  106.90  3.000
 YZE  H17A  C17  N18  108.59  3.000
 YZE  H17   C17  N18  110.44  3.000
 YZE  H17A  C17  C16  109.87  3.000
 YZE  H17   C17  C16  109.92  3.000
 YZE  N18   C17  C16  111.02  3.000
 YZE  HN18  N18  C19  118.89  3.000
 YZE  HN18  N18  C17  117.01  3.000
 YZE  C19   N18  C17  123.12  3.000
 YZE  O27   C19  C20  120.78  3.000
 YZE  O27   C19  N18  123.25  3.000
 YZE  C20   C19  N18  115.97  3.000
 YZE  C26   C20  C21  119.07  3.000
 YZE  C26   C20  C19  122.62  3.000
 YZE  C21   C20  C19  118.27  3.000
 YZE  H21   C21  C22  119.19  3.000
 YZE  H21   C21  C20  119.98  3.000
 YZE  C22   C21  C20  120.83  3.000
 YZE  H22   C22  C23  121.23  3.000
 YZE  H22   C22  C21  119.65  3.000
 YZE  C23   C22  C21  119.12  3.000
 YZE  C25   C23  I24  119.47  3.000
 YZE  C25   C23  C22  121.05  3.000
 YZE  I24   C23  C22  119.48  3.000
 YZE  H25   C25  C26  119.57  3.000
 YZE  C26   C25  C23  119.15  3.000
 YZE  H25   C25  C23  121.28  3.000
 YZE  H26   C26  C25  118.19  3.000
 YZE  H26   C26  C20  121.02  3.000
 YZE  C25   C26  C20  120.76  3.000
 YZE  O30   C28  O29  123.96  3.000
 YZE  O30   C28  C13  111.46  3.000
 YZE  O29   C28  C13  124.56  3.000
 YZE  HO30  O30  C28  110.23  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
 YZE  CONST_01  C23   C22  C21  C20     0.00   0.0  0
 YZE  CONST_02  C23   C25  C26  C20     0.00   0.0  0
 YZE  CONST_03  C25   C26  C20  C21     0.00   0.0  0
 YZE  CONST_04  C25   C23  C22  C21     0.00   0.0  0
 YZE  CONST_05  C26   C20  C21  C22     0.00   0.0  0
 YZE  CONST_06  C26   C25  C23  C22     0.00   0.0  0
 YZE  CONST_07  C22   C21  C20  C19   180.00   0.0  0
 YZE  CONST_08  C25   C26  C20  C19   180.00   0.0  0
 YZE  CONST_09  I24   C23  C22  C21   180.00   0.0  0
 YZE  CONST_10  C26   C25  C23  I24   180.00   0.0  0
 YZE  CONST_11  H22   C22  C21  C20   180.00   0.0  0
 YZE  CONST_12  H25   C25  C26  C20   180.00   0.0  0
 YZE  CONST_13  H26   C26  C20  C21   180.00   0.0  0
 YZE  CONST_14  H21   C21  C22  C23   180.00   0.0  0
 YZE  CONST_15  C20   C19  N18  C17   180.00   0.0  0
 YZE  CONST_16  HN18  N18  C19  C20     0.00   0.0  0
 YZE  CONST_17  O31   C11  N10  C6      0.00   0.0  0
 YZE  CONST_18  O31   C11  N12  C13     0.00   0.0  0
 YZE  CONST_19  O27   C19  N18  C17     0.00   0.0  0
 YZE  CONST_20  N12   C11  N10  C6    180.00   0.0  0
 YZE  CONST_21  C13   N12  C11  N10   180.00   0.0  0
 YZE  CONST_22  HN10  N10  C11  O31   180.00   0.0  0
 YZE  CONST_23  HN12  N12  C11  O31   180.00   0.0  0
 YZE  CONST_24  HO9   O9   C7   C6    180.00   0.0  0
 YZE  CONST_25  HO30  O30  C28  C13   180.00   0.0  0
 YZE  Var_01    C21   C20  C19  N18   153.38  30.0  2
 YZE  Var_02    C6    C5   C4   C2    121.86  30.0  3
 YZE  Var_03    C16   C15  C14  C13  -178.85  30.0  3
 YZE  Var_04    C17   C16  C15  C14  -179.85  30.0  1
 YZE  Var_05    N18   C17  C16  C15  -179.66  30.0  3
 YZE  Var_06    C19   N18  C17  C16  -155.49  30.0  3
 YZE  Var_07    H2    C2   C4   C5    179.22   0.0  2

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
 YZE  chir_01  C6   C5   N10  C7   positiv
 YZE  chir_02  C13  N12  C28  C14  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
 YZE  plan-1  C19   0.020
 YZE  plan-1  C20   0.020
 YZE  plan-1  C21   0.020
 YZE  plan-1  C22   0.020
 YZE  plan-1  C23   0.020
 YZE  plan-1  I24   0.020
 YZE  plan-1  C25   0.020
 YZE  plan-1  C26   0.020
 YZE  plan-1  H21   0.020
 YZE  plan-1  H22   0.020
 YZE  plan-1  H25   0.020
 YZE  plan-1  H26   0.020
 YZE  plan-2  C2    0.020
 YZE  plan-2  C4    0.020
 YZE  plan-2  C5    0.020
 YZE  plan-2  H2    0.020
 YZE  plan-2  H2A   0.020
 YZE  plan-2  H4    0.020
 YZE  plan-3  C6    0.020
 YZE  plan-3  N10   0.020
 YZE  plan-3  C11   0.020
 YZE  plan-3  N12   0.020
 YZE  plan-3  C13   0.020
 YZE  plan-3  O31   0.020
 YZE  plan-3  HN10  0.020
 YZE  plan-3  HN12  0.020
 YZE  plan-4  C17   0.020
 YZE  plan-4  N18   0.020
 YZE  plan-4  C19   0.020
 YZE  plan-4  C20   0.020
 YZE  plan-4  O27   0.020
 YZE  plan-4  HN18  0.020
 YZE  plan-5  C6    0.020
 YZE  plan-5  C7    0.020
 YZE  plan-5  O8    0.020
 YZE  plan-5  O9    0.020
 YZE  plan-5  HO9   0.020
 YZE  plan-6  C13   0.020
 YZE  plan-6  C28   0.020
 YZE  plan-6  O29   0.020
 YZE  plan-6  O30   0.020
 YZE  plan-6  HO30  0.020

