# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 22:57:36 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](CC(C)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
 ZIL  ZIL  N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine  ligand  57  27  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZIL
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
 ZIL  C12  C  C     0   0.769  -89.8217  -28.3184  37.5049
 ZIL  O3   O  O     0  -0.507  -90.1967  -27.2049  37.8095
 ZIL  O4   O  O2    0  -0.480  -90.1683  -29.4328  38.1546
 ZIL  C13  C  CH2   0  -0.234  -90.9945  -29.2762  39.3129
 ZIL  C14  C  CR6   0   0.072  -91.1906  -30.6381  39.9085
 ZIL  C15  C  CR16  0  -0.282  -90.1039  -31.3461  40.4196
 ZIL  C16  C  CR16  0  -0.242  -90.2826  -32.6036  40.9753
 ZIL  C17  C  CR16  0  -0.263  -91.5527  -33.1670  41.0332
 ZIL  C18  C  CR16  0  -0.240  -92.6395  -32.4673  40.5300
 ZIL  C19  C  CR16  0  -0.304  -92.4561  -31.2100  39.9661
 ZIL  N1   N  NH1   0  -0.668  -88.9908  -28.5897  36.4799
 ZIL  C4   C  CH1   0  -0.174  -88.5977  -27.5558  35.5562
 ZIL  C5   C  C     0   0.568  -89.8135  -27.0962  34.7502
 ZIL  O    O  O     0  -0.488  -90.5652  -27.9061  34.2306
 ZIL  C2   C  CH1   0  -0.273  -87.5066  -28.0841  34.6116
 ZIL  C1   C  CH2   0  -0.422  -86.2814  -28.6007  35.3778
 ZIL  C3   C  CH3   0  -0.673  -87.1189  -27.0320  33.5753
 ZIL  C    C  CH3   0  -0.678  -85.5681  -27.5748  36.2475
 ZIL  N    N  NH1   0  -0.623  -89.9571  -25.7669  34.6416
 ZIL  C6   C  CH1   0  -0.238  -91.0552  -25.1620  33.9288
 ZIL  C11  C  C     0   0.555  -90.6472  -23.9299  33.1446
 ZIL  O1   O  O     0  -0.441  -91.4423  -23.2755  32.5181
 ZIL  C7   C  CH2   0  -0.395  -92.2904  -24.8967  34.8047
 ZIL  C8   C  CH1   0  -0.249  -92.2606  -23.6905  35.7464
 ZIL  C9   C  CH3   0  -0.652  -93.5454  -23.6843  36.5718
 ZIL  C10  C  CH3   0  -0.681  -91.0465  -23.6504  36.6711
 ZIL  O2   O  OH1   0  -0.579  -89.3540  -23.6611  33.1995
 ZIL  H23  H  HCH2  0   0.251  -91.9546  -28.8331  39.0399
 ZIL  H24  H  HCH2  0   0.249  -90.5073  -28.6097  40.0285
 ZIL  H25  H  HCR6  0   0.254  -89.1114  -30.9127  40.3864
 ZIL  H26  H  HCR6  0   0.258  -89.4309  -33.1442  41.3676
 ZIL  H27  H  HCR6  0   0.258  -91.6934  -34.1464  41.4719
 ZIL  H28  H  HCR6  0   0.258  -93.6312  -32.8984  40.5731
 ZIL  H29  H  HCR6  0   0.256  -93.3084  -30.6706  39.5705
 ZIL  H22  H  HNH1  0   0.402  -88.8478  -29.5516  36.2135
 ZIL  H9   H  HCH1  0   0.267  -88.1897  -26.7124  36.1208
 ZIL  H5   H  HCH1  0   0.247  -87.9312  -28.9395  34.0734
 ZIL  H3   H  HCH2  0   0.227  -86.5630  -29.4570  35.9953
 ZIL  H4   H  HCH2  0   0.232  -85.5820  -28.9960  34.6360
 ZIL  H6   H  HCH3  0   0.238  -86.2528  -27.3743  33.0083
 ZIL  H7   H  HCH3  0   0.242  -87.9193  -26.8456  32.8596
 ZIL  H8   H  HCH3  0   0.227  -86.8603  -26.0756  34.0318
 ZIL  H    H  HCH3  0   0.236  -84.6762  -28.0148  36.6945
 ZIL  H1   H  HCH3  0   0.225  -85.2463  -26.7011  35.6793
 ZIL  H2   H  HCH3  0   0.222  -86.1953  -27.2247  37.0686
 ZIL  H10  H  HNH1  0   0.403  -89.3594  -25.1823  35.2015
 ZIL  H11  H  HCH1  0   0.314  -91.3655  -25.8852  33.1683
 ZIL  H12  H  HCH2  0   0.243  -93.1547  -24.7975  34.1446
 ZIL  H13  H  HCH2  0   0.241  -92.4573  -25.8078  35.3866
 ZIL  H14  H  HCH1  0   0.225  -92.2558  -22.7796  35.1385
 ZIL  H15  H  HCH3  0   0.229  -93.6055  -22.7916  37.1963
 ZIL  H16  H  HCH3  0   0.216  -93.5858  -24.5551  37.2307
 ZIL  H17  H  HCH3  0   0.227  -94.4329  -23.7065  35.9368
 ZIL  H18  H  HCH3  0   0.213  -90.1174  -23.4396  36.1380
 ZIL  H19  H  HCH3  0   0.235  -91.1608  -22.8541  37.4082
 ZIL  H20  H  HCH3  0   0.234  -90.9262  -24.5915  37.2111
 ZIL  H21  H  HOH1  0   0.487  -89.1573  -22.8709  32.6729

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
 ZIL  O1   C11  double    1.205  0.020  1.205
 ZIL  C11  C6   single    1.516  0.020  1.516
 ZIL  C11  O2   single    1.322  0.020  1.322
 ZIL  C6   C7   single    1.537  0.020  1.537
 ZIL  C6   N    single    1.442  0.020  1.442
 ZIL  C7   C8   single    1.531  0.020  1.531
 ZIL  C3   C2   single    1.527  0.020  1.527
 ZIL  N    C5   single    1.341  0.020  1.341
 ZIL  O    C5   double    1.221  0.020  1.221
 ZIL  C2   C1   single    1.535  0.020  1.535
 ZIL  C2   C4   single    1.537  0.020  1.537
 ZIL  C5   C4   single    1.529  0.020  1.529
 ZIL  C8   C9   single    1.527  0.020  1.527
 ZIL  C8   C10  single    1.527  0.020  1.527
 ZIL  C1   C    single    1.522  0.020  1.522
 ZIL  C4   N1   single    1.441  0.020  1.441
 ZIL  N1   C12  single    1.347  0.020  1.347
 ZIL  C12  O4   single    1.336  0.020  1.336
 ZIL  C12  O3   double    1.214  0.020  1.214
 ZIL  O4   C13  single    1.431  0.020  1.431
 ZIL  C15  C16  aromatic  1.386  0.020  1.386
 ZIL  C15  C14  aromatic  1.394  0.020  1.394
 ZIL  C13  C14  single    1.499  0.020  1.499
 ZIL  C16  C17  aromatic  1.391  0.020  1.391
 ZIL  C14  C19  aromatic  1.390  0.020  1.390
 ZIL  C17  C18  aromatic  1.387  0.020  1.387
 ZIL  C19  C18  aromatic  1.390  0.020  1.390
 ZIL  C13  H24  single    0.970  0.020  1.090
 ZIL  C13  H23  single    0.970  0.020  1.090
 ZIL  C15  H25  single    0.930  0.020  1.080
 ZIL  C16  H26  single    0.930  0.020  1.080
 ZIL  C17  H27  single    0.930  0.020  1.080
 ZIL  C18  H28  single    0.930  0.020  1.080
 ZIL  C19  H29  single    0.930  0.020  1.080
 ZIL  N1   H22  single    0.860  0.020  1.020
 ZIL  C4   H9   single    0.970  0.020  1.090
 ZIL  C2   H5   single    0.970  0.020  1.090
 ZIL  C3   H7   single    0.970  0.020  1.090
 ZIL  C3   H8   single    0.970  0.020  1.090
 ZIL  C3   H6   single    0.970  0.020  1.090
 ZIL  C1   H3   single    0.970  0.020  1.090
 ZIL  C1   H4   single    0.970  0.020  1.090
 ZIL  C    H    single    0.970  0.020  1.090
 ZIL  C    H1   single    0.970  0.020  1.090
 ZIL  C    H2   single    0.970  0.020  1.090
 ZIL  N    H10  single    0.860  0.020  1.020
 ZIL  C6   H11  single    0.970  0.020  1.090
 ZIL  C7   H12  single    0.970  0.020  1.090
 ZIL  C7   H13  single    0.970  0.020  1.090
 ZIL  C8   H14  single    0.970  0.020  1.090
 ZIL  C9   H15  single    0.970  0.020  1.090
 ZIL  C9   H17  single    0.970  0.020  1.090
 ZIL  C9   H16  single    0.970  0.020  1.090
 ZIL  C10  H19  single    0.970  0.020  1.090
 ZIL  C10  H20  single    0.970  0.020  1.090
 ZIL  C10  H18  single    0.970  0.020  1.090
 ZIL  O2   H21  single    0.850  0.020  0.980

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
 ZIL  N1   C12  O4   111.24  3.000
 ZIL  O4   C12  O3   124.27  3.000
 ZIL  N1   C12  O3   124.49  3.000
 ZIL  C13  O4   C12  116.88  3.000
 ZIL  H24  C13  H23  107.95  3.000
 ZIL  H23  C13  C14  110.66  3.000
 ZIL  H24  C13  C14  110.62  3.000
 ZIL  H23  C13  O4   110.46  3.000
 ZIL  H24  C13  O4   109.84  3.000
 ZIL  C14  C13  O4   107.32  3.000
 ZIL  C19  C14  C15  119.05  3.000
 ZIL  C19  C14  C13  120.62  3.000
 ZIL  C15  C14  C13  120.33  3.000
 ZIL  H25  C15  C16  119.55  3.000
 ZIL  H25  C15  C14  119.98  3.000
 ZIL  C16  C15  C14  120.48  3.000
 ZIL  H26  C16  C17  120.08  3.000
 ZIL  H26  C16  C15  119.79  3.000
 ZIL  C17  C16  C15  120.12  3.000
 ZIL  H27  C17  C18  120.11  3.000
 ZIL  H27  C17  C16  120.15  3.000
 ZIL  C18  C17  C16  119.74  3.000
 ZIL  H28  C18  C19  119.82  3.000
 ZIL  H28  C18  C17  120.17  3.000
 ZIL  C19  C18  C17  120.01  3.000
 ZIL  H29  C19  C18  119.64  3.000
 ZIL  H29  C19  C14  119.75  3.000
 ZIL  C18  C19  C14  120.60  3.000
 ZIL  H22  N1   C4   118.45  3.000
 ZIL  H22  N1   C12  118.72  3.000
 ZIL  C4   N1   C12  120.76  3.000
 ZIL  H9   C4   C2   108.51  3.000
 ZIL  H9   C4   C5   109.69  3.000
 ZIL  C2   C4   C5   110.11  3.000
 ZIL  H9   C4   N1   108.91  3.000
 ZIL  C5   C4   N1   109.67  3.000
 ZIL  C2   C4   N1   109.94  3.000
 ZIL  N    C5   O    123.85  3.000
 ZIL  O    C5   C4   120.95  3.000
 ZIL  N    C5   C4   115.18  3.000
 ZIL  H5   C2   C3   107.63  3.000
 ZIL  H5   C2   C1   106.96  3.000
 ZIL  C3   C2   C1   111.60  3.000
 ZIL  H5   C2   C4   107.16  3.000
 ZIL  C1   C2   C4   112.07  3.000
 ZIL  C3   C2   C4   111.13  3.000
 ZIL  H4   C1   H3   105.37  3.000
 ZIL  H4   C1   C    109.36  3.000
 ZIL  H3   C1   C    109.03  3.000
 ZIL  H4   C1   C2   107.07  3.000
 ZIL  H3   C1   C2   109.89  3.000
 ZIL  C    C1   C2   115.62  3.000
 ZIL  H8   C3   H7   107.40  3.000
 ZIL  H8   C3   H6   107.73  3.000
 ZIL  H7   C3   H6   107.19  3.000
 ZIL  H6   C3   C2   109.78  3.000
 ZIL  H8   C3   C2   112.36  3.000
 ZIL  H7   C3   C2   112.16  3.000
 ZIL  H2   C    H1   107.73  3.000
 ZIL  H2   C    H    106.93  3.000
 ZIL  H1   C    H    107.19  3.000
 ZIL  H2   C    C1   112.14  3.000
 ZIL  H1   C    C1   112.36  3.000
 ZIL  H    C    C1   110.21  3.000
 ZIL  H10  N    C6   118.92  3.000
 ZIL  H10  N    C5   117.85  3.000
 ZIL  C6   N    C5   122.49  3.000
 ZIL  H11  C6   C7   106.39  3.000
 ZIL  H11  C6   C11  104.71  3.000
 ZIL  C7   C6   C11  111.75  3.000
 ZIL  H11  C6   N    106.39  3.000
 ZIL  C7   C6   N    113.74  3.000
 ZIL  C11  C6   N    113.05  3.000
 ZIL  O2   C11  O1   123.81  3.000
 ZIL  O2   C11  C6   114.01  3.000
 ZIL  O1   C11  C6   122.17  3.000
 ZIL  H13  C7   H12  106.05  3.000
 ZIL  H13  C7   C8   109.39  3.000
 ZIL  H12  C7   C8   108.41  3.000
 ZIL  H13  C7   C6   106.37  3.000
 ZIL  H12  C7   C6   107.89  3.000
 ZIL  C8   C7   C6   118.10  3.000
 ZIL  H14  C8   C10  108.11  3.000
 ZIL  H14  C8   C9   107.48  3.000
 ZIL  C10  C8   C9   109.98  3.000
 ZIL  H14  C8   C7   108.30  3.000
 ZIL  C10  C8   C7   114.13  3.000
 ZIL  C9   C8   C7   108.62  3.000
 ZIL  H17  C9   H16  107.73  3.000
 ZIL  H16  C9   H15  107.74  3.000
 ZIL  H17  C9   H15  107.75  3.000
 ZIL  H16  C9   C8   110.72  3.000
 ZIL  H17  C9   C8   111.69  3.000
 ZIL  H15  C9   C8   111.04  3.000
 ZIL  H20  C10  H19  107.85  3.000
 ZIL  H20  C10  H18  108.32  3.000
 ZIL  H19  C10  H18  106.15  3.000
 ZIL  H18  C10  C8   112.72  3.000
 ZIL  H20  C10  C8   111.39  3.000
 ZIL  H19  C10  C8   110.18  3.000
 ZIL  H21  O2   C11  109.97  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
 ZIL  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 ZIL  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 ZIL  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 ZIL  CONST_04  C18  C19  C14  C15     0.00   0.0  0
 ZIL  CONST_05  C19  C14  C15  C16     0.00   0.0  0
 ZIL  CONST_06  C19  C18  C17  C16     0.00   0.0  0
 ZIL  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 ZIL  CONST_08  C18  C19  C14  C13   180.00   0.0  0
 ZIL  CONST_09  H26  C16  C15  C14   180.00   0.0  0
 ZIL  CONST_10  H28  C18  C19  C14   180.00   0.0  0
 ZIL  CONST_11  H27  C17  C16  C15   180.00   0.0  0
 ZIL  CONST_12  H29  C19  C14  C15   180.00   0.0  0
 ZIL  CONST_13  H25  C15  C16  C17   180.00   0.0  0
 ZIL  CONST_14  C6   N    C5   C4    180.00   0.0  0
 ZIL  CONST_15  C6   N    C5   O       0.00   0.0  0
 ZIL  CONST_16  H10  N    C5   C4      0.00   0.0  0
 ZIL  CONST_17  H21  O2   C11  C6    180.00   0.0  0
 ZIL  Var_01    C15  C14  C13  O4     64.16  30.0  2
 ZIL  Var_02    C14  C13  O4   C12  -177.10  30.0  3
 ZIL  Var_03    C4   N1   C12  O3     -7.19  30.0  1
 ZIL  Var_04    N1   C12  O4   C13   176.76  30.0  2
 ZIL  Var_05    C9   C8   C7   C6   -176.32  30.0  3
 ZIL  Var_06    H    C    C1   C2   -176.10  30.0  3
 ZIL  Var_07    H15  C9   C8   C7   -175.08  30.0  3
 ZIL  Var_08    H19  C10  C8   C7   -171.75  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
 ZIL  chir_01  C4  C2  C5  N1   negativ
 ZIL  chir_02  C2  C4  C1  C3   positiv
 ZIL  chir_03  C6  N   C7  C11  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
 ZIL  plan-1  C13  0.020
 ZIL  plan-1  C14  0.020
 ZIL  plan-1  C15  0.020
 ZIL  plan-1  C16  0.020
 ZIL  plan-1  C17  0.020
 ZIL  plan-1  C18  0.020
 ZIL  plan-1  C19  0.020
 ZIL  plan-1  H25  0.020
 ZIL  plan-1  H26  0.020
 ZIL  plan-1  H27  0.020
 ZIL  plan-1  H28  0.020
 ZIL  plan-1  H29  0.020
 ZIL  plan-2  C4   0.020
 ZIL  plan-2  C5   0.020
 ZIL  plan-2  O    0.020
 ZIL  plan-2  N    0.020
 ZIL  plan-2  C6   0.020
 ZIL  plan-2  H10  0.020
 ZIL  plan-3  C6   0.020
 ZIL  plan-3  C11  0.020
 ZIL  plan-3  O1   0.020
 ZIL  plan-3  O2   0.020
 ZIL  plan-3  H21  0.020
 ZIL  plan-4  C12  0.020
 ZIL  plan-4  O3   0.020
 ZIL  plan-4  O4   0.020
 ZIL  plan-4  N1   0.020

