# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 06:38:36 2020
#   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  56  27  .  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_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   0.759   1.8700  -0.5837  -1.0122
 ZIL  O3   O  O      0  -0.525   1.8030  -0.8125  -2.2041
 ZIL  O4   O  O2     0  -0.483   2.9970  -0.2227  -0.3840
 ZIL  C13  C  CH2    0  -0.237   4.1691  -0.0623  -1.1885
 ZIL  C14  C  CR6    0   0.076   5.2488   0.4577  -0.2880
 ZIL  C15  C  CR16   0  -0.284   5.2286   1.7853   0.1350
 ZIL  C16  C  CR16   0  -0.243   6.2140   2.2696   0.9820
 ZIL  C17  C  CR16   0  -0.262   7.2344   1.4302   1.4147
 ZIL  C18  C  CR16   0  -0.241   7.2626   0.1072   0.9970
 ZIL  C19  C  CR16   0  -0.300   6.2712  -0.3757   0.1512
 ZIL  N1   N  NH1    0  -0.663   0.8472  -0.6500  -0.1473
 ZIL  C4   C  CH1    0  -0.200  -0.4966  -0.9937  -0.5457
 ZIL  C5   C  C      0   0.579  -1.4419  -0.2762   0.4158
 ZIL  O    O  O      0  -0.508  -1.0972  -0.0216   1.5638
 ZIL  C2   C  CH1    0  -0.221  -0.7160  -2.5251  -0.5606
 ZIL  C1   C  CH2    0  -0.450  -2.0101  -2.9550  -1.2554
 ZIL  C3   C  CH3    0  -0.672  -0.6349  -3.1354   0.8343
 ZIL  C    C  CH3    0  -0.678  -2.1319  -2.5181  -2.7106
 ZIL  N    N  NH1    0  -0.621  -2.6292   0.0664  -0.0879
 ZIL  C6   C  CH1    0  -0.211  -3.6945   0.6104   0.7228
 ZIL  C11  C  C      0   0.424  -4.4288  -0.4656   1.5632
 ZIL  O1   O  O      0  -0.576  -4.1710  -1.6607   1.3398
 ZIL  C7   C  CH2    0  -0.443  -4.6795   1.3759  -0.1599
 ZIL  C8   C  CH1    0  -0.225  -4.0594   2.4665  -1.0375
 ZIL  C9   C  CH3    0  -0.651  -5.1529   3.1740  -1.8318
 ZIL  C10  C  CH3    0  -0.660  -3.2528   3.4707  -0.2207
 ZIL  O2   O  OC    -1  -0.615  -5.2382  -0.0119   2.3965
 ZIL  H23  H  HCH2   0   0.247   4.4606  -1.0180  -1.6292
 ZIL  H24  H  HCH2   0   0.246   3.9747   0.6409  -2.0011
 ZIL  H25  H  HCR6   0   0.254   4.4411   2.4472  -0.2060
 ZIL  H26  H  HCR6   0   0.258   6.1890   3.3030   1.3026
 ZIL  H27  H  HCR6   0   0.258   8.0062   1.8090   2.0723
 ZIL  H28  H  HCR6   0   0.258   8.0543  -0.5512   1.3301
 ZIL  H29  H  HCR6   0   0.256   6.2973  -1.4096  -0.1721
 ZIL  H22  H  HNH1   0   0.396   0.9992  -0.4209   0.8234
 ZIL  H9   H  HCH1   0   0.276  -0.6555  -0.6109  -1.5566
 ZIL  H5   H  HCH1   0   0.233   0.1155  -2.9196  -1.1564
 ZIL  H3   H  HCH2   0   0.229  -2.0426  -4.0476  -1.2188
 ZIL  H4   H  HCH2   0   0.239  -2.8730  -2.6149  -0.6766
 ZIL  H6   H  HCH3   0   0.231  -1.5087  -2.8728   1.4322
 ZIL  H7   H  HCH3   0   0.228  -0.5989  -4.2234   0.7630
 ZIL  H8   H  HCH3   0   0.225   0.2581  -2.8157   1.3724
 ZIL  H    H  HCH3   0   0.237  -2.9815  -3.0045  -3.1904
 ZIL  H1   H  HCH3   0   0.210  -2.2819  -1.4424  -2.8244
 ZIL  H2   H  HCH3   0   0.226  -1.2361  -2.7783  -3.2776
 ZIL  H10  H  HNH1   0   0.386  -2.8619  -0.2511  -1.0151
 ZIL  H11  H  HCH1   0   0.242  -3.2401   1.3149   1.4231
 ZIL  H12  H  HCH2   0   0.225  -5.2207   0.6687  -0.8003
 ZIL  H13  H  HCH2   0   0.230  -5.4270   1.8281   0.4963
 ZIL  H14  H  HCH1   0   0.211  -3.3816   1.9909  -1.7556
 ZIL  H15  H  HCH3   0   0.225  -4.7291   3.9026  -2.5252
 ZIL  H16  H  HCH3   0   0.223  -5.7460   2.4662  -2.4138
 ZIL  H17  H  HCH3   0   0.213  -5.8349   3.7075  -1.1654
 ZIL  H18  H  HCH3   0   0.213  -3.8702   3.9220   0.5603
 ZIL  H19  H  HCH3   0   0.229  -2.3912   3.0079   0.2627
 ZIL  H20  H  HCH3   0   0.226  -2.8773   4.2774  -0.8527

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  deloc     1.243  0.020  1.243
 ZIL  C11  C6   single    1.550  0.020  1.550
 ZIL  C11  O2   deloc     1.247  0.020  1.247
 ZIL  C6   C7   single    1.528  0.020  1.528
 ZIL  C6   N    single    1.445  0.020  1.445
 ZIL  C7   C8   single    1.531  0.020  1.531
 ZIL  C3   C2   single    1.525  0.020  1.525
 ZIL  N    C5   single    1.334  0.020  1.334
 ZIL  O    C5   double    1.225  0.020  1.225
 ZIL  C2   C1   single    1.531  0.020  1.531
 ZIL  C2   C4   single    1.547  0.020  1.547
 ZIL  C5   C4   single    1.527  0.020  1.527
 ZIL  C8   C9   single    1.526  0.020  1.526
 ZIL  C8   C10  single    1.525  0.020  1.525
 ZIL  C1   C    single    1.524  0.020  1.524
 ZIL  C4   N1   single    1.443  0.020  1.443
 ZIL  N1   C12  single    1.341  0.020  1.341
 ZIL  C12  O4   single    1.340  0.020  1.340
 ZIL  C12  O3   double    1.215  0.020  1.215
 ZIL  O4   C13  single    1.431  0.020  1.431
 ZIL  C15  C16  aromatic  1.387  0.020  1.387
 ZIL  C15  C14  aromatic  1.393  0.020  1.393
 ZIL  C13  C14  single    1.499  0.020  1.499
 ZIL  C16  C17  aromatic  1.390  0.020  1.390
 ZIL  C14  C19  aromatic  1.390  0.020  1.390
 ZIL  C17  C18  aromatic  1.388  0.020  1.388
 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

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   110.63  3.000
 ZIL  O4   C12  O3   123.84  3.000
 ZIL  N1   C12  O3   125.53  3.000
 ZIL  C13  O4   C12  117.11  3.000
 ZIL  H24  C13  H23  108.11  3.000
 ZIL  H23  C13  C14  110.71  3.000
 ZIL  H24  C13  C14  110.60  3.000
 ZIL  H23  C13  O4   110.33  3.000
 ZIL  H24  C13  O4   110.17  3.000
 ZIL  C14  C13  O4   106.93  3.000
 ZIL  C19  C14  C15  119.07  3.000
 ZIL  C19  C14  C13  120.77  3.000
 ZIL  C15  C14  C13  120.16  3.000
 ZIL  H25  C15  C16  119.68  3.000
 ZIL  H25  C15  C14  119.80  3.000
 ZIL  C16  C15  C14  120.52  3.000
 ZIL  H26  C16  C17  120.08  3.000
 ZIL  H26  C16  C15  119.87  3.000
 ZIL  C17  C16  C15  120.05  3.000
 ZIL  H27  C17  C18  120.14  3.000
 ZIL  H27  C17  C16  120.07  3.000
 ZIL  C18  C17  C16  119.79  3.000
 ZIL  H28  C18  C19  119.85  3.000
 ZIL  H28  C18  C17  120.15  3.000
 ZIL  C19  C18  C17  120.00  3.000
 ZIL  H29  C19  C18  119.74  3.000
 ZIL  H29  C19  C14  119.70  3.000
 ZIL  C18  C19  C14  120.56  3.000
 ZIL  H22  N1   C4   117.39  3.000
 ZIL  H22  N1   C12  119.63  3.000
 ZIL  C4   N1   C12  122.94  3.000
 ZIL  H9   C4   C2   108.50  3.000
 ZIL  H9   C4   C5   109.14  3.000
 ZIL  C2   C4   C5   112.54  3.000
 ZIL  H9   C4   N1   107.90  3.000
 ZIL  C5   C4   N1   106.90  3.000
 ZIL  C2   C4   N1   111.74  3.000
 ZIL  N    C5   O    123.40  3.000
 ZIL  O    C5   C4   120.88  3.000
 ZIL  N    C5   C4   115.70  3.000
 ZIL  H5   C2   C3   108.23  3.000
 ZIL  H5   C2   C1   107.07  3.000
 ZIL  C3   C2   C1   110.36  3.000
 ZIL  H5   C2   C4   104.71  3.000
 ZIL  C1   C2   C4   113.72  3.000
 ZIL  C3   C2   C4   112.32  3.000
 ZIL  H4   C1   H3   105.64  3.000
 ZIL  H4   C1   C    110.69  3.000
 ZIL  H3   C1   C    108.42  3.000
 ZIL  H4   C1   C2   109.85  3.000
 ZIL  H3   C1   C2   106.89  3.000
 ZIL  C    C1   C2   114.87  3.000
 ZIL  H8   C3   H7   107.31  3.000
 ZIL  H8   C3   H6   108.35  3.000
 ZIL  H7   C3   H6   107.60  3.000
 ZIL  H6   C3   C2   111.25  3.000
 ZIL  H8   C3   C2   112.19  3.000
 ZIL  H7   C3   C2   109.95  3.000
 ZIL  H2   C    H1   107.05  3.000
 ZIL  H2   C    H    107.73  3.000
 ZIL  H1   C    H    106.65  3.000
 ZIL  H2   C    C1   111.22  3.000
 ZIL  H1   C    C1   113.13  3.000
 ZIL  H    C    C1   110.77  3.000
 ZIL  H10  N    C6   117.70  3.000
 ZIL  H10  N    C5   118.16  3.000
 ZIL  C6   N    C5   122.74  3.000
 ZIL  H11  C6   C7   108.38  3.000
 ZIL  H11  C6   C11  107.29  3.000
 ZIL  C7   C6   C11  110.83  3.000
 ZIL  H11  C6   N    107.20  3.000
 ZIL  C7   C6   N    109.86  3.000
 ZIL  C11  C6   N    113.08  3.000
 ZIL  O2   C11  O1   127.19  3.000
 ZIL  O2   C11  C6   114.65  3.000
 ZIL  O1   C11  C6   118.15  3.000
 ZIL  H13  C7   H12  106.26  3.000
 ZIL  H13  C7   C8   109.07  3.000
 ZIL  H12  C7   C8   108.93  3.000
 ZIL  H13  C7   C6   107.54  3.000
 ZIL  H12  C7   C6   109.40  3.000
 ZIL  C8   C7   C6   115.26  3.000
 ZIL  H14  C8   C10  108.03  3.000
 ZIL  H14  C8   C9   107.66  3.000
 ZIL  C10  C8   C9   110.64  3.000
 ZIL  H14  C8   C7   108.48  3.000
 ZIL  C10  C8   C7   112.10  3.000
 ZIL  C9   C8   C7   109.78  3.000
 ZIL  H17  C9   H16  107.62  3.000
 ZIL  H16  C9   H15  107.77  3.000
 ZIL  H17  C9   H15  107.69  3.000
 ZIL  H16  C9   C8   111.49  3.000
 ZIL  H17  C9   C8   110.87  3.000
 ZIL  H15  C9   C8   111.23  3.000
 ZIL  H20  C10  H19  107.36  3.000
 ZIL  H20  C10  H18  107.63  3.000
 ZIL  H19  C10  H18  107.74  3.000
 ZIL  H18  C10  C8   110.84  3.000
 ZIL  H20  C10  C8   111.01  3.000
 ZIL  H19  C10  C8   112.07  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  Var_01    C15  C14  C13  O4    -74.43  30.0  2
 ZIL  Var_02    C14  C13  O4   C12   174.99  30.0  3
 ZIL  Var_03    C4   N1   C12  O3     -0.88  30.0  1
 ZIL  Var_04    N1   C12  O4   C13  -177.82  30.0  1
 ZIL  Var_05    C9   C8   C7   C6   -178.37  30.0  3
 ZIL  Var_06    H    C    C1   C2    169.80  30.0  3
 ZIL  Var_07    H15  C9   C8   C7   -175.47  30.0  3
 ZIL  Var_08    H19  C10  C8   C7     63.92  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-4  C12  0.020
 ZIL  plan-4  O3   0.020
 ZIL  plan-4  O4   0.020
 ZIL  plan-4  N1   0.020

