# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 20:27:22 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)CCCCCCCCCCCn1ccnc1)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
 LEH  LEH  N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine  L-peptide  64  27  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LEH
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
 LEH  O3    O  O     0  -0.501    4.9361   1.5787   0.8218
 LEH  C7    C  C     0   0.576    4.9283   0.7411  -0.0698
 LEH  N1    N  NH1   0  -0.644    6.0400   0.0594  -0.4061
 LEH  C6    C  CH1   0  -0.186    7.3101   0.3530   0.1963
 LEH  C5    C  CH2   0  -0.454    8.3536  -0.6958  -0.2024
 LEH  C4    C  CH1   0  -0.235    8.0140  -2.1262   0.2268
 LEH  C3    C  CH3   0  -0.652    9.1156  -3.0671  -0.2517
 LEH  C2    C  CH3   0  -0.664    7.8182  -2.2433   1.7338
 LEH  C1    C  C     0   0.548    7.7924   1.7348  -0.2178
 LEH  O2    O  OH1   0  -0.592    8.6908   2.2048   0.6368
 LEH  O1    O  O     0  -0.435    7.4371   2.3173  -1.2086
 LEH  C8    C  CH2   0  -0.581    3.6885   0.4134  -0.8684
 LEH  C9    C  CH2   0  -0.416    2.4267   0.3802  -0.0143
 LEH  C10   C  CH2   0  -0.416    1.1704   0.1505  -0.8438
 LEH  C11   C  CH2   0  -0.413   -0.0974   0.1328   0.0012
 LEH  C12   C  CH2   0  -0.412   -1.3655  -0.0671  -0.8187
 LEH  C13   C  CH2   0  -0.412   -2.6346  -0.0430   0.0243
 LEH  C14   C  CH2   0  -0.412   -3.9043  -0.2349  -0.7950
 LEH  C15   C  CH2   0  -0.413   -5.1762  -0.1561   0.0399
 LEH  C16   C  CH2   0  -0.422   -6.4428  -0.3481  -0.7842
 LEH  C17   C  CH2   0  -0.429   -7.7143  -0.2154   0.0434
 LEH  C18   C  CH2   0  -0.293   -8.9602  -0.4179  -0.8066
 LEH  N2    N  NR5   0  -0.397  -10.1874  -0.2499  -0.0529
 LEH  C20   C  CR15  0  -0.109  -10.7140  -1.1243   0.8548
 LEH  C21   C  CR15  0  -0.220  -11.8351  -0.5151   1.3436
 LEH  N3    N  N     0  -0.458  -11.9999   0.7086   0.7599
 LEH  C19   C  CR15  0   0.091  -10.9922   0.8325  -0.0669
 LEH  HN1   H  HNH1  0   0.404    6.0140  -0.5543  -1.2044
 LEH  H6    H  HCH1  0   0.283    7.2038   0.3513   1.2839
 LEH  H5    H  HCH2  0   0.250    8.4941  -0.6637  -1.2879
 LEH  H5A   H  HCH2  0   0.253    9.3110  -0.4141   0.2433
 LEH  H4    H  HCH1  0   0.225    7.0827  -2.4311  -0.2623
 LEH  H3    H  HCH3  0   0.230    8.8934  -4.1007   0.0173
 LEH  H3A   H  HCH3  0   0.228    9.2350  -3.0229  -1.3356
 LEH  H3B   H  HCH3  0   0.217   10.0761  -2.8061   0.1990
 LEH  H2    H  HCH3  0   0.231    6.9723  -1.6536   2.0900
 LEH  H2A   H  HCH3  0   0.234    7.6282  -3.2792   2.0180
 LEH  H2B   H  HCH3  0   0.218    8.7086  -1.9091   2.2722
 LEH  HO2   H  HOH1  0   0.484    9.0260   3.0618   0.3335
 LEH  H8    H  HCH2  0   0.267    3.5895   1.1880  -1.6366
 LEH  H8A   H  HCH2  0   0.250    3.8099  -0.5319  -1.4033
 LEH  H9    H  HCH2  0   0.224    2.5165  -0.4083   0.7394
 LEH  H9A   H  HCH2  0   0.224    2.3338   1.3215   0.5323
 LEH  H10   H  HCH2  0   0.211    1.0884   0.9364  -1.6028
 LEH  H10A  H  HCH2  0   0.211    1.2559  -0.7939  -1.3924
 LEH  H11   H  HCH2  0   0.209   -0.0211  -0.6595   0.7540
 LEH  H11A  H  HCH2  0   0.208   -0.1709   1.0735   0.5587
 LEH  H12   H  HCH2  0   0.207   -1.4279   0.7133  -1.5854
 LEH  H12A  H  HCH2  0   0.207   -1.3052  -1.0182  -1.3596
 LEH  H13   H  HCH2  0   0.208   -2.5760  -0.8212   0.7934
 LEH  H13A  H  HCH2  0   0.206   -2.6905   0.9102   0.5624
 LEH  H14   H  HCH2  0   0.207   -3.9441   0.5246  -1.5839
 LEH  H14A  H  HCH2  0   0.208   -3.8648  -1.2022  -1.3083
 LEH  H15   H  HCH2  0   0.211   -5.1404  -0.9107   0.8333
 LEH  H15A  H  HCH2  0   0.210   -5.2156   0.8149   0.5460
 LEH  H16   H  HCH2  0   0.216   -6.4609   0.3867  -1.5965
 LEH  H16A  H  HCH2  0   0.217   -6.4192  -1.3322  -1.2646
 LEH  H17   H  HCH2  0   0.231   -7.7044  -0.9458   0.8582
 LEH  H17A  H  HCH2  0   0.229   -7.7525   0.7744   0.5079
 LEH  H18   H  HCH2  0   0.260   -8.9799   0.3006  -1.6274
 LEH  H18A  H  HCH2  0   0.259   -8.9620  -1.4133  -1.2536
 LEH  H20   H  HCR5  0   0.286  -10.2623  -2.0796   1.0654
 LEH  H21   H  HCR5  0   0.248  -12.5287  -0.8976   2.0770
 LEH  H19   H  HCR5  0   0.277  -10.7955   1.6799  -0.7070

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
 LEH  O3   C7    double    1.223  0.020  1.223
 LEH  C7   N1    single    1.347  0.020  1.347
 LEH  C7   C8    single    1.511  0.020  1.511
 LEH  C6   N1    single    1.436  0.020  1.436
 LEH  N1   HN1   single    0.860  0.020  1.020
 LEH  C5   C6    single    1.532  0.020  1.532
 LEH  C6   C1    single    1.521  0.020  1.521
 LEH  C6   H6    single    0.970  0.020  1.090
 LEH  C4   C5    single    1.532  0.020  1.532
 LEH  C5   H5    single    0.970  0.020  1.090
 LEH  C5   H5A   single    0.970  0.020  1.090
 LEH  C2   C4    single    1.524  0.020  1.524
 LEH  C4   C3    single    1.526  0.020  1.526
 LEH  C4   H4    single    0.970  0.020  1.090
 LEH  C3   H3    single    0.970  0.020  1.090
 LEH  C3   H3A   single    0.970  0.020  1.090
 LEH  C3   H3B   single    0.970  0.020  1.090
 LEH  C2   H2    single    0.970  0.020  1.090
 LEH  C2   H2A   single    0.970  0.020  1.090
 LEH  C2   H2B   single    0.970  0.020  1.090
 LEH  O1   C1    double    1.203  0.020  1.203
 LEH  C1   O2    single    1.326  0.020  1.326
 LEH  O2   HO2   single    0.850  0.020  0.980
 LEH  C8   C9    single    1.524  0.020  1.524
 LEH  C8   H8    single    0.970  0.020  1.090
 LEH  C8   H8A   single    0.970  0.020  1.090
 LEH  C10  C9    single    1.523  0.020  1.523
 LEH  C9   H9    single    0.970  0.020  1.090
 LEH  C9   H9A   single    0.970  0.020  1.090
 LEH  C11  C10   single    1.524  0.020  1.524
 LEH  C10  H10   single    0.970  0.020  1.090
 LEH  C10  H10A  single    0.970  0.020  1.090
 LEH  C11  C12   single    1.523  0.020  1.523
 LEH  C11  H11   single    0.970  0.020  1.090
 LEH  C11  H11A  single    0.970  0.020  1.090
 LEH  C13  C12   single    1.524  0.020  1.524
 LEH  C12  H12   single    0.970  0.020  1.090
 LEH  C12  H12A  single    0.970  0.020  1.090
 LEH  C13  C14   single    1.523  0.020  1.523
 LEH  C13  H13   single    0.970  0.020  1.090
 LEH  C13  H13A  single    0.970  0.020  1.090
 LEH  C14  C15   single    1.523  0.020  1.523
 LEH  C14  H14   single    0.970  0.020  1.090
 LEH  C14  H14A  single    0.970  0.020  1.090
 LEH  C15  C16   single    1.523  0.020  1.523
 LEH  C15  H15   single    0.970  0.020  1.090
 LEH  C15  H15A  single    0.970  0.020  1.090
 LEH  C16  C17   single    1.523  0.020  1.523
 LEH  C16  H16   single    0.970  0.020  1.090
 LEH  C16  H16A  single    0.970  0.020  1.090
 LEH  C17  C18   single    1.522  0.020  1.522
 LEH  C17  H17   single    0.970  0.020  1.090
 LEH  C17  H17A  single    0.970  0.020  1.090
 LEH  C18  N2    single    1.450  0.020  1.450
 LEH  C18  H18   single    0.970  0.020  1.090
 LEH  C18  H18A  single    0.970  0.020  1.090
 LEH  C20  N2    aromatic  1.366  0.020  1.366
 LEH  N2   C19   aromatic  1.349  0.020  1.349
 LEH  C20  C21   aromatic  1.366  0.020  1.366
 LEH  C20  H20   single    0.930  0.020  1.080
 LEH  C21  N3    aromatic  1.366  0.020  1.366
 LEH  C21  H21   single    0.930  0.020  1.080
 LEH  C19  N3    aromatic  1.309  0.020  1.309
 LEH  C19  H19   single    0.930  0.020  1.080

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
 LEH  C8    C7   N1   115.83  3.000
 LEH  C8    C7   O3   122.62  3.000
 LEH  N1    C7   O3   121.56  3.000
 LEH  HN1   N1   C6   118.67  3.000
 LEH  HN1   N1   C7   119.01  3.000
 LEH  C6    N1   C7   121.46  3.000
 LEH  H6    C6   C1   107.65  3.000
 LEH  H6    C6   C5   108.92  3.000
 LEH  C1    C6   C5   109.58  3.000
 LEH  H6    C6   N1   109.34  3.000
 LEH  C1    C6   N1   110.61  3.000
 LEH  C5    C6   N1   110.69  3.000
 LEH  H5A   C5   H5   106.51  3.000
 LEH  H5A   C5   C4   108.71  3.000
 LEH  H5    C5   C4   109.49  3.000
 LEH  H5A   C5   C6   108.30  3.000
 LEH  H5    C5   C6   108.98  3.000
 LEH  C4    C5   C6   114.54  3.000
 LEH  H4    C4   C2   108.12  3.000
 LEH  H4    C4   C3   107.59  3.000
 LEH  C2    C4   C3   110.82  3.000
 LEH  H4    C4   C5   108.87  3.000
 LEH  C3    C4   C5   109.15  3.000
 LEH  C2    C4   C5   112.16  3.000
 LEH  H3B   C3   H3A  107.68  3.000
 LEH  H3B   C3   H3   107.68  3.000
 LEH  H3A   C3   H3   107.79  3.000
 LEH  H3B   C3   C4   110.98  3.000
 LEH  H3A   C3   C4   111.44  3.000
 LEH  H3    C3   C4   111.10  3.000
 LEH  H2B   C2   H2A  107.70  3.000
 LEH  H2B   C2   H2   107.79  3.000
 LEH  H2A   C2   H2   107.05  3.000
 LEH  H2B   C2   C4   111.04  3.000
 LEH  H2A   C2   C4   110.66  3.000
 LEH  H2    C2   C4   112.39  3.000
 LEH  O1    C1   O2   124.00  3.000
 LEH  O2    C1   C6   111.18  3.000
 LEH  O1    C1   C6   124.79  3.000
 LEH  HO2   O2   C1   110.25  3.000
 LEH  H8A   C8   H8   106.16  3.000
 LEH  H8A   C8   C9   110.33  3.000
 LEH  H8    C8   C9   109.49  3.000
 LEH  H8A   C8   C7   110.81  3.000
 LEH  H8    C8   C7   106.95  3.000
 LEH  C9    C8   C7   112.83  3.000
 LEH  H9A   C9   H9   106.45  3.000
 LEH  H9A   C9   C10  109.41  3.000
 LEH  H9    C9   C10  109.52  3.000
 LEH  H9A   C9   C8   109.39  3.000
 LEH  H9    C9   C8   109.49  3.000
 LEH  C10   C9   C8   112.40  3.000
 LEH  H10A  C10  H10  106.10  3.000
 LEH  H10A  C10  C11  109.43  3.000
 LEH  H10   C10  C11  109.28  3.000
 LEH  H10A  C10  C9   109.78  3.000
 LEH  H10   C10  C9   109.33  3.000
 LEH  C11   C10  C9   112.71  3.000
 LEH  H11A  C11  H11  106.02  3.000
 LEH  H11A  C11  C12  109.31  3.000
 LEH  H11   C11  C12  109.45  3.000
 LEH  H11A  C11  C10  109.14  3.000
 LEH  H11   C11  C10  109.36  3.000
 LEH  C12   C11  C10  113.31  3.000
 LEH  H12A  C12  H12  106.02  3.000
 LEH  H12A  C12  C13  109.42  3.000
 LEH  H12   C12  C13  109.17  3.000
 LEH  H12A  C12  C11  109.50  3.000
 LEH  H12   C12  C11  109.30  3.000
 LEH  C13   C12  C11  113.17  3.000
 LEH  H13A  C13  H13  106.01  3.000
 LEH  H13A  C13  C14  109.34  3.000
 LEH  H13   C13  C14  109.43  3.000
 LEH  H13A  C13  C12  109.14  3.000
 LEH  H13   C13  C12  109.42  3.000
 LEH  C14   C13  C12  113.24  3.000
 LEH  H14A  C14  H14  106.02  3.000
 LEH  H14A  C14  C15  109.42  3.000
 LEH  H14   C14  C15  109.17  3.000
 LEH  H14A  C14  C13  109.46  3.000
 LEH  H14   C14  C13  109.28  3.000
 LEH  C15   C14  C13  113.24  3.000
 LEH  H15A  C15  H15  106.08  3.000
 LEH  H15A  C15  C16  109.37  3.000
 LEH  H15   C15  C16  109.40  3.000
 LEH  H15A  C15  C14  109.20  3.000
 LEH  H15   C15  C14  109.51  3.000
 LEH  C16   C15  C14  113.03  3.000
 LEH  H16A  C16  H16  106.12  3.000
 LEH  H16A  C16  C17  109.54  3.000
 LEH  H16   C16  C17  109.31  3.000
 LEH  H16A  C16  C15  109.43  3.000
 LEH  H16   C16  C15  109.29  3.000
 LEH  C17   C16  C15  112.91  3.000
 LEH  H17A  C17  H17  106.74  3.000
 LEH  H17A  C17  C18  109.20  3.000
 LEH  H17   C17  C18  109.55  3.000
 LEH  H17A  C17  C16  109.79  3.000
 LEH  H17   C17  C16  109.81  3.000
 LEH  C18   C17  C16  111.62  3.000
 LEH  H18A  C18  H18  107.01  3.000
 LEH  H18A  C18  N2   108.50  3.000
 LEH  H18   C18  N2   107.43  3.000
 LEH  H18A  C18  C17  110.58  3.000
 LEH  H18   C18  C17  110.33  3.000
 LEH  N2    C18  C17  112.78  3.000
 LEH  C19   N2   C20  106.89  3.000
 LEH  C19   N2   C18  126.34  3.000
 LEH  C20   N2   C18  126.70  3.000
 LEH  H20   C20  C21  132.02  3.000
 LEH  H20   C20  N2   122.40  3.000
 LEH  C21   C20  N2   105.58  3.000
 LEH  H21   C21  N3   122.03  3.000
 LEH  H21   C21  C20  127.75  3.000
 LEH  N3    C21  C20  110.22  3.000
 LEH  C19   N3   C21  105.18  3.000
 LEH  H19   C19  N3   126.06  3.000
 LEH  H19   C19  N2   121.81  3.000
 LEH  N3    C19  N2   112.13  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
 LEH  CONST_01  N3   C21  C20  N2      0.00   0.0  0
 LEH  CONST_02  C21  N3   C19  N2      0.00   0.0  0
 LEH  CONST_03  N3   C19  N2   C20     0.00   0.0  0
 LEH  CONST_04  C19  N3   C21  C20     0.00   0.0  0
 LEH  CONST_05  C19  N2   C20  C21     0.00   0.0  0
 LEH  CONST_06  C21  C20  N2   C18   180.00   0.0  0
 LEH  CONST_07  N3   C19  N2   C18   180.00   0.0  0
 LEH  CONST_08  H21  C21  C20  N2    180.00   0.0  0
 LEH  CONST_09  H19  C19  N2   C20   180.00   0.0  0
 LEH  CONST_10  H20  C20  C21  N3    180.00   0.0  0
 LEH  CONST_11  C6   N1   C7   O3      0.00   0.0  0
 LEH  CONST_12  C8   C7   N1   C6    180.00   0.0  0
 LEH  CONST_13  HN1  N1   C7   O3    180.00   0.0  0
 LEH  CONST_14  HO2  O2   C1   C6    180.00   0.0  0
 LEH  Var_01    C20  N2   C18  C17   -74.16  30.0  2
 LEH  Var_02    N2   C18  C17  C16  -177.94  30.0  3
 LEH  Var_03    C9   C8   C7   O3    -39.70  30.0  3
 LEH  Var_04    C10  C9   C8   C7    175.80  30.0  3
 LEH  Var_05    C2   C4   C5   C6    -57.81  30.0  2
 LEH  Var_06    C11  C10  C9   C8   -179.31  30.0  1
 LEH  Var_07    C12  C11  C10  C9    178.80  30.0  1
 LEH  Var_08    C13  C12  C11  C10  -178.29  30.0  3
 LEH  Var_09    C14  C13  C12  C11   179.67  30.0  2
 LEH  Var_10    C15  C14  C13  C12  -177.74  30.0  3
 LEH  Var_11    C16  C15  C14  C13   179.98  30.0  3
 LEH  Var_12    C17  C16  C15  C14  -177.78  30.0  3
 LEH  Var_13    C18  C17  C16  C15  -179.76  30.0  3
 LEH  Var_14    H2   C2   C4   C5     63.27  30.0  3
 LEH  Var_15    H3   C3   C4   C5   -178.66  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
 LEH  chir_01  C6  N1  C5  C1  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
 LEH  plan-1  C18  0.020
 LEH  plan-1  N2   0.020
 LEH  plan-1  C20  0.020
 LEH  plan-1  C21  0.020
 LEH  plan-1  N3   0.020
 LEH  plan-1  C19  0.020
 LEH  plan-1  H20  0.020
 LEH  plan-1  H21  0.020
 LEH  plan-1  H19  0.020
 LEH  plan-2  O3   0.020
 LEH  plan-2  C7   0.020
 LEH  plan-2  N1   0.020
 LEH  plan-2  C6   0.020
 LEH  plan-2  C8   0.020
 LEH  plan-2  HN1  0.020
 LEH  plan-3  C6   0.020
 LEH  plan-3  C1   0.020
 LEH  plan-3  O2   0.020
 LEH  plan-3  O1   0.020
 LEH  plan-3  HO2  0.020

