# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 16:48:05 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  63  27  .  2022-03-22  2022-07-25
;
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  -0.520    4.9822   1.6452   0.7577
 LEH  C7    C  C      0   0.566    4.9810   0.8061  -0.1368
 LEH  N1    N  NH1    0  -0.627    6.0567   0.0638  -0.4327
 LEH  C6    C  CH1    0  -0.192    7.3609   0.3442   0.1194
 LEH  C5    C  CH2    0  -0.444    8.2967  -0.8375  -0.1319
 LEH  C4    C  CH1    0  -0.226    7.8349  -2.1838   0.4321
 LEH  C3    C  CH3    0  -0.652    8.8466  -3.2665   0.0678
 LEH  C2    C  CH3    0  -0.660    7.6258  -2.1320   1.9413
 LEH  C1    C  C      0   0.413    7.9862   1.6452  -0.4486
 LEH  O2    O  OC    -1  -0.620    8.9773   2.0687   0.1803
 LEH  O1    O  O      0  -0.597    7.4791   2.1337  -1.4719
 LEH  C8    C  CH2    0  -0.579    3.7447   0.5361  -0.9680
 LEH  C9    C  CH2    0  -0.414    2.4733   0.4799  -0.1291
 LEH  C10   C  CH2    0  -0.415    1.2178   0.3143  -0.9748
 LEH  C11   C  CH2    0  -0.412   -0.0514   0.2538  -0.1342
 LEH  C12   C  CH2    0  -0.412   -1.3231   0.1198  -0.9622
 LEH  C13   C  CH2    0  -0.412   -2.5846   0.0670  -0.1094
 LEH  C14   C  CH2    0  -0.413   -3.8656  -0.0535  -0.9251
 LEH  C15   C  CH2    0  -0.413   -5.1186  -0.0928  -0.0591
 LEH  C16   C  CH2    0  -0.423   -6.4065  -0.2077  -0.8645
 LEH  C17   C  CH2    0  -0.428   -7.6468  -0.2305   0.0196
 LEH  C18   C  CH2    0  -0.296   -8.9264  -0.3437  -0.7968
 LEH  N2    N  NR5    0  -0.396  -10.1150  -0.3435   0.0344
 LEH  C20   C  CR15   0  -0.109  -10.5700  -1.3766   0.8037
 LEH  C21   C  CR15   0  -0.220  -11.6567  -0.8869   1.4712
 LEH  N3    N  N      0  -0.459  -11.8707   0.4186   1.1313
 LEH  C19   C  CR15   0   0.092  -10.9259   0.7080   0.2713
 LEH  HN1   H  HNH1   0   0.385    6.0105  -0.5217  -1.2513
 LEH  H6    H  HCH1   0   0.231    7.2487   0.4776   1.1983
 LEH  H5    H  HCH2   0   0.222    8.4572  -0.9420  -1.2119
 LEH  H5A   H  HCH2   0   0.228    9.2700  -0.5895   0.2990
 LEH  H4    H  HCH1   0   0.212    6.8801  -2.4512  -0.0338
 LEH  H3    H  HCH3   0   0.224    8.5365  -4.2423   0.4456
 LEH  H3A   H  HCH3   0   0.223    8.9682  -3.3526  -1.0136
 LEH  H3B   H  HCH3   0   0.212    9.8281  -3.0435   0.4942
 LEH  H2    H  HCH3   0   0.228    6.8445  -1.4257   2.2238
 LEH  H2A   H  HCH3   0   0.226    7.3365  -3.1104   2.3289
 LEH  H2B   H  HCH3   0   0.212    8.5441  -1.8318   2.4530
 LEH  H8    H  HCH2   0   0.256    3.6623   1.3479  -1.6991
 LEH  H8A   H  HCH2   0   0.242    3.8538  -0.3846  -1.5474
 LEH  H9    H  HCH2   0   0.220    2.5443  -0.3481   0.5837
 LEH  H9A   H  HCH2   0   0.221    2.3912   1.3922   0.4665
 LEH  H10   H  HCH2   0   0.210    1.1446   1.1464  -1.6840
 LEH  H10A  H  HCH2   0   0.210    1.2969  -0.5947  -1.5814
 LEH  H11   H  HCH2   0   0.208    0.0178  -0.5873   0.5647
 LEH  H11A  H  HCH2   0   0.207   -0.1172   1.1556   0.4852
 LEH  H12   H  HCH2   0   0.207   -1.3929   0.9612  -1.6607
 LEH  H12A  H  HCH2   0   0.207   -1.2631  -0.7828  -1.5808
 LEH  H13   H  HCH2   0   0.207   -2.5159  -0.7774   0.5857
 LEH  H13A  H  HCH2   0   0.207   -2.6365   0.9669   0.5142
 LEH  H14   H  HCH2   0   0.208   -3.9338   0.7885  -1.6230
 LEH  H14A  H  HCH2   0   0.208   -3.8214  -0.9570  -1.5435
 LEH  H15   H  HCH2   0   0.211   -5.0504  -0.9349   0.6384
 LEH  H15A  H  HCH2   0   0.210   -5.1585   0.8105   0.5600
 LEH  H16   H  HCH2   0   0.217   -6.4744   0.6308  -1.5661
 LEH  H16A  H  HCH2   0   0.217   -6.3754  -1.1161  -1.4761
 LEH  H17   H  HCH2   0   0.231   -7.5841  -1.0700   0.7185
 LEH  H17A  H  HCH2   0   0.229   -7.6868   0.6804   0.6247
 LEH  H18   H  HCH2   0   0.261   -9.0107   0.4934  -1.4909
 LEH  H18A  H  HCH2   0   0.260   -8.9221  -1.2565  -1.3946
 LEH  H20   H  HCR5   0   0.286  -10.0982  -2.3453   0.8038
 LEH  H21   H  HCR5   0   0.248  -12.2930  -1.4084   2.1698
 LEH  H19   H  HCR5   0   0.277  -10.7816   1.6613  -0.2157

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    1.227  0.020  1.227
 LEH  C7   N1    single    1.340  0.020  1.340
 LEH  C7   C8    single    1.514  0.020  1.514
 LEH  C6   N1    single    1.444  0.020  1.444
 LEH  N1   HN1   single    0.860  0.020  1.020
 LEH  C5   C6    single    1.528  0.020  1.528
 LEH  C6   C1    single    1.551  0.020  1.551
 LEH  C6   H6    single    0.970  0.020  1.090
 LEH  C4   C5    single    1.531  0.020  1.531
 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    deloc     1.242  0.020  1.242
 LEH  C1   O2    deloc     1.248  0.020  1.248
 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    1.524  0.020  1.524
 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  1.310  0.020  1.310
 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   115.82  3.000
 LEH  C8    C7   O3   121.55  3.000
 LEH  N1    C7   O3   122.63  3.000
 LEH  HN1   N1   C6   117.71  3.000
 LEH  HN1   N1   C7   117.68  3.000
 LEH  C6    N1   C7   122.22  3.000
 LEH  H6    C6   C1   107.48  3.000
 LEH  H6    C6   C5   108.64  3.000
 LEH  C1    C6   C5   109.97  3.000
 LEH  H6    C6   N1   107.97  3.000
 LEH  C1    C6   N1   112.77  3.000
 LEH  C5    C6   N1   109.88  3.000
 LEH  H5A   C5   H5   106.23  3.000
 LEH  H5A   C5   C4   108.83  3.000
 LEH  H5    C5   C4   108.86  3.000
 LEH  H5A   C5   C6   107.76  3.000
 LEH  H5    C5   C6   108.98  3.000
 LEH  C4    C5   C6   115.77  3.000
 LEH  H4    C4   C2   108.04  3.000
 LEH  H4    C4   C3   107.64  3.000
 LEH  C2    C4   C3   110.58  3.000
 LEH  H4    C4   C5   108.71  3.000
 LEH  C3    C4   C5   109.64  3.000
 LEH  C2    C4   C5   112.10  3.000
 LEH  H3B   C3   H3A  107.61  3.000
 LEH  H3B   C3   H3   107.62  3.000
 LEH  H3A   C3   H3   107.70  3.000
 LEH  H3B   C3   C4   110.94  3.000
 LEH  H3A   C3   C4   111.49  3.000
 LEH  H3    C3   C4   111.31  3.000
 LEH  H2B   C2   H2A  107.61  3.000
 LEH  H2B   C2   H2   107.62  3.000
 LEH  H2A   C2   H2   107.39  3.000
 LEH  H2B   C2   C4   110.94  3.000
 LEH  H2A   C2   C4   110.94  3.000
 LEH  H2    C2   C4   112.13  3.000
 LEH  O1    C1   O2   127.29  3.000
 LEH  O2    C1   C6   114.85  3.000
 LEH  O1    C1   C6   117.84  3.000
 LEH  H8A   C8   H8   106.13  3.000
 LEH  H8A   C8   C9   110.11  3.000
 LEH  H8    C8   C9   109.38  3.000
 LEH  H8A   C8   C7   111.08  3.000
 LEH  H8    C8   C7   107.19  3.000
 LEH  C9    C8   C7   112.68  3.000
 LEH  H9A   C9   H9   106.35  3.000
 LEH  H9A   C9   C10  109.37  3.000
 LEH  H9    C9   C10  109.43  3.000
 LEH  H9A   C9   C8   109.38  3.000
 LEH  H9    C9   C8   109.40  3.000
 LEH  C10   C9   C8   112.70  3.000
 LEH  H10A  C10  H10  106.06  3.000
 LEH  H10A  C10  C11  109.43  3.000
 LEH  H10   C10  C11  109.36  3.000
 LEH  H10A  C10  C9   109.77  3.000
 LEH  H10   C10  C9   109.39  3.000
 LEH  C11   C10  C9   112.63  3.000
 LEH  H11A  C11  H11  105.95  3.000
 LEH  H11A  C11  C12  109.24  3.000
 LEH  H11   C11  C12  109.38  3.000
 LEH  H11A  C11  C10  109.22  3.000
 LEH  H11   C11  C10  109.25  3.000
 LEH  C12   C11  C10  113.52  3.000
 LEH  H12A  C12  H12  106.02  3.000
 LEH  H12A  C12  C13  109.44  3.000
 LEH  H12   C12  C13  109.31  3.000
 LEH  H12A  C12  C11  109.49  3.000
 LEH  H12   C12  C11  109.40  3.000
 LEH  C13   C12  C11  112.95  3.000
 LEH  H13A  C13  H13  105.95  3.000
 LEH  H13A  C13  C14  109.25  3.000
 LEH  H13   C13  C14  109.35  3.000
 LEH  H13A  C13  C12  109.22  3.000
 LEH  H13   C13  C12  109.26  3.000
 LEH  C14   C13  C12  113.53  3.000
 LEH  H14A  C14  H14  106.05  3.000
 LEH  H14A  C14  C15  109.43  3.000
 LEH  H14   C14  C15  109.31  3.000
 LEH  H14A  C14  C13  109.48  3.000
 LEH  H14   C14  C13  109.43  3.000
 LEH  C15   C14  C13  112.91  3.000
 LEH  H15A  C15  H15  106.03  3.000
 LEH  H15A  C15  C16  109.28  3.000
 LEH  H15   C15  C16  109.34  3.000
 LEH  H15A  C15  C14  109.26  3.000
 LEH  H15   C15  C14  109.30  3.000
 LEH  C16   C15  C14  113.37  3.000
 LEH  H16A  C16  H16  106.19  3.000
 LEH  H16A  C16  C17  109.56  3.000
 LEH  H16   C16  C17  109.43  3.000
 LEH  H16A  C16  C15  109.50  3.000
 LEH  H16   C16  C15  109.47  3.000
 LEH  C17   C16  C15  112.50  3.000
 LEH  H17A  C17  H17  106.71  3.000
 LEH  H17A  C17  C18  109.14  3.000
 LEH  H17   C17  C18  109.49  3.000
 LEH  H17A  C17  C16  109.77  3.000
 LEH  H17   C17  C16  109.60  3.000
 LEH  C18   C17  C16  111.98  3.000
 LEH  H18A  C18  H18  107.08  3.000
 LEH  H18A  C18  N2   108.50  3.000
 LEH  H18   C18  N2   107.53  3.000
 LEH  H18A  C18  C17  110.66  3.000
 LEH  H18   C18  C17  110.43  3.000
 LEH  N2    C18  C17  112.43  3.000
 LEH  C19   N2   C20  106.88  3.000
 LEH  C19   N2   C18  126.40  3.000
 LEH  C20   N2   C18  126.55  3.000
 LEH  H20   C20  C21  132.11  3.000
 LEH  H20   C20  N2   122.28  3.000
 LEH  C21   C20  N2   105.61  3.000
 LEH  H21   C21  N3   122.04  3.000
 LEH  H21   C21  C20  127.73  3.000
 LEH  N3    C21  C20  110.22  3.000
 LEH  C19   N3   C21  105.16  3.000
 LEH  H19   C19  N3   125.96  3.000
 LEH  H19   C19  N2   121.91  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  Var_01    C20  N2   C18  C17   -74.93  30.0  2
 LEH  Var_02    N2   C18  C17  C16  -179.03  30.0  3
 LEH  Var_03    C9   C8   C7   O3    -42.79  30.0  3
 LEH  Var_04    C10  C9   C8   C7    175.63  30.0  3
 LEH  Var_05    C2   C4   C5   C6    -58.44  30.0  2
 LEH  Var_06    C11  C10  C9   C8    179.81  30.0  1
 LEH  Var_07    C12  C11  C10  C9    178.70  30.0  1
 LEH  Var_08    C13  C12  C11  C10  -179.73  30.0  3
 LEH  Var_09    C14  C13  C12  C11   179.44  30.0  1
 LEH  Var_10    C15  C14  C13  C12  -179.50  30.0  3
 LEH  Var_11    C16  C15  C14  C13   179.78  30.0  3
 LEH  Var_12    C17  C16  C15  C14  -179.39  30.0  3
 LEH  Var_13    C18  C17  C16  C15   179.93  30.0  3
 LEH  Var_14    H2   C2   C4   C5     62.23  30.0  3
 LEH  Var_15    H3   C3   C4   C5   -179.21  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

