# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:37:40 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)C(N)=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
 41M  41M  N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysinamide  ligand  54  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_41M
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
 41M  N1   N  NR15  0  -0.656  -6.5770   1.0412   0.8837
 41M  C2   C  CR5   0   0.643  -7.7994   1.2263   0.3143
 41M  N3   N  NR15  0  -0.661  -8.3457  -0.0018   0.1317
 41M  C4   C  C     0  -0.064  -6.2792  -0.3395   1.1668
 41M  C5   C  C     0  -0.045  -7.4912  -1.0876   0.5353
 41M  C6   C  CH2   0  -0.570  -6.9905  -1.9436  -0.6333
 41M  S7   S  S2    0  -0.025  -5.4827  -1.1468  -1.2401
 41M  C8   C  CR15  0  -0.360  -4.9928  -0.8286   0.4877
 41M  C9   C  CH2   0  -0.421  -3.8158   0.1230   0.5990
 41M  C10  C  CH2   0  -0.419  -2.5366  -0.4269  -0.0205
 41M  C11  C  CH2   0  -0.414  -1.3427   0.4961   0.1849
 41M  C12  C  CH2   0  -0.579  -0.0828  -0.0573  -0.4677
 41M  C13  C  C     0   0.562   1.1260   0.8362  -0.2885
 41M  N14  N  NH1   0  -0.646   2.2946   0.1963  -0.1371
 41M  C15  C  CH2   0  -0.234   3.5645   0.8806  -0.0092
 41M  C16  C  CH2   0  -0.476   4.7151  -0.1126  -0.0362
 41M  C17  C  CH2   0  -0.410   6.0642   0.5790   0.1107
 41M  C18  C  CH2   0  -0.424   7.2211  -0.4097   0.0598
 41M  C19  C  CH1   0  -0.213   8.5917   0.2470   0.2642
 41M  C20  C  C     0   0.488   9.6569  -0.8545   0.2775
 41M  N21  N  NH2   0  -0.797   9.8175  -1.4739   1.4561
 41M  O22  O  O     0  -0.529  -8.3105   2.2990   0.0305
 41M  O23  O  O     0  -0.511   1.0464   2.0589  -0.3075
 41M  N24  N  NH2   0  -0.777   8.8251   1.2612  -0.7391
 41M  O25  O  O     0  -0.491  10.2877  -1.1546  -0.7264
 41M  H1   H  HNR5  0   0.399  -6.1263   1.7939   1.3758
 41M  H2   H  HNR5  0   0.399  -9.1741  -0.1368  -0.4230
 41M  H3   H  H     0   0.281  -6.2077  -0.5164   2.2438
 41M  H4   H  H     0   0.278  -7.9947  -1.7297   1.2617
 41M  H5   H  HCH2  0   0.274  -6.7564  -2.9511  -0.2855
 41M  H6   H  HCH2  0   0.289  -7.7268  -2.0236  -1.4326
 41M  H7   H  HCR5  0   0.275  -4.7225  -1.7902   0.9377
 41M  H8   H  HCH2  0   0.233  -4.0700   1.0796   0.1351
 41M  H9   H  HCH2  0   0.240  -3.6433   0.3240   1.6619
 41M  H10  H  HCH2  0   0.220  -2.3182  -1.4105   0.4083
 41M  H11  H  HCH2  0   0.221  -2.6871  -0.5883  -1.0929
 41M  H12  H  HCH2  0   0.226  -1.5670   1.4838  -0.2244
 41M  H13  H  HCH2  0   0.225  -1.1708   0.6342   1.2566
 41M  H14  H  HCH2  0   0.247   0.1237  -1.0622  -0.0905
 41M  H15  H  HCH2  0   0.266  -0.2480  -0.1671  -1.5451
 41M  H16  H  HNH1  0   0.398   2.2937  -0.8099  -0.0968
 41M  H17  H  HCH2  0   0.230   3.6790   1.5984  -0.8254
 41M  H18  H  HCH2  0   0.227   3.5922   1.4547   0.9225
 41M  H19  H  HCH2  0   0.229   4.5869  -0.8437   0.7689
 41M  H20  H  HCH2  0   0.230   4.6893  -0.6730  -0.9766
 41M  H21  H  HCH2  0   0.228   6.1850   1.3253  -0.6769
 41M  H22  H  HCH2  0   0.216   6.0942   1.1241   1.0604
 41M  H23  H  HCH2  0   0.233   7.0751  -1.1756   0.8265
 41M  H24  H  HCH2  0   0.227   7.2172  -0.9340  -0.9027
 41M  H25  H  HCH1  0   0.249   8.5885   0.7365   1.2446
 41M  H26  H  HNH2  0   0.406   9.2807  -1.2156   2.2663
 41M  H27  H  HNH2  0   0.399  10.4357  -2.2641   1.5453
 41M  H28  H  HNH2  0   0.350   9.7207   1.7055  -0.5801
 41M  H29  H  HNH2  0   0.339   8.8929   0.8230  -1.6503

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
 41M  O22  C2   double  1.222  0.020  1.222
 41M  C2   N1   single  1.361  0.020  1.361
 41M  C2   N3   single  1.357  0.020  1.357
 41M  N1   C4   single  1.441  0.020  1.441
 41M  C11  C12  single  1.523  0.020  1.523
 41M  C11  C10  single  1.523  0.020  1.523
 41M  C9   C10  single  1.524  0.020  1.524
 41M  C9   C8   single  1.518  0.020  1.518
 41M  C12  C13  single  1.514  0.020  1.514
 41M  N3   C5   single  1.439  0.020  1.439
 41M  C4   C8   single  1.535  0.020  1.535
 41M  C4   C5   single  1.558  0.020  1.558
 41M  C8   S7   single  1.824  0.020  1.824
 41M  O23  C13  double  1.225  0.020  1.225
 41M  S7   C6   single  1.810  0.020  1.810
 41M  C13  N14  single  1.341  0.020  1.341
 41M  C5   C6   single  1.533  0.020  1.533
 41M  N14  C15  single  1.448  0.020  1.448
 41M  C15  C16  single  1.520  0.020  1.520
 41M  C16  C17  single  1.523  0.020  1.523
 41M  C17  C18  single  1.523  0.020  1.523
 41M  C18  C19  single  1.534  0.020  1.534
 41M  C19  N24  single  1.446  0.020  1.446
 41M  C19  C20  single  1.532  0.020  1.532
 41M  C20  N21  single  1.341  0.020  1.341
 41M  C20  O25  double  1.223  0.020  1.223
 41M  N1   H1   single  0.890  0.020  1.040
 41M  N3   H2   single  0.860  0.020  1.020
 41M  C4   H3   single  0.970  0.020  1.090
 41M  C5   H4   single  0.970  0.020  1.090
 41M  C6   H5   single  0.970  0.020  1.090
 41M  C6   H6   single  0.970  0.020  1.090
 41M  C8   H7   single  0.970  0.020  1.090
 41M  C9   H8   single  0.970  0.020  1.090
 41M  C9   H9   single  0.970  0.020  1.090
 41M  C10  H10  single  0.970  0.020  1.090
 41M  C10  H11  single  0.970  0.020  1.090
 41M  C11  H12  single  0.970  0.020  1.090
 41M  C11  H13  single  0.970  0.020  1.090
 41M  C12  H14  single  0.970  0.020  1.090
 41M  C12  H15  single  0.970  0.020  1.090
 41M  N14  H16  single  0.860  0.020  1.020
 41M  C15  H17  single  0.970  0.020  1.090
 41M  C15  H18  single  0.970  0.020  1.090
 41M  C16  H19  single  0.970  0.020  1.090
 41M  C16  H20  single  0.970  0.020  1.090
 41M  C17  H21  single  0.970  0.020  1.090
 41M  C17  H22  single  0.970  0.020  1.090
 41M  C18  H23  single  0.970  0.020  1.090
 41M  C18  H24  single  0.970  0.020  1.090
 41M  C19  H25  single  0.970  0.020  1.090
 41M  N21  H26  single  0.860  0.020  1.020
 41M  N21  H27  single  0.860  0.020  1.020
 41M  N24  H28  single  0.890  0.020  1.040
 41M  N24  H29  single  0.890  0.020  1.040

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
 41M  H1   N1   C4   121.89  3.000
 41M  H1   N1   C2   120.35  3.000
 41M  C4   N1   C2   113.47  3.000
 41M  O22  C2   N3   126.53  3.000
 41M  N3   C2   N1   107.15  3.000
 41M  O22  C2   N1   126.32  3.000
 41M  H2   N3   C5   122.83  3.000
 41M  H2   N3   C2   121.82  3.000
 41M  C5   N3   C2   113.96  3.000
 41M  H3   C4   C8   109.24  3.000
 41M  H3   C4   C5   111.86  3.000
 41M  C8   C4   C5   108.65  3.000
 41M  H3   C4   N1   111.22  3.000
 41M  C5   C4   N1   102.69  3.000
 41M  C8   C4   N1   113.07  3.000
 41M  H4   C5   C6   109.23  3.000
 41M  H4   C5   C4   111.80  3.000
 41M  C6   C5   C4   108.85  3.000
 41M  H4   C5   N3   110.86  3.000
 41M  C6   C5   N3   113.67  3.000
 41M  C4   C5   N3   102.32  3.000
 41M  H6   C6   H5   108.12  3.000
 41M  H6   C6   S7   110.45  3.000
 41M  H5   C6   S7   109.55  3.000
 41M  H6   C6   C5   112.30  3.000
 41M  H5   C6   C5   110.04  3.000
 41M  S7   C6   C5   106.38  3.000
 41M  C8   S7   C6    89.02  3.000
 41M  H7   C8   C9   109.20  3.000
 41M  H7   C8   S7   107.59  3.000
 41M  C9   C8   S7   112.78  3.000
 41M  H7   C8   C4   107.74  3.000
 41M  S7   C8   C4   104.46  3.000
 41M  C9   C8   C4   114.70  3.000
 41M  H9   C9   H8   106.72  3.000
 41M  H9   C9   C10  109.17  3.000
 41M  H8   C9   C10  109.78  3.000
 41M  H9   C9   C8   107.96  3.000
 41M  H8   C9   C8   109.71  3.000
 41M  C10  C9   C8   113.27  3.000
 41M  H11  C10  H10  106.17  3.000
 41M  H11  C10  C11  109.22  3.000
 41M  H10  C10  C11  109.59  3.000
 41M  H11  C10  C9   109.63  3.000
 41M  H10  C10  C9   109.41  3.000
 41M  C11  C10  C9   112.62  3.000
 41M  H13  C11  H12  106.57  3.000
 41M  H13  C11  C12  109.61  3.000
 41M  H12  C11  C12  109.75  3.000
 41M  H13  C11  C10  109.37  3.000
 41M  H12  C11  C10  109.66  3.000
 41M  C12  C11  C10  111.75  3.000
 41M  H15  C12  H14  106.00  3.000
 41M  H15  C12  C13  107.22  3.000
 41M  H14  C12  C13  110.54  3.000
 41M  H15  C12  C11  109.46  3.000
 41M  H14  C12  C11  110.03  3.000
 41M  C13  C12  C11  113.29  3.000
 41M  O23  C13  N14  122.31  3.000
 41M  N14  C13  C12  115.32  3.000
 41M  O23  C13  C12  122.36  3.000
 41M  H16  N14  C15  117.99  3.000
 41M  H16  N14  C13  118.72  3.000
 41M  C15  N14  C13  123.28  3.000
 41M  H18  C15  H17  106.77  3.000
 41M  H18  C15  C16  109.79  3.000
 41M  H17  C15  C16  109.66  3.000
 41M  H18  C15  N14  110.19  3.000
 41M  H17  C15  N14  109.65  3.000
 41M  C16  C15  N14  110.69  3.000
 41M  H20  C16  H19  106.67  3.000
 41M  H20  C16  C17  109.64  3.000
 41M  H19  C16  C17  109.63  3.000
 41M  H20  C16  C15  109.38  3.000
 41M  H19  C16  C15  109.55  3.000
 41M  C17  C16  C15  111.84  3.000
 41M  H22  C17  H21  106.40  3.000
 41M  H22  C17  C18  109.35  3.000
 41M  H21  C17  C18  109.61  3.000
 41M  H22  C17  C16  109.50  3.000
 41M  H21  C17  C16  109.80  3.000
 41M  C18  C17  C16  112.02  3.000
 41M  H24  C18  H23  106.27  3.000
 41M  H24  C18  C19  108.97  3.000
 41M  H23  C18  C19  109.01  3.000
 41M  H24  C18  C17  109.71  3.000
 41M  H23  C18  C17  109.26  3.000
 41M  C19  C18  C17  113.36  3.000
 41M  H25  C19  N24  107.94  3.000
 41M  H25  C19  C20  108.38  3.000
 41M  N24  C19  C20  113.46  3.000
 41M  H25  C19  C18  107.93  3.000
 41M  C20  C19  C18  108.34  3.000
 41M  N24  C19  C18  110.62  3.000
 41M  O25  C20  N21  123.11  3.000
 41M  O25  C20  C19  121.85  3.000
 41M  N21  C20  C19  115.02  3.000
 41M  H27  N21  H26  117.25  3.000
 41M  H27  N21  C20  120.90  3.000
 41M  H26  N21  C20  121.70  3.000
 41M  H29  N24  H28  105.77  3.000
 41M  H29  N24  C19  109.36  3.000
 41M  H28  N24  C19  109.99  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
 41M  CONST_01  C5   N3   C2   N1      0.00   0.0  0
 41M  CONST_02  C4   N1   C2   N3      0.00   0.0  0
 41M  CONST_03  O22  C2   N1   C4    180.00   0.0  0
 41M  CONST_04  O22  C2   N3   C5    180.00   0.0  0
 41M  CONST_05  H2   N3   C2   N1    180.00   0.0  0
 41M  CONST_07  C15  N14  C13  C12   180.00   0.0  0
 41M  CONST_08  O23  C13  N14  C15     0.00   0.0  0
 41M  CONST_09  H16  N14  C13  C12     0.00   0.0  0
 41M  CONST_10  H26  N21  C20  C19     0.00   0.0  0
 41M  CONST_11  H27  N21  C20  C19   180.00   0.0  0
 41M  Var_01    H5   C6   S7   C8    -78.19  30.0  1
 41M  Var_02    C11  C10  C9   C8   -175.98  30.0  3
 41M  Var_03    C12  C11  C10  C9   -178.75  30.0  1
 41M  Var_04    C13  C12  C11  C10   179.82  30.0  3
 41M  Var_05    O23  C13  C12  C11   -36.80  30.0  3
 41M  Var_06    C16  C15  N14  C13  -172.55  30.0  3
 41M  Var_07    C17  C16  C15  N14  -179.43  30.0  3
 41M  Var_08    C18  C17  C16  C15  -179.00  30.0  3
 41M  Var_09    C19  C18  C17  C16  -177.57  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
 41M  chir_01  C4   N1   C8   C5   positiv
 41M  chir_02  C5   N3   C4   C6   positiv
 41M  chir_03  C8   S7   C9   C4   negativ
 41M  chir_04  C19  C18  N24  C20  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
 41M  plan-1  C12  0.020
 41M  plan-1  C13  0.020
 41M  plan-1  N14  0.020
 41M  plan-1  C15  0.020
 41M  plan-1  O23  0.020
 41M  plan-1  H16  0.020
 41M  plan-2  C19  0.020
 41M  plan-2  C20  0.020
 41M  plan-2  N21  0.020
 41M  plan-2  O25  0.020
 41M  plan-2  H26  0.020
 41M  plan-2  H27  0.020
 41M  plan-3  N1   0.020
 41M  plan-3  C2   0.020
 41M  plan-3  N3   0.020
 41M  plan-3  C4   0.020
 41M  plan-3  C5   0.020
 41M  plan-3  O22  0.020
 41M  plan-3  H1   0.020
 41M  plan-3  H2   0.020

