# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:46:55 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N~2~-[(2S)-2-{[1-(4-carboxybenzyl)-1H-1,2,3-triazol-4-yl]methyl}-3-methylbutanoyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](Cc1cn(Cc2ccc(cc2)C(O)=O)nn1)C(=O)N[C@@H](CCCCN)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
 D38  D38  N~2~-[(2S)-2-{[1-(4-carboxybenzyl)-1H-1,2,3-triazol-4-yl]methyl}-3-methylbutanoyl]-L-lysine  ligand  63  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D38
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
 D38  C1    C  CR16  0  -0.241   5.8758   1.2727   1.5439
 D38  C2    C  CR6   0  -0.092   7.1170   1.0549   0.9460
 D38  C3    C  CR16  0  -0.242   7.1902   0.9013  -0.4356
 D38  C4    C  CR16  0  -0.293   6.0363   0.9592  -1.2027
 D38  C5    C  CR6   0   0.125   4.8003   1.1771  -0.6086
 D38  C6    C  CR16  0  -0.266   4.7301   1.3360   0.7736
 D38  C7    C  C     0   0.534   8.3177   0.9928   1.8154
 D38  O8    O  O     0  -0.437   8.2815   1.1016   3.0177
 D38  O9    O  OH1   0  -0.593   9.4401   0.8049   1.1363
 D38  C10   C  CH2   0  -0.380   3.5579   1.2529  -1.4542
 D38  N11   N  NR5   0  -0.252   2.5504   0.3088  -1.0137
 D38  C12   C  CR15  0  -0.089   1.3490   0.5561  -0.4645
 D38  C13   C  CR5   0   0.158   0.8347  -0.6887  -0.1980
 D38  N14   N  N     0  -0.308   1.7531  -1.5974  -0.5980
 D38  N15   N  N     0  -0.098   2.7800  -0.9887  -1.0841
 D38  C16   C  CH2   0  -0.509  -0.4767  -1.0613   0.3983
 D38  C17   C  CH1   0  -0.373  -1.6334  -1.0424  -0.6162
 D38  C18   C  CH1   0  -0.227  -1.4003  -1.9535  -1.8405
 D38  C19   C  CH3   0  -0.657  -1.2010  -3.4264  -1.5020
 D38  C20   C  CH3   0  -0.674  -2.4991  -1.7840  -2.8860
 D38  C21   C  C     0   0.600  -2.9197  -1.3749   0.1170
 D38  N22   N  NH1   0  -0.643  -3.9737  -0.5803  -0.1489
 D38  C23   C  CH1   0  -0.172  -5.2451  -0.7930   0.4849
 D38  C24   C  C     0   0.543  -5.8763  -2.0952   0.0165
 D38  O25   O  O     0  -0.428  -5.6628  -2.6242  -1.0426
 D38  O26   O  OH1   0  -0.592  -6.7387  -2.5558   0.9128
 D38  O27   O  O     0  -0.495  -3.0013  -2.2888   0.9262
 D38  C28   C  CH2   0  -0.466  -6.1953   0.3751   0.2051
 D38  C29   C  CH2   0  -0.422  -5.6906   1.6999   0.7677
 D38  C30   C  CH2   0  -0.428  -6.7285   2.8074   0.6400
 D38  C31   C  CH2   0  -0.273  -6.2303   4.1398   1.1775
 D38  N32   N  NH2   0  -0.800  -7.2540   5.1678   1.0527
 D38  H1    H  HCR6  0   0.269   5.8049   1.3948   2.6162
 D38  H3    H  HCR6  0   0.271   8.1372   0.7274  -0.9271
 D38  H4    H  HCR6  0   0.268   6.1041   0.8325  -2.2759
 D38  H6    H  HCR6  0   0.264   3.7762   1.5121   1.2562
 D38  HO9   H  HOH1  0   0.489  10.1937   0.7715   1.7440
 D38  H10   H  HCH2  0   0.299   3.1133   2.2464  -1.3995
 D38  H10A  H  HCH2  0   0.300   3.7886   1.0551  -2.5004
 D38  H12   H  HCR5  0   0.310   0.9695   1.5515  -0.3062
 D38  H16   H  HCH2  0   0.260  -0.3931  -2.0461   0.8577
 D38  H16A  H  HCH2  0   0.268  -0.7109  -0.3616   1.2037
 D38  H17   H  HCH1  0   0.262  -1.7103  -0.0204  -1.0040
 D38  H18   H  HCH1  0   0.238  -0.4701  -1.5934  -2.2912
 D38  H19   H  HCH3  0   0.221  -2.1099  -3.8812  -1.1075
 D38  H19A  H  HCH3  0   0.225  -0.9237  -3.9765  -2.4027
 D38  H19B  H  HCH3  0   0.229  -0.4035  -3.5767  -0.7741
 D38  H20   H  HCH3  0   0.223  -2.6486  -0.7338  -3.1453
 D38  H20A  H  HCH3  0   0.232  -2.2318  -2.3111  -3.8031
 D38  H20B  H  HCH3  0   0.233  -3.4546  -2.1833  -2.5435
 D38  HN22  H  HNH1  0   0.402  -3.9025   0.1064  -0.8823
 D38  H23   H  HCH1  0   0.281  -5.0988  -0.8630   1.5668
 D38  HO26  H  HOH1  0   0.484  -7.1731  -3.3554   0.5798
 D38  H28   H  HCH2  0   0.245  -6.3644   0.4612  -0.8727
 D38  H28A  H  HCH2  0   0.258  -7.1635   0.1427   0.6543
 D38  H29   H  HCH2  0   0.224  -5.4263   1.5647   1.8212
 D38  H29A  H  HCH2  0   0.223  -4.7728   2.0067   0.2581
 D38  H30   H  HCH2  0   0.217  -7.0158   2.9307  -0.4086
 D38  H30A  H  HCH2  0   0.216  -7.6364   2.5137   1.1787
 D38  H31   H  HCH2  0   0.188  -5.8764   3.9982   2.2093
 D38  H31A  H  HCH2  0   0.213  -5.3574   4.4532   0.5978
 D38  HN32  H  HNH2  0   0.337  -8.0236   4.9455   1.6727
 D38  HN3A  H  HNH2  0   0.345  -6.8871   6.0509   1.3842

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
 D38  C2   C1    aromatic  1.395  0.020  1.395
 D38  C1   C6    aromatic  1.382  0.020  1.382
 D38  C1   H1    single    0.930  0.020  1.080
 D38  C7   C2    single    1.484  0.020  1.484
 D38  C2   C3    aromatic  1.392  0.020  1.392
 D38  C3   C4    aromatic  1.387  0.020  1.387
 D38  C3   H3    single    0.930  0.020  1.080
 D38  C4   C5    aromatic  1.389  0.020  1.389
 D38  C4   H4    single    0.930  0.020  1.080
 D38  C6   C5    aromatic  1.393  0.020  1.393
 D38  C5   C10   single    1.505  0.020  1.505
 D38  C6   H6    single    0.930  0.020  1.080
 D38  O8   C7    double    1.208  0.020  1.208
 D38  O9   C7    single    1.325  0.020  1.325
 D38  O9   HO9   single    0.850  0.020  0.980
 D38  C10  N11   single    1.449  0.020  1.449
 D38  C10  H10   single    0.970  0.020  1.090
 D38  C10  H10A  single    0.970  0.020  1.090
 D38  C12  N11   aromatic  1.344  0.020  1.344
 D38  N11  N15   aromatic  1.320  0.020  1.320
 D38  C12  C13   aromatic  1.373  0.020  1.373
 D38  C12  H12   single    0.930  0.020  1.080
 D38  C16  C13   single    1.488  0.020  1.488
 D38  C13  N14   aromatic  1.352  0.020  1.352
 D38  N14  N15   aromatic  1.289  0.020  1.289
 D38  C16  C17   single    1.539  0.020  1.539
 D38  C16  H16   single    0.970  0.020  1.090
 D38  C16  H16A  single    0.970  0.020  1.090
 D38  C18  C17   single    1.544  0.020  1.544
 D38  C17  C21   single    1.517  0.020  1.517
 D38  C17  H17   single    0.970  0.020  1.090
 D38  C20  C18   single    1.526  0.020  1.526
 D38  C18  C19   single    1.524  0.020  1.524
 D38  C18  H18   single    0.970  0.020  1.090
 D38  C19  H19   single    0.970  0.020  1.090
 D38  C19  H19A  single    0.970  0.020  1.090
 D38  C19  H19B  single    0.970  0.020  1.090
 D38  C20  H20   single    0.970  0.020  1.090
 D38  C20  H20A  single    0.970  0.020  1.090
 D38  C20  H20B  single    0.970  0.020  1.090
 D38  C21  N22   single    1.346  0.020  1.346
 D38  C21  O27   double    1.223  0.020  1.223
 D38  N22  C23   single    1.437  0.020  1.437
 D38  N22  HN22  single    0.860  0.020  1.020
 D38  C23  C28   single    1.532  0.020  1.532
 D38  C23  C24   single    1.521  0.020  1.521
 D38  C23  H23   single    0.970  0.020  1.090
 D38  O25  C24   double    1.203  0.020  1.203
 D38  C24  O26   single    1.326  0.020  1.326
 D38  O26  HO26  single    0.850  0.020  0.980
 D38  C28  C29   single    1.525  0.020  1.525
 D38  C28  H28   single    0.970  0.020  1.090
 D38  C28  H28A  single    0.970  0.020  1.090
 D38  C29  C30   single    1.523  0.020  1.523
 D38  C29  H29   single    0.970  0.020  1.090
 D38  C29  H29A  single    0.970  0.020  1.090
 D38  C30  C31   single    1.521  0.020  1.521
 D38  C30  H30   single    0.970  0.020  1.090
 D38  C30  H30A  single    0.970  0.020  1.090
 D38  C31  N32   single    1.456  0.020  1.456
 D38  C31  H31   single    0.970  0.020  1.090
 D38  C31  H31A  single    0.970  0.020  1.090
 D38  N32  HN32  single    0.890  0.020  1.040
 D38  N32  HN3A  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
 D38  H1    C1   C6    119.54  3.000
 D38  H1    C1   C2    120.07  3.000
 D38  C6    C1   C2    120.39  3.000
 D38  C7    C2   C3    122.30  3.000
 D38  C3    C2   C1    119.31  3.000
 D38  C7    C2   C1    118.39  3.000
 D38  H3    C3   C4    118.96  3.000
 D38  H3    C3   C2    121.00  3.000
 D38  C4    C3   C2    120.04  3.000
 D38  H4    C4   C5    119.87  3.000
 D38  H4    C4   C3    119.42  3.000
 D38  C5    C4   C3    120.70  3.000
 D38  C10   C5   C6    120.67  3.000
 D38  C10   C5   C4    120.16  3.000
 D38  C6    C5   C4    119.16  3.000
 D38  H6    C6   C5    120.33  3.000
 D38  H6    C6   C1    119.28  3.000
 D38  C5    C6   C1    120.40  3.000
 D38  O9    C7   O8    123.25  3.000
 D38  O9    C7   C2    113.02  3.000
 D38  O8    C7   C2    123.73  3.000
 D38  HO9   O9   C7    110.01  3.000
 D38  H10A  C10  H10   107.47  3.000
 D38  H10A  C10  N11   108.71  3.000
 D38  H10   C10  N11   107.16  3.000
 D38  H10A  C10  C5    110.83  3.000
 D38  H10   C10  C5    110.77  3.000
 D38  N11   C10  C5    111.73  3.000
 D38  N15   N11  C12   110.99  3.000
 D38  N15   N11  C10   120.23  3.000
 D38  C12   N11  C10   128.74  3.000
 D38  H12   C12  C13   132.64  3.000
 D38  H12   C12  N11   123.03  3.000
 D38  C13   C12  N11   104.32  3.000
 D38  C16   C13  N14   123.28  3.000
 D38  N14   C13  C12   107.30  3.000
 D38  C16   C13  C12   129.41  3.000
 D38  N15   N14  C13   109.59  3.000
 D38  N14   N15  N11   107.80  3.000
 D38  H16A  C16  H16   106.53  3.000
 D38  H16A  C16  C17   108.49  3.000
 D38  H16   C16  C17   110.28  3.000
 D38  H16A  C16  C13   108.90  3.000
 D38  H16   C16  C13   109.12  3.000
 D38  C17   C16  C13   113.28  3.000
 D38  H17   C17  C21   108.41  3.000
 D38  H17   C17  C18   106.28  3.000
 D38  C21   C17  C18   112.45  3.000
 D38  H17   C17  C16   107.31  3.000
 D38  C21   C17  C16   108.42  3.000
 D38  C18   C17  C16   113.71  3.000
 D38  H18   C18  C20   107.05  3.000
 D38  H18   C18  C19   107.35  3.000
 D38  C20   C18  C19   110.70  3.000
 D38  H18   C18  C17   105.11  3.000
 D38  C19   C18  C17   114.45  3.000
 D38  C20   C18  C17   111.66  3.000
 D38  H19B  C19  H19A  107.20  3.000
 D38  H19B  C19  H19   108.10  3.000
 D38  H19A  C19  H19   107.48  3.000
 D38  H19B  C19  C18   112.15  3.000
 D38  H19A  C19  C18   109.70  3.000
 D38  H19   C19  C18   111.99  3.000
 D38  H20B  C20  H20A  107.55  3.000
 D38  H20B  C20  H20   107.86  3.000
 D38  H20A  C20  H20   107.37  3.000
 D38  H20B  C20  C18   112.02  3.000
 D38  H20A  C20  C18   110.24  3.000
 D38  H20   C20  C18   111.60  3.000
 D38  O27   C21  N22   121.28  3.000
 D38  O27   C21  C17   122.67  3.000
 D38  N22   C21  C17   116.03  3.000
 D38  HN22  N22  C23   119.00  3.000
 D38  HN22  N22  C21   119.40  3.000
 D38  C23   N22  C21   121.22  3.000
 D38  H23   C23  C28   108.21  3.000
 D38  H23   C23  C24   107.78  3.000
 D38  C28   C23  C24   109.83  3.000
 D38  H23   C23  N22   109.11  3.000
 D38  C24   C23  N22   110.98  3.000
 D38  C28   C23  N22   110.83  3.000
 D38  O26   C24  O25   123.89  3.000
 D38  O26   C24  C23   111.03  3.000
 D38  O25   C24  C23   125.03  3.000
 D38  HO26  O26  C24   110.23  3.000
 D38  H28A  C28  H28   106.55  3.000
 D38  H28A  C28  C29   109.05  3.000
 D38  H28   C28  C29   110.24  3.000
 D38  H28A  C28  C23   108.21  3.000
 D38  H28   C28  C23   109.62  3.000
 D38  C29   C28  C23   112.94  3.000
 D38  H29A  C29  H29   106.28  3.000
 D38  H29A  C29  C30   109.19  3.000
 D38  H29   C29  C30   109.57  3.000
 D38  H29A  C29  C28   110.46  3.000
 D38  H29   C29  C28   109.12  3.000
 D38  C30   C29  C28   112.04  3.000
 D38  H30A  C30  H30   106.49  3.000
 D38  H30A  C30  C31   109.42  3.000
 D38  H30   C30  C31   109.03  3.000
 D38  H30A  C30  C29   109.17  3.000
 D38  H30   C30  C29   109.95  3.000
 D38  C31   C30  C29   112.60  3.000
 D38  H31A  C31  H31   106.10  3.000
 D38  H31A  C31  N32   108.27  3.000
 D38  H31   C31  N32   113.42  3.000
 D38  H31A  C31  C30   108.98  3.000
 D38  H31   C31  C30   108.91  3.000
 D38  N32   C31  C30   110.97  3.000
 D38  HN3A  N32  HN32  105.45  3.000
 D38  HN3A  N32  C31   109.46  3.000
 D38  HN32  N32  C31   109.08  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
 D38  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 D38  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 D38  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 D38  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 D38  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 D38  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 D38  CONST_07  N14   C13  C12  N11     0.00   0.0  0
 D38  CONST_08  C13   N14  N15  N11     0.00   0.0  0
 D38  CONST_09  N14   N15  N11  C12     0.00   0.0  0
 D38  CONST_10  N15   N14  C13  C12     0.00   0.0  0
 D38  CONST_11  N15   N11  C12  C13     0.00   0.0  0
 D38  CONST_12  C10   C5   C6   C1    180.00   0.0  0
 D38  CONST_13  C10   C5   C4   C3    180.00   0.0  0
 D38  CONST_14  C7    C2   C3   C4    180.00   0.0  0
 D38  CONST_15  C7    C2   C1   C6    180.00   0.0  0
 D38  CONST_16  C13   C12  N11  C10   180.00   0.0  0
 D38  CONST_17  N14   N15  N11  C10   180.00   0.0  0
 D38  CONST_18  C16   C13  C12  N11   180.00   0.0  0
 D38  CONST_19  C16   C13  N14  N15   180.00   0.0  0
 D38  CONST_20  H3    C3   C2   C1    180.00   0.0  0
 D38  CONST_21  H6    C6   C1   C2    180.00   0.0  0
 D38  CONST_22  H4    C4   C3   C2    180.00   0.0  0
 D38  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 D38  CONST_24  H12   C12  C13  N14   180.00   0.0  0
 D38  CONST_25  HO9   O9   C7   C2    180.00   0.0  0
 D38  CONST_26  C23   N22  C21  C17   180.00   0.0  0
 D38  CONST_27  O27   C21  N22  C23     0.00   0.0  0
 D38  CONST_28  HN22  N22  C21  C17     0.00   0.0  0
 D38  CONST_29  HO26  O26  C24  C23   180.00   0.0  0
 D38  Var_01    N11   C10  C5   C4    124.99  30.0  2
 D38  Var_02    C12   N11  C10  C5    113.25  30.0  2
 D38  Var_03    O8    C7   C2   C1      1.08  30.0  3
 D38  Var_04    C17   C16  C13  C12    81.21  30.0  1
 D38  Var_05    C30   C29  C28  C23  -172.53  30.0  3
 D38  Var_06    C31   C30  C29  C28  -179.11  30.0  3
 D38  Var_07    N32   C31  C30  C29  -179.33  30.0  3
 D38  Var_08    H20   C20  C18  C17    51.69  30.0  3
 D38  Var_09    H19   C19  C18  C17    67.60  30.0  3
 D38  Var_10    HN32  N32  C31  C30    67.21  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
 D38  chir_01  C17  C16  C18  C21  negativ
 D38  chir_02  C23  N22  C28  C24  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
 D38  plan-1  C10   0.020
 D38  plan-1  N11   0.020
 D38  plan-1  C12   0.020
 D38  plan-1  C13   0.020
 D38  plan-1  N14   0.020
 D38  plan-1  N15   0.020
 D38  plan-1  C16   0.020
 D38  plan-1  H12   0.020
 D38  plan-2  C1    0.020
 D38  plan-2  C2    0.020
 D38  plan-2  C3    0.020
 D38  plan-2  C4    0.020
 D38  plan-2  C5    0.020
 D38  plan-2  C6    0.020
 D38  plan-2  C7    0.020
 D38  plan-2  C10   0.020
 D38  plan-2  H1    0.020
 D38  plan-2  H3    0.020
 D38  plan-2  H4    0.020
 D38  plan-2  H6    0.020
 D38  plan-3  C17   0.020
 D38  plan-3  C21   0.020
 D38  plan-3  N22   0.020
 D38  plan-3  C23   0.020
 D38  plan-3  O27   0.020
 D38  plan-3  HN22  0.020
 D38  plan-4  C2    0.020
 D38  plan-4  C7    0.020
 D38  plan-4  O8    0.020
 D38  plan-4  O9    0.020
 D38  plan-4  HO9   0.020
 D38  plan-5  C23   0.020
 D38  plan-5  C24   0.020
 D38  plan-5  O25   0.020
 D38  plan-5  O26   0.020
 D38  plan-5  HO26  0.020

