# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 18:20:17 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  61  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  -0.276   5.9520   1.4576   1.6055
 D38  C2    C  CR6    0  -0.107   7.1734   1.2081   0.9807
 D38  C3    C  CR16   0  -0.275   7.1809   1.0152  -0.3966
 D38  C4    C  CR16   0  -0.298   6.0026   1.0613  -1.1298
 D38  C5    C  CR6    0   0.114   4.7894   1.3113  -0.5017
 D38  C6    C  CR16   0  -0.272   4.7754   1.5130   0.8764
 D38  C7    C  C      0   0.397   8.4663   1.1454   1.7849
 D38  O8    O  O      0  -0.592   8.3646   1.3033   3.0165
 D38  O9    O  OC    -1  -0.593   9.5129   0.9409   1.1408
 D38  C10   C  CH2    0  -0.385   3.5167   1.3714  -1.3013
 D38  N11   N  NR5    0  -0.247   2.5460   0.3894  -0.8527
 D38  C12   C  CR15   0  -0.091   1.3568   0.5961  -0.2623
 D38  C13   C  CR5    0   0.156   0.8751  -0.6658  -0.0128
 D38  N14   N  N      0  -0.313   1.8005  -1.5435  -0.4624
 D38  N15   N  N      0  -0.103   2.8002  -0.8996  -0.9631
 D38  C16   C  CH2    0  -0.506  -0.4152  -1.0789   0.6036
 D38  C17   C  CH1    0  -0.376  -1.5926  -1.0469  -0.3856
 D38  C18   C  CH1    0  -0.219  -1.4033  -2.0084  -1.5798
 D38  C19   C  CH3    0  -0.662  -1.4397  -3.4825  -1.1905
 D38  C20   C  CH3    0  -0.686  -2.4079  -1.7315  -2.6947
 D38  C21   C  C      0   0.603  -2.8836  -1.3237   0.3698
 D38  N22   N  NH1    0  -0.632  -3.9473  -0.5994  -0.0047
 D38  C23   C  CH1    0  -0.178  -5.2730  -0.8522   0.5085
 D38  C24   C  C      0   0.409  -5.8773  -2.1921   0.0144
 D38  O25   O  O      0  -0.578  -5.3602  -2.7418  -0.9731
 D38  O26   O  OC    -1  -0.619  -6.8727  -2.5830   0.6577
 D38  O27   O  O      0  -0.518  -2.9331  -2.1371   1.2860
 D38  C28   C  CH2    0  -0.461  -6.1985   0.3077   0.1440
 D38  C29   C  CH2    0  -0.415  -5.7476   1.6614   0.6832
 D38  C30   C  CH2    0  -0.425  -6.7806   2.7549   0.4412
 D38  C31   C  CH2    0  -0.273  -6.3253   4.1182   0.9382
 D38  N32   N  NH2    0  -0.801  -7.3484   5.1283   0.7039
 D38  H1    H  HCR6   0   0.245   5.9255   1.6115   2.6760
 D38  H3    H  HCR6   0   0.244   8.1174   0.8183  -0.9009
 D38  H4    H  HCR6   0   0.250   6.0291   0.9022  -2.2016
 D38  H6    H  HCR6   0   0.248   3.8392   1.7140   1.3858
 D38  H10   H  HCH2   0   0.290   3.0415   2.3478  -1.2104
 D38  H10A  H  HCH2   0   0.293   3.7154   1.2019  -2.3593
 D38  H12   H  HCR5   0   0.307   0.9607   1.5788  -0.0699
 D38  H16   H  HCH2   0   0.254  -0.3052  -2.0781   1.0259
 D38  H16A  H  HCH2   0   0.260  -0.6386  -0.4101   1.4375
 D38  H17   H  HCH1   0   0.251  -1.6405  -0.0336  -0.8017
 D38  H18   H  HCH1   0   0.233  -0.4065  -1.7926  -1.9767
 D38  H19   H  HCH3   0   0.225  -2.4410  -3.7855  -0.8828
 D38  H19A  H  HCH3   0   0.222  -1.1547  -4.0985  -2.0451
 D38  H19B  H  HCH3   0   0.224  -0.7491  -3.7152  -0.3793
 D38  H20   H  HCH3   0   0.217  -2.3758  -0.6866  -3.0126
 D38  H20A  H  HCH3   0   0.224  -2.1811  -2.3442  -3.5695
 D38  H20B  H  HCH3   0   0.245  -3.4247  -1.9645  -2.3756
 D38  HN22  H  HNH1   0   0.386  -3.8612  -0.0172  -0.8226
 D38  H23   H  HCH1   0   0.226  -5.2102  -0.9000   1.5999
 D38  H28   H  HCH2   0   0.219  -6.3058   0.3626  -0.9459
 D38  H28A  H  HCH2   0   0.234  -7.1898   0.0754   0.5382
 D38  H29   H  HCH2   0   0.212  -5.5524   1.5734   1.7571
 D38  H29A  H  HCH2   0   0.213  -4.7985   1.9558   0.2251
 D38  H30   H  HCH2   0   0.212  -7.0071   2.8236  -0.6273
 D38  H30A  H  HCH2   0   0.211  -7.7181   2.4809   0.9383
 D38  H31   H  HCH2   0   0.186  -6.0294   4.0320   1.9942
 D38  H31A  H  HCH2   0   0.211  -5.4237   4.4124   0.3933
 D38  HN32  H  HNH2   0   0.336  -8.1514   4.9260   1.2874
 D38  HN3A  H  HNH2   0   0.344  -7.0095   6.0300   1.0144

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  1.394  0.020  1.394
 D38  C1   C6    aromatic  1.385  0.020  1.385
 D38  C1   H1    single    0.930  0.020  1.080
 D38  C7   C2    single    1.524  0.020  1.524
 D38  C2   C3    aromatic  1.391  0.020  1.391
 D38  C3   C4    aromatic  1.389  0.020  1.389
 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    1.504  0.020  1.504
 D38  C6   H6    single    0.930  0.020  1.080
 D38  O8   C7    deloc     1.246  0.020  1.246
 D38  O9   C7    deloc     1.246  0.020  1.246
 D38  C10  N11   single    1.452  0.020  1.452
 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  1.318  0.020  1.318
 D38  C12  C13   aromatic  1.374  0.020  1.374
 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  1.290  0.020  1.290
 D38  C16  C17   single    1.538  0.020  1.538
 D38  C16  H16   single    0.970  0.020  1.090
 D38  C16  H16A  single    0.970  0.020  1.090
 D38  C18  C17   single    1.545  0.020  1.545
 D38  C17  C21   single    1.521  0.020  1.521
 D38  C17  H17   single    0.970  0.020  1.090
 D38  C20  C18   single    1.526  0.020  1.526
 D38  C18  C19   single    1.525  0.020  1.525
 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    1.340  0.020  1.340
 D38  C21  O27   double    1.226  0.020  1.226
 D38  N22  C23   single    1.444  0.020  1.444
 D38  N22  HN22  single    0.860  0.020  1.020
 D38  C23  C28   single    1.528  0.020  1.528
 D38  C23  C24   single    1.551  0.020  1.551
 D38  C23  H23   single    0.970  0.020  1.090
 D38  O25  C24   deloc     1.243  0.020  1.243
 D38  C24  O26   deloc     1.248  0.020  1.248
 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    1.524  0.020  1.524
 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    1.457  0.020  1.457
 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    119.62  3.000
 D38  H1    C1   C2    119.36  3.000
 D38  C6    C1   C2    121.02  3.000
 D38  C7    C2   C3    120.82  3.000
 D38  C3    C2   C1    118.24  3.000
 D38  C7    C2   C1    120.93  3.000
 D38  H3    C3   C4    119.64  3.000
 D38  H3    C3   C2    119.44  3.000
 D38  C4    C3   C2    120.92  3.000
 D38  H4    C4   C5    119.67  3.000
 D38  H4    C4   C3    119.77  3.000
 D38  C5    C4   C3    120.56  3.000
 D38  C10   C5   C6    120.77  3.000
 D38  C10   C5   C4    120.39  3.000
 D38  C6    C5   C4    118.84  3.000
 D38  H6    C6   C5    120.01  3.000
 D38  H6    C6   C1    119.56  3.000
 D38  C5    C6   C1    120.42  3.000
 D38  O9    C7   O8    126.90  3.000
 D38  O9    C7   C2    116.53  3.000
 D38  O8    C7   C2    116.57  3.000
 D38  H10A  C10  H10   107.45  3.000
 D38  H10A  C10  N11   108.46  3.000
 D38  H10   C10  N11   106.78  3.000
 D38  H10A  C10  C5    110.83  3.000
 D38  H10   C10  C5    111.13  3.000
 D38  N11   C10  C5    111.99  3.000
 D38  N15   N11  C12   110.97  3.000
 D38  N15   N11  C10   120.43  3.000
 D38  C12   N11  C10   128.57  3.000
 D38  H12   C12  C13   132.60  3.000
 D38  H12   C12  N11   122.99  3.000
 D38  C13   C12  N11   104.41  3.000
 D38  C16   C13  N14   123.41  3.000
 D38  N14   C13  C12   107.21  3.000
 D38  C16   C13  C12   129.36  3.000
 D38  N15   N14  C13   109.59  3.000
 D38  N14   N15  N11   107.82  3.000
 D38  H16A  C16  H16   106.62  3.000
 D38  H16A  C16  C17   108.77  3.000
 D38  H16   C16  C17   110.21  3.000
 D38  H16A  C16  C13   108.88  3.000
 D38  H16   C16  C13   109.11  3.000
 D38  C17   C16  C13   113.05  3.000
 D38  H17   C17  C21   108.63  3.000
 D38  H17   C17  C18   106.69  3.000
 D38  C21   C17  C18   112.01  3.000
 D38  H17   C17  C16   107.26  3.000
 D38  C21   C17  C16   109.06  3.000
 D38  C18   C17  C16   112.98  3.000
 D38  H18   C18  C20   107.39  3.000
 D38  H18   C18  C19   107.75  3.000
 D38  C20   C18  C19   110.25  3.000
 D38  H18   C18  C17   105.62  3.000
 D38  C19   C18  C17   113.66  3.000
 D38  C20   C18  C17   111.79  3.000
 D38  H19B  C19  H19A  107.26  3.000
 D38  H19B  C19  H19   108.20  3.000
 D38  H19A  C19  H19   107.69  3.000
 D38  H19B  C19  C18   112.40  3.000
 D38  H19A  C19  C18   109.84  3.000
 D38  H19   C19  C18   111.26  3.000
 D38  H20B  C20  H20A  107.95  3.000
 D38  H20B  C20  H20   108.47  3.000
 D38  H20A  C20  H20   107.30  3.000
 D38  H20B  C20  C18   111.17  3.000
 D38  H20A  C20  C18   110.29  3.000
 D38  H20   C20  C18   111.52  3.000
 D38  O27   C21  N22   122.36  3.000
 D38  O27   C21  C17   121.74  3.000
 D38  N22   C21  C17   115.88  3.000
 D38  HN22  N22  C23   117.91  3.000
 D38  HN22  N22  C21   118.12  3.000
 D38  C23   N22  C21   122.32  3.000
 D38  H23   C23  C28   107.81  3.000
 D38  H23   C23  C24   107.60  3.000
 D38  C28   C23  C24   110.11  3.000
 D38  H23   C23  N22   108.03  3.000
 D38  C24   C23  N22   113.32  3.000
 D38  C28   C23  N22   109.78  3.000
 D38  O26   C24  O25   127.07  3.000
 D38  O26   C24  C23   114.66  3.000
 D38  O25   C24  C23   118.24  3.000
 D38  H28A  C28  H28   106.30  3.000
 D38  H28A  C28  C29   109.24  3.000
 D38  H28   C28  C29   109.62  3.000
 D38  H28A  C28  C23   107.59  3.000
 D38  H28   C28  C23   109.54  3.000
 D38  C29   C28  C23   114.23  3.000
 D38  H29A  C29  H29   106.11  3.000
 D38  H29A  C29  C30   109.18  3.000
 D38  H29   C29  C30   109.53  3.000
 D38  H29A  C29  C28   110.31  3.000
 D38  H29   C29  C28   109.15  3.000
 D38  C30   C29  C28   112.36  3.000
 D38  H30A  C30  H30   106.34  3.000
 D38  H30A  C30  C31   109.39  3.000
 D38  H30   C30  C31   108.96  3.000
 D38  H30A  C30  C29   109.18  3.000
 D38  H30   C30  C29   109.90  3.000
 D38  C31   C30  C29   112.86  3.000
 D38  H31A  C31  H31   106.12  3.000
 D38  H31A  C31  N32   108.20  3.000
 D38  H31   C31  N32   113.43  3.000
 D38  H31A  C31  C30   108.97  3.000
 D38  H31   C31  C30   108.91  3.000
 D38  N32   C31  C30   111.02  3.000
 D38  HN3A  N32  HN32  105.47  3.000
 D38  HN3A  N32  C31   109.46  3.000
 D38  HN32  N32  C31   109.00  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  C23   N22  C21  C17   180.00   0.0  0
 D38  CONST_26  O27   C21  N22  C23     0.00   0.0  0
 D38  CONST_27  HN22  N22  C21  C17     0.00   0.0  0
 D38  Var_01    N11   C10  C5   C4    121.06  30.0  2
 D38  Var_02    C12   N11  C10  C5    113.40  30.0  2
 D38  Var_03    O8    C7   C2   C1      1.26  30.0  2
 D38  Var_04    C17   C16  C13  C12    80.63  30.0  1
 D38  Var_05    C30   C29  C28  C23  -173.09  30.0  3
 D38  Var_06    C31   C30  C29  C28  -178.32  30.0  3
 D38  Var_07    N32   C31  C30  C29  -179.22  30.0  3
 D38  Var_08    H20   C20  C18  C17    54.41  30.0  3
 D38  Var_09    H19   C19  C18  C17    69.19  30.0  3
 D38  Var_10    HN32  N32  C31  C30    67.00  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-5  C23   0.020
 D38  plan-5  C24   0.020
 D38  plan-5  O25   0.020
 D38  plan-5  O26   0.020

