# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 16:45:19 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@@H](N)C(O)=O)C(=O)N[C@H](C)C(O)=O)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
 J0J  J0J  D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine  ligand  63  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J0J
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
 J0J  N03   N  NH2   0  -0.810  21.7065  -4.0486  -16.7086
 J0J  C02   C  CH1   0  -0.189  22.1900  -4.2112  -15.3482
 J0J  C01   C  CH3   0  -0.673  21.9408  -2.9347  -14.5496
 J0J  C04   C  C     0   0.540  23.6849  -4.5017  -15.3333
 J0J  O05   O  O     0  -0.507  24.2438  -4.9758  -14.3515
 J0J  N06   N  NH1   0  -0.644  24.3446  -4.1666  -16.4469
 J0J  C07   C  CH1   0  -0.123  25.7681  -4.3257  -16.5643
 J0J  C30   C  C     0   0.531  26.1494  -5.7778  -16.3166
 J0J  O31   O  O     0  -0.437  25.5253  -6.7179  -16.7351
 J0J  C08   C  CH2   0  -0.478  26.1940  -3.8999  -17.9726
 J0J  C09   C  CH2   0  -0.605  27.6946  -3.9678  -18.2022
 J0J  C10   C  C     0   0.582  28.1040  -3.3443  -19.5219
 J0J  O11   O  O     0  -0.491  27.3442  -2.6827  -20.2119
 J0J  O32   O  OH1   0  -0.587  27.2864  -5.8837  -15.6443
 J0J  C22   C  C     0   0.560  29.3678  -3.8802  -22.2810
 J0J  C13   C  CH1   0  -0.213  29.9265  -3.0693  -21.1070
 J0J  C14   C  CH2   0  -0.457  31.4582  -3.1300  -21.0954
 J0J  C15   C  CH2   0  -0.438  32.0470  -4.5360  -21.1565
 J0J  C16   C  CH2   0  -0.445  33.5688  -4.4921  -21.1015
 J0J  C17   C  CH1   0  -0.208  34.2439  -5.8582  -21.2453
 J0J  C19   C  C     0   0.542  33.9409  -6.4257  -22.6206
 J0J  O23   O  O     0  -0.476  28.7847  -4.9375  -22.1258
 J0J  O20   O  O     0  -0.453  34.1564  -5.8181  -23.6422
 J0J  O21   O  OH1   0  -0.581  33.4409  -7.6512  -22.6019
 J0J  N12   N  NH1   0  -0.639  29.3900  -3.5450  -19.8629
 J0J  N18   N  NH2   0  -0.795  33.8283  -6.7435  -20.1760
 J0J  N24   N  NH1   0  -0.628  29.6346  -3.3433  -23.4855
 J0J  C25   C  CH1   0  -0.223  29.3128  -3.9766  -24.7381
 J0J  C26   C  CH3   0  -0.654  30.5247  -4.0393  -25.6562
 J0J  C27   C  C     0   0.561  28.1189  -3.3203  -25.4178
 J0J  O28   O  O     0  -0.440  27.9691  -3.2784  -26.6127
 J0J  O29   O  OH1   0  -0.578  27.2437  -2.8410  -24.5496
 J0J  HN03  H  HNH2  0   0.360  21.5751  -4.9519  -17.1462
 J0J  HN0A  H  HNH2  0   0.363  20.7974  -3.6045  -16.6995
 J0J  H02   H  HCH1  0   0.244  21.7113  -5.0446  -14.8185
 J0J  H01   H  HCH3  0   0.233  22.4290  -2.0801  -15.0199
 J0J  H01A  H  HCH3  0   0.244  22.3139  -3.0295  -13.5312
 J0J  H01B  H  HCH3  0   0.245  20.8708  -2.7289  -14.4955
 J0J  HN06  H  HNH1  0   0.406  23.8000  -3.7973  -17.2148
 J0J  H07   H  HCH1  0   0.278  26.2813  -3.6962  -15.8308
 J0J  H08   H  HCH2  0   0.255  25.6691  -4.5191  -18.7041
 J0J  H08A  H  HCH2  0   0.268  25.8493  -2.8746  -18.1182
 J0J  H09   H  HCH2  0   0.283  28.2282  -3.4469  -17.4005
 J0J  H09A  H  HCH2  0   0.273  28.0542  -4.9996  -18.1815
 J0J  HO32  H  HOH1  0   0.482  27.5410  -6.8156  -15.5648
 J0J  H13   H  HCH1  0   0.289  29.6337  -2.0234  -21.2400
 J0J  H14   H  HCH2  0   0.249  31.8343  -2.5466  -21.9389
 J0J  H14A  H  HCH2  0   0.257  31.8064  -2.6147  -20.1959
 J0J  H15   H  HCH2  0   0.233  31.6645  -5.1576  -20.3437
 J0J  H15A  H  HCH2  0   0.230  31.7305  -5.0176  -22.0867
 J0J  H16   H  HCH2  0   0.240  33.9477  -3.8330  -21.8853
 J0J  H16A  H  HCH2  0   0.246  33.8925  -4.0530  -20.1533
 J0J  H17   H  HCH1  0   0.268  35.3302  -5.6746  -21.2545
 J0J  HO21  H  HOH1  0   0.479  33.2959  -7.9564  -23.5104
 J0J  HN12  H  HNH1  0   0.403  29.9522  -4.1671  -19.3042
 J0J  HN18  H  HNH2  0   0.353  34.3894  -7.5860  -20.1756
 J0J  HN1A  H  HNH2  0   0.352  34.0212  -6.2874  -19.2929
 J0J  HN24  H  HNH1  0   0.406  30.0957  -2.4467  -23.5245
 J0J  H25   H  HCH1  0   0.303  28.9947  -4.9983  -24.5075
 J0J  H26   H  HCH3  0   0.239  30.8783  -3.0429  -25.9227
 J0J  H26A  H  HCH3  0   0.244  31.3343  -4.5673  -25.1541
 J0J  H26B  H  HCH3  0   0.248  30.2919  -4.5743  -26.5740
 J0J  HO29  H  HOH1  0   0.483  26.4840  -2.4665  -25.0205

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
 J0J  H01B  C01   single  0.970  0.020  1.090
 J0J  C01   H01A  single  0.970  0.020  1.090
 J0J  C01   H01   single  0.970  0.020  1.090
 J0J  C01   C02   single  1.526  0.020  1.526
 J0J  C04   C02   single  1.523  0.020  1.523
 J0J  C02   N03   single  1.453  0.020  1.453
 J0J  C02   H02   single  0.970  0.020  1.090
 J0J  N03   HN03  single  0.890  0.020  1.040
 J0J  N03   HN0A  single  0.890  0.020  1.040
 J0J  N06   C04   single  1.337  0.020  1.337
 J0J  C04   O05   double  1.225  0.020  1.225
 J0J  C07   N06   single  1.437  0.020  1.437
 J0J  HN06  N06   single  0.860  0.020  1.020
 J0J  C08   C07   single  1.532  0.020  1.532
 J0J  C30   C07   single  1.522  0.020  1.522
 J0J  C07   H07   single  0.970  0.020  1.090
 J0J  H08   C08   single  0.970  0.020  1.090
 J0J  C09   C08   single  1.520  0.020  1.520
 J0J  C08   H08A  single  0.970  0.020  1.090
 J0J  C10   C09   single  1.516  0.020  1.516
 J0J  H09   C09   single  0.970  0.020  1.090
 J0J  C09   H09A  single  0.970  0.020  1.090
 J0J  O11   C10   double  1.221  0.020  1.221
 J0J  N12   C10   single  1.345  0.020  1.345
 J0J  C13   N12   single  1.436  0.020  1.436
 J0J  N12   HN12  single  0.860  0.020  1.020
 J0J  C22   C13   single  1.532  0.020  1.532
 J0J  H13   C13   single  0.970  0.020  1.090
 J0J  C13   C14   single  1.533  0.020  1.533
 J0J  H14   C14   single  0.970  0.020  1.090
 J0J  C14   C15   single  1.525  0.020  1.525
 J0J  C14   H14A  single  0.970  0.020  1.090
 J0J  H15   C15   single  0.970  0.020  1.090
 J0J  C15   C16   single  1.523  0.020  1.523
 J0J  C15   H15A  single  0.970  0.020  1.090
 J0J  H16   C16   single  0.970  0.020  1.090
 J0J  C17   C16   single  1.531  0.020  1.531
 J0J  C16   H16A  single  0.970  0.020  1.090
 J0J  C19   C17   single  1.518  0.020  1.518
 J0J  C17   H17   single  0.970  0.020  1.090
 J0J  C17   N18   single  1.449  0.020  1.449
 J0J  HN18  N18   single  0.890  0.020  1.040
 J0J  N18   HN1A  single  0.890  0.020  1.040
 J0J  O20   C19   double  1.208  0.020  1.208
 J0J  O21   C19   single  1.324  0.020  1.324
 J0J  O21   HO21  single  0.850  0.020  0.980
 J0J  N24   C22   single  1.345  0.020  1.345
 J0J  C22   O23   double  1.217  0.020  1.217
 J0J  C25   N24   single  1.440  0.020  1.440
 J0J  N24   HN24  single  0.860  0.020  1.020
 J0J  C27   C25   single  1.523  0.020  1.523
 J0J  C26   C25   single  1.522  0.020  1.522
 J0J  C25   H25   single  0.970  0.020  1.090
 J0J  H26B  C26   single  0.970  0.020  1.090
 J0J  H26   C26   single  0.970  0.020  1.090
 J0J  C26   H26A  single  0.970  0.020  1.090
 J0J  O28   C27   double  1.205  0.020  1.205
 J0J  C27   O29   single  1.323  0.020  1.323
 J0J  O29   HO29  single  0.850  0.020  0.980
 J0J  O31   C30   double  1.203  0.020  1.203
 J0J  C30   O32   single  1.325  0.020  1.325
 J0J  O32   HO32  single  0.850  0.020  0.980

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
 J0J  HN0A  N03  HN03  106.20  3.000
 J0J  HN0A  N03  C02   109.86  3.000
 J0J  HN03  N03  C02   110.37  3.000
 J0J  H02   C02  C04   106.18  3.000
 J0J  H02   C02  C01   108.13  3.000
 J0J  C04   C02  C01   108.34  3.000
 J0J  H02   C02  N03   113.07  3.000
 J0J  C04   C02  N03   110.93  3.000
 J0J  C01   C02  N03   110.00  3.000
 J0J  H01B  C01  H01A  107.83  3.000
 J0J  H01A  C01  H01   108.55  3.000
 J0J  H01B  C01  H01   108.21  3.000
 J0J  H01   C01  C02   110.89  3.000
 J0J  H01A  C01  C02   111.14  3.000
 J0J  H01B  C01  C02   110.12  3.000
 J0J  N06   C04  O05   122.64  3.000
 J0J  O05   C04  C02   121.97  3.000
 J0J  N06   C04  C02   115.36  3.000
 J0J  HN06  N06  C07   120.79  3.000
 J0J  HN06  N06  C04   117.28  3.000
 J0J  C07   N06  C04   121.94  3.000
 J0J  H07   C07  C08   109.02  3.000
 J0J  H07   C07  C30   108.81  3.000
 J0J  C08   C07  C30   110.20  3.000
 J0J  H07   C07  N06   110.25  3.000
 J0J  C30   C07  N06   109.91  3.000
 J0J  C08   C07  N06   108.65  3.000
 J0J  O32   C30  O31   123.99  3.000
 J0J  O32   C30  C07   111.95  3.000
 J0J  O31   C30  C07   123.97  3.000
 J0J  H08A  C08  H08   106.93  3.000
 J0J  H08A  C08  C09   109.49  3.000
 J0J  H08   C08  C09   110.36  3.000
 J0J  H08A  C08  C07   107.22  3.000
 J0J  C09   C08  C07   113.65  3.000
 J0J  H08   C08  C07   108.93  3.000
 J0J  H09A  C09  H09   105.96  3.000
 J0J  H09A  C09  C10   108.42  3.000
 J0J  H09   C09  C10   108.07  3.000
 J0J  H09A  C09  C08   111.36  3.000
 J0J  H09   C09  C08   110.45  3.000
 J0J  C10   C09  C08   112.32  3.000
 J0J  N12   C10  O11   122.16  3.000
 J0J  N12   C10  C09   114.67  3.000
 J0J  O11   C10  C09   123.14  3.000
 J0J  HO32  O32  C30   110.11  3.000
 J0J  N24   C22  O23   123.76  3.000
 J0J  O23   C22  C13   122.45  3.000
 J0J  N24   C22  C13   113.73  3.000
 J0J  H13   C13  N12   108.78  3.000
 J0J  H13   C13  C14   107.82  3.000
 J0J  N12   C13  C14   110.71  3.000
 J0J  C14   C13  C22   110.44  3.000
 J0J  H13   C13  C22   108.37  3.000
 J0J  N12   C13  C22   110.63  3.000
 J0J  H14A  C14  H14   105.89  3.000
 J0J  H14A  C14  C15   110.14  3.000
 J0J  H14   C14  C15   109.17  3.000
 J0J  H14A  C14  C13   107.80  3.000
 J0J  C15   C14  C13   114.95  3.000
 J0J  H14   C14  C13   108.48  3.000
 J0J  H15A  C15  H15   106.31  3.000
 J0J  H15A  C15  C16   109.40  3.000
 J0J  H15   C15  C16   109.83  3.000
 J0J  H15A  C15  C14   109.15  3.000
 J0J  C16   C15  C14   110.95  3.000
 J0J  H15   C15  C14   111.07  3.000
 J0J  H16A  C16  H16   106.09  3.000
 J0J  H16A  C16  C17   108.01  3.000
 J0J  H16   C16  C17   108.55  3.000
 J0J  H16A  C16  C15   109.79  3.000
 J0J  C17   C16  C15   114.30  3.000
 J0J  H16   C16  C15   109.76  3.000
 J0J  H17   C17  N18   113.00  3.000
 J0J  N18   C17  C19   112.51  3.000
 J0J  H17   C17  C19   104.57  3.000
 J0J  N18   C17  C16   110.45  3.000
 J0J  H17   C17  C16   106.68  3.000
 J0J  C19   C17  C16   109.31  3.000
 J0J  O21   C19  O20   123.02  3.000
 J0J  O21   C19  C17   114.12  3.000
 J0J  O20   C19  C17   122.85  3.000
 J0J  HO21  O21  C19   109.56  3.000
 J0J  HN12  N12  C13   118.45  3.000
 J0J  HN12  N12  C10   119.00  3.000
 J0J  C13   N12  C10   121.83  3.000
 J0J  HN1A  N18  HN18  105.60  3.000
 J0J  HN1A  N18  C17   108.29  3.000
 J0J  HN18  N18  C17   110.48  3.000
 J0J  HN24  N24  C25   117.34  3.000
 J0J  HN24  N24  C22   118.68  3.000
 J0J  C25   N24  C22   123.98  3.000
 J0J  H25   C25  C27   105.58  3.000
 J0J  H25   C25  C26   108.67  3.000
 J0J  C27   C25  C26   111.90  3.000
 J0J  H25   C25  N24   106.99  3.000
 J0J  C26   C25  N24   111.41  3.000
 J0J  C27   C25  N24   111.96  3.000
 J0J  H26B  C26  H26A  108.04  3.000
 J0J  H26A  C26  H26   108.33  3.000
 J0J  H26B  C26  H26   108.22  3.000
 J0J  H26A  C26  C25   109.50  3.000
 J0J  H26   C26  C25   111.60  3.000
 J0J  H26B  C26  C25   111.04  3.000
 J0J  O29   C27  O28   123.78  3.000
 J0J  O29   C27  C25   112.46  3.000
 J0J  O28   C27  C25   123.72  3.000
 J0J  HO29  O29  C27   109.87  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
 J0J  CONST_01  C07   N06  C04  C02   180.00   0.0  0
 J0J  CONST_02  C07   N06  C04  O05     0.00   0.0  0
 J0J  CONST_03  C13   N12  C10  C09   180.00   0.0  0
 J0J  CONST_04  C13   N12  C10  O11     0.00   0.0  0
 J0J  CONST_05  C25   N24  C22  C13   180.00   0.0  0
 J0J  CONST_06  C25   N24  C22  O23     0.00   0.0  0
 J0J  CONST_07  HN06  N06  C04  C02     0.00   0.0  0
 J0J  CONST_08  HN12  N12  C10  C09     0.00   0.0  0
 J0J  CONST_09  HN24  N24  C22  C13     0.00   0.0  0
 J0J  CONST_10  HO32  O32  C30  C07   180.00   0.0  0
 J0J  CONST_11  HO21  O21  C19  C17   180.00   0.0  0
 J0J  CONST_12  HO29  O29  C27  C25   180.00   0.0  0
 J0J  Var_01    C10   C09  C08  C07  -171.26  30.0  1
 J0J  Var_02    O11   C10  C09  C08    10.75  30.0  1
 J0J  Var_03    C16   C15  C14  C13  -178.45  30.0  3
 J0J  Var_04    C17   C16  C15  C14  -176.39  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
 J0J  chir_01  C02  C01  C04  N03  positiv
 J0J  chir_02  C07  N06  C08  C30  positiv
 J0J  chir_03  C13  N12  C22  C14  positiv
 J0J  chir_04  C17  N18  C16  C19  positiv
 J0J  chir_05  C25  N24  C27  C26  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
 J0J  plan-1  C02   0.020
 J0J  plan-1  C04   0.020
 J0J  plan-1  O05   0.020
 J0J  plan-1  N06   0.020
 J0J  plan-1  C07   0.020
 J0J  plan-1  HN06  0.020
 J0J  plan-2  C09   0.020
 J0J  plan-2  C10   0.020
 J0J  plan-2  O11   0.020
 J0J  plan-2  C13   0.020
 J0J  plan-2  N12   0.020
 J0J  plan-2  HN12  0.020
 J0J  plan-3  C22   0.020
 J0J  plan-3  C13   0.020
 J0J  plan-3  O23   0.020
 J0J  plan-3  N24   0.020
 J0J  plan-3  C25   0.020
 J0J  plan-3  HN24  0.020
 J0J  plan-4  C07   0.020
 J0J  plan-4  C30   0.020
 J0J  plan-4  O31   0.020
 J0J  plan-4  O32   0.020
 J0J  plan-4  HO32  0.020
 J0J  plan-5  C17   0.020
 J0J  plan-5  C19   0.020
 J0J  plan-5  O20   0.020
 J0J  plan-5  O21   0.020
 J0J  plan-5  HO21  0.020
 J0J  plan-6  C25   0.020
 J0J  plan-6  C27   0.020
 J0J  plan-6  O28   0.020
 J0J  plan-6  O29   0.020
 J0J  plan-6  HO29  0.020

