# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 11:30:11 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (2R,3R,4S)-3-(acetylamino)-4-amino-2-[(2-phenylethyl)(propyl)carbamoyl]-3,4-dihydro-2H-pyran-6-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(CCc1ccccc1)C(=O)[C@@H]2OC(=C[C@H](N)[C@H]2NC(C)=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
 DPC  DPC  '(2R,3R,4S)-3-(acetylamino)-4-amino-2-[(2-phenylethyl)(propyl)carbamoyl]-3,4-dihydro-2H-pyran-6-carboxylic acid (non-preferred name)'  L-saccharide  54  28  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DPC
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
 DPC  C1    C  C      0   0.374  -3.0396  -1.2326  -3.8579
 DPC  O1A   O  O      0  -0.589  -3.1692  -1.4555  -5.0750
 DPC  O1B   O  OC    -1  -0.594  -3.8974  -1.3432  -2.9675
 DPC  C2    C  C      0   0.167  -1.6605  -0.7607  -3.4065
 DPC  C3    C  C1     0  -0.362  -0.6534  -0.5237  -4.2457
 DPC  C4    C  CH1    0  -0.086   0.7105  -0.0891  -3.8074
 DPC  C5    C  CH1    0  -0.123   0.8616  -0.3578  -2.3135
 DPC  N5    N  NH1    0  -0.648   2.0098   0.3466  -1.7978
 DPC  C10   C  C      0   0.525   2.8898  -0.1393  -0.8942
 DPC  O10   O  O      0  -0.486   2.8294  -1.2713  -0.4437
 DPC  C11   C  CH3    0  -0.784   3.9485   0.8425  -0.4582
 DPC  C6    C  CH1    0  -0.036  -0.4226   0.0815  -1.5888
 DPC  O6    O  O2     0  -0.476  -1.5594  -0.6044  -2.0634
 DPC  C7    C  C      0   0.533  -0.3105  -0.2833  -0.1106
 DPC  O7    O  O      0  -0.484  -0.3124  -1.4649   0.1961
 DPC  N8    N  NT     0  -0.455  -0.1410   0.7015   0.7933
 DPC  C81   C  CH2    0  -0.315   0.1808   0.3248   2.1606
 DPC  C82   C  CH2    0  -0.518  -1.0537  -0.0125   3.0017
 DPC  CG    C  CR6    0   0.129  -0.6648  -0.3383   4.4160
 DPC  CD1   C  CR16   0  -0.314  -0.8181   0.5951   5.4380
 DPC  CD2   C  CR16   0  -0.303  -0.0995  -1.5753   4.7241
 DPC  CE1   C  CR16   0  -0.240  -0.4239   0.3007   6.7373
 DPC  CE2   C  CR16   0  -0.240   0.2986  -1.8730   6.0198
 DPC  CZ    C  CR16   0  -0.272   0.1363  -0.9349   7.0320
 DPC  C9    C  CH2    0  -0.329  -0.4511   2.1103   0.5860
 DPC  C91   C  CH2    0  -0.426   0.7629   2.9856   0.3095
 DPC  C92   C  CH3    0  -0.666   0.3936   4.4614   0.3002
 DPC  NE    N  NH2    0  -0.796   1.7304  -0.8262  -4.5400
 DPC  H3    H  H      0   0.251  -0.8313  -0.6554  -5.3044
 DPC  H4    H  HCH1   0   0.221   0.7977   1.0007  -3.9615
 DPC  H5    H  HCH1   0   0.276   1.0094  -1.4285  -2.1608
 DPC  HN5   H  HNH1   0   0.401   2.1538   1.2865  -2.1336
 DPC  H111  H  HCH3   0   0.269   4.9111   0.3406  -0.3815
 DPC  H112  H  HCH3   0   0.251   4.0474   1.6972  -1.1245
 DPC  H113  H  HCH3   0   0.267   3.6946   1.2194   0.5343
 DPC  H6    H  HCH1   0   0.254  -0.5544   1.1557  -1.7600
 DPC  H811  H  HCH2   0   0.260   0.8675  -0.5215   2.1461
 DPC  H812  H  HCH2   0   0.258   0.7184   1.1601   2.6153
 DPC  H821  H  HCH2   0   0.248  -1.7464   0.8323   2.9912
 DPC  H822  H  HCH2   0   0.257  -1.5741  -0.8588   2.5490
 DPC  HD1   H  HCR6   0   0.246  -1.2553   1.5618   5.2153
 DPC  HD2   H  HCR6   0   0.248   0.0254  -2.3155   3.9417
 DPC  HE1   H  HCR6   0   0.253  -0.5572   1.0365   7.5202
 DPC  HE2   H  HCR6   0   0.253   0.7329  -2.8395   6.2420
 DPC  HZ    H  HCR6   0   0.254   0.4420  -1.1679   8.0438
 DPC  H91   H  HCH2   0   0.258  -0.9492   2.4638   1.4930
 DPC  H92   H  HCH2   0   0.263  -1.1897   2.2264  -0.2064
 DPC  H911  H  HCH2   0   0.216   1.1997   2.7102  -0.6520
 DPC  H912  H  HCH2   0   0.230   1.5303   2.7990   1.0657
 DPC  H921  H  HCH3   0   0.237   1.2611   5.0812   0.0753
 DPC  H922  H  HCH3   0   0.224  -0.3686   4.6753  -0.4511
 DPC  H923  H  HCH3   0   0.225   0.0019   4.7767   1.2686
 DPC  HNE1  H  HNH2   0   0.351   1.6268  -0.6372  -5.5299
 DPC  HNE2  H  HNH2   0   0.346   2.6444  -0.4647  -4.2934

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
 DPC  C1   O1A   deloc     1.244  0.020  1.244
 DPC  C1   O1B   deloc     1.241  0.020  1.241
 DPC  C1   C2    single    1.526  0.020  1.526
 DPC  C2   C3    double    1.332  0.020  1.332
 DPC  C2   O6    single    1.356  0.020  1.356
 DPC  C3   C4    single    1.497  0.020  1.497
 DPC  C3   H3    single    0.930  0.020  1.080
 DPC  C4   C5    single    1.525  0.020  1.525
 DPC  C4   NE    single    1.456  0.020  1.456
 DPC  C4   H4    single    0.970  0.020  1.090
 DPC  C5   N5    single    1.442  0.020  1.442
 DPC  C5   C6    single    1.539  0.020  1.539
 DPC  C5   H5    single    0.970  0.020  1.090
 DPC  N5   C10   single    1.352  0.020  1.352
 DPC  N5   HN5   single    0.860  0.020  1.020
 DPC  C10  O10   double    1.220  0.020  1.220
 DPC  C10  C11   single    1.508  0.020  1.508
 DPC  C11  H111  single    0.970  0.020  1.090
 DPC  C11  H112  single    0.970  0.020  1.090
 DPC  C11  H113  single    0.970  0.020  1.090
 DPC  C6   O6    single    1.410  0.020  1.410
 DPC  C6   C7    single    1.527  0.020  1.527
 DPC  C6   H6    single    0.970  0.020  1.090
 DPC  C7   O7    double    1.221  0.020  1.221
 DPC  C7   N8    single    1.347  0.020  1.347
 DPC  N8   C81   single    1.454  0.020  1.454
 DPC  N8   C9    single    1.457  0.020  1.457
 DPC  C81  C82   single    1.531  0.020  1.531
 DPC  C81  H811  single    0.970  0.020  1.090
 DPC  C81  H812  single    0.970  0.020  1.090
 DPC  C82  CG    single    1.503  0.020  1.503
 DPC  C82  H821  single    0.970  0.020  1.090
 DPC  C82  H822  single    0.970  0.020  1.090
 DPC  CG   CD1   aromatic  1.392  0.020  1.392
 DPC  CG   CD2   aromatic  1.395  0.020  1.395
 DPC  CD1  CE1   aromatic  1.389  0.020  1.389
 DPC  CD1  HD1   single    0.930  0.020  1.080
 DPC  CD2  CE2   aromatic  1.388  0.020  1.388
 DPC  CD2  HD2   single    0.930  0.020  1.080
 DPC  CE1  CZ    aromatic  1.388  0.020  1.388
 DPC  CE1  HE1   single    0.930  0.020  1.080
 DPC  CE2  CZ    aromatic  1.390  0.020  1.390
 DPC  CE2  HE2   single    0.930  0.020  1.080
 DPC  CZ   HZ    single    0.930  0.020  1.080
 DPC  C9   C91   single    1.522  0.020  1.522
 DPC  C9   H91   single    0.970  0.020  1.090
 DPC  C9   H92   single    0.970  0.020  1.090
 DPC  C91  C92   single    1.521  0.020  1.521
 DPC  C91  H911  single    0.970  0.020  1.090
 DPC  C91  H912  single    0.970  0.020  1.090
 DPC  C92  H921  single    0.970  0.020  1.090
 DPC  C92  H922  single    0.970  0.020  1.090
 DPC  C92  H923  single    0.970  0.020  1.090
 DPC  NE   HNE1  single    0.890  0.020  1.040
 DPC  NE   HNE2  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
 DPC  C2    C1   O1B   116.10  3.000
 DPC  C2    C1   O1A   116.04  3.000
 DPC  O1B   C1   O1A   127.86  3.000
 DPC  O6    C2   C3    123.17  3.000
 DPC  O6    C2   C1    113.33  3.000
 DPC  C3    C2   C1    123.50  3.000
 DPC  H3    C3   C4    118.15  3.000
 DPC  H3    C3   C2    118.08  3.000
 DPC  C4    C3   C2    123.77  3.000
 DPC  H4    C4   NE    111.97  3.000
 DPC  H4    C4   C5    107.62  3.000
 DPC  NE    C4   C5    109.52  3.000
 DPC  H4    C4   C3    108.52  3.000
 DPC  NE    C4   C3    110.11  3.000
 DPC  C5    C4   C3    109.02  3.000
 DPC  H5    C5   C6    109.10  3.000
 DPC  H5    C5   N5    108.73  3.000
 DPC  C6    C5   N5    110.89  3.000
 DPC  H5    C5   C4    108.85  3.000
 DPC  C6    C5   C4    109.17  3.000
 DPC  N5    C5   C4    110.06  3.000
 DPC  HN5   N5   C10   117.69  3.000
 DPC  HN5   N5   C5    116.73  3.000
 DPC  C10   N5   C5    125.57  3.000
 DPC  C11   C10  O10   122.14  3.000
 DPC  C11   C10  N5    114.60  3.000
 DPC  O10   C10  N5    123.25  3.000
 DPC  H113  C11  H112  107.86  3.000
 DPC  H113  C11  H111  107.51  3.000
 DPC  H112  C11  H111  108.96  3.000
 DPC  H113  C11  C10   108.93  3.000
 DPC  H112  C11  C10   113.46  3.000
 DPC  H111  C11  C10   109.94  3.000
 DPC  H6    C6   C7    113.23  3.000
 DPC  H6    C6   O6    109.11  3.000
 DPC  C7    C6   O6    105.60  3.000
 DPC  H6    C6   C5    107.86  3.000
 DPC  C7    C6   C5    109.06  3.000
 DPC  O6    C6   C5    112.06  3.000
 DPC  C6    O6   C2    116.72  3.000
 DPC  N8    C7   O7    122.62  3.000
 DPC  N8    C7   C6    118.95  3.000
 DPC  O7    C7   C6    118.32  3.000
 DPC  C9    N8   C81   115.54  3.000
 DPC  C9    N8   C7    125.76  3.000
 DPC  C81   N8   C7    117.98  3.000
 DPC  H812  C81  H811  106.81  3.000
 DPC  H812  C81  C82   109.66  3.000
 DPC  H811  C81  C82   110.13  3.000
 DPC  H812  C81  N8    107.59  3.000
 DPC  H811  C81  N8    109.15  3.000
 DPC  C82   C81  N8    113.27  3.000
 DPC  H822  C82  H821  107.05  3.000
 DPC  H822  C82  CG    110.22  3.000
 DPC  H821  C82  CG    109.93  3.000
 DPC  H822  C82  C81   109.10  3.000
 DPC  H821  C82  C81   109.60  3.000
 DPC  CG    C82  C81   110.86  3.000
 DPC  CD2   CG   CD1   118.49  3.000
 DPC  CD2   CG   C82   120.34  3.000
 DPC  CD1   CG   C82   121.13  3.000
 DPC  HD1   CD1  CE1   119.70  3.000
 DPC  HD1   CD1  CG    119.43  3.000
 DPC  CE1   CD1  CG    120.87  3.000
 DPC  HD2   CD2  CE2   119.62  3.000
 DPC  HD2   CD2  CG    119.53  3.000
 DPC  CE2   CD2  CG    120.85  3.000
 DPC  HE1   CE1  CZ    120.07  3.000
 DPC  HE1   CE1  CD1   119.83  3.000
 DPC  CZ    CE1  CD1   120.10  3.000
 DPC  HE2   CE2  CZ    120.00  3.000
 DPC  HE2   CE2  CD2   119.88  3.000
 DPC  CZ    CE2  CD2   120.12  3.000
 DPC  HZ    CZ   CE2   120.17  3.000
 DPC  HZ    CZ   CE1   120.26  3.000
 DPC  CE2   CZ   CE1   119.56  3.000
 DPC  H92   C9   H91   105.07  3.000
 DPC  H92   C9   C91   110.33  3.000
 DPC  H91   C9   C91   109.15  3.000
 DPC  H92   C9   N8    110.53  3.000
 DPC  H91   C9   N8    106.94  3.000
 DPC  C91   C9   N8    114.34  3.000
 DPC  H912  C91  H911  106.59  3.000
 DPC  H912  C91  C92   109.88  3.000
 DPC  H911  C91  C92   109.67  3.000
 DPC  H912  C91  C9    109.63  3.000
 DPC  H911  C91  C9    109.52  3.000
 DPC  C92   C91  C9    111.43  3.000
 DPC  H923  C92  H922  107.67  3.000
 DPC  H923  C92  H921  107.74  3.000
 DPC  H922  C92  H921  107.61  3.000
 DPC  H923  C92  C91   111.22  3.000
 DPC  H922  C92  C91   111.33  3.000
 DPC  H921  C92  C91   111.09  3.000
 DPC  HNE2  NE   HNE1  105.28  3.000
 DPC  HNE2  NE   C4    109.19  3.000
 DPC  HNE1  NE   C4    108.99  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
 DPC  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 DPC  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 DPC  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 DPC  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 DPC  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 DPC  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 DPC  CONST_07  CE1   CD1  CG   C82   180.00   0.0  0
 DPC  CONST_08  CE2   CD2  CG   C82   180.00   0.0  0
 DPC  CONST_09  HE1   CE1  CD1  CG    180.00   0.0  0
 DPC  CONST_10  HE2   CE2  CD2  CG    180.00   0.0  0
 DPC  CONST_11  HD2   CD2  CG   CD1   180.00   0.0  0
 DPC  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 DPC  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 DPC  CONST_14  O10   C10  N5   C5      0.00   0.0  0
 DPC  CONST_15  C11   C10  N5   C5    180.00   0.0  0
 DPC  CONST_16  C81   N8   C7   C6    180.00   0.0  0
 DPC  CONST_18  C81   N8   C7   O7      0.00   0.0  0
 DPC  CONST_20  HN5   N5   C10  O10   180.00   0.0  0
 DPC  Var_01    O6    C2   C3   C4      1.42  30.0  1
 DPC  Var_02    C3    C2   C1   O1A     3.44  30.0  2
 DPC  Var_03    CD1   CG   C82  C81   101.55  30.0  2
 DPC  Var_04    CG    C82  C81  N8   -177.66  30.0  3
 DPC  Var_05    C82   C81  N8   C7    -84.39  30.0  3
 DPC  Var_06    C91   C9   N8   C7   -102.34  30.0  3
 DPC  Var_07    C92   C91  C9   N8   -171.91  30.0  3
 DPC  Var_08    H111  C11  C10  N5   -139.17  30.0  3
 DPC  Var_09    H921  C92  C91  C9   -178.47  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
 DPC  chir_01  C4  C3  C5  NE  negativ
 DPC  chir_02  C5  N5  C6  C4  negativ
 DPC  chir_03  C6  O6  C7  C5  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
 DPC  plan-1  C82  0.020
 DPC  plan-1  CG   0.020
 DPC  plan-1  CD1  0.020
 DPC  plan-1  CD2  0.020
 DPC  plan-1  CE1  0.020
 DPC  plan-1  CE2  0.020
 DPC  plan-1  CZ   0.020
 DPC  plan-1  HD1  0.020
 DPC  plan-1  HD2  0.020
 DPC  plan-1  HE1  0.020
 DPC  plan-1  HE2  0.020
 DPC  plan-1  HZ   0.020
 DPC  plan-2  C6   0.020
 DPC  plan-2  C7   0.020
 DPC  plan-2  O7   0.020
 DPC  plan-2  N8   0.020
 DPC  plan-2  C81  0.020
 DPC  plan-2  C9   0.020
 DPC  plan-3  C5   0.020
 DPC  plan-3  N5   0.020
 DPC  plan-3  C10  0.020
 DPC  plan-3  O10  0.020
 DPC  plan-3  C11  0.020
 DPC  plan-3  HN5  0.020
 DPC  plan-4  C1   0.020
 DPC  plan-4  O1A  0.020
 DPC  plan-4  O1B  0.020
 DPC  plan-4  C2   0.020

