# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:26:48 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: (2R,4S,5R,6R)-5-(acetylamino)-4-amino-6-[(2-phenylethyl)(propyl)carbamoyl]tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(CCc1ccccc1)C(=O)[C@@H]2O[C@H](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
 G21  G21  '(2R,4S,5R,6R)-5-(acetylamino)-4-amino-6-[(2-phenylethyl)(propyl)carbamoyl]tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  56  28  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G21
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
 G21  C1    C  C      0   0.393  23.8330  20.2997  63.8985
 G21  O1A   O  O      0  -0.616  24.5165  21.3042  63.6154
 G21  O1B   O  OC    -1  -0.668  22.4761  20.4455  63.6445
 G21  C2    C  CH1    0  -0.096  24.2526  19.1129  64.4696
 G21  C3    C  CH2    0  -0.504  23.5678  17.7844  64.4749
 G21  C4    C  CH1    0  -0.058  24.1741  16.8540  63.4148
 G21  C5    C  CH1    0  -0.099  25.6932  16.8259  63.5785
 G21  N5    N  NH1    0  -0.640  26.3090  16.1061  62.4836
 G21  C10   C  C      0   0.522  27.2322  15.1310  62.6058
 G21  O10   O  O      0  -0.494  27.6257  14.7043  63.6819
 G21  C11   C  CH3    0  -0.783  27.7792  14.6113  61.2989
 G21  C6    C  CH1    0  -0.016  26.2513  18.2596  63.6539
 G21  O6    O  O2     0  -0.505  25.6343  18.9771  64.6917
 G21  C7    C  C      0   0.535  27.7412  18.2140  63.9839
 G21  O7    O  O      0  -0.497  28.0825  17.8671  65.1068
 G21  N8    N  NT     0  -0.454  28.6379  18.5518  63.0335
 G21  C81   C  CH2    0  -0.312  30.0537  18.4296  63.3430
 G21  C82   C  CH2    0  -0.529  30.5964  17.0311  63.0319
 G21  CG    C  CR6    0   0.137  32.0653  16.9420  63.3313
 G21  CD1   C  CR16   0  -0.307  32.5135  16.5240  64.5824
 G21  CD2   C  CR16   0  -0.306  33.0099  17.3170  62.3780
 G21  CE1   C  CR16   0  -0.238  33.8703  16.4787  64.8744
 G21  CE2   C  CR16   0  -0.237  34.3675  17.2749  62.6653
 G21  CZ    C  CR16   0  -0.270  34.8024  16.8548  63.9159
 G21  C9    C  CH2    0  -0.346  28.2937  18.9865  61.6841
 G21  C91   C  CH2    0  -0.424  27.9241  20.4625  61.5819
 G21  C92   C  CH3    0  -0.670  29.0255  21.4083  62.0386
 G21  NE    N  NH2    0  -0.799  23.6497  15.5039  63.5447
 G21  H2    H  HCH1   0   0.442  21.9846  19.6932  63.9884
 G21  H31   H  HCH2   0   0.200  23.6614  17.2805  65.4476
 G21  H32   H  HCH2   0   0.213  22.4914  17.8515  64.2897
 G21  H4    H  HCH1   0   0.188  23.9575  17.3063  62.4314
 G21  H5    H  HCH1   0   0.248  25.9317  16.3026  64.5063
 G21  HN5   H  HNH1   0   0.400  26.0441  16.3873  61.5516
 G21  H111  H  HCH3   0   0.261  27.8515  13.5256  61.3340
 G21  H112  H  HCH3   0   0.248  27.1854  14.8965  60.4323
 G21  H113  H  HCH3   0   0.269  28.7886  15.0020  61.1592
 G21  H6    H  HCH1   0   0.222  26.0446  18.7473  62.6941
 G21  H811  H  HCH2   0   0.257  30.5963  19.1698  62.7538
 G21  H812  H  HCH2   0   0.257  30.2237  18.6723  64.3907
 G21  H821  H  HCH2   0   0.251  30.0467  16.2917  63.6169
 G21  H822  H  HCH2   0   0.250  30.4154  16.8058  61.9773
 G21  HD1   H  HCR6   0   0.246  31.7907  16.2273  65.3339
 G21  HD2   H  HCR6   0   0.245  32.6775  17.6406  61.3980
 G21  HE1   H  HCR6   0   0.251  34.2000  16.1460  65.8506
 G21  HE2   H  HCR6   0   0.251  35.0870  17.5659  61.9105
 G21  HZ    H  HCR6   0   0.251  35.8606  16.8174  64.1406
 G21  H91   H  HCH2   0   0.260  29.1641  18.7886  61.0551
 G21  H92   H  HCH2   0   0.256  27.4965  18.3672  61.2744
 G21  H911  H  HCH2   0   0.227  27.6788  20.6632  60.5356
 G21  H912  H  HCH2   0   0.224  27.0109  20.6617  62.1502
 G21  H921  H  HCH3   0   0.236  28.7253  22.4468  61.8983
 G21  H922  H  HCH3   0   0.226  29.2576  21.2787  63.0965
 G21  H923  H  HCH3   0   0.219  29.9461  21.2513  61.4732
 G21  HNE1  H  HNH2   0   0.341  24.0080  14.9232  62.7958
 G21  HNE2  H  HNH2   0   0.343  22.6455  15.5259  63.4128

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
 G21  C1   O1A   deloc     1.248  0.020  1.248
 G21  C1   O1B   deloc     1.388  0.020  1.388
 G21  C1   C2    single    1.382  0.020  1.382
 G21  C2   C3    single    1.495  0.020  1.495
 G21  C2   O6    single    1.406  0.020  1.406
 G21  C2   H2    single    0.970  0.020  1.090
 G21  C3   C4    single    1.535  0.020  1.535
 G21  C3   H31   single    0.970  0.020  1.090
 G21  C3   H32   single    0.970  0.020  1.090
 G21  C4   C5    single    1.528  0.020  1.528
 G21  C4   NE    single    1.454  0.020  1.454
 G21  C4   H4    single    0.970  0.020  1.090
 G21  C5   N5    single    1.448  0.020  1.448
 G21  C5   C6    single    1.540  0.020  1.540
 G21  C5   H5    single    0.970  0.020  1.090
 G21  N5   C10   single    1.348  0.020  1.348
 G21  N5   HN5   single    0.860  0.020  1.020
 G21  C10  O10   double    1.223  0.020  1.223
 G21  C10  C11   single    1.509  0.020  1.509
 G21  C11  H111  single    0.970  0.020  1.090
 G21  C11  H112  single    0.970  0.020  1.090
 G21  C11  H113  single    0.970  0.020  1.090
 G21  C6   O6    single    1.405  0.020  1.405
 G21  C6   C7    single    1.527  0.020  1.527
 G21  C6   H6    single    0.970  0.020  1.090
 G21  C7   O7    double    1.224  0.020  1.224
 G21  C7   N8    single    1.350  0.020  1.350
 G21  N8   C81   single    1.454  0.020  1.454
 G21  N8   C9    single    1.459  0.020  1.459
 G21  C81  C82   single    1.532  0.020  1.532
 G21  C81  H811  single    0.970  0.020  1.090
 G21  C81  H812  single    0.970  0.020  1.090
 G21  C82  CG    single    1.502  0.020  1.502
 G21  C82  H821  single    0.970  0.020  1.090
 G21  C82  H822  single    0.970  0.020  1.090
 G21  CG   CD1   aromatic  1.393  0.020  1.393
 G21  CG   CD2   aromatic  1.393  0.020  1.393
 G21  CD1  CE1   aromatic  1.389  0.020  1.389
 G21  CD1  HD1   single    0.930  0.020  1.080
 G21  CD2  CE2   aromatic  1.388  0.020  1.388
 G21  CD2  HD2   single    0.930  0.020  1.080
 G21  CE1  CZ    aromatic  1.389  0.020  1.389
 G21  CE1  HE1   single    0.930  0.020  1.080
 G21  CE2  CZ    aromatic  1.389  0.020  1.389
 G21  CE2  HE2   single    0.930  0.020  1.080
 G21  CZ   HZ    single    0.930  0.020  1.080
 G21  C9   C91   single    1.525  0.020  1.525
 G21  C9   H91   single    0.970  0.020  1.090
 G21  C9   H92   single    0.970  0.020  1.090
 G21  C91  C92   single    1.522  0.020  1.522
 G21  C91  H911  single    0.970  0.020  1.090
 G21  C91  H912  single    0.970  0.020  1.090
 G21  C92  H921  single    0.970  0.020  1.090
 G21  C92  H922  single    0.970  0.020  1.090
 G21  C92  H923  single    0.970  0.020  1.090
 G21  NE   HNE1  single    0.890  0.020  1.040
 G21  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
 G21  C2    C1   O1B   117.55  3.000
 G21  C2    C1   O1A   128.23  3.000
 G21  O1B   C1   O1A   114.17  3.000
 G21  H2    C2   O6    171.04  3.000
 G21  H2    C2   C3     77.40  3.000
 G21  O6    C2   C3    111.34  3.000
 G21  H2    C2   C1     54.57  3.000
 G21  O6    C2   C1    116.52  3.000
 G21  C3    C2   C1    128.72  3.000
 G21  H32   C3   H31   105.16  3.000
 G21  H32   C3   C4    107.99  3.000
 G21  H31   C3   C4    107.43  3.000
 G21  H32   C3   C2    113.30  3.000
 G21  H31   C3   C2    111.81  3.000
 G21  C4    C3   C2    110.81  3.000
 G21  H4    C4   NE    112.90  3.000
 G21  H4    C4   C5    107.34  3.000
 G21  NE    C4   C5    109.38  3.000
 G21  H4    C4   C3    106.82  3.000
 G21  NE    C4   C3    111.01  3.000
 G21  C5    C4   C3    109.25  3.000
 G21  H5    C5   C6    108.99  3.000
 G21  H5    C5   N5    108.15  3.000
 G21  C6    C5   N5    110.23  3.000
 G21  H5    C5   C4    108.49  3.000
 G21  C6    C5   C4    110.39  3.000
 G21  N5    C5   C4    110.55  3.000
 G21  HN5   N5   C10   117.72  3.000
 G21  HN5   N5   C5    116.63  3.000
 G21  C10   N5   C5    125.61  3.000
 G21  C11   C10  O10   121.69  3.000
 G21  C11   C10  N5    114.76  3.000
 G21  O10   C10  N5    123.54  3.000
 G21  H113  C11  H112  107.99  3.000
 G21  H113  C11  H111  107.44  3.000
 G21  H112  C11  H111  108.86  3.000
 G21  H113  C11  C10   108.83  3.000
 G21  H112  C11  C10   113.66  3.000
 G21  H111  C11  C10   109.86  3.000
 G21  H6    C6   C7    112.74  3.000
 G21  H6    C6   O6    109.68  3.000
 G21  C7    C6   O6    106.52  3.000
 G21  H6    C6   C5    107.63  3.000
 G21  C7    C6   C5    109.66  3.000
 G21  O6    C6   C5    110.64  3.000
 G21  C6    O6   C2    111.37  3.000
 G21  N8    C7   O7    122.12  3.000
 G21  N8    C7   C6    119.26  3.000
 G21  O7    C7   C6    118.62  3.000
 G21  C9    N8   C81   116.84  3.000
 G21  C9    N8   C7    124.69  3.000
 G21  C81   N8   C7    118.42  3.000
 G21  H812  C81  H811  106.91  3.000
 G21  H812  C81  C82   110.09  3.000
 G21  H811  C81  C82   109.49  3.000
 G21  H812  C81  N8    109.76  3.000
 G21  H811  C81  N8    108.20  3.000
 G21  C82   C81  N8    112.23  3.000
 G21  H822  C82  H821  107.10  3.000
 G21  H822  C82  CG    109.99  3.000
 G21  H821  C82  CG    110.22  3.000
 G21  H822  C82  C81   108.98  3.000
 G21  H821  C82  C81   109.34  3.000
 G21  CG    C82  C81   111.11  3.000
 G21  CD2   CG   CD1   118.49  3.000
 G21  CD2   CG   C82   120.71  3.000
 G21  CD1   CG   C82   120.77  3.000
 G21  HD1   CD1  CE1   119.78  3.000
 G21  HD1   CD1  CG    119.35  3.000
 G21  CE1   CD1  CG    120.86  3.000
 G21  HD2   CD2  CE2   119.73  3.000
 G21  HD2   CD2  CG    119.39  3.000
 G21  CE2   CD2  CG    120.88  3.000
 G21  HE1   CE1  CZ    120.08  3.000
 G21  HE1   CE1  CD1   119.81  3.000
 G21  CZ    CE1  CD1   120.11  3.000
 G21  HE2   CE2  CZ    120.06  3.000
 G21  HE2   CE2  CD2   119.83  3.000
 G21  CZ    CE2  CD2   120.11  3.000
 G21  HZ    CZ   CE2   120.23  3.000
 G21  HZ    CZ   CE1   120.22  3.000
 G21  CE2   CZ   CE1   119.55  3.000
 G21  H92   C9   H91   105.28  3.000
 G21  H92   C9   C91   110.35  3.000
 G21  H91   C9   C91   109.27  3.000
 G21  H92   C9   N8    110.56  3.000
 G21  H91   C9   N8    106.90  3.000
 G21  C91   C9   N8    114.05  3.000
 G21  H912  C91  H911  106.05  3.000
 G21  H912  C91  C92   109.58  3.000
 G21  H911  C91  C92   109.60  3.000
 G21  H912  C91  C9    110.11  3.000
 G21  H911  C91  C9    107.23  3.000
 G21  C92   C91  C9    113.95  3.000
 G21  H923  C92  H922  107.81  3.000
 G21  H923  C92  H921  107.61  3.000
 G21  H922  C92  H921  107.25  3.000
 G21  H923  C92  C91   111.44  3.000
 G21  H922  C92  C91   111.78  3.000
 G21  H921  C92  C91   110.74  3.000
 G21  HNE2  NE   HNE1  105.47  3.000
 G21  HNE2  NE   C4    109.01  3.000
 G21  HNE1  NE   C4    109.79  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
 G21  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 G21  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 G21  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 G21  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 G21  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 G21  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 G21  CONST_07  CE1   CD1  CG   C82   180.00   0.0  0
 G21  CONST_08  CE2   CD2  CG   C82   180.00   0.0  0
 G21  CONST_09  HE1   CE1  CD1  CG    180.00   0.0  0
 G21  CONST_10  HE2   CE2  CD2  CG    180.00   0.0  0
 G21  CONST_11  HD2   CD2  CG   CD1   180.00   0.0  0
 G21  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 G21  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 G21  CONST_14  O10   C10  N5   C5      0.00   0.0  0
 G21  CONST_15  C11   C10  N5   C5    180.00   0.0  0
 G21  CONST_16  C81   N8   C7   C6    180.00   0.0  0
 G21  CONST_17  C9    N8   C7   C6      0.00   0.0  0
 G21  CONST_18  C81   N8   C7   O7      0.00   0.0  0
 G21  CONST_19  C9    N8   C7   O7    180.00   0.0  0
 G21  CONST_20  HN5   N5   C10  O10   180.00   0.0  0
 G21  Var_01    CD1   CG   C82  C81    91.52  30.0  2
 G21  Var_02    CG    C82  C81  N8    178.72  30.0  3
 G21  Var_03    C82   C81  N8   C7     87.87  30.0  3
 G21  Var_04    C91   C9   N8   C7     82.08  30.0  3
 G21  Var_05    C92   C91  C9   N8     59.10  30.0  3
 G21  Var_06    H111  C11  C10  N5   -137.26  30.0  3
 G21  Var_07    H921  C92  C91  C9    177.24  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
 G21  chir_01  C2  C1  C3  O6  negativ
 G21  chir_02  C4  NE  C5  C3  positiv
 G21  chir_03  C5  N5  C6  C4  negativ
 G21  chir_04  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
 G21  plan-1  C82  0.020
 G21  plan-1  CG   0.020
 G21  plan-1  CD1  0.020
 G21  plan-1  CD2  0.020
 G21  plan-1  CE1  0.020
 G21  plan-1  CE2  0.020
 G21  plan-1  CZ   0.020
 G21  plan-1  HD1  0.020
 G21  plan-1  HD2  0.020
 G21  plan-1  HE1  0.020
 G21  plan-1  HE2  0.020
 G21  plan-1  HZ   0.020
 G21  plan-2  C6   0.020
 G21  plan-2  C7   0.020
 G21  plan-2  O7   0.020
 G21  plan-2  N8   0.020
 G21  plan-2  C81  0.020
 G21  plan-2  C9   0.020
 G21  plan-3  C5   0.020
 G21  plan-3  N5   0.020
 G21  plan-3  C10  0.020
 G21  plan-3  O10  0.020
 G21  plan-3  C11  0.020
 G21  plan-3  HN5  0.020
 G21  plan-4  C1   0.020
 G21  plan-4  O1A  0.020
 G21  plan-4  O1B  0.020
 G21  plan-4  C2   0.020

