# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 15:22:52 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@@H]1[C@@H](O)C[C@@](OCc2ccccc2)(O[C@H]1[C@H](O)[C@H](O)CO)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
 PH5  PH5  'benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  56  29  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PH5
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
 PH5  C1    C  C     0   0.476  -0.8268  -1.0539  -2.3034
 PH5  O1A   O  O     0  -0.418  -0.9329  -2.0667  -2.9454
 PH5  O1B   O  OH1   0  -0.566  -0.7879   0.1565  -2.8245
 PH5  C2    C  CT    0   0.461  -0.7884  -1.0571  -0.7527
 PH5  O2    O  O2    0  -0.495  -2.0858  -1.1865  -0.2809
 PH5  C3    C  CH2   0  -0.544  -0.0069  -2.2565  -0.2335
 PH5  C4    C  CH1   0   0.064   1.4893  -2.0915  -0.4673
 PH5  O4    O  OH1   0  -0.659   2.2234  -3.1323   0.1248
 PH5  C5    C  CH1   0  -0.109   1.9556  -0.7766   0.1485
 PH5  N5    N  NH1   0  -0.646   3.3498  -0.5388  -0.1216
 PH5  C10   C  C     0   0.560   4.3329  -0.6423   0.7990
 PH5  O10   O  O     0  -0.491   4.1213  -0.8372   1.9846
 PH5  C11   C  CH2   0  -0.585   5.7288  -0.4838   0.2300
 PH5  C12   C  CH3   0  -0.657   6.8169  -0.4489   1.2870
 PH5  C6    C  CH1   0   0.017   1.1182   0.3829  -0.4063
 PH5  O6    O  O2    0  -0.510  -0.2683   0.1347  -0.2491
 PH5  C7    C  CH1   0  -0.020   1.3831   1.6954   0.3313
 PH5  O7    O  OH1   0  -0.659   0.9979   1.6030   1.6813
 PH5  C8    C  CH1   0  -0.021   0.7272   2.8948  -0.3797
 PH5  O8    O  OH1   0  -0.657   1.1742   2.9840  -1.7133
 PH5  C9    C  CH2   0  -0.160   0.9794   4.1839   0.3865
 PH5  O9    O  OH1   0  -0.671   0.3198   5.2393  -0.2741
 PH5  CB    C  CH2   0  -0.254  -3.0461  -0.1990  -0.6618
 PH5  CG    C  CR6   0   0.090  -4.2487  -0.4112   0.2069
 PH5  CD1   C  CR16  0  -0.290  -4.3140   0.1695   1.4707
 PH5  CD2   C  CR16  0  -0.293  -5.2960  -1.2213  -0.2197
 PH5  CE1   C  CR16  0  -0.243  -5.4107  -0.0503   2.2919
 PH5  CE2   C  CR16  0  -0.243  -6.3953  -1.4445   0.5990
 PH5  CZ    C  CR16  0  -0.262  -6.4535  -0.8592   1.8569
 PH5  H1B   H  HOH1  0   0.487  -0.8566   0.1040  -3.7910
 PH5  H3C1  H  HCH2  0   0.272  -0.3688  -3.1740  -0.7001
 PH5  H3C2  H  HCH2  0   0.265  -0.1920  -2.3345   0.8418
 PH5  H4    H  HCH1  0   0.210   1.6882  -2.0533  -1.5502
 PH5  HA    H  HOH1  0   0.455   2.0517  -3.9418  -0.3666
 PH5  H5    H  HCH1  0   0.266   1.8287  -0.8310   1.2319
 PH5  HB    H  HNH1  0   0.397   3.6235  -0.4404  -1.0883
 PH5  H111  H  HCH2  0   0.262   5.7586   0.4226  -0.3808
 PH5  H112  H  HCH2  0   0.267   5.9030  -1.3094  -0.4667
 PH5  H121  H  HCH3  0   0.227   6.6916   0.3930   1.9671
 PH5  H122  H  HCH3  0   0.228   6.8288  -1.3616   1.8812
 PH5  H123  H  HCH3  0   0.233   7.7932  -0.3497   0.8138
 PH5  H6    H  HCH1  0   0.241   1.3721   0.5239  -1.4648
 PH5  H7    H  HCH1  0   0.246   2.4668   1.8585   0.3354
 PH5  HC    H  HOH1  0   0.443   0.0687   1.3479   1.7134
 PH5  H8    H  HCH1  0   0.235  -0.3545   2.7314  -0.4391
 PH5  HD    H  HOH1  0   0.443   2.1048   3.2339  -1.7080
 PH5  H9C1  H  HCH2  0   0.208   0.6241   4.0673   1.4149
 PH5  H9C2  H  HCH2  0   0.187   2.0656   4.3587   0.4436
 PH5  H9    H  HOH1  0   0.455   0.4354   6.0345   0.2532
 PH5  HBC1  H  HCH2  0   0.247  -2.6510   0.8097  -0.5218
 PH5  HBC2  H  HCH2  0   0.234  -3.3249  -0.3131  -1.7151
 PH5  HD1   H  HCR6  0   0.250  -3.5042   0.8035   1.8125
 PH5  HD2   H  HCR6  0   0.253  -5.2541  -1.6779  -1.2017
 PH5  HE1   H  HCR6  0   0.258  -5.4538   0.4110   3.2699
 PH5  HE2   H  HCR6  0   0.258  -7.2060  -2.0735   0.2548
 PH5  HZ    H  HCR6  0   0.259  -7.3094  -1.0300   2.4971

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
 PH5  C1   O1A   double    1.204  0.020  1.204
 PH5  C1   O1B   single    1.318  0.020  1.318
 PH5  C1   C2    single    1.551  0.020  1.551
 PH5  O1B  H1B   single    0.850  0.020  0.980
 PH5  C2   O2    single    1.387  0.020  1.387
 PH5  C2   C3    single    1.523  0.020  1.523
 PH5  C2   O6    single    1.394  0.020  1.394
 PH5  O2   CB    single    1.429  0.020  1.429
 PH5  C3   C4    single    1.523  0.020  1.523
 PH5  C3   H3C1  single    0.970  0.020  1.090
 PH5  C3   H3C2  single    0.970  0.020  1.090
 PH5  C4   O4    single    1.405  0.020  1.405
 PH5  C4   C5    single    1.525  0.020  1.525
 PH5  C4   H4    single    0.970  0.020  1.090
 PH5  O4   HA    single    0.850  0.020  0.980
 PH5  C5   N5    single    1.440  0.020  1.440
 PH5  C5   C6    single    1.534  0.020  1.534
 PH5  C5   H5    single    0.970  0.020  1.090
 PH5  N5   C10   single    1.351  0.020  1.351
 PH5  N5   HB    single    0.860  0.020  1.020
 PH5  C10  O10   double    1.220  0.020  1.220
 PH5  C10  C11   single    1.516  0.020  1.516
 PH5  C11  C12   single    1.517  0.020  1.517
 PH5  C11  H111  single    0.970  0.020  1.090
 PH5  C11  H112  single    0.970  0.020  1.090
 PH5  C12  H121  single    0.970  0.020  1.090
 PH5  C12  H122  single    0.970  0.020  1.090
 PH5  C12  H123  single    0.970  0.020  1.090
 PH5  C6   O6    single    1.417  0.020  1.417
 PH5  C6   C7    single    1.529  0.020  1.529
 PH5  C6   H6    single    0.970  0.020  1.090
 PH5  C7   O7    single    1.407  0.020  1.407
 PH5  C7   C8    single    1.541  0.020  1.541
 PH5  C7   H7    single    0.970  0.020  1.090
 PH5  O7   HC    single    0.850  0.020  0.980
 PH5  C8   O8    single    1.409  0.020  1.409
 PH5  C8   C9    single    1.521  0.020  1.521
 PH5  C8   H8    single    0.970  0.020  1.090
 PH5  O8   HD    single    0.850  0.020  0.980
 PH5  C9   O9    single    1.409  0.020  1.409
 PH5  C9   H9C1  single    0.970  0.020  1.090
 PH5  C9   H9C2  single    0.970  0.020  1.090
 PH5  O9   H9    single    0.850  0.020  0.980
 PH5  CB   CG    single    1.499  0.020  1.499
 PH5  CB   HBC1  single    0.970  0.020  1.090
 PH5  CB   HBC2  single    0.970  0.020  1.090
 PH5  CG   CD1   aromatic  1.392  0.020  1.392
 PH5  CG   CD2   aromatic  1.391  0.020  1.391
 PH5  CD1  CE1   aromatic  1.388  0.020  1.388
 PH5  CD1  HD1   single    0.930  0.020  1.080
 PH5  CD2  CE2   aromatic  1.389  0.020  1.389
 PH5  CD2  HD2   single    0.930  0.020  1.080
 PH5  CE1  CZ    aromatic  1.390  0.020  1.390
 PH5  CE1  HE1   single    0.930  0.020  1.080
 PH5  CE2  CZ    aromatic  1.389  0.020  1.389
 PH5  CE2  HE2   single    0.930  0.020  1.080
 PH5  CZ   HZ    single    0.930  0.020  1.080

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
 PH5  C2    C1   O1B   113.35  3.000
 PH5  C2    C1   O1A   122.25  3.000
 PH5  O1B   C1   O1A   124.35  3.000
 PH5  H1B   O1B  C1    110.00  3.000
 PH5  O6    C2   C3    111.02  3.000
 PH5  O6    C2   O2    107.81  3.000
 PH5  C3    C2   O2    106.90  3.000
 PH5  O6    C2   C1    111.62  3.000
 PH5  C3    C2   C1    110.81  3.000
 PH5  O2    C2   C1    108.49  3.000
 PH5  CB    O2   C2    118.27  3.000
 PH5  H3C2  C3   H3C1  107.71  3.000
 PH5  H3C2  C3   C4    108.96  3.000
 PH5  H3C1  C3   C4    110.57  3.000
 PH5  H3C2  C3   C2    107.73  3.000
 PH5  H3C1  C3   C2    110.26  3.000
 PH5  C4    C3   C2    111.49  3.000
 PH5  H4    C4   C5    108.17  3.000
 PH5  H4    C4   O4    110.22  3.000
 PH5  C5    C4   O4    107.99  3.000
 PH5  H4    C4   C3    109.39  3.000
 PH5  C5    C4   C3    109.38  3.000
 PH5  O4    C4   C3    111.62  3.000
 PH5  HA    O4   C4    108.35  3.000
 PH5  H5    C5   C6    109.44  3.000
 PH5  H5    C5   N5    107.87  3.000
 PH5  C6    C5   N5    109.63  3.000
 PH5  H5    C5   C4    108.79  3.000
 PH5  C6    C5   C4    109.80  3.000
 PH5  N5    C5   C4    111.27  3.000
 PH5  HB    N5   C10   117.57  3.000
 PH5  HB    N5   C5    117.27  3.000
 PH5  C10   N5   C5    124.34  3.000
 PH5  C11   C10  O10   122.76  3.000
 PH5  C11   C10  N5    113.98  3.000
 PH5  O10   C10  N5    123.25  3.000
 PH5  H112  C11  H111  105.39  3.000
 PH5  H112  C11  C12   110.29  3.000
 PH5  H111  C11  C12   110.52  3.000
 PH5  H112  C11  C10   107.86  3.000
 PH5  H111  C11  C10   108.75  3.000
 PH5  C12   C11  C10   113.66  3.000
 PH5  H123  C12  H122  107.67  3.000
 PH5  H123  C12  H121  107.69  3.000
 PH5  H122  C12  H121  107.95  3.000
 PH5  H123  C12  C11   110.01  3.000
 PH5  H122  C12  C11   111.63  3.000
 PH5  H121  C12  C11   111.73  3.000
 PH5  H6    C6   C7    108.36  3.000
 PH5  H6    C6   O6    110.84  3.000
 PH5  C7    C6   O6    105.45  3.000
 PH5  H6    C6   C5    108.63  3.000
 PH5  C7    C6   C5    112.32  3.000
 PH5  O6    C6   C5    111.19  3.000
 PH5  C6    O6   C2    118.33  3.000
 PH5  H7    C7   C8    107.87  3.000
 PH5  H7    C7   O7    106.08  3.000
 PH5  C8    C7   O7    112.17  3.000
 PH5  H7    C7   C6    107.52  3.000
 PH5  C8    C7   C6    111.83  3.000
 PH5  O7    C7   C6    111.05  3.000
 PH5  HC    O7   C7    108.26  3.000
 PH5  H8    C8   C9    108.51  3.000
 PH5  H8    C8   O8    105.74  3.000
 PH5  C9    C8   O8    111.75  3.000
 PH5  H8    C8   C7    109.22  3.000
 PH5  C9    C8   C7    110.90  3.000
 PH5  O8    C8   C7    110.54  3.000
 PH5  HD    O8   C8    108.51  3.000
 PH5  H9C2  C9   H9C1  106.76  3.000
 PH5  H9C2  C9   O9    111.53  3.000
 PH5  H9C1  C9   O9    111.62  3.000
 PH5  H9C2  C9   C8    108.91  3.000
 PH5  H9C1  C9   C8    109.23  3.000
 PH5  O9    C9   C8    108.73  3.000
 PH5  H9    O9   C9    107.83  3.000
 PH5  HBC2  CB   HBC1  108.15  3.000
 PH5  HBC2  CB   CG    109.77  3.000
 PH5  HBC1  CB   CG    110.29  3.000
 PH5  HBC2  CB   O2    110.81  3.000
 PH5  HBC1  CB   O2    111.15  3.000
 PH5  CG    CB   O2    106.67  3.000
 PH5  CD2   CG   CD1   119.07  3.000
 PH5  CD2   CG   CB    120.59  3.000
 PH5  CD1   CG   CB    120.31  3.000
 PH5  HD1   CD1  CE1   119.78  3.000
 PH5  HD1   CD1  CG    119.68  3.000
 PH5  CE1   CD1  CG    120.54  3.000
 PH5  HD2   CD2  CE2   119.81  3.000
 PH5  HD2   CD2  CG    119.61  3.000
 PH5  CE2   CD2  CG    120.58  3.000
 PH5  HE1   CE1  CZ    120.07  3.000
 PH5  HE1   CE1  CD1   119.92  3.000
 PH5  CZ    CE1  CD1   120.01  3.000
 PH5  HE2   CE2  CZ    120.11  3.000
 PH5  HE2   CE2  CD2   119.92  3.000
 PH5  CZ    CE2  CD2   119.97  3.000
 PH5  HZ    CZ   CE2   120.16  3.000
 PH5  HZ    CZ   CE1   120.01  3.000
 PH5  CE2   CZ   CE1   119.83  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
 PH5  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 PH5  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 PH5  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 PH5  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 PH5  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 PH5  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 PH5  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 PH5  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 PH5  CONST_09  HE1   CE1  CD1  CG    180.00   0.0  0
 PH5  CONST_10  HE2   CE2  CD2  CG    180.00   0.0  0
 PH5  CONST_11  HD2   CD2  CG   CD1   180.00   0.0  0
 PH5  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 PH5  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 PH5  CONST_14  O10   C10  N5   C5      0.00   0.0  0
 PH5  CONST_15  C11   C10  N5   C5    180.00   0.0  0
 PH5  CONST_16  H1B   O1B  C1   C2    180.00   0.0  0
 PH5  CONST_17  HB    N5   C10  O10   180.00   0.0  0
 PH5  Var_01    CG    CB   O2   C2   -168.05  30.0  3
 PH5  Var_02    CD1   CG   CB   O2     85.35  30.0  2
 PH5  Var_03    C12   C11  C10  N5    173.66  30.0  3
 PH5  Var_04    H121  C12  C11  C10   -61.34  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
 PH5  chir_01  C2  O2  C3  O6  positiv
 PH5  chir_02  C4  O4  C5  C3  positiv
 PH5  chir_03  C5  N5  C6  C4  negativ
 PH5  chir_04  C6  O6  C7  C5  negativ
 PH5  chir_05  C7  O7  C6  C8  negativ
 PH5  chir_06  C8  O8  C7  C9  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
 PH5  plan-1  CB   0.020
 PH5  plan-1  CG   0.020
 PH5  plan-1  CD1  0.020
 PH5  plan-1  CD2  0.020
 PH5  plan-1  CE1  0.020
 PH5  plan-1  CE2  0.020
 PH5  plan-1  CZ   0.020
 PH5  plan-1  HD1  0.020
 PH5  plan-1  HD2  0.020
 PH5  plan-1  HE1  0.020
 PH5  plan-1  HE2  0.020
 PH5  plan-1  HZ   0.020
 PH5  plan-2  C5   0.020
 PH5  plan-2  N5   0.020
 PH5  plan-2  C10  0.020
 PH5  plan-2  O10  0.020
 PH5  plan-2  C11  0.020
 PH5  plan-2  HB   0.020
 PH5  plan-3  C1   0.020
 PH5  plan-3  O1A  0.020
 PH5  plan-3  O1B  0.020
 PH5  plan-3  C2   0.020
 PH5  plan-3  H1B  0.020

