# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 04:30:08 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  55  29  .  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
;

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   0.357  -0.6940  -1.2286  -2.4097
 PH5  O1A   O  O      0  -0.593  -0.7396  -2.3433  -2.9638
 PH5  O1B   O  OC    -1  -0.575  -0.6559  -0.1140  -2.9526
 PH5  C2    C  CT     0   0.435  -0.7512  -1.2679  -0.8438
 PH5  O2    O  O2     0  -0.515  -2.0687  -1.4546  -0.4244
 PH5  C3    C  CH2    0  -0.525   0.0593  -2.4129  -0.2531
 PH5  C4    C  CH1    0   0.065   1.5493  -2.1753  -0.4509
 PH5  O4    O  OH1    0  -0.666   2.3334  -3.1647   0.1739
 PH5  C5    C  CH1    0  -0.112   1.9408  -0.8279   0.1462
 PH5  N5    N  NH1    0  -0.643   3.3208  -0.5167  -0.1324
 PH5  C10   C  C      0   0.556   4.3068  -0.4989   0.7869
 PH5  O10   O  O      0  -0.496   4.1152  -0.6708   1.9807
 PH5  C11   C  CH2    0  -0.584   5.6840  -0.2289   0.2111
 PH5  C12   C  CH3    0  -0.657   6.7862  -0.2090   1.2542
 PH5  C6    C  CH1    0   0.029   1.0345   0.2798  -0.4121
 PH5  O6    O  O2     0  -0.521  -0.3240  -0.0577  -0.2623
 PH5  C7    C  CH1    0  -0.012   1.2082   1.5996   0.3404
 PH5  O7    O  OH1    0  -0.667   0.7355   1.4846   1.6625
 PH5  C8    C  CH1    0  -0.024   0.5480   2.7673  -0.4165
 PH5  O8    O  OH1    0  -0.660   1.1767   2.9549  -1.6650
 PH5  C9    C  CH2    0  -0.160   0.5587   4.0405   0.4152
 PH5  O9    O  OH1    0  -0.672  -0.0585   5.0690  -0.3253
 PH5  CB    C  CH2    0  -0.229  -3.0373  -0.5394  -0.9083
 PH5  CG    C  CR6    0   0.089  -4.1444  -0.4497   0.1033
 PH5  CD1   C  CR16   0  -0.292  -3.8510  -0.1758   1.4386
 PH5  CD2   C  CR16   0  -0.316  -5.4730  -0.6088  -0.2726
 PH5  CE1   C  CR16   0  -0.242  -4.8674  -0.0577   2.3740
 PH5  CE2   C  CR16   0  -0.241  -6.4954  -0.4867   0.6621
 PH5  CZ    C  CR16   0  -0.269  -6.1948  -0.2121   1.9880
 PH5  H3C1  H  HCH2   0   0.246  -0.2361  -3.3565  -0.7134
 PH5  H3C2  H  HCH2   0   0.232  -0.1522  -2.4806   0.8195
 PH5  H4    H  HCH1   0   0.199   1.7641  -2.1481  -1.5309
 PH5  HA    H  HOH1   0   0.450   2.1643  -4.0029  -0.2674
 PH5  H5    H  HCH1   0   0.254   1.8217  -0.8798   1.2307
 PH5  HB    H  HNH1   0   0.393   3.5813  -0.4122  -1.1017
 PH5  H111  H  HCH2   0   0.264   5.6532   0.7228  -0.3276
 PH5  H112  H  HCH2   0   0.263   5.8943  -0.9869  -0.5488
 PH5  H121  H  HCH3   0   0.227   6.6285   0.5764   1.9922
 PH5  H122  H  HCH3   0   0.227   6.8551  -1.1583   1.7843
 PH5  H123  H  HCH3   0   0.232   7.7484  -0.0267   0.7768
 PH5  H6    H  HCH1   0   0.230   1.2843   0.4416  -1.4677
 PH5  H7    H  HCH1   0   0.236   2.2801   1.8165   0.4172
 PH5  HC    H  HOH1   0   0.441  -0.1446   1.0919   1.6200
 PH5  H8    H  HCH1   0   0.235  -0.4906   2.5051  -0.6453
 PH5  HD    H  HOH1   0   0.440   2.0795   3.2540  -1.5101
 PH5  H9C1  H  HCH2   0   0.205   0.0376   3.8584   1.3603
 PH5  H9C2  H  HCH2   0   0.185   1.5993   4.2962   0.6710
 PH5  H9    H  HOH1   0   0.454  -0.0804   5.8558   0.2261
 PH5  HBC1  H  HCH2   0   0.242  -2.6052   0.4527  -1.0618
 PH5  HBC2  H  HCH2   0   0.223  -3.4378  -0.8698  -1.8742
 PH5  HD1   H  HCR6   0   0.248  -2.8199  -0.0519   1.7467
 PH5  HD2   H  HCR6   0   0.251  -5.7147  -0.8335  -1.3049
 PH5  HE1   H  HCR6   0   0.254  -4.6254   0.1552   3.4074
 PH5  HE2   H  HCR6   0   0.254  -7.5249  -0.6142   0.3530
 PH5  HZ    H  HCR6   0   0.254  -6.9878  -0.1205   2.7188

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   deloc     1.246  0.020  1.246
 PH5  C1   O1B   deloc     1.240  0.020  1.240
 PH5  C1   C2    single    1.567  0.020  1.567
 PH5  C2   O2    single    1.395  0.020  1.395
 PH5  C2   C3    single    1.522  0.020  1.522
 PH5  C2   O6    single    1.409  0.020  1.409
 PH5  O2   CB    single    1.418  0.020  1.418
 PH5  C3   C4    single    1.522  0.020  1.522
 PH5  C3   H3C1  single    0.970  0.020  1.090
 PH5  C3   H3C2  single    0.970  0.020  1.090
 PH5  C4   O4    single    1.409  0.020  1.409
 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    1.442  0.020  1.442
 PH5  C5   C6    single    1.536  0.020  1.536
 PH5  C5   H5    single    0.970  0.020  1.090
 PH5  N5   C10   single    1.348  0.020  1.348
 PH5  N5   HB    single    0.860  0.020  1.020
 PH5  C10  O10   double    1.221  0.020  1.221
 PH5  C10  C11   single    1.517  0.020  1.517
 PH5  C11  C12   single    1.518  0.020  1.518
 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    1.408  0.020  1.408
 PH5  C6   C7    single    1.529  0.020  1.529
 PH5  C6   H6    single    0.970  0.020  1.090
 PH5  C7   O7    single    1.409  0.020  1.409
 PH5  C7   C8    single    1.540  0.020  1.540
 PH5  C7   H7    single    0.970  0.020  1.090
 PH5  O7   HC    single    0.850  0.020  0.980
 PH5  C8   O8    single    1.410  0.020  1.410
 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    1.410  0.020  1.410
 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    1.502  0.020  1.502
 PH5  CB   HBC1  single    0.970  0.020  1.090
 PH5  CB   HBC2  single    0.970  0.020  1.090
 PH5  CG   CD1   aromatic  1.394  0.020  1.394
 PH5  CG   CD2   aromatic  1.390  0.020  1.390
 PH5  CD1  CE1   aromatic  1.386  0.020  1.386
 PH5  CD1  HD1   single    0.930  0.020  1.080
 PH5  CD2  CE2   aromatic  1.391  0.020  1.391
 PH5  CD2  HD2   single    0.930  0.020  1.080
 PH5  CE1  CZ    aromatic  1.391  0.020  1.391
 PH5  CE1  HE1   single    0.930  0.020  1.080
 PH5  CE2  CZ    aromatic  1.387  0.020  1.387
 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   117.44  3.000
 PH5  C2    C1   O1A   114.88  3.000
 PH5  O1B   C1   O1A   127.63  3.000
 PH5  O6    C2   C3    108.94  3.000
 PH5  O6    C2   O2    106.09  3.000
 PH5  C3    C2   O2    106.59  3.000
 PH5  O6    C2   C1    112.32  3.000
 PH5  C3    C2   C1    112.77  3.000
 PH5  O2    C2   C1    109.76  3.000
 PH5  CB    O2   C2    117.14  3.000
 PH5  H3C2  C3   H3C1  107.91  3.000
 PH5  H3C2  C3   C4    109.03  3.000
 PH5  H3C1  C3   C4    110.21  3.000
 PH5  H3C2  C3   C2    108.88  3.000
 PH5  H3C1  C3   C2    110.05  3.000
 PH5  C4    C3   C2    110.70  3.000
 PH5  H4    C4   C5    108.19  3.000
 PH5  H4    C4   O4    110.10  3.000
 PH5  C5    C4   O4    107.70  3.000
 PH5  H4    C4   C3    108.80  3.000
 PH5  C5    C4   C3    109.78  3.000
 PH5  O4    C4   C3    112.19  3.000
 PH5  HA    O4   C4    108.10  3.000
 PH5  H5    C5   C6    109.31  3.000
 PH5  H5    C5   N5    107.85  3.000
 PH5  C6    C5   N5    109.80  3.000
 PH5  H5    C5   C4    108.59  3.000
 PH5  C6    C5   C4    110.08  3.000
 PH5  N5    C5   C4    111.15  3.000
 PH5  HB    N5   C10   117.70  3.000
 PH5  HB    N5   C5    117.06  3.000
 PH5  C10   N5   C5    124.83  3.000
 PH5  C11   C10  O10   122.58  3.000
 PH5  C11   C10  N5    114.05  3.000
 PH5  O10   C10  N5    123.37  3.000
 PH5  H112  C11  H111  105.44  3.000
 PH5  H112  C11  C12   110.30  3.000
 PH5  H111  C11  C12   110.34  3.000
 PH5  H112  C11  C10   108.35  3.000
 PH5  H111  C11  C10   108.43  3.000
 PH5  C12   C11  C10   113.63  3.000
 PH5  H123  C12  H122  107.65  3.000
 PH5  H123  C12  H121  107.70  3.000
 PH5  H122  C12  H121  107.93  3.000
 PH5  H123  C12  C11   110.02  3.000
 PH5  H122  C12  C11   111.65  3.000
 PH5  H121  C12  C11   111.71  3.000
 PH5  H6    C6   C7    108.69  3.000
 PH5  H6    C6   O6    110.95  3.000
 PH5  C7    C6   O6    105.32  3.000
 PH5  H6    C6   C5    108.77  3.000
 PH5  C7    C6   C5    112.12  3.000
 PH5  O6    C6   C5    110.96  3.000
 PH5  C6    O6   C2    117.04  3.000
 PH5  H7    C7   C8    107.67  3.000
 PH5  H7    C7   O7    106.17  3.000
 PH5  C8    C7   O7    112.29  3.000
 PH5  H7    C7   C6    108.44  3.000
 PH5  C8    C7   C6    111.34  3.000
 PH5  O7    C7   C6    110.69  3.000
 PH5  HC    O7   C7    107.34  3.000
 PH5  H8    C8   C9    108.74  3.000
 PH5  H8    C8   O8    105.64  3.000
 PH5  C9    C8   O8    111.69  3.000
 PH5  H8    C8   C7    109.12  3.000
 PH5  C9    C8   C7    111.28  3.000
 PH5  O8    C8   C7    110.17  3.000
 PH5  HD    O8   C8    108.46  3.000
 PH5  H9C2  C9   H9C1  106.73  3.000
 PH5  H9C2  C9   O9    111.48  3.000
 PH5  H9C1  C9   O9    111.50  3.000
 PH5  H9C2  C9   C8    109.15  3.000
 PH5  H9C1  C9   C8    109.25  3.000
 PH5  O9    C9   C8    108.69  3.000
 PH5  H9    O9   C9    107.81  3.000
 PH5  HBC2  CB   HBC1  107.11  3.000
 PH5  HBC2  CB   CG    110.00  3.000
 PH5  HBC1  CB   CG    109.37  3.000
 PH5  HBC2  CB   O2    110.84  3.000
 PH5  HBC1  CB   O2    111.33  3.000
 PH5  CG    CB   O2    108.19  3.000
 PH5  CD2   CG   CD1   118.86  3.000
 PH5  CD2   CG   CB    121.03  3.000
 PH5  CD1   CG   CB    120.10  3.000
 PH5  HD1   CD1  CE1   119.75  3.000
 PH5  HD1   CD1  CG    119.68  3.000
 PH5  CE1   CD1  CG    120.57  3.000
 PH5  HD2   CD2  CE2   119.63  3.000
 PH5  HD2   CD2  CG    119.64  3.000
 PH5  CE2   CD2  CG    120.73  3.000
 PH5  HE1   CE1  CZ    120.00  3.000
 PH5  HE1   CE1  CD1   119.80  3.000
 PH5  CZ    CE1  CD1   120.20  3.000
 PH5  HE2   CE2  CZ    120.16  3.000
 PH5  HE2   CE2  CD2   119.80  3.000
 PH5  CZ    CE2  CD2   120.04  3.000
 PH5  HZ    CZ   CE2   120.23  3.000
 PH5  HZ    CZ   CE1   120.16  3.000
 PH5  CE2   CZ   CE1   119.61  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  HB    N5   C10  O10   180.00   0.0  0
 PH5  Var_01    CG    CB   O2   C2   -152.20  30.0  3
 PH5  Var_02    CD1   CG   CB   O2     52.50  30.0  2
 PH5  Var_03    C12   C11  C10  N5    179.92  30.0  3
 PH5  Var_04    H121  C12  C11  C10   -61.32  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

