# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:34:26 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (1R)-4-(acetylamino)-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@H](O[C@H]1[C@H](O)[C@H](O)CO)[P](O)(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
 EQP  EQP  (1R)-4-(acetylamino)-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol  D-saccharide  39  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EQP
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
 EQP  P1    P  P      0   1.169  43.1784  52.2752  45.6063
 EQP  C2    C  CH1    0  -0.266  42.8899  51.2945  47.1849
 EQP  C3    C  CH2    0  -0.463  41.5562  51.5900  47.8552
 EQP  C4    C  CH1    0   0.076  41.4029  50.7952  49.1378
 EQP  C5    C  CH1    0  -0.130  42.6194  51.0197  50.0427
 EQP  C6    C  CH1    0   0.069  43.9034  50.7315  49.2468
 EQP  C7    C  CH1    0   0.014  45.1753  50.9480  50.0596
 EQP  C8    C  CH1    0   0.004  46.4356  50.6146  49.2448
 EQP  C9    C  CH2    0  -0.200  47.7163  51.0192  49.9586
 EQP  C11   C  CH3    0  -0.779  42.4096  49.5503  53.5441
 EQP  N5    N  NH1    0  -0.644  42.5270  50.1820  51.2186
 EQP  O1P   O  O      0  -0.899  42.0345  51.8039  44.6992
 EQP  O2P   O  OP    -1  -0.899  43.0817  53.7469  46.0265
 EQP  O3P   O  OP    -1  -0.895  44.5685  51.8414  45.1288
 EQP  O4    O  OH1    0  -0.667  40.2002  51.1622  49.7769
 EQP  O6    O  O2     0  -0.508  43.9468  51.5451  48.1075
 EQP  O7    O  OH1    0  -0.675  45.2081  52.2841  50.5098
 EQP  O8    O  OH1    0  -0.675  46.3894  49.2252  48.9869
 EQP  O9    O  OH1    0  -0.671  47.7269  50.4981  51.2687
 EQP  O10   O  O      0  -0.492  42.4299  51.8138  52.7886
 EQP  H2    H  HCH1   0   0.157  42.9077  50.2210  46.9218
 EQP  H32   H  HCH2   0   0.204  41.4893  52.6612  48.0735
 EQP  H31   H  HCH2   0   0.220  40.7459  51.3492  47.1637
 EQP  H4    H  HCH1   0   0.181  41.3842  49.7233  48.8767
 EQP  H5    H  HCH1   0   0.251  42.6274  52.0588  50.3749
 EQP  H6    H  HCH1   0   0.199  43.8801  49.6678  48.9536
 EQP  H7    H  HCH1   0   0.218  45.1354  50.2526  50.9072
 EQP  H8    H  HCH1   0   0.214  46.4130  51.1885  48.3090
 EQP  H92   H  HCH2   0   0.210  48.5686  50.6515  49.3691
 EQP  H91   H  HCH2   0   0.200  47.7915  52.1132  49.9538
 EQP  H111  H  HCH3   0   0.261  41.5639  49.7256  54.2081
 EQP  H113  H  HCH3   0   0.247  42.3312  48.5418  53.1421
 EQP  H112  H  HCH3   0   0.264  43.3135  49.6063  54.1517
 EQP  HN5   H  HNH1   0   0.396  42.5541  49.1842  51.0706
 EQP  HO4   H  HOH1   0   0.442  40.0914  50.6016  50.5520
 EQP  HO7   H  HOH1   0   0.451  45.7238  52.3146  51.3207
 EQP  HO8   H  HOH1   0   0.450  47.0461  49.0200  48.3149
 EQP  HO9   H  HOH1   0   0.454  48.5255  50.8024  51.7086
 EQP  C10   C  C      0   0.512  42.4544  50.6289  52.4888

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
 EQP  P1   C2    single  1.881  0.020  1.881
 EQP  P1   O1P   deloc   1.534  0.020  1.534
 EQP  P1   O2P   deloc   1.534  0.020  1.534
 EQP  P1   O3P   deloc   1.532  0.020  1.532
 EQP  C2   C3    single  1.522  0.020  1.522
 EQP  C2   O6    single  1.425  0.020  1.425
 EQP  C2   H2    single  0.970  0.020  1.090
 EQP  C3   C4    single  1.517  0.020  1.517
 EQP  C3   H32   single  0.970  0.020  1.090
 EQP  C3   H31   single  0.970  0.020  1.090
 EQP  C4   C5    single  1.533  0.020  1.533
 EQP  C4   O4    single  1.411  0.020  1.411
 EQP  C4   H4    single  0.970  0.020  1.090
 EQP  C5   C6    single  1.538  0.020  1.538
 EQP  C5   N5    single  1.447  0.020  1.447
 EQP  C5   H5    single  0.970  0.020  1.090
 EQP  C6   C7    single  1.525  0.020  1.525
 EQP  C6   O6    single  1.401  0.020  1.401
 EQP  C6   H6    single  0.970  0.020  1.090
 EQP  C7   C8    single  1.537  0.020  1.537
 EQP  C7   O7    single  1.410  0.020  1.410
 EQP  C7   H7    single  0.970  0.020  1.090
 EQP  C8   C9    single  1.521  0.020  1.521
 EQP  C8   O8    single  1.414  0.020  1.414
 EQP  C8   H8    single  0.970  0.020  1.090
 EQP  C9   O9    single  1.410  0.020  1.410
 EQP  C9   H92   single  0.970  0.020  1.090
 EQP  C9   H91   single  0.970  0.020  1.090
 EQP  C10  C11   single  1.510  0.020  1.510
 EQP  C10  N5    single  1.348  0.020  1.348
 EQP  C10  O10   double  1.222  0.020  1.222
 EQP  C11  H111  single  0.970  0.020  1.090
 EQP  C11  H113  single  0.970  0.020  1.090
 EQP  C11  H112  single  0.970  0.020  1.090
 EQP  N5   HN5   single  0.860  0.020  1.020
 EQP  O4   HO4   single  0.850  0.020  0.980
 EQP  O7   HO7   single  0.850  0.020  0.980
 EQP  O8   HO8   single  0.850  0.020  0.980
 EQP  O9   HO9   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
 EQP  O3P   P1   O2P   114.47  3.000
 EQP  O3P   P1   O1P   113.90  3.000
 EQP  O2P   P1   O1P   114.19  3.000
 EQP  O3P   P1   C2    104.66  3.000
 EQP  O2P   P1   C2    105.12  3.000
 EQP  O1P   P1   C2    102.81  3.000
 EQP  H2    C2   O6    108.23  3.000
 EQP  H2    C2   C3    107.91  3.000
 EQP  O6    C2   C3    109.31  3.000
 EQP  H2    C2   P1    107.71  3.000
 EQP  O6    C2   P1    109.75  3.000
 EQP  C3    C2   P1    113.76  3.000
 EQP  H31   C3   H32   107.25  3.000
 EQP  H31   C3   C4    110.18  3.000
 EQP  H32   C3   C4    109.74  3.000
 EQP  H31   C3   C2    109.18  3.000
 EQP  H32   C3   C2    109.35  3.000
 EQP  C4    C3   C2    111.06  3.000
 EQP  H4    C4   O4    110.21  3.000
 EQP  H4    C4   C5    107.19  3.000
 EQP  O4    C4   C5    111.79  3.000
 EQP  H4    C4   C3    108.10  3.000
 EQP  O4    C4   C3    109.45  3.000
 EQP  C5    C4   C3    110.02  3.000
 EQP  H5    C5   N5    107.73  3.000
 EQP  H5    C5   C6    109.26  3.000
 EQP  N5    C5   C6    111.44  3.000
 EQP  H5    C5   C4    108.98  3.000
 EQP  N5    C5   C4    110.14  3.000
 EQP  C6    C5   C4    109.25  3.000
 EQP  H6    C6   O6    110.14  3.000
 EQP  H6    C6   C7    107.22  3.000
 EQP  O6    C6   C7    108.99  3.000
 EQP  H6    C6   C5    107.48  3.000
 EQP  O6    C6   C5    109.75  3.000
 EQP  C7    C6   C5    113.20  3.000
 EQP  H7    C7   O7    110.78  3.000
 EQP  H7    C7   C8    107.57  3.000
 EQP  O7    C7   C8    110.83  3.000
 EQP  H7    C7   C6    106.95  3.000
 EQP  O7    C7   C6    108.91  3.000
 EQP  C8    C7   C6    111.74  3.000
 EQP  H8    C8   O8    110.95  3.000
 EQP  H8    C8   C9    106.15  3.000
 EQP  O8    C8   C9    111.99  3.000
 EQP  H8    C8   C7    108.76  3.000
 EQP  O8    C8   C7    106.44  3.000
 EQP  C9    C8   C7    112.57  3.000
 EQP  H91   C9   H92   106.14  3.000
 EQP  H91   C9   O9    111.85  3.000
 EQP  H92   C9   O9    111.64  3.000
 EQP  H91   C9   C8    108.73  3.000
 EQP  H92   C9   C8    108.19  3.000
 EQP  O9    C9   C8    110.13  3.000
 EQP  H112  C11  H113  108.24  3.000
 EQP  H112  C11  H111  107.20  3.000
 EQP  H113  C11  H111  108.55  3.000
 EQP  H112  C11  C10   109.16  3.000
 EQP  H113  C11  C10   113.95  3.000
 EQP  H111  C11  C10   109.52  3.000
 EQP  HN5   N5   C10   117.86  3.000
 EQP  HN5   N5   C5    116.85  3.000
 EQP  C10   N5   C5    125.25  3.000
 EQP  HO4   O4   C4    108.03  3.000
 EQP  C6    O6   C2    113.67  3.000
 EQP  HO7   O7   C7    108.16  3.000
 EQP  HO8   O8   C8    108.35  3.000
 EQP  HO9   O9   C9    108.33  3.000
 EQP  O10   C10  N5    123.60  3.000
 EQP  O10   C10  C11   121.36  3.000
 EQP  N5    C10  C11   115.04  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
 EQP  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 EQP  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 EQP  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 EQP  Var_01    H111  C11  C10  N5   -128.17  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
 EQP  chir_01  C2  P1  C3  O6  positiv
 EQP  chir_02  C4  O4  C5  C3  positiv
 EQP  chir_03  C5  N5  C6  C4  negativ
 EQP  chir_04  C6  O6  C5  C7  positiv
 EQP  chir_05  C7  O7  C6  C8  negativ
 EQP  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
 EQP  plan-1  C5   0.020
 EQP  plan-1  C11  0.020
 EQP  plan-1  N5   0.020
 EQP  plan-1  O10  0.020
 EQP  plan-1  HN5  0.020
 EQP  plan-1  C10  0.020

