# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:23:13 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (1S)-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
 AXP  AXP  (1S)-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_AXP
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
 AXP  P1    P  P      0   1.155  -0.1070   0.1347  -3.2762
 AXP  C2    C  CH1    0  -0.244  -0.3349  -0.3127  -1.4736
 AXP  C3    C  CH2    0  -0.471   0.6602  -1.4071  -1.0899
 AXP  C4    C  CH1    0   0.014   0.9331  -1.5441   0.4009
 AXP  C5    C  CH1    0  -0.129   1.1220  -0.1463   0.9987
 AXP  C6    C  CH1    0  -0.021  -0.0637   0.7700   0.6650
 AXP  C7    C  CH1    0  -0.055  -1.4624   0.4572   1.2414
 AXP  C8    C  CH1    0  -0.022  -1.5520   0.3366   2.7756
 AXP  C9    C  CH2    0  -0.167  -2.9886   0.0247   3.1839
 AXP  C11   C  CH3    0  -0.760   4.6359   0.9301   0.0605
 AXP  N5    N  NH1    0  -0.662   2.3002   0.4543   0.4007
 AXP  O1P   O  O      0  -0.825  -0.3344  -1.1931  -4.0106
 AXP  O2P   O  OP    -1  -0.975   1.3405   0.6453  -3.3399
 AXP  O3P   O  OP    -1  -0.993  -1.1606   1.2016  -3.5849
 AXP  O4    O  OH1    0  -0.675  -0.1161  -2.1807   1.1139
 AXP  O6    O  O2     0  -0.504  -0.1291   0.8946  -0.7360
 AXP  O7    O  OH1    0  -0.664  -2.3569   1.4565   0.7935
 AXP  O8    O  OH1    0  -0.619  -0.6760  -0.6200   3.3223
 AXP  O9    O  OH1    0  -0.672  -3.0637   0.0027   4.5920
 AXP  O10   O  O      0  -0.464   3.7732  -0.1884   1.9905
 AXP  H2    H  HCH1   0   0.167  -1.3593  -0.6741  -1.2989
 AXP  H31   H  HCH2   0   0.233   1.6149  -1.1923  -1.5761
 AXP  H32   H  HCH2   0   0.237   0.3234  -2.3590  -1.5078
 AXP  H4    H  HCH1   0   0.218   1.8616  -2.1126   0.5437
 AXP  H5    H  HCH1   0   0.283   1.2835  -0.2006   2.0726
 AXP  H6    H  HCH1   0   0.278   0.2048   1.7693   1.0388
 AXP  H7    H  HCH1   0   0.320  -1.8430  -0.4688   0.8046
 AXP  H8    H  HCH1   0   0.189  -1.2801   1.3008   3.2193
 AXP  H91   H  HCH2   0   0.148  -3.6628   0.7762   2.7616
 AXP  H92   H  HCH2   0   0.201  -3.2732  -0.9453   2.7485
 AXP  H111  H  HCH3   0   0.258   5.2949   1.5424   0.6739
 AXP  H112  H  HCH3   0   0.197   5.2360   0.1175  -0.3516
 AXP  H113  H  HCH3   0   0.313   4.2692   1.5323  -0.7687
 AXP  HN5   H  HNH1   0   0.383   2.1875   0.8351  -0.5293
 AXP  HO4   H  HOH1   0   0.457  -0.3955  -2.9692   0.6375
 AXP  HO7   H  HOH1   0   0.442  -2.0515   2.3110   1.1181
 AXP  HO8   H  HOH1   0   0.453  -0.6123  -1.3664   2.7058
 AXP  HO9   H  HOH1   0   0.452  -3.9846  -0.1259   4.8333
 AXP  C10   C  C      0   0.526   3.5365   0.3474   0.9146

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
 AXP  P1   C2    single  1.871  0.020  1.871
 AXP  P1   O1P   deloc   1.534  0.020  1.534
 AXP  P1   O2P   deloc   1.536  0.020  1.536
 AXP  P1   O3P   deloc   1.531  0.020  1.531
 AXP  C2   C3    single  1.528  0.020  1.528
 AXP  C2   O6    single  1.430  0.020  1.430
 AXP  C2   H2    single  0.970  0.020  1.090
 AXP  C3   C4    single  1.522  0.020  1.522
 AXP  C3   H31   single  0.970  0.020  1.090
 AXP  C3   H32   single  0.970  0.020  1.090
 AXP  C4   C5    single  1.532  0.020  1.532
 AXP  C4   O4    single  1.419  0.020  1.419
 AXP  C4   H4    single  0.970  0.020  1.090
 AXP  C5   C6    single  1.535  0.020  1.535
 AXP  C5   N5    single  1.451  0.020  1.451
 AXP  C5   H5    single  0.970  0.020  1.090
 AXP  C6   C7    single  1.545  0.020  1.545
 AXP  C6   O6    single  1.408  0.020  1.408
 AXP  C6   H6    single  0.970  0.020  1.090
 AXP  C7   C8    single  1.542  0.020  1.542
 AXP  C7   O7    single  1.414  0.020  1.414
 AXP  C7   H7    single  0.970  0.020  1.090
 AXP  C8   C9    single  1.526  0.020  1.526
 AXP  C8   O8    single  1.408  0.020  1.408
 AXP  C8   H8    single  0.970  0.020  1.090
 AXP  C9   O9    single  1.410  0.020  1.410
 AXP  C9   H91   single  0.970  0.020  1.090
 AXP  C9   H92   single  0.970  0.020  1.090
 AXP  C10  C11   single  1.509  0.020  1.509
 AXP  C10  N5    single  1.343  0.020  1.343
 AXP  C10  O10   double  1.225  0.020  1.225
 AXP  C11  H111  single  0.970  0.020  1.090
 AXP  C11  H112  single  0.970  0.020  1.090
 AXP  C11  H113  single  0.970  0.020  1.090
 AXP  N5   HN5   single  0.860  0.020  1.020
 AXP  O4   HO4   single  0.850  0.020  0.980
 AXP  O7   HO7   single  0.850  0.020  0.980
 AXP  O8   HO8   single  0.850  0.020  0.980
 AXP  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
 AXP  O3P   P1   O2P   114.11  3.000
 AXP  O3P   P1   O1P   113.86  3.000
 AXP  O2P   P1   O1P   114.05  3.000
 AXP  O3P   P1   C2    106.08  3.000
 AXP  O2P   P1   C2    103.54  3.000
 AXP  O1P   P1   C2    103.66  3.000
 AXP  H2    C2   O6    109.24  3.000
 AXP  H2    C2   C3    109.34  3.000
 AXP  O6    C2   C3    112.43  3.000
 AXP  H2    C2   P1    110.18  3.000
 AXP  O6    C2   P1    106.11  3.000
 AXP  C3    C2   P1    109.50  3.000
 AXP  H32   C3   H31   105.68  3.000
 AXP  H32   C3   C4    110.58  3.000
 AXP  H31   C3   C4    107.28  3.000
 AXP  H32   C3   C2    109.09  3.000
 AXP  H31   C3   C2    108.45  3.000
 AXP  C4    C3   C2    115.29  3.000
 AXP  H4    C4   O4    109.12  3.000
 AXP  H4    C4   C5    108.50  3.000
 AXP  O4    C4   C5    107.72  3.000
 AXP  H4    C4   C3    109.00  3.000
 AXP  O4    C4   C3    113.58  3.000
 AXP  C5    C4   C3    108.80  3.000
 AXP  H5    C5   N5    107.88  3.000
 AXP  H5    C5   C6    111.05  3.000
 AXP  N5    C5   C6    106.88  3.000
 AXP  H5    C5   C4    110.99  3.000
 AXP  N5    C5   C4    108.48  3.000
 AXP  C6    C5   C4    111.38  3.000
 AXP  H6    C6   O6    105.61  3.000
 AXP  H6    C6   C7    106.15  3.000
 AXP  O6    C6   C7    110.31  3.000
 AXP  H6    C6   C5    106.25  3.000
 AXP  O6    C6   C5    107.76  3.000
 AXP  C7    C6   C5    119.82  3.000
 AXP  H7    C7   O7    104.60  3.000
 AXP  H7    C7   C8    108.15  3.000
 AXP  O7    C7   C8    109.50  3.000
 AXP  H7    C7   C6    109.75  3.000
 AXP  O7    C7   C6    108.15  3.000
 AXP  C8    C7   C6    116.09  3.000
 AXP  H8    C8   O8    106.64  3.000
 AXP  H8    C8   C9    107.77  3.000
 AXP  O8    C8   C9    110.07  3.000
 AXP  H8    C8   C7    108.65  3.000
 AXP  O8    C8   C7    113.80  3.000
 AXP  C9    C8   C7    109.70  3.000
 AXP  H92   C9   H91   107.05  3.000
 AXP  H92   C9   O9    111.56  3.000
 AXP  H91   C9   O9    111.30  3.000
 AXP  H92   C9   C8    108.53  3.000
 AXP  H91   C9   C8    109.66  3.000
 AXP  O9    C9   C8    108.69  3.000
 AXP  H113  C11  H112  108.04  3.000
 AXP  H113  C11  H111  108.78  3.000
 AXP  H112  C11  H111  107.38  3.000
 AXP  H113  C11  C10   113.54  3.000
 AXP  H112  C11  C10   109.08  3.000
 AXP  H111  C11  C10   109.82  3.000
 AXP  HN5   N5   C10   118.98  3.000
 AXP  HN5   N5   C5    116.37  3.000
 AXP  C10   N5   C5    123.82  3.000
 AXP  HO4   O4   C4    109.47  3.000
 AXP  C6    O6   C2    116.44  3.000
 AXP  HO7   O7   C7    108.63  3.000
 AXP  HO8   O8   C8    108.48  3.000
 AXP  HO9   O9   C9    107.69  3.000
 AXP  O10   C10  N5    123.28  3.000
 AXP  O10   C10  C11   121.68  3.000
 AXP  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
 AXP  CONST_01  C11   C10  N5   C5   180.00   0.0  0
 AXP  CONST_02  O10   C10  N5   C5     0.00   0.0  0
 AXP  CONST_03  HN5   N5   C10  C11    0.00   0.0  0
 AXP  Var_01    H111  C11  C10  N5   133.29  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
 AXP  chir_01  C2  P1  C3  O6  negativ
 AXP  chir_02  C4  O4  C5  C3  positiv
 AXP  chir_03  C5  N5  C6  C4  negativ
 AXP  chir_04  C6  O6  C5  C7  positiv
 AXP  chir_05  C7  O7  C6  C8  negativ
 AXP  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
 AXP  plan-1  C5   0.020
 AXP  plan-1  C11  0.020
 AXP  plan-1  N5   0.020
 AXP  plan-1  O10  0.020
 AXP  plan-1  HN5  0.020
 AXP  plan-1  C10  0.020

