# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 26 13:31:51 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-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol"  D-saccharide  41  21  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   1.385  43.1090  52.2020  45.6527
 EQP  C2    C  CH1   0  -0.269  42.8605  51.2307  47.1731
 EQP  C3    C  CH2   0  -0.494  41.5289  51.5691  47.8314
 EQP  C4    C  CH1   0   0.074  41.3999  50.7657  49.1131
 EQP  C5    C  CH1   0  -0.130  42.6286  51.0014  50.0000
 EQP  C6    C  CH1   0   0.048  43.9090  50.6927  49.2076
 EQP  C7    C  CH1   0   0.011  45.1819  50.9567  50.0015
 EQP  C8    C  CH1   0   0.004  46.4476  50.6026  49.2043
 EQP  C9    C  CH2   0  -0.199  47.7198  51.0098  49.9323
 EQP  C11   C  CH3   0  -0.780  42.4013  49.6161  53.5278
 EQP  N5    N  NH1   0  -0.647  42.5449  50.1861  51.1878
 EQP  O1P   O  O     0  -0.700  42.0115  52.0695  44.6652
 EQP  O2P   O  OH1   0  -0.747  43.3752  53.7073  46.1555
 EQP  O3P   O  OH1   0  -0.737  44.5581  51.6881  45.2064
 EQP  O4    O  OH1   0  -0.658  40.2076  51.1398  49.7541
 EQP  O6    O  O2    0  -0.498  43.9400  51.4831  48.0347
 EQP  O7    O  OH1   0  -0.673  45.1982  52.3094  50.3941
 EQP  O8    O  OH1   0  -0.673  46.3923  49.2113  48.9676
 EQP  O9    O  OH1   0  -0.670  47.7107  50.4959  51.2443
 EQP  O10   O  O     0  -0.487  42.4497  51.8590  52.7128
 EQP  H2    H  HCH1  0   0.265  42.8443  50.1710  46.8681
 EQP  H32   H  HCH2  0   0.250  41.4800  52.6382  48.0604
 EQP  H31   H  HCH2  0   0.265  40.7067  51.3329  47.1535
 EQP  H4    H  HCH1  0   0.205  41.3804  49.6958  48.8473
 EQP  H5    H  HCH1  0   0.266  42.6422  52.0465  50.3123
 EQP  H6    H  HCH1  0   0.233  43.8967  49.6264  48.9335
 EQP  H7    H  HCH1  0   0.232  45.1453  50.2931  50.8736
 EQP  H8    H  HCH1  0   0.216  46.4440  51.1643  48.2606
 EQP  H92   H  HCH2  0   0.212  48.5784  50.6366  49.3555
 EQP  H91   H  HCH2  0   0.202  47.7967  52.1036  49.9210
 EQP  H111  H  HCH3  0   0.264  41.5359  49.8018  54.1632
 EQP  H113  H  HCH3  0   0.248  42.3412  48.5973  53.1501
 EQP  H112  H  HCH3  0   0.266  43.2872  49.6965  54.1584
 EQP  HN5   H  HNH1  0   0.401  42.5596  49.1848  51.0610
 EQP  HOP2  H  HOH1  0   0.492  42.7035  54.3382  45.8653
 EQP  HOP3  H  HOH1  0   0.494  44.8809  52.0635  44.3750
 EQP  HO4   H  HOH1  0   0.450  40.0799  50.5630  50.5144
 EQP  HO7   H  HOH1  0   0.455  45.6779  52.3780  51.2244
 EQP  HO8   H  HOH1  0   0.452  47.0742  48.9835  48.3283
 EQP  HO9   H  HOH1  0   0.456  48.4967  50.8115  51.6986
 EQP  C10   C  C     0   0.516  42.4659  50.6668  52.4476

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  1.821  0.020  1.821
 EQP  P1   O1P   double  1.482  0.020  1.482
 EQP  P1   O2P   single  1.609  0.020  1.609
 EQP  P1   O3P   single  1.601  0.020  1.601
 EQP  C2   C3    single  1.523  0.020  1.523
 EQP  C2   O6    single  1.404  0.020  1.404
 EQP  C2   H2    single  0.970  0.020  1.090
 EQP  C3   C4    single  1.518  0.020  1.518
 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  1.404  0.020  1.404
 EQP  C4   H4    single  0.970  0.020  1.090
 EQP  C5   C6    single  1.537  0.020  1.537
 EQP  C5   N5    single  1.443  0.020  1.443
 EQP  C5   H5    single  0.970  0.020  1.090
 EQP  C6   C7    single  1.523  0.020  1.523
 EQP  C6   O6    single  1.415  0.020  1.415
 EQP  C6   H6    single  0.970  0.020  1.090
 EQP  C7   C8    single  1.537  0.020  1.537
 EQP  C7   O7    single  1.409  0.020  1.409
 EQP  C7   H7    single  0.970  0.020  1.090
 EQP  C8   C9    single  1.521  0.020  1.521
 EQP  C8   O8    single  1.412  0.020  1.412
 EQP  C8   H8    single  0.970  0.020  1.090
 EQP  C9   O9    single  1.409  0.020  1.409
 EQP  C9   H92   single  0.970  0.020  1.090
 EQP  C9   H91   single  0.970  0.020  1.090
 EQP  C10  C11   single  1.508  0.020  1.508
 EQP  C10  N5    single  1.351  0.020  1.351
 EQP  C10  O10   double  1.221  0.020  1.221
 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  O2P  HOP2  single  0.850  0.020  0.980
 EQP  O3P  HOP3  single  0.850  0.020  0.980
 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   103.75  3.000
 EQP  O3P   P1   O1P   117.12  3.000
 EQP  O2P   P1   O1P   114.47  3.000
 EQP  O3P   P1   C2    100.66  3.000
 EQP  O2P   P1   C2    105.10  3.000
 EQP  O1P   P1   C2    114.05  3.000
 EQP  H2    C2   O6    110.71  3.000
 EQP  H2    C2   C3    108.67  3.000
 EQP  O6    C2   C3    111.53  3.000
 EQP  H2    C2   P1    106.48  3.000
 EQP  O6    C2   P1    108.15  3.000
 EQP  C3    C2   P1    111.20  3.000
 EQP  H31   C3   H32   107.92  3.000
 EQP  H31   C3   C4    110.23  3.000
 EQP  H32   C3   C4    109.66  3.000
 EQP  H31   C3   C2    110.00  3.000
 EQP  H32   C3   C2    110.27  3.000
 EQP  C4    C3   C2    108.76  3.000
 EQP  H4    C4   O4    110.70  3.000
 EQP  H4    C4   C5    107.62  3.000
 EQP  O4    C4   C5    112.04  3.000
 EQP  H4    C4   C3    108.14  3.000
 EQP  O4    C4   C3    108.45  3.000
 EQP  C5    C4   C3    109.81  3.000
 EQP  H5    C5   N5    107.84  3.000
 EQP  H5    C5   C6    109.24  3.000
 EQP  N5    C5   C6    111.04  3.000
 EQP  H5    C5   C4    108.83  3.000
 EQP  N5    C5   C4    110.04  3.000
 EQP  C6    C5   C4    109.78  3.000
 EQP  H6    C6   O6    109.56  3.000
 EQP  H6    C6   C7    107.88  3.000
 EQP  O6    C6   C7    108.47  3.000
 EQP  H6    C6   C5    108.28  3.000
 EQP  O6    C6   C5    109.48  3.000
 EQP  C7    C6   C5    113.12  3.000
 EQP  H7    C7   O7    111.09  3.000
 EQP  H7    C7   C8    107.49  3.000
 EQP  O7    C7   C8    110.87  3.000
 EQP  H7    C7   C6    106.36  3.000
 EQP  O7    C7   C6    108.75  3.000
 EQP  C8    C7   C6    112.20  3.000
 EQP  H8    C8   O8    111.08  3.000
 EQP  H8    C8   C9    106.09  3.000
 EQP  O8    C8   C9    112.13  3.000
 EQP  H8    C8   C7    108.97  3.000
 EQP  O8    C8   C7    106.35  3.000
 EQP  C9    C8   C7    112.26  3.000
 EQP  H91   C9   H92   106.16  3.000
 EQP  H91   C9   O9    111.95  3.000
 EQP  H92   C9   O9    111.69  3.000
 EQP  H91   C9   C8    108.71  3.000
 EQP  H92   C9   C8    108.13  3.000
 EQP  O9    C9   C8    110.03  3.000
 EQP  H112  C11  H113  108.34  3.000
 EQP  H112  C11  H111  107.19  3.000
 EQP  H113  C11  H111  108.55  3.000
 EQP  H112  C11  C10   109.15  3.000
 EQP  H113  C11  C10   113.95  3.000
 EQP  H111  C11  C10   109.45  3.000
 EQP  HN5   N5   C10   118.10  3.000
 EQP  HN5   N5   C5    117.15  3.000
 EQP  C10   N5   C5    124.75  3.000
 EQP  HOP2  O2P  P1    113.70  3.000
 EQP  HOP3  O3P  P1    114.64  3.000
 EQP  HO4   O4   C4    108.27  3.000
 EQP  C6    O6   C2    113.05  3.000
 EQP  HO7   O7   C7    108.37  3.000
 EQP  HO8   O8   C8    108.47  3.000
 EQP  HO9   O9   C9    108.37  3.000
 EQP  O10   C10  N5    123.42  3.000
 EQP  O10   C10  C11   121.59  3.000
 EQP  N5    C10  C11   114.99  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  CONST_04  HN5   N5   C10  O10   180.00   0.0  0
 EQP  Var_01    H111  C11  C10  N5   -126.67  30.0  3
 EQP  Var_02    H113  C11  C10  N5     -4.93  30.0  3
 EQP  Var_03    H112  C11  C10  N5    116.31  30.0  3
 EQP  Var_04    H111  C11  C10  O10    53.48  30.0  3
 EQP  Var_05    H113  C11  C10  O10   175.22  30.0  3
 EQP  Var_06    H112  C11  C10  O10   -63.54  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

