# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 12:08:08 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,3S,4S,5S)-4-hydroxy-2,5-bis(hydroxymethyl)-5-{[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydrofuran-3-yl (2R,3R,4S,5S)-2,4,5-trihydroxytetrahydro-2H-pyran-3-yl hydrogen (R)-phosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O[P](O)(=O)O[C@H]3[C@H](O)OC[C@H](O)[C@@H]3O)[C@@H]2O)[C@H](O)[C@H](O)[C@H]1O
#
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
 AGR  AGR  '(2R,3S,4S,5S)-4-hydroxy-2,5-bis(hydroxymethyl)-5-{[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydrofuran-3-yl (2R,3R,4S,5S)-2,4,5-trihydroxytetrahydro-2H-pyran-3-yl hydrogen (R)-phosphate (non-preferred name)'  saccharide  66  36  .  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 (reasonable std)
;

data_comp_AGR
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
 AGR  O2   O  OH1    0  -0.698   3.9493  -2.9295  -0.5639
 AGR  C2   C  CH1    0   0.043   4.3204  -1.6562  -0.1074
 AGR  C3   C  CH1    0  -0.063   4.3427  -1.6321   1.4244
 AGR  O3   O  OH1    0  -0.688   3.1371  -2.0486   2.0192
 AGR  C4   C  CH1    0   0.007   4.7336  -0.2217   1.9018
 AGR  O4   O  OH1    0  -0.672   6.0642   0.0894   1.5564
 AGR  C5   C  CH1    0  -0.018   3.8150   0.8127   1.2699
 AGR  C6   C  CH2    0  -0.159   4.2058   2.2327   1.6182
 AGR  O6   O  OH1    0  -0.659   3.1531   3.0935   1.2495
 AGR  O5   O  O2     0  -0.491   3.8068   0.6967  -0.1470
 AGR  C1   C  CH1    0   0.195   3.4089  -0.5435  -0.6415
 AGR  O1   O  O2     0  -0.546   2.1019  -0.8453  -0.2326
 AGR  CBH  C  CT     0   0.501   0.9885  -0.7682  -1.0957
 AGR  CAO  C  CH2    0  -0.164   0.7660  -2.1103  -1.7730
 AGR  OAD  O  OH1    0  -0.671   1.9167  -2.4623  -2.5132
 AGR  CBD  C  CH1    0  -0.051  -0.2031  -0.3545  -0.2237
 AGR  OAK  O  OH1    0  -0.705  -0.1816  -1.0059   1.0043
 AGR  OAR  O  O2     0  -0.510   1.1333   0.2402  -2.0431
 AGR  CBC  C  CH1    0   0.008   0.4279   1.4190  -1.6471
 AGR  CAN  C  CH2    0  -0.173   1.2879   2.6468  -1.7998
 AGR  OAC  O  OH1    0  -0.675   1.5550   2.8495  -3.1696
 AGR  CBG  C  CH1    0  -0.032  -0.0273   1.1668  -0.2119
 AGR  OAU  O  O2     0  -0.624  -1.1819   1.9394   0.0218
 AGR  O15  O  O      0  -0.791  -1.4602   0.8330   2.3048
 AGR  P1   P  P      0   1.380  -2.0376   1.9109   1.4197
 AGR  OAL  O  OP    -1  -0.761  -2.1884   3.3079   1.9153
 AGR  OBA  O  O2     0  -0.618  -3.5141   1.4871   0.8676
 AGR  CBO  C  CH1    0  -0.011  -3.8236   0.1691   0.4694
 AGR  CBM  C  CH1    0   0.025  -4.3153   0.1708  -0.9754
 AGR  O14  O  OH1    0  -0.647  -3.2963   0.6503  -1.8074
 AGR  CBL  C  CH1    0  -0.030  -4.7921  -1.2286  -1.3621
 AGR  O10  O  OH1    0  -0.658  -3.6726  -2.0804  -1.3958
 AGR  CBN  C  CH2    0  -0.232  -5.8357  -1.6823  -0.3518
 AGR  OAX  O  O2     0  -0.489  -5.3226  -1.6529   0.9609
 AGR  C8   C  CH1    0   0.278  -4.9458  -0.3577   1.3676
 AGR  OAH  O  OH1    0  -0.648  -4.4941  -0.4219   2.6647
 AGR  H1   H  HOH1   0   0.452   3.3211  -2.8430  -1.2995
 AGR  H2   H  HCH1   0   0.213   5.3343  -1.4097  -0.4496
 AGR  H3   H  HCH1   0   0.241   5.1137  -2.3325   1.7711
 AGR  H4   H  HOH1   0   0.448   2.3948  -1.7191   1.4946
 AGR  H5   H  HCH1   0   0.229   4.5862  -0.1780   2.9907
 AGR  H6   H  HOH1   0   0.454   6.6451  -0.5426   1.9914
 AGR  H7   H  HCH1   0   0.230   2.8070   0.6429   1.6715
 AGR  H8   H  HCH2   0   0.199   4.3974   2.2751   2.6990
 AGR  H9   H  HCH2   0   0.207   5.1416   2.4971   1.1141
 AGR  H10  H  HOH1   0   0.455   3.4597   3.9995   1.3447
 AGR  H11  H  HCH1   0   0.258   3.4918  -0.4669  -1.7287
 AGR  H12  H  HCH2   0   0.221   0.5445  -2.8545  -0.9994
 AGR  H13  H  HCH2   0   0.225  -0.1145  -2.0333  -2.4200
 AGR  H14  H  HOH1   0   0.476   1.7497  -3.3015  -2.9545
 AGR  H15  H  HCH1   0   0.233  -1.1265  -0.5746  -0.7857
 AGR  H16  H  HOH1   0   0.455  -0.6746  -0.4193   1.6312
 AGR  H17  H  HCH1   0   0.237  -0.4647   1.5129  -2.2789
 AGR  H18  H  HCH2   0   0.196   0.7350   3.4916  -1.3666
 AGR  H19  H  HCH2   0   0.223   2.2035   2.5239  -1.2117
 AGR  H20  H  HOH1   0   0.455   2.1258   3.6187  -3.2496
 AGR  H21  H  HCH1   0   0.246   0.7667   1.4397   0.4969
 AGR  H23  H  HCH1   0   0.245  -2.9648  -0.5038   0.5678
 AGR  H24  H  HCH1   0   0.213  -5.1987   0.8284  -1.0222
 AGR  H25  H  HOH1   0   0.448  -3.6327   0.6766  -2.7090
 AGR  H26  H  HCH1   0   0.227  -5.2824  -1.1722  -2.3465
 AGR  H27  H  HOH1   0   0.452  -3.9591  -2.9442  -1.7085
 AGR  H28  H  HCH2   0   0.212  -6.7290  -1.0470  -0.4438
 AGR  H29  H  HCH2   0   0.253  -6.1491  -2.7089  -0.5530
 AGR  H30  H  HCH1   0   0.183  -5.8189   0.3149   1.2758
 AGR  H31  H  HOH1   0   0.462  -5.2502  -0.4752   3.2586

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
 AGR  CBN  OAX  single  1.410  0.020  1.410
 AGR  CBN  CBL  single  1.522  0.020  1.522
 AGR  OAX  C8   single  1.409  0.020  1.409
 AGR  C8   OAH  single  1.375  0.020  1.375
 AGR  C8   CBO  single  1.531  0.020  1.531
 AGR  CBL  O10  single  1.407  0.020  1.407
 AGR  CBL  CBM  single  1.528  0.020  1.528
 AGR  CBM  CBO  single  1.526  0.020  1.526
 AGR  CBM  O14  single  1.400  0.020  1.400
 AGR  CBO  OBA  single  1.411  0.020  1.411
 AGR  OBA  P1   single  1.632  0.020  1.632
 AGR  O15  P1   deloc   1.510  0.020  1.510
 AGR  P1   OAL  deloc   1.490  0.020  1.490
 AGR  P1   OAU  single  1.639  0.020  1.639
 AGR  CAN  OAC  single  1.410  0.020  1.410
 AGR  CAN  CBC  single  1.507  0.020  1.507
 AGR  OAU  CBG  single  1.409  0.020  1.409
 AGR  C6   O6   single  1.409  0.020  1.409
 AGR  C6   C5   single  1.513  0.020  1.513
 AGR  CBC  CBG  single  1.527  0.020  1.527
 AGR  CBC  OAR  single  1.430  0.020  1.430
 AGR  CBG  CBD  single  1.532  0.020  1.532
 AGR  C5   O5   single  1.422  0.020  1.422
 AGR  C5   C4   single  1.521  0.020  1.521
 AGR  OAR  CBH  single  1.391  0.020  1.391
 AGR  CBD  OAK  single  1.390  0.020  1.390
 AGR  CBD  CBH  single  1.533  0.020  1.533
 AGR  O5   C1   single  1.393  0.020  1.393
 AGR  O4   C4   single  1.409  0.020  1.409
 AGR  C4   C3   single  1.540  0.020  1.540
 AGR  CBH  O1   single  1.411  0.020  1.411
 AGR  CBH  CAO  single  1.520  0.020  1.520
 AGR  O1   C1   single  1.402  0.020  1.402
 AGR  C1   C2   single  1.534  0.020  1.534
 AGR  C3   C2   single  1.532  0.020  1.532
 AGR  C3   O3   single  1.407  0.020  1.407
 AGR  CAO  OAD  single  1.413  0.020  1.413
 AGR  C2   O2   single  1.403  0.020  1.403
 AGR  O2   H1   single  0.850  0.020  0.980
 AGR  C2   H2   single  0.970  0.020  1.090
 AGR  C3   H3   single  0.970  0.020  1.090
 AGR  O3   H4   single  0.850  0.020  0.980
 AGR  C4   H5   single  0.970  0.020  1.090
 AGR  O4   H6   single  0.850  0.020  0.980
 AGR  C5   H7   single  0.970  0.020  1.090
 AGR  C6   H8   single  0.970  0.020  1.090
 AGR  C6   H9   single  0.970  0.020  1.090
 AGR  O6   H10  single  0.850  0.020  0.980
 AGR  C1   H11  single  0.970  0.020  1.090
 AGR  CAO  H12  single  0.970  0.020  1.090
 AGR  CAO  H13  single  0.970  0.020  1.090
 AGR  OAD  H14  single  0.850  0.020  0.980
 AGR  CBD  H15  single  0.970  0.020  1.090
 AGR  OAK  H16  single  0.850  0.020  0.980
 AGR  CBC  H17  single  0.970  0.020  1.090
 AGR  CAN  H18  single  0.970  0.020  1.090
 AGR  CAN  H19  single  0.970  0.020  1.090
 AGR  OAC  H20  single  0.850  0.020  0.980
 AGR  CBG  H21  single  0.970  0.020  1.090
 AGR  CBO  H23  single  0.970  0.020  1.090
 AGR  CBM  H24  single  0.970  0.020  1.090
 AGR  O14  H25  single  0.850  0.020  0.980
 AGR  CBL  H26  single  0.970  0.020  1.090
 AGR  O10  H27  single  0.850  0.020  0.980
 AGR  CBN  H28  single  0.970  0.020  1.090
 AGR  CBN  H29  single  0.970  0.020  1.090
 AGR  C8   H30  single  0.970  0.020  1.090
 AGR  OAH  H31  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
 AGR  H1   O2   C2   109.67  3.000
 AGR  H2   C2   C1   106.10  3.000
 AGR  H2   C2   C3   107.13  3.000
 AGR  C1   C2   C3   110.20  3.000
 AGR  H2   C2   O2   110.28  3.000
 AGR  C3   C2   O2   110.09  3.000
 AGR  C1   C2   O2   112.83  3.000
 AGR  H3   C3   C4   107.95  3.000
 AGR  H3   C3   O3   106.22  3.000
 AGR  C4   C3   O3   110.95  3.000
 AGR  H3   C3   C2   108.42  3.000
 AGR  O3   C3   C2   113.91  3.000
 AGR  C4   C3   C2   109.16  3.000
 AGR  H4   O3   C3   109.12  3.000
 AGR  H5   C4   C5   107.66  3.000
 AGR  H5   C4   O4   111.13  3.000
 AGR  C5   C4   O4   108.56  3.000
 AGR  H5   C4   C3   108.02  3.000
 AGR  O4   C4   C3   111.46  3.000
 AGR  C5   C4   C3   109.93  3.000
 AGR  H6   O4   C4   108.31  3.000
 AGR  H7   C5   O5   110.28  3.000
 AGR  H7   C5   C6   107.34  3.000
 AGR  O5   C5   C6   107.91  3.000
 AGR  H7   C5   C4   107.29  3.000
 AGR  O5   C5   C4   111.22  3.000
 AGR  C6   C5   C4   112.74  3.000
 AGR  H9   C6   H8   107.13  3.000
 AGR  H9   C6   O6   111.74  3.000
 AGR  H8   C6   O6   111.36  3.000
 AGR  H9   C6   C5   109.95  3.000
 AGR  H8   C6   C5   107.92  3.000
 AGR  O6   C6   C5   108.67  3.000
 AGR  H10  O6   C6   108.16  3.000
 AGR  C1   O5   C5   115.35  3.000
 AGR  H11  C1   O1   112.07  3.000
 AGR  H11  C1   O5   105.61  3.000
 AGR  O1   C1   O5   110.75  3.000
 AGR  H11  C1   C2   110.61  3.000
 AGR  O1   C1   C2   107.22  3.000
 AGR  O5   C1   C2   110.63  3.000
 AGR  CBH  O1   C1   123.05  3.000
 AGR  OAR  CBH  CBD  105.82  3.000
 AGR  CBD  CBH  CAO  112.21  3.000
 AGR  OAR  CBH  CAO  110.60  3.000
 AGR  CAO  CBH  O1   109.87  3.000
 AGR  CBD  CBH  O1   106.27  3.000
 AGR  OAR  CBH  O1   111.97  3.000
 AGR  H13  CAO  H12  107.59  3.000
 AGR  H13  CAO  OAD  111.27  3.000
 AGR  H12  CAO  OAD  111.42  3.000
 AGR  H13  CAO  CBH  108.59  3.000
 AGR  H12  CAO  CBH  108.34  3.000
 AGR  OAD  CAO  CBH  109.53  3.000
 AGR  H14  OAD  CAO  108.43  3.000
 AGR  H15  CBD  CBG  107.35  3.000
 AGR  H15  CBD  OAK  111.68  3.000
 AGR  CBG  CBD  OAK  117.18  3.000
 AGR  H15  CBD  CBH  107.88  3.000
 AGR  OAK  CBD  CBH  111.34  3.000
 AGR  CBG  CBD  CBH  100.56  3.000
 AGR  H16  OAK  CBD  105.90  3.000
 AGR  CBC  OAR  CBH  110.95  3.000
 AGR  H17  CBC  CBG  108.23  3.000
 AGR  H17  CBC  CAN  109.64  3.000
 AGR  CBG  CBC  CAN  113.58  3.000
 AGR  H17  CBC  OAR  108.20  3.000
 AGR  CBG  CBC  OAR  105.74  3.000
 AGR  CAN  CBC  OAR  111.23  3.000
 AGR  H19  CAN  H18  107.18  3.000
 AGR  H19  CAN  OAC  112.30  3.000
 AGR  H18  CAN  OAC  111.58  3.000
 AGR  H19  CAN  CBC  109.35  3.000
 AGR  H18  CAN  CBC  107.42  3.000
 AGR  OAC  CAN  CBC  108.88  3.000
 AGR  H20  OAC  CAN  107.96  3.000
 AGR  H21  CBG  OAU  110.43  3.000
 AGR  H21  CBG  CBC  110.49  3.000
 AGR  OAU  CBG  CBC  108.05  3.000
 AGR  H21  CBG  CBD  109.55  3.000
 AGR  CBC  CBG  CBD  101.01  3.000
 AGR  OAU  CBG  CBD  116.87  3.000
 AGR  P1   OAU  CBG  124.04  3.000
 AGR  OBA  P1   OAL  105.33  3.000
 AGR  OAL  P1   O15  120.88  3.000
 AGR  OBA  P1   O15  111.03  3.000
 AGR  OAL  P1   OAU  108.67  3.000
 AGR  O15  P1   OAU  108.23  3.000
 AGR  OBA  P1   OAU  100.85  3.000
 AGR  CBO  OBA  P1   122.43  3.000
 AGR  H23  CBO  C8   108.10  3.000
 AGR  H23  CBO  CBM  109.77  3.000
 AGR  C8   CBO  CBM  108.64  3.000
 AGR  H23  CBO  OBA  112.11  3.000
 AGR  CBM  CBO  OBA  109.68  3.000
 AGR  C8   CBO  OBA  108.46  3.000
 AGR  H24  CBM  CBL  106.59  3.000
 AGR  H24  CBM  O14  110.72  3.000
 AGR  CBL  CBM  O14  112.98  3.000
 AGR  H24  CBM  CBO  107.40  3.000
 AGR  O14  CBM  CBO  109.17  3.000
 AGR  CBL  CBM  CBO  109.82  3.000
 AGR  H25  O14  CBM  108.15  3.000
 AGR  H26  CBL  CBN  107.66  3.000
 AGR  H26  CBL  O10  111.33  3.000
 AGR  CBN  CBL  O10  112.39  3.000
 AGR  H26  CBL  CBM  108.56  3.000
 AGR  O10  CBL  CBM  108.19  3.000
 AGR  CBN  CBL  CBM  108.60  3.000
 AGR  H27  O10  CBL  108.32  3.000
 AGR  H29  CBN  H28  107.12  3.000
 AGR  H29  CBN  OAX  107.20  3.000
 AGR  H28  CBN  OAX  111.18  3.000
 AGR  H29  CBN  CBL  110.78  3.000
 AGR  H28  CBN  CBL  109.22  3.000
 AGR  OAX  CBN  CBL  111.25  3.000
 AGR  C8   OAX  CBN  112.67  3.000
 AGR  H30  C8   OAH  111.47  3.000
 AGR  H30  C8   OAX  108.90  3.000
 AGR  OAH  C8   OAX  108.49  3.000
 AGR  H30  C8   CBO  108.71  3.000
 AGR  OAH  C8   CBO  109.19  3.000
 AGR  OAX  C8   CBO  110.06  3.000
 AGR  H31  OAH  C8   109.06  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
 AGR  Var_01  H28  CBN  OAX  C8    -60.10  30.0  1
 AGR  Var_02  OBA  P1   OAU  CBG  -122.51  30.0  1

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
 AGR  chir_01  C2   C1   C3   O2   negativ
 AGR  chir_02  C3   O3   C2   C4   negativ
 AGR  chir_03  C4   O4   C5   C3   negativ
 AGR  chir_04  C5   O5   C4   C6   negativ
 AGR  chir_05  C1   O5   O1   C2   positiv
 AGR  chir_06  CBH  OAR  CBD  CAO  negativ
 AGR  chir_07  CBD  OAK  CBH  CBG  positiv
 AGR  chir_08  CBC  OAR  CBG  CAN  negativ
 AGR  chir_09  CBG  OAU  CBC  CBD  positiv
 AGR  chir_11  CBO  C8   CBM  OBA  negativ
 AGR  chir_12  CBM  O14  CBO  CBL  positiv
 AGR  chir_13  CBL  O10  CBM  CBN  positiv
 AGR  chir_14  C8   OAX  OAH  CBO  negativ

