# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 20:14:40 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (1S,2R,3R,4S,5R,6S)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[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
 4MY  4MY  '(1S,2R,3R,4S,5R,6S)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]'  ligand  36  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4MY
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
 4MY  C1    C  CH1    0   0.024   0.6506   2.2966  -0.5107
 4MY  C2    C  CH1    0  -0.028  -0.7758   2.3407   0.0225
 4MY  C3    C  CH1    0   0.031  -1.5010   1.0308  -0.2580
 4MY  C4    C  CH1    0   0.106  -0.7185  -0.1616   0.3174
 4MY  C5    C  CH1    0   0.030   0.6876  -0.1811  -0.3257
 4MY  C6    C  CH1    0   0.110   1.4412   1.1139   0.0445
 4MY  O11   O  OH1    0  -0.601   1.3148   3.5108  -0.2054
 4MY  O12   O  OH1    0  -0.654  -0.7843   2.6030   1.4151
 4MY  O13   O  O2     0  -0.658  -2.8126   1.0552   0.2162
 4MY  O14   O  O2     0  -0.600  -1.4054  -1.3387   0.0516
 4MY  O15   O  O2     0  -0.638   1.4082  -1.2904   0.0863
 4MY  O16   O  O2     0  -0.593   2.7306   1.1415  -0.4776
 4MY  O23   O  O      0  -0.893  -3.7534   3.2990  -0.6548
 4MY  O24   O  OP    -1  -1.019  -2.8613  -3.2862   0.5096
 4MY  O25   O  OP    -1  -1.022   2.7583  -3.3713  -0.1361
 4MY  O26   O  OP    -1  -0.970   4.4103  -0.0582   1.0914
 4MY  O33   O  OP    -1  -0.890  -3.9066   1.2023  -2.1065
 4MY  O34   O  OP    -1  -0.946  -0.7188  -3.0307   1.8996
 4MY  O35   O  O      0  -0.797   0.7213  -3.0765  -1.6652
 4MY  O36   O  OP    -1  -1.090   5.1139   1.8265  -0.4947
 4MY  O43   O  OP    -1  -1.004  -5.2752   1.3732   0.0653
 4MY  O44   O  O      0  -0.893  -2.6640  -1.4549   2.3006
 4MY  O45   O  OP    -1  -1.024   2.7875  -1.6744  -2.0652
 4MY  O46   O  O      0  -0.741   3.7013   2.3330   1.5935
 4MY  H1    H  HCH1   0   0.105   0.5902   2.1688  -1.6045
 4MY  H2    H  HCH1   0   0.176  -1.3183   3.1388  -0.5043
 4MY  H3    H  HCH1   0   0.228  -1.4990   0.9099  -1.3551
 4MY  H4    H  HCH1   0   0.181  -0.5955  -0.0093   1.3999
 4MY  H5    H  HCH1   0   0.157   0.5506  -0.1838  -1.4217
 4MY  H6    H  HCH1   0   0.200   1.4585   1.1940   1.1410
 4MY  HO11  H  HOH1   0   0.427   0.8586   4.2076  -0.6889
 4MY  HO12  H  HOH1   0   0.454  -0.1040   3.2684   1.5685
 4MY  P3    P  P      0   1.204  -4.0241   1.7916  -0.7006
 4MY  P4    P  P      0   1.224  -1.9393  -2.3457   1.2907
 4MY  P5    P  P      0   1.238   1.9514  -2.4286  -1.0285
 4MY  P6    P  P      0   1.166   4.0849   1.3165   0.5180

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
 4MY  O11  C1    single  1.417  0.020  1.417
 4MY  C2   C1    single  1.523  0.020  1.523
 4MY  C1   C6    single  1.527  0.020  1.527
 4MY  C1   H1    single  0.970  0.020  1.090
 4MY  O12  C2    single  1.417  0.020  1.417
 4MY  C2   C3    single  1.523  0.020  1.523
 4MY  C2   H2    single  0.970  0.020  1.090
 4MY  O13  C3    single  1.395  0.020  1.395
 4MY  C3   C4    single  1.538  0.020  1.538
 4MY  C3   H3    single  0.970  0.020  1.090
 4MY  O23  P3    deloc   1.532  0.020  1.532
 4MY  P3   O13   single  1.688  0.020  1.688
 4MY  P3   O43   deloc   1.525  0.020  1.525
 4MY  P3   O33   deloc   1.529  0.020  1.529
 4MY  C4   C5    single  1.546  0.020  1.546
 4MY  C4   O14   single  1.389  0.020  1.389
 4MY  C4   H4    single  0.970  0.020  1.090
 4MY  O44  P4    deloc   1.529  0.020  1.529
 4MY  O14  P4    single  1.683  0.020  1.683
 4MY  P4   O24   deloc   1.531  0.020  1.531
 4MY  P4   O34   deloc   1.526  0.020  1.526
 4MY  C6   C5    single  1.543  0.020  1.543
 4MY  C5   O15   single  1.385  0.020  1.385
 4MY  C5   H5    single  0.970  0.020  1.090
 4MY  O15  P5    single  1.683  0.020  1.683
 4MY  O35  P5    deloc   1.529  0.020  1.529
 4MY  P5   O25   deloc   1.529  0.020  1.529
 4MY  P5   O45   deloc   1.531  0.020  1.531
 4MY  C6   O16   single  1.391  0.020  1.391
 4MY  C6   H6    single  0.970  0.020  1.090
 4MY  O46  P6    deloc   1.529  0.020  1.529
 4MY  O26  P6    deloc   1.525  0.020  1.525
 4MY  P6   O16   single  1.690  0.020  1.690
 4MY  P6   O36   deloc   1.531  0.020  1.531
 4MY  O11  HO11  single  0.850  0.020  0.980
 4MY  O12  HO12  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
 4MY  H1    C1   O11  109.79  3.000
 4MY  H1    C1   C6   107.41  3.000
 4MY  O11   C1   C6   110.04  3.000
 4MY  H1    C1   C2   107.41  3.000
 4MY  C6    C1   C2   112.33  3.000
 4MY  O11   C1   C2   109.79  3.000
 4MY  H2    C2   O12  109.49  3.000
 4MY  H2    C2   C3   107.52  3.000
 4MY  O12   C2   C3   109.71  3.000
 4MY  H2    C2   C1   108.38  3.000
 4MY  C3    C2   C1   110.88  3.000
 4MY  O12   C2   C1   110.79  3.000
 4MY  H3    C3   O13  109.97  3.000
 4MY  H3    C3   C4   106.62  3.000
 4MY  O13   C3   C4   111.39  3.000
 4MY  H3    C3   C2   106.04  3.000
 4MY  C4    C3   C2   110.83  3.000
 4MY  O13   C3   C2   111.72  3.000
 4MY  H4    C4   O14  111.16  3.000
 4MY  H4    C4   C5   108.01  3.000
 4MY  O14   C4   C5   111.07  3.000
 4MY  H4    C4   C3   108.53  3.000
 4MY  O14   C4   C3   109.51  3.000
 4MY  C5    C4   C3   108.47  3.000
 4MY  H5    C5   O15  110.96  3.000
 4MY  H5    C5   C6   107.49  3.000
 4MY  O15   C5   C6   110.28  3.000
 4MY  H5    C5   C4   107.45  3.000
 4MY  O15   C5   C4   111.06  3.000
 4MY  C6    C5   C4   109.49  3.000
 4MY  H6    C6   O16  110.99  3.000
 4MY  H6    C6   C5   107.94  3.000
 4MY  O16   C6   C5   112.28  3.000
 4MY  H6    C6   C1   108.32  3.000
 4MY  O16   C6   C1   109.15  3.000
 4MY  C5    C6   C1   108.05  3.000
 4MY  HO11  O11  C1   106.84  3.000
 4MY  HO12  O12  C2   106.26  3.000
 4MY  P3    O13  C3   119.85  3.000
 4MY  P4    O14  C4   121.54  3.000
 4MY  P5    O15  C5   120.82  3.000
 4MY  P6    O16  C6   121.58  3.000
 4MY  O43   P3   O33  114.78  3.000
 4MY  O33   P3   O23  113.15  3.000
 4MY  O43   P3   O23  113.56  3.000
 4MY  O33   P3   O13  106.03  3.000
 4MY  O43   P3   O13  101.32  3.000
 4MY  O23   P3   O13  106.62  3.000
 4MY  O44   P4   O34  112.14  3.000
 4MY  O34   P4   O24  114.16  3.000
 4MY  O44   P4   O24  114.16  3.000
 4MY  O34   P4   O14  107.97  3.000
 4MY  O24   P4   O14  100.54  3.000
 4MY  O44   P4   O14  106.74  3.000
 4MY  O45   P5   O35  111.49  3.000
 4MY  O45   P5   O25  114.27  3.000
 4MY  O35   P5   O25  113.98  3.000
 4MY  O45   P5   O15  106.96  3.000
 4MY  O25   P5   O15  101.58  3.000
 4MY  O35   P5   O15  107.62  3.000
 4MY  O46   P6   O36  114.36  3.000
 4MY  O36   P6   O26  113.93  3.000
 4MY  O46   P6   O26  112.86  3.000
 4MY  O36   P6   O16  100.57  3.000
 4MY  O26   P6   O16  107.41  3.000
 4MY  O46   P6   O16  106.39  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
 4MY  Var_01  O23  P3  O13  C3  -70.23  30.0  3
 4MY  Var_02  O44  P4  O14  C4   48.92  30.0  3
 4MY  Var_03  O35  P5  O15  C5  -64.07  30.0  3
 4MY  Var_04  O46  P6  O16  C6  -39.45  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
 4MY  chir_01  C1  O11  C2  C6  positiv
 4MY  chir_02  C2  O12  C1  C3  negativ
 4MY  chir_03  C3  O13  C4  C2  positiv
 4MY  chir_04  C4  O14  C5  C3  negativ
 4MY  chir_05  C5  O15  C6  C4  positiv
 4MY  chir_06  C6  O16  C1  C5  negativ

