# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:24:07 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: (3~{S},3'~{S},4'~{S},5'~{S},6'~{R})-5-[(4-ethylphenyl)methyl]-6'-(hydroxymethyl)spiro[1~{H}-2-benzofuran-3,2'-oxane]-3',4',5'-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(Cc2ccc3CO[C@]4(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)c3c2)cc1
#
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
 RT2  RT2  (3~{S},3'~{S},4'~{S},5'~{S},6'~{R})-5-[(4-ethylphenyl)methyl]-6'-(hydroxymethyl)spiro[1~{H}-2-benzofuran-3,2'-oxane]-3',4',5'-triol  ligand  54  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RT2
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
 RT2  C10   C  CR6   0   0.143   8.5522   2.7630  -19.3253
 RT2  C13   C  CR56  0  -0.005  11.0295   2.8843  -18.0731
 RT2  C17   C  CH1   0  -0.027  12.6026   1.0882  -20.5623
 RT2  C20   C  CH1   0  -0.012  13.7742   3.5126  -21.6020
 RT2  C22   C  CH2   0  -0.182  13.7796   4.6892  -22.5536
 RT2  C28   C  CR16  0  -0.328   8.6517   2.9802  -17.9520
 RT2  C01   C  CH3   0  -0.651   8.1183  -2.9099  -23.2366
 RT2  C03   C  CR6   0   0.117   6.8029  -1.0981  -22.0958
 RT2  C04   C  CR16  0  -0.292   6.8274   0.1059  -22.7915
 RT2  C05   C  CR16  0  -0.307   6.9434   1.3185  -22.1228
 RT2  C06   C  CR6   0   0.115   7.0394   1.3637  -20.7369
 RT2  C07   C  CR16  0  -0.270   7.0089   0.1590  -20.0373
 RT2  C08   C  CR16  0  -0.294   6.8915  -1.0494  -20.7052
 RT2  C09   C  CH2   0  -0.586   7.2069   2.6702  -20.0033
 RT2  C11   C  CR16  0  -0.370   9.7174   2.6085  -20.0751
 RT2  C12   C  CR56  0   0.070  10.9403   2.6525  -19.4328
 RT2  C14   C  CH2   0  -0.185  12.4705   2.9269  -17.6821
 RT2  O15   O  O     0  -0.537  13.1794   2.7047  -18.8947
 RT2  C16   C  CR5   0   0.489  12.3222   2.4974  -19.9973
 RT2  C18   C  CH1   0  -0.003  13.9798   1.0731  -21.2234
 RT2  C19   C  CH1   0   0.041  14.0721   2.1728  -22.2735
 RT2  O21   O  O2    0  -0.503  12.5019   3.4758  -20.9721
 RT2  O23   O  OH1   0  -0.671  12.8488   4.4756  -23.5869
 RT2  O24   O  OH1   0  -0.679  15.3669   2.2536  -22.8195
 RT2  O25   O  OH1   0  -0.673  14.2568  -0.1527  -21.8555
 RT2  O26   O  OH1   0  -0.660  11.6421   0.7198  -21.5183
 RT2  C27   C  CR16  0  -0.297   9.8858   3.0537  -17.3144
 RT2  H171  H  HCH1  0   0.244  12.6020   0.3869  -19.7166
 RT2  H201  H  HCH1  0   0.229  14.5604   3.7073  -20.8586
 RT2  H222  H  HCH2  0   0.211  14.7989   4.8092  -22.9357
 RT2  H221  H  HCH2  0   0.213  13.5494   5.5971  -21.9798
 RT2  H281  H  HCR6  0   0.253   7.7458   3.0968  -17.3690
 RT2  H011  H  HCH3  0   0.229   8.0495  -3.8621  -23.7643
 RT2  H012  H  HCH3  0   0.224   8.6111  -2.1952  -23.8972
 RT2  H013  H  HCH3  0   0.224   8.7596  -3.0557  -22.3663
 RT2  H021  H  HCH2  0   0.237   6.1063  -2.3110  -23.7116
 RT2  H022  H  HCH2  0   0.237   6.2538  -3.1601  -22.1885
 RT2  H051  H  HCR6  0   0.245   6.9575   2.2411  -22.6919
 RT2  H071  H  HCR6  0   0.242   7.0794   0.1648  -18.9553
 RT2  H081  H  HCR6  0   0.242   6.8650  -1.9710  -20.1347
 RT2  H092  H  HCH2  0   0.267   7.0905   3.4983  -20.7079
 RT2  H091  H  HCH2  0   0.265   6.4176   2.7855  -19.2566
 RT2  H111  H  HCR6  0   0.252   9.6519   2.4583  -21.1459
 RT2  H141  H  HCH2  0   0.242  12.7290   2.1499  -16.9561
 RT2  H142  H  HCH2  0   0.243  12.7537   3.8915  -17.2497
 RT2  H181  H  HCH1  0   0.227  14.7286   1.2866  -20.4480
 RT2  H191  H  HCH1  0   0.219  13.3250   1.9884  -23.0561
 RT2  H231  H  HOH1  0   0.458  12.9438   5.1881  -24.2247
 RT2  H241  H  HOH1  0   0.451  15.5806   1.3960  -23.2012
 RT2  H251  H  HOH1  0   0.456  14.4955  -0.8002  -21.1852
 RT2  H261  H  HOH1  0   0.454  10.8765   0.3630  -21.0589
 RT2  H271  H  HCR6  0   0.255   9.9400   3.2345  -16.2482
 RT2  H041  H  HCR6  0   0.242   6.7551   0.1012  -23.8733
 RT2  C02   C  CH2   0  -0.503   6.7344  -2.4121  -22.8233

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
 RT2  C01  C02   single    1.528  0.020  1.528
 RT2  O23  C22   single    1.407  0.020  1.407
 RT2  C02  C03   single    1.503  0.020  1.503
 RT2  C22  C20   single    1.513  0.020  1.513
 RT2  C04  C03   aromatic  1.391  0.020  1.391
 RT2  C04  C05   aromatic  1.390  0.020  1.390
 RT2  O24  C19   single    1.408  0.020  1.408
 RT2  C03  C08   aromatic  1.394  0.020  1.394
 RT2  C19  C20   single    1.528  0.020  1.528
 RT2  C19  C18   single    1.523  0.020  1.523
 RT2  C05  C06   aromatic  1.390  0.020  1.390
 RT2  O25  C18   single    1.407  0.020  1.407
 RT2  C20  O21   single    1.420  0.020  1.420
 RT2  O26  C17   single    1.404  0.020  1.404
 RT2  C08  C07   aromatic  1.386  0.020  1.386
 RT2  C18  C17   single    1.528  0.020  1.528
 RT2  O21  C16   single    1.393  0.020  1.393
 RT2  C06  C07   aromatic  1.393  0.020  1.393
 RT2  C06  C09   single    1.508  0.020  1.508
 RT2  C17  C16   single    1.544  0.020  1.544
 RT2  C16  C12   single    1.501  0.020  1.501
 RT2  C16  O15   single    1.412  0.020  1.412
 RT2  C11  C12   aromatic  1.382  0.020  1.382
 RT2  C11  C10   aromatic  1.394  0.020  1.394
 RT2  C09  C10   single    1.509  0.020  1.509
 RT2  C12  C13   aromatic  1.382  0.020  1.382
 RT2  C10  C28   aromatic  1.394  0.020  1.394
 RT2  O15  C14   single    1.422  0.020  1.422
 RT2  C13  C14   single    1.494  0.020  1.494
 RT2  C13  C27   aromatic  1.383  0.020  1.383
 RT2  C28  C27   aromatic  1.391  0.020  1.391
 RT2  C17  H171  single    0.970  0.020  1.090
 RT2  C20  H201  single    0.970  0.020  1.090
 RT2  C22  H222  single    0.970  0.020  1.090
 RT2  C22  H221  single    0.970  0.020  1.090
 RT2  C28  H281  single    0.930  0.020  1.080
 RT2  C01  H011  single    0.970  0.020  1.090
 RT2  C01  H012  single    0.970  0.020  1.090
 RT2  C01  H013  single    0.970  0.020  1.090
 RT2  C02  H021  single    0.970  0.020  1.090
 RT2  C02  H022  single    0.970  0.020  1.090
 RT2  C04  H041  single    0.930  0.020  1.080
 RT2  C05  H051  single    0.930  0.020  1.080
 RT2  C07  H071  single    0.930  0.020  1.080
 RT2  C08  H081  single    0.930  0.020  1.080
 RT2  C09  H092  single    0.970  0.020  1.090
 RT2  C09  H091  single    0.970  0.020  1.090
 RT2  C11  H111  single    0.930  0.020  1.080
 RT2  C14  H141  single    0.970  0.020  1.090
 RT2  C14  H142  single    0.970  0.020  1.090
 RT2  C18  H181  single    0.970  0.020  1.090
 RT2  C19  H191  single    0.970  0.020  1.090
 RT2  O23  H231  single    0.850  0.020  0.980
 RT2  O24  H241  single    0.850  0.020  0.980
 RT2  O25  H251  single    0.850  0.020  0.980
 RT2  O26  H261  single    0.850  0.020  0.980
 RT2  C27  H271  single    0.930  0.020  1.080

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
 RT2  C11   C10  C09   119.77  3.000
 RT2  C09   C10  C28   121.05  3.000
 RT2  C11   C10  C28   119.17  3.000
 RT2  C27   C13  C14   130.59  3.000
 RT2  C27   C13  C12   120.45  3.000
 RT2  C14   C13  C12   108.94  3.000
 RT2  H171  C17  O26   110.87  3.000
 RT2  H171  C17  C18   109.10  3.000
 RT2  O26   C17  C18   108.62  3.000
 RT2  H171  C17  C16   107.51  3.000
 RT2  C18   C17  C16   109.34  3.000
 RT2  O26   C17  C16   111.37  3.000
 RT2  H201  C20  O21   110.20  3.000
 RT2  H201  C20  C19   108.24  3.000
 RT2  O21   C20  C19   110.30  3.000
 RT2  H201  C20  C22   106.56  3.000
 RT2  O21   C20  C22   107.59  3.000
 RT2  C19   C20  C22   113.87  3.000
 RT2  H221  C22  H222  106.66  3.000
 RT2  H221  C22  O23   111.74  3.000
 RT2  H222  C22  O23   112.09  3.000
 RT2  H221  C22  C20   108.27  3.000
 RT2  H222  C22  C20   107.93  3.000
 RT2  O23   C22  C20   109.97  3.000
 RT2  H281  C28  C27   119.30  3.000
 RT2  H281  C28  C10   119.15  3.000
 RT2  C27   C28  C10   121.54  3.000
 RT2  H013  C01  H012  107.76  3.000
 RT2  H013  C01  H011  107.84  3.000
 RT2  H012  C01  H011  107.90  3.000
 RT2  H013  C01  C02   111.12  3.000
 RT2  H012  C01  C02   111.07  3.000
 RT2  H011  C01  C02   110.99  3.000
 RT2  C08   C03  C04   117.87  3.000
 RT2  C08   C03  C02   121.07  3.000
 RT2  C04   C03  C02   121.02  3.000
 RT2  H041  C04  C05   119.31  3.000
 RT2  H041  C04  C03   119.61  3.000
 RT2  C05   C04  C03   121.08  3.000
 RT2  H051  C05  C06   119.66  3.000
 RT2  H051  C05  C04   119.41  3.000
 RT2  C06   C05  C04   120.93  3.000
 RT2  C09   C06  C07   120.48  3.000
 RT2  C09   C06  C05   121.40  3.000
 RT2  C07   C06  C05   118.10  3.000
 RT2  H071  C07  C08   119.42  3.000
 RT2  H071  C07  C06   119.67  3.000
 RT2  C08   C07  C06   120.91  3.000
 RT2  H081  C08  C07   119.32  3.000
 RT2  H081  C08  C03   119.57  3.000
 RT2  C07   C08  C03   121.11  3.000
 RT2  H091  C09  H092  106.47  3.000
 RT2  H091  C09  C06   110.10  3.000
 RT2  H092  C09  C06   109.32  3.000
 RT2  H091  C09  C10   109.29  3.000
 RT2  H092  C09  C10   109.74  3.000
 RT2  C06   C09  C10   111.77  3.000
 RT2  H111  C11  C12   121.16  3.000
 RT2  H111  C11  C10   119.76  3.000
 RT2  C12   C11  C10   119.08  3.000
 RT2  C16   C12  C11   129.54  3.000
 RT2  C11   C12  C13   121.31  3.000
 RT2  C16   C12  C13   109.14  3.000
 RT2  H142  C14  H141  107.61  3.000
 RT2  H142  C14  O15   110.22  3.000
 RT2  H141  C14  O15   109.69  3.000
 RT2  H142  C14  C13   112.23  3.000
 RT2  H141  C14  C13   112.41  3.000
 RT2  O15   C14  C13   104.67  3.000
 RT2  C16   O15  C14   112.71  3.000
 RT2  O21   C16  O15   111.41  3.000
 RT2  O15   C16  C12   104.49  3.000
 RT2  O21   C16  C12   108.03  3.000
 RT2  O15   C16  C17   108.03  3.000
 RT2  C12   C16  C17   113.53  3.000
 RT2  O21   C16  C17   111.20  3.000
 RT2  H181  C18  O25   110.62  3.000
 RT2  H181  C18  C19   107.75  3.000
 RT2  O25   C18  C19   107.90  3.000
 RT2  H181  C18  C17   107.88  3.000
 RT2  O25   C18  C17   112.37  3.000
 RT2  C19   C18  C17   110.23  3.000
 RT2  H191  C19  O24   111.05  3.000
 RT2  H191  C19  C18   109.21  3.000
 RT2  O24   C19  C18   111.38  3.000
 RT2  H191  C19  C20   109.15  3.000
 RT2  C18   C19  C20   108.55  3.000
 RT2  O24   C19  C20   107.43  3.000
 RT2  C16   O21  C20   116.37  3.000
 RT2  H231  O23  C22   108.03  3.000
 RT2  H241  O24  C19   107.87  3.000
 RT2  H251  O25  C18   108.80  3.000
 RT2  H261  O26  C17   108.46  3.000
 RT2  H271  C27  C28   120.30  3.000
 RT2  H271  C27  C13   121.29  3.000
 RT2  C28   C27  C13   118.41  3.000
 RT2  H022  C02  H021  106.43  3.000
 RT2  H022  C02  C03   109.71  3.000
 RT2  H021  C02  C03   109.80  3.000
 RT2  H022  C02  C01   109.42  3.000
 RT2  H021  C02  C01   109.32  3.000
 RT2  C03   C02  C01   111.99  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
 RT2  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 RT2  CONST_02  C13   C27  C28  C10     0.00   0.0  0
 RT2  CONST_03  C12   C11  C10  C28     0.00   0.0  0
 RT2  CONST_04  C12   C13  C27  C28     0.00   0.0  0
 RT2  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 RT2  CONST_06  C06   C07  C08  C03     0.00   0.0  0
 RT2  CONST_07  C07   C08  C03  C04     0.00   0.0  0
 RT2  CONST_08  C07   C06  C05  C04     0.00   0.0  0
 RT2  CONST_09  C08   C03  C04  C05     0.00   0.0  0
 RT2  CONST_10  C08   C07  C06  C05     0.00   0.0  0
 RT2  CONST_11  C27   C13  C12  C11     0.00   0.0  0
 RT2  CONST_12  C27   C28  C10  C11     0.00   0.0  0
 RT2  CONST_13  C05   C04  C03  C02   180.00   0.0  0
 RT2  CONST_14  C07   C08  C03  C02   180.00   0.0  0
 RT2  CONST_15  C09   C06  C05  C04   180.00   0.0  0
 RT2  CONST_16  C09   C06  C07  C08   180.00   0.0  0
 RT2  CONST_17  C12   C11  C10  C09   180.00   0.0  0
 RT2  CONST_18  C27   C28  C10  C09   180.00   0.0  0
 RT2  CONST_19  H271  C27  C28  C10   180.00   0.0  0
 RT2  CONST_20  H111  C11  C12  C13   180.00   0.0  0
 RT2  CONST_21  H281  C28  C27  C13   180.00   0.0  0
 RT2  CONST_22  H051  C05  C04  C03   180.00   0.0  0
 RT2  CONST_23  H071  C07  C08  C03   180.00   0.0  0
 RT2  CONST_24  H081  C08  C03  C04   180.00   0.0  0
 RT2  CONST_25  H041  C04  C05  C06   180.00   0.0  0
 RT2  Var_01    O15   C14  C13  C12    -0.09  30.0  1
 RT2  Var_02    C05   C06  C09  C10  -113.67  30.0  2
 RT2  Var_03    C06   C09  C10  C28  -122.80  30.0  1
 RT2  Var_04    C04   C03  C02  C01    85.52  30.0  2
 RT2  Var_05    H011  C01  C02  C03  -179.88  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
 RT2  chir_01  C17  O26  C18  C16  negativ
 RT2  chir_02  C20  O21  C19  C22  negativ
 RT2  chir_03  C16  O15  C17  C12  negativ
 RT2  chir_04  C18  O25  C17  C19  positiv
 RT2  chir_05  C19  O24  C18  C20  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
 RT2  plan-1  C03   0.020
 RT2  plan-1  C04   0.020
 RT2  plan-1  C05   0.020
 RT2  plan-1  C06   0.020
 RT2  plan-1  C07   0.020
 RT2  plan-1  C08   0.020
 RT2  plan-1  C09   0.020
 RT2  plan-1  H051  0.020
 RT2  plan-1  H071  0.020
 RT2  plan-1  H081  0.020
 RT2  plan-1  H041  0.020
 RT2  plan-1  C02   0.020
 RT2  plan-2  C10   0.020
 RT2  plan-2  C13   0.020
 RT2  plan-2  C28   0.020
 RT2  plan-2  C09   0.020
 RT2  plan-2  C11   0.020
 RT2  plan-2  C12   0.020
 RT2  plan-2  C14   0.020
 RT2  plan-2  C16   0.020
 RT2  plan-2  C27   0.020
 RT2  plan-2  H281  0.020
 RT2  plan-2  H111  0.020
 RT2  plan-2  H271  0.020

