# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:02:02 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]([C@@H]1Cc2cc3cc(O)c(C)c(O)c3c(O)c2C(=O)[C@H]1O)C(=O)[C@@H](O)[C@@H](C)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
 CPH  CPH  (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose  ligand  54  30  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CPH
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
 CPH  C1    C  C     0   0.422  -0.0192   2.3940  -0.0262
 CPH  O1    O  O     0  -0.492   0.3732   3.3401   0.6677
 CPH  C2    C  CH1   0  -0.020  -1.4094   2.4721  -0.6409
 CPH  C3    C  CH1   0  -0.379  -2.0121   1.0949  -0.8887
 CPH  C4    C  CH2   0  -0.516  -1.0366   0.2357  -1.6903
 CPH  C5    C  CR16  0  -0.473   3.2822  -2.0741  -1.0585
 CPH  C6    C  CR6   0   0.369   4.5797  -2.0995  -0.5921
 CPH  C7    C  CR6   0  -0.150   5.1381  -1.0206   0.1284
 CPH  C8    C  CR6   0   0.372   4.3457   0.0872   0.3712
 CPH  O8    O  OH1   0  -0.630   4.8983   1.0973   1.0541
 CPH  C9    C  CR6   0   0.437   2.1399   1.2511   0.1364
 CPH  O9    O  OH1   0  -0.671   2.6075   2.2726   0.8495
 CPH  C1'   C  CH1   0  -0.012  -2.4695   0.5029   0.4557
 CPH  O1'   O  O2    0  -0.471  -1.4287   0.5742   1.3764
 CPH  C10   C  CR16  0  -0.457   1.1380  -0.9138  -1.3051
 CPH  C2'   C  C     0   0.330  -2.9459  -0.9289   0.2612
 CPH  O2'   O  O     0  -0.376  -2.2668  -1.8710   0.5908
 CPH  C3'   C  CH1   0  -0.072  -4.3010  -1.1557  -0.3857
 CPH  O3'   O  OH1   0  -0.667  -4.4569  -2.5031  -0.7229
 CPH  C4'   C  CH1   0   0.001  -5.4005  -0.6889   0.5885
 CPH  O4'   O  OH1   0  -0.659  -5.1936  -1.2433   1.8692
 CPH  C4A   C  CR6   0   0.142   0.3384   0.1654  -1.0966
 CPH  C5'   C  CH3   0  -0.683  -6.7910  -0.9796   0.0496
 CPH  C5A   C  CR66  0   0.152   2.4754  -0.9576  -0.8235
 CPH  C8A   C  CR66  0  -0.202   2.9974   0.1460  -0.0970
 CPH  C9A   C  CR6   0  -0.196   0.8354   1.2777  -0.3584
 CPH  CC7   C  CH3   0  -0.774   6.5609  -1.1001   0.6040
 CPH  O6    O  OH1   0  -0.620   5.3006  -3.2015  -0.8512
 CPH  O2    O  OH1   0  -0.654  -1.2758   3.1155  -1.8888
 CPH  CME   C  CH3   0  -0.408  -1.8463   0.5339   2.7241
 CPH  H2    H  HCH1  0   0.257  -2.0521   3.0473   0.0384
 CPH  H3    H  HCH1  0   0.294  -2.9151   1.2399  -1.4889
 CPH  H4    H  HCH2  0   0.268  -1.4258  -0.7708  -1.8542
 CPH  H4A   H  HCH2  0   0.283  -0.9528   0.6724  -2.6893
 CPH  H5    H  HCR6  0   0.257   2.8886  -2.9198  -1.6082
 CPH  HO8   H  HOH1  0   0.489   4.2492   1.8092   1.1828
 CPH  HO9   H  HOH1  0   0.494   1.8597   2.9358   0.9531
 CPH  H1'   H  HCH1  0   0.254  -3.3201   1.1170   0.7918
 CPH  H10   H  HCR6  0   0.244   0.7615  -1.7685  -1.8549
 CPH  H3'   H  HCH1  0   0.257  -4.3681  -0.5366  -1.2912
 CPH  HO3'  H  HOH1  0   0.450  -3.7413  -2.9977  -0.3000
 CPH  H4'   H  HCH1  0   0.244  -5.3013   0.3930   0.7125
 CPH  HO4'  H  HOH1  0   0.445  -5.3414  -2.1941   1.8150
 CPH  H5'   H  HCH3  0   0.234  -6.9574  -2.0498  -0.0793
 CPH  H5'A  H  HCH3  0   0.243  -7.5447  -0.5979   0.7385
 CPH  H5'B  H  HCH3  0   0.233  -6.9467  -0.4960  -0.9154
 CPH  HC7   H  HCH3  0   0.255   7.2595  -1.2228  -0.2280
 CPH  HC7A  H  HCH3  0   0.277   6.8630  -0.2023   1.1340
 CPH  HC7B  H  HCH3  0   0.255   6.7147  -1.9373   1.2906
 CPH  HO6   H  HOH1  0   0.488   6.1955  -3.1314  -0.5006
 CPH  HO2   H  HOH1  0   0.463  -1.0569   4.0417  -1.7397
 CPH  HME   H  HCH3  0   0.242  -0.9651   0.6962   3.3417
 CPH  HMEA  H  HCH3  0   0.214  -2.5761   1.3212   2.9403
 CPH  HMEB  H  HCH3  0   0.220  -2.2887  -0.4283   2.9965

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
 CPH  O1   C1    double    1.237  0.020  1.237
 CPH  C9A  C1    single    1.445  0.020  1.445
 CPH  C1   C2    single    1.522  0.020  1.522
 CPH  C2   O2    single    1.410  0.020  1.410
 CPH  C2   C3    single    1.524  0.020  1.524
 CPH  C2   H2    single    0.970  0.020  1.090
 CPH  C3   C4    single    1.527  0.020  1.527
 CPH  C3   C1'   single    1.539  0.020  1.539
 CPH  C3   H3    single    0.970  0.020  1.090
 CPH  C4A  C4    single    1.499  0.020  1.499
 CPH  C4   H4    single    0.970  0.020  1.090
 CPH  C4   H4A   single    0.970  0.020  1.090
 CPH  C6   C5    aromatic  1.379  0.020  1.379
 CPH  C5   C5A   aromatic  1.397  0.020  1.397
 CPH  C5   H5    single    0.930  0.020  1.080
 CPH  C7   C6    aromatic  1.412  0.020  1.412
 CPH  O6   C6    single    1.342  0.020  1.342
 CPH  CC7  C7    single    1.502  0.020  1.502
 CPH  C7   C8    aromatic  1.384  0.020  1.384
 CPH  O8   C8    single    1.339  0.020  1.339
 CPH  C8   C8A   aromatic  1.428  0.020  1.428
 CPH  O8   HO8   single    0.850  0.020  0.980
 CPH  O9   C9    single    1.331  0.020  1.331
 CPH  C8A  C9    aromatic  1.418  0.020  1.418
 CPH  C9   C9A   aromatic  1.396  0.020  1.396
 CPH  O9   HO9   single    0.850  0.020  0.980
 CPH  C2'  C1'   single    1.521  0.020  1.521
 CPH  C1'  O1'   single    1.391  0.020  1.391
 CPH  C1'  H1'   single    0.970  0.020  1.090
 CPH  O1'  CME   single    1.411  0.020  1.411
 CPH  C5A  C10   aromatic  1.422  0.020  1.422
 CPH  C10  C4A   aromatic  1.359  0.020  1.359
 CPH  C10  H10   single    0.930  0.020  1.080
 CPH  O2'  C2'   double    1.207  0.020  1.207
 CPH  C2'  C3'   single    1.519  0.020  1.519
 CPH  O3'  C3'   single    1.398  0.020  1.398
 CPH  C3'  C4'   single    1.541  0.020  1.541
 CPH  C3'  H3'   single    0.970  0.020  1.090
 CPH  O3'  HO3'  single    0.850  0.020  0.980
 CPH  O4'  C4'   single    1.411  0.020  1.411
 CPH  C4'  C5'   single    1.519  0.020  1.519
 CPH  C4'  H4'   single    0.970  0.020  1.090
 CPH  O4'  HO4'  single    0.850  0.020  0.980
 CPH  C9A  C4A   aromatic  1.424  0.020  1.424
 CPH  C5'  H5'   single    0.970  0.020  1.090
 CPH  C5'  H5'A  single    0.970  0.020  1.090
 CPH  C5'  H5'B  single    0.970  0.020  1.090
 CPH  C8A  C5A   aromatic  1.421  0.020  1.421
 CPH  CC7  HC7   single    0.970  0.020  1.090
 CPH  CC7  HC7A  single    0.970  0.020  1.090
 CPH  CC7  HC7B  single    0.970  0.020  1.090
 CPH  O6   HO6   single    0.850  0.020  0.980
 CPH  O2   HO2   single    0.850  0.020  0.980
 CPH  CME  HME   single    0.970  0.020  1.090
 CPH  CME  HMEA  single    0.970  0.020  1.090
 CPH  CME  HMEB  single    0.970  0.020  1.090

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
 CPH  C9A   C1   C2    119.15  3.000
 CPH  C2    C1   O1    118.49  3.000
 CPH  C9A   C1   O1    122.16  3.000
 CPH  H2    C2   O2    111.34  3.000
 CPH  H2    C2   C3    110.04  3.000
 CPH  O2    C2   C3    107.82  3.000
 CPH  H2    C2   C1    108.16  3.000
 CPH  C3    C2   C1    112.37  3.000
 CPH  O2    C2   C1    107.11  3.000
 CPH  H3    C3   C1'   106.56  3.000
 CPH  H3    C3   C4    108.29  3.000
 CPH  C1'   C3   C4    115.59  3.000
 CPH  H3    C3   C2    107.22  3.000
 CPH  C1'   C3   C2    108.86  3.000
 CPH  C4    C3   C2    109.95  3.000
 CPH  H4A   C4   H4    104.98  3.000
 CPH  H4A   C4   C4A   108.07  3.000
 CPH  H4    C4   C4A   110.08  3.000
 CPH  H4A   C4   C3    107.68  3.000
 CPH  H4    C4   C3    111.71  3.000
 CPH  C4A   C4   C3    113.85  3.000
 CPH  H5    C5   C5A   119.97  3.000
 CPH  H5    C5   C6    119.96  3.000
 CPH  C5A   C5   C6    120.07  3.000
 CPH  O6    C6   C7    120.89  3.000
 CPH  O6    C6   C5    117.08  3.000
 CPH  C7    C6   C5    122.04  3.000
 CPH  CC7   C7   C8    121.96  3.000
 CPH  C8    C7   C6    118.35  3.000
 CPH  CC7   C7   C6    119.70  3.000
 CPH  C8A   C8   O8    121.72  3.000
 CPH  C8A   C8   C7    121.07  3.000
 CPH  O8    C8   C7    117.21  3.000
 CPH  HO8   O8   C8    110.15  3.000
 CPH  C9A   C9   C8A   121.45  3.000
 CPH  C9A   C9   O9    120.26  3.000
 CPH  C8A   C9   O9    118.29  3.000
 CPH  HO9   O9   C9    107.48  3.000
 CPH  H1'   C1'  C2'   108.77  3.000
 CPH  H1'   C1'  O1'   110.31  3.000
 CPH  C2'   C1'  O1'   111.53  3.000
 CPH  H1'   C1'  C3    106.36  3.000
 CPH  O1'   C1'  C3    109.64  3.000
 CPH  C2'   C1'  C3    110.10  3.000
 CPH  CME   O1'  C1'   114.14  3.000
 CPH  H10   C10  C5A   118.30  3.000
 CPH  H10   C10  C4A   119.98  3.000
 CPH  C5A   C10  C4A   121.71  3.000
 CPH  C3'   C2'  O2'   120.11  3.000
 CPH  C3'   C2'  C1'   118.32  3.000
 CPH  O2'   C2'  C1'   121.56  3.000
 CPH  H3'   C3'  C4'   107.86  3.000
 CPH  H3'   C3'  O3'   109.73  3.000
 CPH  C4'   C3'  O3'   111.40  3.000
 CPH  H3'   C3'  C2'   108.74  3.000
 CPH  C4'   C3'  C2'   108.78  3.000
 CPH  O3'   C3'  C2'   110.26  3.000
 CPH  HO3'  O3'  C3'   107.76  3.000
 CPH  H4'   C4'  C5'   108.21  3.000
 CPH  H4'   C4'  O4'   105.81  3.000
 CPH  C5'   C4'  O4'   112.39  3.000
 CPH  H4'   C4'  C3'   107.86  3.000
 CPH  C5'   C4'  C3'   111.76  3.000
 CPH  O4'   C4'  C3'   110.50  3.000
 CPH  HO4'  O4'  C4'   108.31  3.000
 CPH  C9A   C4A  C10   119.62  3.000
 CPH  C9A   C4A  C4    119.25  3.000
 CPH  C10   C4A  C4    121.06  3.000
 CPH  H5'B  C5'  H5'A  107.77  3.000
 CPH  H5'B  C5'  H5'   107.98  3.000
 CPH  H5'A  C5'  H5'   108.23  3.000
 CPH  H5'B  C5'  C4'   111.08  3.000
 CPH  H5'A  C5'  C4'   109.98  3.000
 CPH  H5'   C5'  C4'   111.67  3.000
 CPH  C8A   C5A  C10   119.66  3.000
 CPH  C8A   C5A  C5    119.64  3.000
 CPH  C10   C5A  C5    120.71  3.000
 CPH  C5A   C8A  C9    117.86  3.000
 CPH  C5A   C8A  C8    118.85  3.000
 CPH  C9    C8A  C8    123.29  3.000
 CPH  C4A   C9A  C9    119.67  3.000
 CPH  C4A   C9A  C1    121.08  3.000
 CPH  C9    C9A  C1    119.09  3.000
 CPH  HC7B  CC7  HC7A  106.71  3.000
 CPH  HC7B  CC7  HC7   107.58  3.000
 CPH  HC7A  CC7  HC7   106.65  3.000
 CPH  HC7B  CC7  C7    111.87  3.000
 CPH  HC7A  CC7  C7    111.99  3.000
 CPH  HC7   CC7  C7    111.73  3.000
 CPH  HO6   O6   C6    111.64  3.000
 CPH  HO2   O2   C2    108.86  3.000
 CPH  HMEB  CME  HMEA  108.29  3.000
 CPH  HMEB  CME  HME   108.51  3.000
 CPH  HMEA  CME  HME   108.69  3.000
 CPH  HMEB  CME  O1'   112.50  3.000
 CPH  HMEA  CME  O1'   111.42  3.000
 CPH  HME   CME  O1'   107.34  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
 CPH  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 CPH  CONST_02  C4A  C10  C5A  C5    180.00   0.0  0
 CPH  CONST_03  C8   C8A  C5A  C5      0.00   0.0  0
 CPH  CONST_04  C9   C8A  C5A  C5    180.00   0.0  0
 CPH  CONST_05  C10  C5A  C5   C6    180.00   0.0  0
 CPH  CONST_06  C8A  C5A  C5   C6      0.00   0.0  0
 CPH  CONST_07  C8A  C8   C7   C6      0.00   0.0  0
 CPH  CONST_08  C5A  C5   C6   C7      0.00   0.0  0
 CPH  CONST_09  C9   C8A  C8   C7    180.00   0.0  0
 CPH  CONST_10  C5A  C8A  C8   C7      0.00   0.0  0
 CPH  CONST_11  C9A  C9   C8A  C8    180.00   0.0  0
 CPH  CONST_12  C10  C5A  C8A  C8    180.00   0.0  0
 CPH  CONST_13  C10  C5A  C8A  C9      0.00   0.0  0
 CPH  CONST_14  C10  C4A  C9A  C9      0.00   0.0  0
 CPH  CONST_15  C8A  C5A  C10  C4A     0.00   0.0  0
 CPH  CONST_16  C8A  C9   C9A  C4A     0.00   0.0  0
 CPH  CONST_17  C9A  C4A  C10  C5A     0.00   0.0  0
 CPH  CONST_18  C9A  C9   C8A  C5A     0.00   0.0  0
 CPH  CONST_19  O9   C9   C9A  C1      0.00   0.0  0
 CPH  CONST_20  CC7  C7   C6   C5    180.00   0.0  0
 CPH  CONST_21  O8   C8   C7   C6    180.00   0.0  0
 CPH  CONST_22  O6   C6   C7   C8    180.00   0.0  0
 CPH  CONST_23  O9   C9   C8A  C8      0.00   0.0  0
 CPH  CONST_24  C9   C8A  C8   O8      0.00   0.0  0
 CPH  CONST_25  C5A  C8A  C8   O8    180.00   0.0  0
 CPH  CONST_26  C5A  C8A  C9   O9    180.00   0.0  0
 CPH  CONST_27  C4A  C9A  C9   O9    180.00   0.0  0
 CPH  CONST_28  O6   C6   C5   C5A   180.00   0.0  0
 CPH  CONST_29  CC7  C7   C8   C8A   180.00   0.0  0
 CPH  CONST_30  H10  C10  C4A  C4      0.00   0.0  0
 CPH  CONST_31  H5   C5   C6   C7    180.00   0.0  0
 CPH  Var_01    C9   C9A  C1   C2    175.89  30.0  1
 CPH  Var_02    C10  C4A  C4   C3    152.41  30.0  1
 CPH  Var_03    HC7  CC7  C7   C6     59.90  30.0  2
 CPH  Var_04    HME  CME  O1'  C1'  -174.45  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
 CPH  chir_01  C2   C1   O2   C3   negativ
 CPH  chir_02  C3   C1'  C4   C2   positiv
 CPH  chir_03  C1'  O1'  C2'  C3   positiv
 CPH  chir_04  C3'  O3'  C4'  C2'  negativ
 CPH  chir_05  C4'  O4'  C3'  C5'  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
 CPH  plan-1  C1   0.020
 CPH  plan-1  O1   0.020
 CPH  plan-1  C2   0.020
 CPH  plan-1  C9A  0.020
 CPH  plan-2  C1   0.020
 CPH  plan-2  C4   0.020
 CPH  plan-2  C5   0.020
 CPH  plan-2  C6   0.020
 CPH  plan-2  C7   0.020
 CPH  plan-2  C8   0.020
 CPH  plan-2  O8   0.020
 CPH  plan-2  C9   0.020
 CPH  plan-2  O9   0.020
 CPH  plan-2  C10  0.020
 CPH  plan-2  C4A  0.020
 CPH  plan-2  C5A  0.020
 CPH  plan-2  C8A  0.020
 CPH  plan-2  C9A  0.020
 CPH  plan-2  CC7  0.020
 CPH  plan-2  O6   0.020
 CPH  plan-2  H5   0.020
 CPH  plan-2  H10  0.020
 CPH  plan-3  C1'  0.020
 CPH  plan-3  C2'  0.020
 CPH  plan-3  O2'  0.020
 CPH  plan-3  C3'  0.020

