# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 06:47:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (1S)-5-deoxy-1-C-[(2R)-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-1-O-methyl-D-xylulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]([C@H]1CC(=O)c2c(O)c3c(O)c(C)ccc3cc2C1)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
 CRH  CRH  (1S)-5-deoxy-1-C-[(2R)-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-1-O-methyl-D-xylulose  ligand  52  28  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CRH
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
 CRH  C1    C  C     0   0.448  -1.5271   0.2114  -0.3188
 CRH  C2    C  CH2   0  -0.588  -1.0448   0.3007   1.1030
 CRH  C3    C  CH1   0  -0.310   0.4018  -0.1529   1.2748
 CRH  C4    C  CH2   0  -0.502   1.2795   0.6204   0.2953
 CRH  C5    C  CR16  0  -0.350   2.2230   0.2617  -4.5522
 CRH  C6    C  CR16  0  -0.272   1.7928   0.1235  -5.8495
 CRH  C7    C  CR6   0  -0.029   0.4398  -0.0202  -6.1826
 CRH  C8    C  CR6   0   0.348  -0.4962  -0.0220  -5.1593
 CRH  C9    C  CR6   0   0.441  -1.0011   0.1246  -2.7113
 CRH  C10   C  CR16  0  -0.453   1.7190   0.4118  -2.1520
 CRH  C11   C  CR66  0   0.130   1.2948   0.2659  -3.5010
 CRH  C12   C  CR66  0  -0.169  -0.0874   0.1226  -3.8014
 CRH  C13   C  CR6   0  -0.209  -0.5587   0.2627  -1.3942
 CRH  C14   C  CR6   0   0.134   0.8326   0.4209  -1.1219
 CRH  C15   C  CH3   0  -0.707   0.0038  -0.1747  -7.6092
 CRH  O1    O  O     0  -0.485  -2.7381   0.1004  -0.5426
 CRH  O8    O  OH1   0  -0.622  -1.7776  -0.1649  -5.5208
 CRH  O9    O  OH1   0  -0.662  -2.2940  -0.0134  -2.9774
 CRH  C1'   C  CH1   0   0.003   0.9094   0.0365   2.7111
 CRH  C2'   C  C     0   0.328  -0.0150  -0.6889   3.6879
 CRH  C3'   C  CH1   0  -0.084  -1.0020   0.1339   4.4901
 CRH  C4'   C  CH1   0   0.007  -0.2495   0.9114   5.5909
 CRH  C4M   C  CH3   0  -0.682  -1.1936   1.8150   6.3683
 CRH  O1'   O  O2    0  -0.482   2.2016  -0.4881   2.7686
 CRH  O2'   O  O     0  -0.373   0.0293  -1.8893   3.8131
 CRH  O3'   O  OH1   0  -0.665  -2.0005  -0.6771   5.0368
 CRH  O4'   O  OH1   0  -0.656   0.4551   0.0278   6.4315
 CRH  H21   H  HCH2  0   0.289  -1.7439  -0.2731   1.7148
 CRH  H22   H  HCH2  0   0.290  -1.1467   1.3505   1.4071
 CRH  H3    H  HCH1  0   0.273   0.4619  -1.2233   1.0451
 CRH  H41   H  HCH2  0   0.259   1.2235   1.6877   0.5421
 CRH  H42   H  HCH2  0   0.276   2.3249   0.3305   0.3921
 CRH  H5    H  HCR6  0   0.253   3.2774   0.3689  -4.3330
 CRH  H6    H  HCR6  0   0.257   2.5220   0.1234  -6.6507
 CRH  H10   H  HCR6  0   0.248   2.7794   0.5216  -1.9582
 CRH  H151  H  HCH3  0   0.243  -0.6979   0.6056  -7.9088
 CRH  H152  H  HCH3  0   0.243   0.8605  -0.1234  -8.2791
 CRH  H153  H  HCH3  0   0.244  -0.4920  -1.1319  -7.7814
 CRH  HO8   H  HOH1  0   0.487  -2.3533  -0.1587  -4.7394
 CRH  HO9   H  HOH1  0   0.496  -2.7855   0.0046  -2.1006
 CRH  H1'   H  HCH1  0   0.237   0.9080   1.1147   2.9433
 CRH  H3'   H  HCH1  0   0.261  -1.4620   0.8756   3.8234
 CRH  H4'   H  HCH1  0   0.242   0.5080   1.5377   5.1105
 CRH  H1'1  H  HCH3  0   0.245   3.9443  -0.5045   3.7953
 CRH  H1'2  H  HCH3  0   0.213   3.0164   0.9925   3.9835
 CRH  H1'3  H  HCH3  0   0.220   2.5140  -0.4811   4.8366
 CRH  H4'1  H  HCH3  0   0.245  -0.6378   2.3926   7.1070
 CRH  H4'2  H  HCH3  0   0.234  -1.6962   2.5182   5.7039
 CRH  H4'3  H  HCH3  0   0.233  -1.9584   1.2386   6.8907
 CRH  HO3   H  HOH1  0   0.451  -1.6844  -1.5905   5.0257
 CRH  HO4   H  HOH1  0   0.445  -0.1840  -0.4927   6.9317
 CRH  C1M   C  CH3   0  -0.422   2.9407  -0.0975   3.9055

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
 CRH  C1   C2    single    1.504  0.020  1.504
 CRH  C1   C13   single    1.448  0.020  1.448
 CRH  C1   O1    double    1.236  0.020  1.236
 CRH  C2   C3    single    1.526  0.020  1.526
 CRH  C2   H21   single    0.970  0.020  1.090
 CRH  C2   H22   single    0.970  0.020  1.090
 CRH  C3   C4    single    1.526  0.020  1.526
 CRH  C3   C1'   single    1.535  0.020  1.535
 CRH  C3   H3    single    0.970  0.020  1.090
 CRH  C4   C14   single    1.499  0.020  1.499
 CRH  C4   H41   single    0.970  0.020  1.090
 CRH  C4   H42   single    0.970  0.020  1.090
 CRH  C5   C6    aromatic  1.374  0.020  1.374
 CRH  C5   C11   aromatic  1.402  0.020  1.402
 CRH  C5   H5    single    0.930  0.020  1.080
 CRH  C6   C7    aromatic  1.401  0.020  1.401
 CRH  C6   H6    single    0.930  0.020  1.080
 CRH  C7   C8    aromatic  1.387  0.020  1.387
 CRH  C7   C15   single    1.500  0.020  1.500
 CRH  C8   C12   aromatic  1.425  0.020  1.425
 CRH  C8   O8    single    1.339  0.020  1.339
 CRH  C9   C12   aromatic  1.422  0.020  1.422
 CRH  C9   C13   aromatic  1.396  0.020  1.396
 CRH  C9   O9    single    1.327  0.020  1.327
 CRH  C10  C11   aromatic  1.422  0.020  1.422
 CRH  C10  C14   aromatic  1.359  0.020  1.359
 CRH  C10  H10   single    0.930  0.020  1.080
 CRH  C11  C12   aromatic  1.422  0.020  1.422
 CRH  C13  C14   aromatic  1.426  0.020  1.426
 CRH  C15  H151  single    0.970  0.020  1.090
 CRH  C15  H152  single    0.970  0.020  1.090
 CRH  C15  H153  single    0.970  0.020  1.090
 CRH  O8   HO8   single    0.850  0.020  0.980
 CRH  O9   HO9   single    0.850  0.020  0.980
 CRH  C1'  C2'   single    1.528  0.020  1.528
 CRH  C1'  O1'   single    1.396  0.020  1.396
 CRH  C1'  H1'   single    0.970  0.020  1.090
 CRH  C2'  C3'   single    1.515  0.020  1.515
 CRH  C2'  O2'   double    1.208  0.020  1.208
 CRH  C3'  C4'   single    1.544  0.020  1.544
 CRH  C3'  O3'   single    1.398  0.020  1.398
 CRH  C3'  H3'   single    0.970  0.020  1.090
 CRH  C4'  C4M   single    1.520  0.020  1.520
 CRH  C4'  O4'   single    1.408  0.020  1.408
 CRH  C4'  H4'   single    0.970  0.020  1.090
 CRH  C1M  O1'   single    1.411  0.020  1.411
 CRH  C1M  H1'1  single    0.970  0.020  1.090
 CRH  C1M  H1'2  single    0.970  0.020  1.090
 CRH  C1M  H1'3  single    0.970  0.020  1.090
 CRH  C4M  H4'1  single    0.970  0.020  1.090
 CRH  C4M  H4'2  single    0.970  0.020  1.090
 CRH  C4M  H4'3  single    0.970  0.020  1.090
 CRH  O3'  HO3   single    0.850  0.020  0.980
 CRH  O4'  HO4   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
 CRH  O1    C1   C13   121.58  3.000
 CRH  O1    C1   C2    119.37  3.000
 CRH  C13   C1   C2    119.04  3.000
 CRH  H22   C2   H21   106.73  3.000
 CRH  H22   C2   C3    109.95  3.000
 CRH  H21   C2   C3    112.81  3.000
 CRH  H22   C2   C1    106.79  3.000
 CRH  H21   C2   C1    107.05  3.000
 CRH  C3    C2   C1    113.13  3.000
 CRH  H3    C3   C1'   107.36  3.000
 CRH  H3    C3   C4    109.19  3.000
 CRH  C1'   C3   C4    110.36  3.000
 CRH  H3    C3   C2    108.58  3.000
 CRH  C1'   C3   C2    112.47  3.000
 CRH  C4    C3   C2    108.81  3.000
 CRH  H42   C4   H41   106.73  3.000
 CRH  H42   C4   C14   109.56  3.000
 CRH  H41   C4   C14   109.08  3.000
 CRH  H42   C4   C3    111.11  3.000
 CRH  H41   C4   C3    108.62  3.000
 CRH  C14   C4   C3    111.59  3.000
 CRH  H5    C5   C11   119.52  3.000
 CRH  H5    C5   C6    120.42  3.000
 CRH  C11   C5   C6    120.06  3.000
 CRH  H6    C6   C7    118.31  3.000
 CRH  H6    C6   C5    119.18  3.000
 CRH  C7    C6   C5    122.51  3.000
 CRH  C15   C7   C8    120.37  3.000
 CRH  C15   C7   C6    121.17  3.000
 CRH  C8    C7   C6    118.46  3.000
 CRH  O8    C8   C12   122.85  3.000
 CRH  O8    C8   C7    116.54  3.000
 CRH  C12   C8   C7    120.61  3.000
 CRH  O9    C9   C13   120.53  3.000
 CRH  O9    C9   C12   118.16  3.000
 CRH  C13   C9   C12   121.30  3.000
 CRH  H10   C10  C14   120.14  3.000
 CRH  H10   C10  C11   118.17  3.000
 CRH  C14   C10  C11   121.69  3.000
 CRH  C12   C11  C10   120.06  3.000
 CRH  C12   C11  C5    119.00  3.000
 CRH  C10   C11  C5    120.94  3.000
 CRH  C11   C12  C9    117.54  3.000
 CRH  C11   C12  C8    119.36  3.000
 CRH  C9    C12  C8    123.09  3.000
 CRH  C14   C13  C9    120.00  3.000
 CRH  C14   C13  C1    120.96  3.000
 CRH  C9    C13  C1    119.02  3.000
 CRH  C13   C14  C10   119.39  3.000
 CRH  C13   C14  C4    119.08  3.000
 CRH  C10   C14  C4    121.53  3.000
 CRH  H153  C15  H152  107.55  3.000
 CRH  H153  C15  H151  106.95  3.000
 CRH  H152  C15  H151  107.66  3.000
 CRH  H153  C15  C7    111.87  3.000
 CRH  H152  C15  C7    110.59  3.000
 CRH  H151  C15  C7    111.99  3.000
 CRH  HO8   O8   C8    110.46  3.000
 CRH  HO9   O9   C9    107.43  3.000
 CRH  H1'   C1'  O1'   111.10  3.000
 CRH  H1'   C1'  C2'   109.20  3.000
 CRH  O1'   C1'  C2'   110.81  3.000
 CRH  H1'   C1'  C3    108.49  3.000
 CRH  O1'   C1'  C3    107.35  3.000
 CRH  C2'   C1'  C3    109.85  3.000
 CRH  O2'   C2'  C3'   120.58  3.000
 CRH  O2'   C2'  C1'   121.07  3.000
 CRH  C3'   C2'  C1'   118.35  3.000
 CRH  H3'   C3'  O3'   109.27  3.000
 CRH  H3'   C3'  C4'   107.27  3.000
 CRH  O3'   C3'  C4'   111.20  3.000
 CRH  H3'   C3'  C2'   108.56  3.000
 CRH  O3'   C3'  C2'   110.94  3.000
 CRH  C4'   C3'  C2'   109.49  3.000
 CRH  H4'   C4'  O4'   105.95  3.000
 CRH  H4'   C4'  C4M   108.31  3.000
 CRH  O4'   C4'  C4M   112.23  3.000
 CRH  H4'   C4'  C3'   108.22  3.000
 CRH  O4'   C4'  C3'   110.70  3.000
 CRH  C4M   C4'  C3'   111.18  3.000
 CRH  H4'3  C4M  H4'2  108.02  3.000
 CRH  H4'3  C4M  H4'1  108.23  3.000
 CRH  H4'2  C4M  H4'1  107.84  3.000
 CRH  H4'3  C4M  C4'   111.48  3.000
 CRH  H4'2  C4M  C4'   110.98  3.000
 CRH  H4'1  C4M  C4'   110.17  3.000
 CRH  C1M   O1'  C1'   114.45  3.000
 CRH  HO3   O3'  C3'   108.07  3.000
 CRH  HO4   O4'  C4'   108.46  3.000
 CRH  H1'3  C1M  H1'2  108.38  3.000
 CRH  H1'3  C1M  H1'1  108.34  3.000
 CRH  H1'2  C1M  H1'1  108.39  3.000
 CRH  H1'3  C1M  O1'   112.62  3.000
 CRH  H1'2  C1M  O1'   111.65  3.000
 CRH  H1'1  C1M  O1'   107.33  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
 CRH  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 CRH  CONST_02  C14   C10  C11  C5    180.00   0.0  0
 CRH  CONST_03  C8    C12  C11  C5      0.00   0.0  0
 CRH  CONST_04  C9    C12  C11  C5    180.00   0.0  0
 CRH  CONST_05  C10   C11  C5   C6    180.00   0.0  0
 CRH  CONST_06  C12   C11  C5   C6      0.00   0.0  0
 CRH  CONST_07  C12   C8   C7   C6      0.00   0.0  0
 CRH  CONST_08  C11   C5   C6   C7      0.00   0.0  0
 CRH  CONST_09  C9    C12  C8   C7    180.00   0.0  0
 CRH  CONST_10  C11   C12  C8   C7      0.00   0.0  0
 CRH  CONST_11  C13   C9   C12  C8    180.00   0.0  0
 CRH  CONST_12  C10   C11  C12  C8    180.00   0.0  0
 CRH  CONST_13  C10   C11  C12  C9      0.00   0.0  0
 CRH  CONST_14  C10   C14  C13  C9      0.00   0.0  0
 CRH  CONST_15  C13   C14  C10  C11     0.00   0.0  0
 CRH  CONST_16  C13   C9   C12  C11     0.00   0.0  0
 CRH  CONST_17  C14   C13  C9   C12     0.00   0.0  0
 CRH  CONST_18  C14   C10  C11  C12     0.00   0.0  0
 CRH  CONST_19  O9    C9   C13  C1      0.00   0.0  0
 CRH  CONST_20  C15   C7   C6   C5    180.00   0.0  0
 CRH  CONST_21  O8    C8   C7   C6    180.00   0.0  0
 CRH  CONST_22  O9    C9   C12  C8      0.00   0.0  0
 CRH  CONST_23  O8    C8   C12  C9      0.00   0.0  0
 CRH  CONST_24  O8    C8   C12  C11   180.00   0.0  0
 CRH  CONST_25  O9    C9   C12  C11   180.00   0.0  0
 CRH  CONST_26  C15   C7   C8   C12   180.00   0.0  0
 CRH  CONST_27  O9    C9   C13  C14   180.00   0.0  0
 CRH  CONST_28  H10   C10  C14  C4      0.00   0.0  0
 CRH  CONST_29  H5    C5   C6   C7    180.00   0.0  0
 CRH  CONST_30  H6    C6   C7   C8    180.00   0.0  0
 CRH  Var_01    C9    C13  C1   C2    177.39  30.0  1
 CRH  Var_02    C13   C1   C2   C3    -24.67  30.0  1
 CRH  Var_03    C10   C14  C4   C3   -147.18  30.0  1
 CRH  Var_04    H151  C15  C7   C6   -121.90  30.0  2
 CRH  Var_05    H1'1  C1M  O1'  C1'  -175.73  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
 CRH  chir_01  C3   C2   C4   C1'  negativ
 CRH  chir_02  C1'  O1'  C2'  C3   positiv
 CRH  chir_03  C3'  O3'  C4'  C2'  negativ
 CRH  chir_04  C4'  O4'  C3'  C4M  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
 CRH  plan-1  C1   0.020
 CRH  plan-1  C2   0.020
 CRH  plan-1  C13  0.020
 CRH  plan-1  O1   0.020
 CRH  plan-2  C1   0.020
 CRH  plan-2  C4   0.020
 CRH  plan-2  C5   0.020
 CRH  plan-2  C6   0.020
 CRH  plan-2  C7   0.020
 CRH  plan-2  C8   0.020
 CRH  plan-2  C9   0.020
 CRH  plan-2  C10  0.020
 CRH  plan-2  C11  0.020
 CRH  plan-2  C12  0.020
 CRH  plan-2  C13  0.020
 CRH  plan-2  C14  0.020
 CRH  plan-2  C15  0.020
 CRH  plan-2  O8   0.020
 CRH  plan-2  O9   0.020
 CRH  plan-2  H5   0.020
 CRH  plan-2  H6   0.020
 CRH  plan-2  H10  0.020
 CRH  plan-3  C1'  0.020
 CRH  plan-3  C2'  0.020
 CRH  plan-3  C3'  0.020
 CRH  plan-3  O2'  0.020

