# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 09:01:38 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3R)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCC[C@H](C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2)O1
#
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
 9CU  9CU  (3R)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one  ligand  41  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9CU
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
 9CU  C16  C  CH3   0  -0.680  -4.0590   0.8049   2.5592
 9CU  C7   C  CH1   0   0.034  -0.3320  -0.7350  -0.3252
 9CU  C6   C  CH2   0  -0.533   0.8499  -1.6555  -0.5419
 9CU  C9   C  CR6   0  -0.344   2.1894   0.4069  -0.2439
 9CU  C2   C  CR16  0  -0.495   4.4563   0.3544   0.6076
 9CU  C14  C  CH2   0  -0.452  -5.3174  -0.1759  -0.9665
 9CU  C15  C  CH2   0  -0.441  -4.0984  -1.0310  -1.2956
 9CU  C8   C  C     0   0.613   1.0648   1.1583  -0.7789
 9CU  C5   C  CR6   0   0.171   2.1142  -0.9871  -0.0983
 9CU  C4   C  CR16  0  -0.447   3.1793  -1.7007   0.3987
 9CU  C12  C  CH1   0   0.051  -4.0663   0.6288   1.0549
 9CU  C3   C  CR6   0   0.410   4.3514  -1.0223   0.7588
 9CU  C10  C  CH2   0  -0.487  -1.6190  -1.2867  -0.9036
 9CU  C1   C  CR6   0   0.399   3.3843   1.0759   0.0945
 9CU  C13  C  CH2   0  -0.436  -5.3933   0.0930   0.5324
 9CU  O5   O  O2    0  -0.503  -3.0074  -0.2507   0.7151
 9CU  C11  C  CH1   0   0.062  -2.8466  -0.4198  -0.6792
 9CU  O3   O  O2    0  -0.446  -0.0902   0.5407  -0.9583
 9CU  O4   O  O     0  -0.488   1.1365   2.3406  -1.0853
 9CU  O2   O  OH1   0  -0.616   5.3533  -1.7603   1.2460
 9CU  O1   O  OH1   0  -0.622   3.5272   2.3886  -0.0573
 9CU  H1   H  HCH3  0   0.223  -4.2678  -0.1379   3.0684
 9CU  H2   H  HCH3  0   0.234  -3.0974   1.1808   2.9106
 9CU  H3   H  HCH3  0   0.228  -4.8259   1.5213   2.8544
 9CU  H4   H  HCH1  0   0.262  -0.4507  -0.5488   0.7466
 9CU  H5   H  HCH2  0   0.279   0.6870  -2.5828   0.0088
 9CU  H6   H  HCH2  0   0.273   0.9306  -1.9242  -1.6008
 9CU  H7   H  HCR6  0   0.285   5.3666   0.8760   0.8805
 9CU  H8   H  HCH2  0   0.217  -5.2465   0.7752  -1.5044
 9CU  H9   H  HCH2  0   0.236  -6.2310  -0.6610  -1.3157
 9CU  H10  H  HCH2  0   0.218  -4.2349  -2.0474  -0.9104
 9CU  H11  H  HCH2  0   0.234  -3.9696  -1.1134  -2.3776
 9CU  H12  H  HCR6  0   0.266   3.1202  -2.7754   0.5156
 9CU  H13  H  HCH1  0   0.192  -3.8790   1.6068   0.5814
 9CU  H14  H  HCH2  0   0.247  -1.4923  -1.4502  -1.9775
 9CU  H15  H  HCH2  0   0.247  -1.7877  -2.2712  -0.4563
 9CU  H16  H  HCH2  0   0.231  -6.1861   0.8116   0.7548
 9CU  H17  H  HCH2  0   0.215  -5.6410  -0.8314   1.0654
 9CU  H18  H  HCH1  0   0.202  -2.6875   0.5656  -1.1469
 9CU  H19  H  HOH1  0   0.482   6.1140  -1.2078   1.4616
 9CU  H20  H  HOH1  0   0.477   2.7075   2.7341  -0.4748

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
 9CU  O1   C1   single    1.329  0.020  1.329
 9CU  O4   C8   double    1.224  0.020  1.224
 9CU  C1   C2   aromatic  1.390  0.020  1.390
 9CU  C1   C9   aromatic  1.411  0.020  1.411
 9CU  C2   C3   aromatic  1.389  0.020  1.389
 9CU  C8   C9   single    1.454  0.020  1.454
 9CU  C8   O3   single    1.322  0.020  1.322
 9CU  C9   C5   aromatic  1.404  0.020  1.404
 9CU  C3   O2   single    1.336  0.020  1.336
 9CU  C3   C4   aromatic  1.401  0.020  1.401
 9CU  O3   C7   single    1.445  0.020  1.445
 9CU  C5   C4   aromatic  1.375  0.020  1.375
 9CU  C5   C6   single    1.497  0.020  1.497
 9CU  C6   C7   single    1.514  0.020  1.514
 9CU  C7   C10  single    1.515  0.020  1.515
 9CU  C10  C11  single    1.520  0.020  1.520
 9CU  C11  C15  single    1.523  0.020  1.523
 9CU  C11  O5   single    1.414  0.020  1.414
 9CU  C15  C14  single    1.525  0.020  1.525
 9CU  O5   C12  single    1.418  0.020  1.418
 9CU  C14  C13  single    1.525  0.020  1.525
 9CU  C12  C13  single    1.523  0.020  1.523
 9CU  C12  C16  single    1.515  0.020  1.515
 9CU  C16  H1   single    0.970  0.020  1.090
 9CU  C16  H2   single    0.970  0.020  1.090
 9CU  C16  H3   single    0.970  0.020  1.090
 9CU  C7   H4   single    0.970  0.020  1.090
 9CU  C6   H5   single    0.970  0.020  1.090
 9CU  C6   H6   single    0.970  0.020  1.090
 9CU  C2   H7   single    0.930  0.020  1.080
 9CU  C14  H8   single    0.970  0.020  1.090
 9CU  C14  H9   single    0.970  0.020  1.090
 9CU  C15  H10  single    0.970  0.020  1.090
 9CU  C15  H11  single    0.970  0.020  1.090
 9CU  C4   H12  single    0.930  0.020  1.080
 9CU  C12  H13  single    0.970  0.020  1.090
 9CU  C10  H14  single    0.970  0.020  1.090
 9CU  C10  H15  single    0.970  0.020  1.090
 9CU  C13  H16  single    0.970  0.020  1.090
 9CU  C13  H17  single    0.970  0.020  1.090
 9CU  C11  H18  single    0.970  0.020  1.090
 9CU  O2   H19  single    0.850  0.020  0.980
 9CU  O1   H20  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
 9CU  H3   C16  H2   107.85  3.000
 9CU  H3   C16  H1   107.86  3.000
 9CU  H2   C16  H1   108.42  3.000
 9CU  H3   C16  C12  110.00  3.000
 9CU  H2   C16  C12  111.37  3.000
 9CU  H1   C16  C12  111.22  3.000
 9CU  H4   C7   O3   107.28  3.000
 9CU  H4   C7   C10  110.10  3.000
 9CU  O3   C7   C10  107.25  3.000
 9CU  H4   C7   C6   109.17  3.000
 9CU  C10  C7   C6   112.78  3.000
 9CU  O3   C7   C6   110.10  3.000
 9CU  H6   C6   H5   106.89  3.000
 9CU  H6   C6   C5   109.49  3.000
 9CU  H5   C6   C5   110.86  3.000
 9CU  H6   C6   C7   110.19  3.000
 9CU  H5   C6   C7   109.15  3.000
 9CU  C5   C6   C7   110.21  3.000
 9CU  C1   C9   C5   119.44  3.000
 9CU  C5   C9   C8   120.65  3.000
 9CU  C1   C9   C8   119.88  3.000
 9CU  H7   C2   C1   119.38  3.000
 9CU  H7   C2   C3   120.86  3.000
 9CU  C1   C2   C3   119.76  3.000
 9CU  H9   C14  H8   106.44  3.000
 9CU  H9   C14  C13  110.56  3.000
 9CU  H8   C14  C13  109.45  3.000
 9CU  H9   C14  C15  110.54  3.000
 9CU  H8   C14  C15  109.22  3.000
 9CU  C13  C14  C15  110.54  3.000
 9CU  H11  C15  H10  107.03  3.000
 9CU  H11  C15  C11  109.52  3.000
 9CU  H10  C15  C11  109.41  3.000
 9CU  H11  C15  C14  110.50  3.000
 9CU  H10  C15  C14  110.17  3.000
 9CU  C11  C15  C14  110.16  3.000
 9CU  O4   C8   O3   117.95  3.000
 9CU  O3   C8   C9   118.95  3.000
 9CU  O4   C8   C9   123.09  3.000
 9CU  C4   C5   C9   120.76  3.000
 9CU  C4   C5   C6   121.97  3.000
 9CU  C9   C5   C6   117.25  3.000
 9CU  H12  C4   C3   119.90  3.000
 9CU  H12  C4   C5   120.79  3.000
 9CU  C3   C4   C5   119.31  3.000
 9CU  H13  C12  O5   108.68  3.000
 9CU  H13  C12  C13  108.22  3.000
 9CU  O5   C12  C13  110.50  3.000
 9CU  H13  C12  C16  108.82  3.000
 9CU  C13  C12  C16  112.69  3.000
 9CU  O5   C12  C16  107.85  3.000
 9CU  O2   C3   C4   116.96  3.000
 9CU  C4   C3   C2   121.00  3.000
 9CU  O2   C3   C2   122.04  3.000
 9CU  H15  C10  H14  106.54  3.000
 9CU  H15  C10  C11  109.16  3.000
 9CU  H14  C10  C11  108.90  3.000
 9CU  H15  C10  C7   107.61  3.000
 9CU  H14  C10  C7   109.32  3.000
 9CU  C11  C10  C7   114.97  3.000
 9CU  O1   C1   C2   118.15  3.000
 9CU  C2   C1   C9   119.70  3.000
 9CU  O1   C1   C9   122.15  3.000
 9CU  H17  C13  H16  106.97  3.000
 9CU  H17  C13  C12  109.08  3.000
 9CU  H16  C13  C12  109.32  3.000
 9CU  H17  C13  C14  109.92  3.000
 9CU  H16  C13  C14  110.62  3.000
 9CU  C12  C13  C14  110.85  3.000
 9CU  C11  O5   C12  113.30  3.000
 9CU  H18  C11  O5   109.14  3.000
 9CU  H18  C11  C10  109.31  3.000
 9CU  O5   C11  C10  107.81  3.000
 9CU  H18  C11  C15  107.79  3.000
 9CU  O5   C11  C15  110.71  3.000
 9CU  C10  C11  C15  112.04  3.000
 9CU  C8   O3   C7   119.96  3.000
 9CU  H19  O2   C3   110.88  3.000
 9CU  H20  O1   C1   107.82  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
 9CU  CONST_01  C3   C2   C1   C9     0.00   0.0  0
 9CU  CONST_02  C3   C4   C5   C9     0.00   0.0  0
 9CU  CONST_03  C5   C9   C1   C2     0.00   0.0  0
 9CU  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 9CU  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 9CU  CONST_06  C1   C9   C5   C4     0.00   0.0  0
 9CU  CONST_07  O1   C1   C9   C8     0.00   0.0  0
 9CU  CONST_08  O1   C1   C9   C5   180.00   0.0  0
 9CU  CONST_09  O2   C3   C4   C5   180.00   0.0  0
 9CU  CONST_10  O1   C1   C2   C3   180.00   0.0  0
 9CU  CONST_11  O2   C3   C2   C1   180.00   0.0  0
 9CU  CONST_12  H12  C4   C5   C6     0.00   0.0  0
 9CU  CONST_13  H7   C2   C1   C9   180.00   0.0  0
 9CU  Var_01    C9   C8   O3   C7    15.72  30.0  1
 9CU  Var_02    C9   C5   C6   C7   -32.27  30.0  1
 9CU  Var_03    C12  C13  C14  C15   51.07  30.0  1
 9CU  Var_04    O3   C8   C9   C5     9.00  30.0  1
 9CU  Var_05    C11  C15  C14  C13  -51.39  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
 9CU  chir_01  C7   O3  C6   C10  positiv
 9CU  chir_02  C12  O5  C13  C16  negativ
 9CU  chir_03  C11  O5  C15  C10  positiv

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
 9CU  plan-1  C9   0.020
 9CU  plan-1  C8   0.020
 9CU  plan-1  O3   0.020
 9CU  plan-1  O4   0.020
 9CU  plan-2  C6   0.020
 9CU  plan-2  C9   0.020
 9CU  plan-2  C2   0.020
 9CU  plan-2  C8   0.020
 9CU  plan-2  C5   0.020
 9CU  plan-2  C4   0.020
 9CU  plan-2  C3   0.020
 9CU  plan-2  C1   0.020
 9CU  plan-2  O2   0.020
 9CU  plan-2  O1   0.020
 9CU  plan-2  H7   0.020
 9CU  plan-2  H12  0.020

