# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:58:00 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C1=Cc2ccc(O)cc2OC1=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
 YZ9  YZ9  'ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate'  ligand  27  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YZ9
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
 YZ9  C3    C  CH3   0  -0.686   0.9359  -0.1780   5.4688
 YZ9  C11   C  CH2   0  -0.185  -0.3046  -0.0284   4.6229
 YZ9  O1    O  O     0  -0.456  -2.0143   0.1032   2.5741
 YZ9  O2    O  O2    0  -0.443   0.1078   0.0080   3.2464
 YZ9  C6    C  CR16  0  -0.286  -1.7423   0.0052  -2.5081
 YZ9  C5    C  CR16  0  -0.120  -1.2249   0.0515  -0.0713
 YZ9  C4    C  CR16  0  -0.463   1.0026   0.1654  -3.0147
 YZ9  O3    O  O     0  -0.468   1.4198   0.2019  -0.7156
 YZ9  C2    C  CR66  0   0.002  -0.8413   0.0663  -1.4328
 YZ9  C1    C  CR66  0   0.413   0.5236   0.1450  -1.7172
 YZ9  C7    C  CR6   0   0.558   1.1056   0.1904   0.6170
 YZ9  C12   C  C     0   0.622  -0.8302   0.0746   2.3266
 YZ9  O4    O  OH1   0  -0.606   0.4648   0.1192  -5.3384
 YZ9  O5    O  OC    0  -0.397   2.0347   0.2620   1.3739
 YZ9  C10   C  CR16  0  -0.336  -1.2935   0.0229  -3.8029
 YZ9  C9    C  CR6   0  -0.376  -0.3133   0.1038   0.9367
 YZ9  C8    C  CR6   0   0.390   0.0874   0.1043  -4.0604
 YZ9  H31   H  HCH3  0   0.239   0.6469  -0.2039   6.5191
 YZ9  H32   H  HCH3  0   0.236   1.4655  -1.1037   5.2447
 YZ9  H33   H  HCH3  0   0.237   1.6202   0.6587   5.3307
 YZ9  H111  H  HCH2  0   0.237  -0.9893  -0.8637   4.7803
 YZ9  H112  H  HCH2  0   0.238  -0.8358   0.8933   4.8689
 YZ9  H6    H  HCR6  0   0.281  -2.8037  -0.0571  -2.3048
 YZ9  H5    H  HCR6  0   0.297  -2.2802  -0.0088   0.1656
 YZ9  H4    H  HCR6  0   0.302   2.0678   0.2282  -3.2013
 YZ9  HO4   H  HOH1  0   0.487   1.4249   0.1733  -5.4203
 YZ9  H10   H  HCR6  0   0.284  -1.9879  -0.0250  -4.6306

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
 YZ9  C3   C11   single    1.509  0.020  1.509
 YZ9  C3   H31   single    0.970  0.020  1.090
 YZ9  C3   H32   single    0.970  0.020  1.090
 YZ9  C3   H33   single    0.970  0.020  1.090
 YZ9  C11  O2    single    1.437  0.020  1.437
 YZ9  C11  H111  single    0.970  0.020  1.090
 YZ9  C11  H112  single    0.970  0.020  1.090
 YZ9  O1   C12   double    1.210  0.020  1.210
 YZ9  O2   C12   single    1.315  0.020  1.315
 YZ9  C6   C2    aromatic  1.404  0.020  1.404
 YZ9  C6   C10   aromatic  1.370  0.020  1.370
 YZ9  C6   H6    single    0.930  0.020  1.080
 YZ9  C5   C2    aromatic  1.415  0.020  1.415
 YZ9  C5   C9    aromatic  1.360  0.020  1.360
 YZ9  C5   H5    single    0.930  0.020  1.080
 YZ9  C4   C1    aromatic  1.383  0.020  1.383
 YZ9  C4   C8    aromatic  1.391  0.020  1.391
 YZ9  C4   H4    single    0.930  0.020  1.080
 YZ9  O3   C1    aromatic  1.345  0.020  1.345
 YZ9  O3   C7    aromatic  1.369  0.020  1.369
 YZ9  C2   C1    aromatic  1.396  0.020  1.396
 YZ9  C7   O5    double    1.200  0.020  1.200
 YZ9  C7   C9    aromatic  1.457  0.020  1.457
 YZ9  C12  C9    single    1.483  0.020  1.483
 YZ9  O4   C8    single    1.333  0.020  1.333
 YZ9  O4   HO4   single    0.850  0.020  0.980
 YZ9  C10  C8    aromatic  1.407  0.020  1.407
 YZ9  C10  H10   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
 YZ9  H33   C3   H32   108.73  3.000
 YZ9  H33   C3   H31   107.87  3.000
 YZ9  H32   C3   H31   107.87  3.000
 YZ9  H33   C3   C11   111.66  3.000
 YZ9  H32   C3   C11   111.62  3.000
 YZ9  H31   C3   C11   108.95  3.000
 YZ9  H112  C11  H111  107.95  3.000
 YZ9  H112  C11  O2    109.51  3.000
 YZ9  H111  C11  O2    109.72  3.000
 YZ9  H112  C11  C3    110.94  3.000
 YZ9  H111  C11  C3    111.04  3.000
 YZ9  O2    C11  C3    107.67  3.000
 YZ9  C12   O2   C11   117.80  3.000
 YZ9  H6    C6   C10   119.95  3.000
 YZ9  H6    C6   C2    119.20  3.000
 YZ9  C10   C6   C2    120.85  3.000
 YZ9  H5    C5   C9    119.54  3.000
 YZ9  H5    C5   C2    118.37  3.000
 YZ9  C9    C5   C2    122.08  3.000
 YZ9  H4    C4   C8    121.33  3.000
 YZ9  H4    C4   C1    120.19  3.000
 YZ9  C8    C4   C1    118.47  3.000
 YZ9  C7    O3   C1    124.85  3.000
 YZ9  C1    C2   C5    117.49  3.000
 YZ9  C1    C2   C6    118.27  3.000
 YZ9  C5    C2   C6    124.23  3.000
 YZ9  C2    C1   O3    120.13  3.000
 YZ9  C2    C1   C4    122.02  3.000
 YZ9  O3    C1   C4    117.85  3.000
 YZ9  C9    C7   O5    128.23  3.000
 YZ9  C9    C7   O3    115.94  3.000
 YZ9  O5    C7   O3    115.82  3.000
 YZ9  C9    C12  O2    114.06  3.000
 YZ9  C9    C12  O1    122.16  3.000
 YZ9  O2    C12  O1    123.78  3.000
 YZ9  HO4   O4   C8    111.33  3.000
 YZ9  H10   C10  C8    119.51  3.000
 YZ9  H10   C10  C6    120.81  3.000
 YZ9  C8    C10  C6    119.68  3.000
 YZ9  C12   C9   C7    123.11  3.000
 YZ9  C12   C9   C5    117.40  3.000
 YZ9  C7    C9   C5    119.50  3.000
 YZ9  C10   C8   O4    117.01  3.000
 YZ9  C10   C8   C4    120.71  3.000
 YZ9  O4    C8   C4    122.28  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
 YZ9  CONST_01  C9    C5   C2   C6    180.00   0.0  0
 YZ9  CONST_02  C4    C1   C2   C6      0.00   0.0  0
 YZ9  CONST_03  O3    C1   C2   C6    180.00   0.0  0
 YZ9  CONST_04  C4    C8   C10  C6      0.00   0.0  0
 YZ9  CONST_05  C10   C6   C2   C5    180.00   0.0  0
 YZ9  CONST_06  C4    C1   C2   C5    180.00   0.0  0
 YZ9  CONST_07  O3    C1   C2   C5      0.00   0.0  0
 YZ9  CONST_08  O3    C7   C9   C5      0.00   0.0  0
 YZ9  CONST_09  C7    O3   C1   C4    180.00   0.0  0
 YZ9  CONST_10  C8    C4   C1   O3    180.00   0.0  0
 YZ9  CONST_11  C8    C10  C6   C2      0.00   0.0  0
 YZ9  CONST_12  C7    C9   C5   C2      0.00   0.0  0
 YZ9  CONST_13  C8    C4   C1   C2      0.00   0.0  0
 YZ9  CONST_14  C7    O3   C1   C2      0.00   0.0  0
 YZ9  CONST_15  C10   C8   C4   C1      0.00   0.0  0
 YZ9  CONST_16  C9    C7   O3   C1      0.00   0.0  0
 YZ9  CONST_17  C10   C6   C2   C1      0.00   0.0  0
 YZ9  CONST_18  C9    C5   C2   C1      0.00   0.0  0
 YZ9  CONST_19  O4    C8   C10  C6    180.00   0.0  0
 YZ9  CONST_20  O5    C7   C9   C5    180.00   0.0  0
 YZ9  CONST_21  C12   C9   C7   O3    180.00   0.0  0
 YZ9  CONST_22  C12   C9   C5   C2    180.00   0.0  0
 YZ9  CONST_23  O4    C8   C4   C1    180.00   0.0  0
 YZ9  CONST_24  O5    C7   O3   C1    180.00   0.0  0
 YZ9  CONST_25  H5    C5   C2   C6      0.00   0.0  0
 YZ9  CONST_26  H6    C6   C2   C5      0.00   0.0  0
 YZ9  CONST_27  H10   C10  C8   C4    180.00   0.0  0
 YZ9  CONST_28  H4    C4   C1   O3      0.00   0.0  0
 YZ9  Var_01    C5    C9   C12  O1     -5.38  30.0  2
 YZ9  Var_02    C9    C12  O2   C11  -179.83  30.0  3
 YZ9  Var_03    H31   C3   C11  O2    179.78  30.0  3
 YZ9  Var_04    H111  C11  O2   C12    56.04  30.0  1

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
 YZ9  plan-1  O3   0.020
 YZ9  plan-1  C7   0.020
 YZ9  plan-1  O5   0.020
 YZ9  plan-1  C9   0.020
 YZ9  plan-2  C6   0.020
 YZ9  plan-2  C5   0.020
 YZ9  plan-2  C4   0.020
 YZ9  plan-2  O3   0.020
 YZ9  plan-2  C2   0.020
 YZ9  plan-2  C1   0.020
 YZ9  plan-2  O4   0.020
 YZ9  plan-2  C10  0.020
 YZ9  plan-2  C8   0.020
 YZ9  plan-2  H6   0.020
 YZ9  plan-2  H4   0.020
 YZ9  plan-2  H10  0.020
 YZ9  plan-3  O1   0.020
 YZ9  plan-3  O2   0.020
 YZ9  plan-3  C12  0.020
 YZ9  plan-3  C9   0.020

