# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:10:38 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (1R)-1,6-dimethyl-1,2-dihydrophenanthro[1,2-b]furan-10,11-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1COC2=C1C(=O)C(=O)c3c2ccc4c(C)cccc34
#
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
 1YL  1YL  (1R)-1,6-dimethyl-1,2-dihydrophenanthro[1,2-b]furan-10,11-dione  ligand  35  21  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1YL
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
 1YL  C18  C  CH3   0  -0.757   4.7015   1.9676   0.1113
 1YL  C4   C  CR6   0   0.103   3.9239   0.6858   0.0759
 1YL  C3   C  CR16  0  -0.324   4.5740  -0.5179   0.1196
 1YL  C2   C  CR16  0  -0.212   3.8558  -1.7260   0.0967
 1YL  C1   C  CR16  0  -0.367   2.4915  -1.7423   0.0241
 1YL  C10  C  CR66  0   0.167   1.7573  -0.5291  -0.0298
 1YL  C5   C  CR66  0   0.047   2.4986   0.6935   0.0009
 1YL  C6   C  CR16  0  -0.317   1.8073   1.9200  -0.0454
 1YL  C7   C  CR16  0  -0.278   0.4442   1.9715  -0.1144
 1YL  C8   C  CR66  0  -0.027  -0.2960   0.7812  -0.1377
 1YL  C9   C  CR66  0  -0.066   0.3295  -0.4621  -0.1016
 1YL  C11  C  CR6   0   0.234  -0.5376  -1.6706  -0.1591
 1YL  O21  O  O     0  -0.351  -0.1249  -2.8022  -0.2354
 1YL  C12  C  CR6   0   0.254  -2.0862  -1.5234  -0.1306
 1YL  O20  O  O     0  -0.393  -2.7486  -2.5407  -0.0734
 1YL  C13  C  CR6   0  -0.220  -2.5968  -0.2018  -0.1924
 1YL  C14  C  CR6   0   0.492  -1.7494   0.8472  -0.1993
 1YL  O19  O  O2    0  -0.456  -2.3445   2.0249  -0.2539
 1YL  C16  C  CH2   0  -0.189  -3.7672   1.7950  -0.4410
 1YL  C15  C  CH1   0  -0.309  -4.0111   0.3010  -0.1545
 1YL  C17  C  CH3   0  -0.660  -4.6933   0.0428   1.1859
 1YL  H1   H  HCH3  0   0.253   4.4460   2.5735   0.9822
 1YL  H2   H  HCH3  0   0.262   5.7698   1.7637   0.1553
 1YL  H3   H  HCH3  0   0.253   4.5187   2.5827  -0.7715
 1YL  H4   H  HCR6  0   0.260   5.6552  -0.5444   0.1746
 1YL  H5   H  HCR6  0   0.265   4.3963  -2.6628   0.1382
 1YL  H6   H  HCR6  0   0.274   1.9834  -2.6896   0.0080
 1YL  H7   H  HCR6  0   0.276   2.3632   2.8473  -0.0284
 1YL  H8   H  HCR6  0   0.274  -0.0564   2.9286  -0.1499
 1YL  H11  H  HCH2  0   0.260  -4.3011   2.4637   0.2326
 1YL  H12  H  HCH2  0   0.265  -4.0049   2.0632  -1.4706
 1YL  H13  H  HCH1  0   0.278  -4.6124  -0.1352  -0.9548
 1YL  H14  H  HCH3  0   0.230  -4.1397   0.5037   2.0054
 1YL  H15  H  HCH3  0   0.241  -5.7045   0.4512   1.1875
 1YL  H16  H  HCH3  0   0.242  -4.7657  -1.0253   1.3859

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
 1YL  C2   C1   aromatic  1.366  0.020  1.366
 1YL  C2   C3   aromatic  1.406  0.020  1.406
 1YL  O21  C11  double    1.207  0.020  1.207
 1YL  C1   C10  aromatic  1.419  0.020  1.419
 1YL  O20  C12  double    1.215  0.020  1.215
 1YL  C3   C4   aromatic  1.369  0.020  1.369
 1YL  C11  C12  single    1.556  0.020  1.556
 1YL  C11  C9   single    1.489  0.020  1.489
 1YL  C12  C13  single    1.418  0.020  1.418
 1YL  C10  C9   aromatic  1.431  0.020  1.431
 1YL  C10  C5   aromatic  1.430  0.020  1.430
 1YL  C9   C8   aromatic  1.392  0.020  1.392
 1YL  C4   C5   aromatic  1.427  0.020  1.427
 1YL  C4   C18  single    1.500  0.020  1.500
 1YL  C5   C6   aromatic  1.409  0.020  1.409
 1YL  C13  C15  single    1.501  0.020  1.501
 1YL  C13  C14  double    1.349  0.020  1.349
 1YL  C8   C14  single    1.456  0.020  1.456
 1YL  C8   C7   aromatic  1.402  0.020  1.402
 1YL  C15  C17  single    1.526  0.020  1.526
 1YL  C15  C16  single    1.541  0.020  1.541
 1YL  C14  O19  single    1.321  0.020  1.321
 1YL  C6   C7   aromatic  1.366  0.020  1.366
 1YL  C16  O19  single    1.453  0.020  1.453
 1YL  C18  H1   single    0.970  0.020  1.090
 1YL  C18  H2   single    0.970  0.020  1.090
 1YL  C18  H3   single    0.970  0.020  1.090
 1YL  C3   H4   single    0.930  0.020  1.080
 1YL  C2   H5   single    0.930  0.020  1.080
 1YL  C1   H6   single    0.930  0.020  1.080
 1YL  C6   H7   single    0.930  0.020  1.080
 1YL  C7   H8   single    0.930  0.020  1.080
 1YL  C16  H11  single    0.970  0.020  1.090
 1YL  C16  H12  single    0.970  0.020  1.090
 1YL  C15  H13  single    0.970  0.020  1.090
 1YL  C17  H14  single    0.970  0.020  1.090
 1YL  C17  H15  single    0.970  0.020  1.090
 1YL  C17  H16  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
 1YL  H3   C18  H2   107.62  3.000
 1YL  H3   C18  H1   107.06  3.000
 1YL  H2   C18  H1   107.55  3.000
 1YL  H3   C18  C4   112.07  3.000
 1YL  H2   C18  C4   110.48  3.000
 1YL  H1   C18  C4   111.84  3.000
 1YL  C5   C4   C3   118.73  3.000
 1YL  C5   C4   C18  120.96  3.000
 1YL  C3   C4   C18  120.30  3.000
 1YL  H4   C3   C2   119.34  3.000
 1YL  H4   C3   C4   119.83  3.000
 1YL  C2   C3   C4   120.84  3.000
 1YL  H5   C2   C1   119.36  3.000
 1YL  H5   C2   C3   119.22  3.000
 1YL  C1   C2   C3   121.42  3.000
 1YL  H6   C1   C10  120.55  3.000
 1YL  H6   C1   C2   118.90  3.000
 1YL  C10  C1   C2   120.56  3.000
 1YL  C9   C10  C5   118.57  3.000
 1YL  C5   C10  C1   117.50  3.000
 1YL  C9   C10  C1   123.92  3.000
 1YL  C6   C5   C10  119.29  3.000
 1YL  C6   C5   C4   119.77  3.000
 1YL  C10  C5   C4   120.94  3.000
 1YL  H7   C6   C7   118.78  3.000
 1YL  H7   C6   C5   119.59  3.000
 1YL  C7   C6   C5   121.62  3.000
 1YL  H8   C7   C8   120.45  3.000
 1YL  H8   C7   C6   119.83  3.000
 1YL  C8   C7   C6   119.72  3.000
 1YL  C14  C8   C9   119.34  3.000
 1YL  C14  C8   C7   119.29  3.000
 1YL  C9   C8   C7   121.38  3.000
 1YL  C11  C9   C8   117.54  3.000
 1YL  C8   C9   C10  119.42  3.000
 1YL  C11  C9   C10  123.03  3.000
 1YL  C12  C11  O21  115.48  3.000
 1YL  C12  C11  C9   120.15  3.000
 1YL  O21  C11  C9   124.37  3.000
 1YL  C13  C12  O20  125.86  3.000
 1YL  C13  C12  C11  116.47  3.000
 1YL  O20  C12  C11  117.66  3.000
 1YL  C15  C13  C14  109.36  3.000
 1YL  C14  C13  C12  119.93  3.000
 1YL  C15  C13  C12  130.55  3.000
 1YL  O19  C14  C13  114.25  3.000
 1YL  O19  C14  C8   119.47  3.000
 1YL  C13  C14  C8   126.28  3.000
 1YL  C16  O19  C14  107.78  3.000
 1YL  H12  C16  H11  109.04  3.000
 1YL  H12  C16  C15  112.32  3.000
 1YL  H11  C16  C15  113.76  3.000
 1YL  H12  C16  O19  107.22  3.000
 1YL  H11  C16  O19  107.65  3.000
 1YL  C15  C16  O19  106.52  3.000
 1YL  H13  C15  C17  109.27  3.000
 1YL  H13  C15  C16  109.77  3.000
 1YL  C17  C15  C16  113.46  3.000
 1YL  H13  C15  C13  111.50  3.000
 1YL  C16  C15  C13   99.84  3.000
 1YL  C17  C15  C13  112.75  3.000
 1YL  H16  C17  H15  107.77  3.000
 1YL  H16  C17  H14  108.07  3.000
 1YL  H15  C17  H14  108.13  3.000
 1YL  H16  C17  C15  110.91  3.000
 1YL  H15  C17  C15  110.64  3.000
 1YL  H14  C17  C15  111.19  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
 1YL  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 1YL  CONST_02  C1   C10  C5   C4      0.00   0.0  0
 1YL  CONST_03  C9   C10  C5   C4    180.00   0.0  0
 1YL  CONST_04  C7   C6   C5   C4    180.00   0.0  0
 1YL  CONST_05  C10  C1   C2   C3      0.00   0.0  0
 1YL  CONST_06  C10  C5   C4   C3      0.00   0.0  0
 1YL  CONST_07  C6   C5   C4   C3    180.00   0.0  0
 1YL  CONST_08  C9   C10  C1   C2    180.00   0.0  0
 1YL  CONST_09  C5   C10  C1   C2      0.00   0.0  0
 1YL  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 1YL  CONST_11  C8   C9   C10  C1    180.00   0.0  0
 1YL  CONST_12  C6   C5   C10  C1    180.00   0.0  0
 1YL  CONST_13  C7   C8   C9   C10     0.00   0.0  0
 1YL  CONST_14  C7   C6   C5   C10     0.00   0.0  0
 1YL  CONST_15  C8   C9   C10  C5      0.00   0.0  0
 1YL  CONST_16  C8   C7   C6   C5      0.00   0.0  0
 1YL  CONST_17  C9   C10  C5   C6      0.00   0.0  0
 1YL  CONST_18  C9   C8   C7   C6      0.00   0.0  0
 1YL  CONST_19  C2   C3   C4   C18   180.00   0.0  0
 1YL  CONST_20  C10  C5   C4   C18   180.00   0.0  0
 1YL  CONST_21  C6   C5   C4   C18     0.00   0.0  0
 1YL  CONST_22  H5   C2   C3   C4    180.00   0.0  0
 1YL  CONST_23  H7   C6   C5   C4      0.00   0.0  0
 1YL  CONST_24  H6   C1   C2   C3    180.00   0.0  0
 1YL  CONST_25  H4   C3   C2   C1    180.00   0.0  0
 1YL  CONST_26  H8   C7   C6   C5    180.00   0.0  0
 1YL  Var_01    C15  C16  O19  C14    13.42  30.0  1
 1YL  Var_02    H1   C18  C4   C3   -118.82  30.0  2

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
 1YL  chir_01  C15  C13  C17  C16  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
 1YL  plan-1  C18  0.020
 1YL  plan-1  C4   0.020
 1YL  plan-1  C3   0.020
 1YL  plan-1  C2   0.020
 1YL  plan-1  C1   0.020
 1YL  plan-1  C10  0.020
 1YL  plan-1  C5   0.020
 1YL  plan-1  C6   0.020
 1YL  plan-1  C7   0.020
 1YL  plan-1  C8   0.020
 1YL  plan-1  C9   0.020
 1YL  plan-1  C11  0.020
 1YL  plan-1  O21  0.020
 1YL  plan-1  C12  0.020
 1YL  plan-1  O20  0.020
 1YL  plan-1  C13  0.020
 1YL  plan-1  C14  0.020
 1YL  plan-1  O19  0.020
 1YL  plan-1  C15  0.020
 1YL  plan-1  H4   0.020
 1YL  plan-1  H5   0.020
 1YL  plan-1  H6   0.020
 1YL  plan-1  H7   0.020
 1YL  plan-1  H8   0.020

