# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:57:06 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: [(3S)-9-hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C2C(=Cc3cccc(O)c3C2=O)C[C@@H](CC(O)=O)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
 SDN  SDN  '[(3S)-9-hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetic acid'  ligand  34  21  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SDN
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
 SDN  O4    O  OH1    0  -0.637   4.1769  -1.7535   0.4653
 SDN  C11   C  CR6    0   0.378   3.9112  -0.4566   0.3310
 SDN  C12   C  CR66   0  -0.249   2.5928   0.0070   0.1016
 SDN  C13   C  CR6    0   0.386   1.4960  -0.9499   0.0090
 SDN  O5    O  O      0  -0.525   1.7253  -2.1703   0.1416
 SDN  C14   C  CR6    0  -0.184   0.1638  -0.4191  -0.2086
 SDN  C15   C  C      0   0.422  -0.9429  -1.2505  -0.3010
 SDN  O3    O  O2     0  -0.420  -2.1637  -0.7798  -0.3113
 SDN  C16   C  CH3    0  -0.741  -0.9311  -2.7355  -0.4079
 SDN  C10   C  CR16   0  -0.373   4.9594   0.4547   0.4209
 SDN  C9    C  CR16   0  -0.227   4.7054   1.8123   0.2875
 SDN  C8    C  CR16   0  -0.371   3.4244   2.2877   0.0658
 SDN  C7    C  CR66   0   0.175   2.3572   1.3926  -0.0295
 SDN  C6    C  CR16   0  -0.470   1.0200   1.8595  -0.2693
 SDN  C5    C  CR6    0   0.171  -0.0198   1.0076  -0.3575
 SDN  C4    C  CH2    0  -0.537  -1.4015   1.4723  -0.6943
 SDN  C3    C  CH1    0   0.039  -2.4182   0.6084   0.0134
 SDN  C2    C  CH2    0  -0.614  -3.8467   0.8924  -0.3742
 SDN  C1    C  C      0   0.420  -4.8980   0.0693   0.3981
 SDN  O2    O  O      0  -0.605  -4.6169  -0.2418   1.5712
 SDN  O1    O  OC    -1  -0.615  -5.9563  -0.1792  -0.2103
 SDN  HO4   H  HOH1   0   0.476   3.3044  -2.2243   0.3731
 SDN  H161  H  HCH3   0   0.276  -0.6503  -3.1826   0.5467
 SDN  H162  H  HCH3   0   0.264  -1.9241  -3.0918  -0.6741
 SDN  H163  H  HCH3   0   0.269  -0.2113  -3.0838  -1.1440
 SDN  H10   H  HCR6   0   0.261   5.9647   0.0939   0.5963
 SDN  H9    H  HCR6   0   0.262   5.5290   2.5111   0.3599
 SDN  H8    H  HCR6   0   0.251   3.2438   3.3502  -0.0349
 SDN  H6    H  HCR6   0   0.245   0.8625   2.9239  -0.3970
 SDN  H41   H  HCH2   0   0.274  -1.5420   2.5140  -0.4033
 SDN  H42   H  HCH2   0   0.265  -1.5583   1.4182  -1.7778
 SDN  H3    H  HCH1   0   0.254  -2.2971   0.7000   1.0969
 SDN  H21   H  HCH2   0   0.252  -4.0315   1.9517  -0.1639
 SDN  H22   H  HCH2   0   0.228  -3.9707   0.7721  -1.4537

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
 SDN  C9   C10   aromatic  1.388  0.020  1.388
 SDN  C9   C8    aromatic  1.384  0.020  1.384
 SDN  C10  C11   aromatic  1.392  0.020  1.392
 SDN  C8   C7    aromatic  1.396  0.020  1.396
 SDN  C11  O4    single    1.331  0.020  1.331
 SDN  C11  C12   aromatic  1.416  0.020  1.416
 SDN  C7   C12   aromatic  1.412  0.020  1.412
 SDN  C7   C6    single    1.437  0.020  1.437
 SDN  C12  C13   single    1.459  0.020  1.459
 SDN  C6   C5    double    1.347  0.020  1.347
 SDN  C13  O5    double    1.249  0.020  1.249
 SDN  C13  C14   single    1.450  0.020  1.450
 SDN  C5   C14   single    1.446  0.020  1.446
 SDN  C5   C4    single    1.496  0.020  1.496
 SDN  C14  C15   double    1.387  0.020  1.387
 SDN  C4   C3    single    1.510  0.020  1.510
 SDN  C15  C16   single    1.489  0.020  1.489
 SDN  C15  O3    single    1.308  0.020  1.308
 SDN  C3   O3    single    1.448  0.020  1.448
 SDN  C3   C2    single    1.507  0.020  1.507
 SDN  C2   C1    single    1.542  0.020  1.542
 SDN  C1   O2    deloc     1.246  0.020  1.246
 SDN  C1   O1    deloc     1.246  0.020  1.246
 SDN  O4   HO4   single    0.850  0.020  0.980
 SDN  C16  H161  single    0.970  0.020  1.090
 SDN  C16  H162  single    0.970  0.020  1.090
 SDN  C16  H163  single    0.970  0.020  1.090
 SDN  C10  H10   single    0.930  0.020  1.080
 SDN  C9   H9    single    0.930  0.020  1.080
 SDN  C8   H8    single    0.930  0.020  1.080
 SDN  C6   H6    single    0.930  0.020  1.080
 SDN  C4   H41   single    0.970  0.020  1.090
 SDN  C4   H42   single    0.970  0.020  1.090
 SDN  C3   H3    single    0.970  0.020  1.090
 SDN  C2   H21   single    0.970  0.020  1.090
 SDN  C2   H22   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
 SDN  HO4   O4   C11   106.05  3.000
 SDN  C10   C11  C12   119.81  3.000
 SDN  C12   C11  O4    121.42  3.000
 SDN  C10   C11  O4    118.77  3.000
 SDN  C7    C12  C13   120.84  3.000
 SDN  C13   C12  C11   119.70  3.000
 SDN  C7    C12  C11   119.45  3.000
 SDN  C14   C13  O5    122.83  3.000
 SDN  C14   C13  C12   117.39  3.000
 SDN  O5    C13  C12   119.76  3.000
 SDN  C5    C14  C15   118.88  3.000
 SDN  C15   C14  C13   121.56  3.000
 SDN  C5    C14  C13   119.54  3.000
 SDN  C16   C15  O3    111.45  3.000
 SDN  O3    C15  C14   121.96  3.000
 SDN  C16   C15  C14   126.59  3.000
 SDN  C3    O3   C15   120.47  3.000
 SDN  H163  C16  H162  109.50  3.000
 SDN  H163  C16  H161  106.90  3.000
 SDN  H162  C16  H161  108.36  3.000
 SDN  H163  C16  C15   111.93  3.000
 SDN  H162  C16  C15   109.69  3.000
 SDN  H161  C16  C15   110.36  3.000
 SDN  H10   C10  C9    120.78  3.000
 SDN  H10   C10  C11   119.45  3.000
 SDN  C9    C10  C11   119.77  3.000
 SDN  H9    C9   C8    119.55  3.000
 SDN  H9    C9   C10   119.07  3.000
 SDN  C8    C9   C10   121.38  3.000
 SDN  H8    C8   C7    119.70  3.000
 SDN  H8    C8   C9    120.42  3.000
 SDN  C7    C8   C9    119.88  3.000
 SDN  C6    C7   C8    120.97  3.000
 SDN  C6    C7   C12   119.33  3.000
 SDN  C8    C7   C12   119.70  3.000
 SDN  H6    C6   C5    120.09  3.000
 SDN  H6    C6   C7    118.31  3.000
 SDN  C5    C6   C7    121.59  3.000
 SDN  C4    C5   C6    122.08  3.000
 SDN  C4    C5   C14   116.54  3.000
 SDN  C6    C5   C14   121.28  3.000
 SDN  H42   C4   H41   107.01  3.000
 SDN  H42   C4   C3    109.80  3.000
 SDN  H41   C4   C3    109.55  3.000
 SDN  H42   C4   C5    109.83  3.000
 SDN  H41   C4   C5    110.83  3.000
 SDN  C3    C4   C5    109.78  3.000
 SDN  H3    C3   C2    110.11  3.000
 SDN  H3    C3   C4    109.98  3.000
 SDN  C2    C3   C4    114.19  3.000
 SDN  H3    C3   O3    106.43  3.000
 SDN  C2    C3   O3    106.83  3.000
 SDN  C4    C3   O3    108.96  3.000
 SDN  H22   C2   H21   106.07  3.000
 SDN  H22   C2   C1    111.00  3.000
 SDN  H21   C2   C1    107.75  3.000
 SDN  H22   C2   C3    109.92  3.000
 SDN  H21   C2   C3    107.02  3.000
 SDN  C1    C2   C3    114.63  3.000
 SDN  O1    C1   O2    127.00  3.000
 SDN  O1    C1   C2    116.16  3.000
 SDN  O2    C1   C2    116.80  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
 SDN  CONST_01  C8    C9   C10  C11    0.00   0.0  0
 SDN  CONST_02  C8    C7   C12  C11    0.00   0.0  0
 SDN  CONST_03  C9    C10  C11  C12    0.00   0.0  0
 SDN  CONST_04  C9    C8   C7   C12    0.00   0.0  0
 SDN  CONST_05  C7    C8   C9   C10    0.00   0.0  0
 SDN  CONST_06  C7    C12  C11  C10    0.00   0.0  0
 SDN  CONST_07  C9    C10  C11  O4   180.00   0.0  0
 SDN  CONST_08  C7    C12  C11  O4   180.00   0.0  0
 SDN  CONST_09  C13   C12  C11  O4     0.00   0.0  0
 SDN  CONST_10  H9    C9   C10  C11  180.00   0.0  0
 SDN  CONST_11  H10   C10  C11  C12  180.00   0.0  0
 SDN  CONST_12  H8    C8   C7   C12  180.00   0.0  0
 SDN  Var_01    O3    C15  C14  C13  170.36   0.0  0
 SDN  Var_02    C7    C6   C5   C14    0.26   0.0  0
 SDN  Var_03    C5    C14  C15  O3   -10.75   0.0  0
 SDN  Var_04    C3    C4   C5   C14   36.30  30.0  1
 SDN  Var_05    H161  C16  C15  C14   72.57  30.0  3
 SDN  Var_06    O2    C1   C2   C3    31.62  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
 SDN  chir_01  C3  C4  O3  C2  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
 SDN  plan-1  C2   0.020
 SDN  plan-1  C1   0.020
 SDN  plan-1  O2   0.020
 SDN  plan-1  O1   0.020
 SDN  plan-2  O4   0.020
 SDN  plan-2  C11  0.020
 SDN  plan-2  C12  0.020
 SDN  plan-2  C13  0.020
 SDN  plan-2  O5   0.020
 SDN  plan-2  C14  0.020
 SDN  plan-2  C15  0.020
 SDN  plan-2  O3   0.020
 SDN  plan-2  C16  0.020
 SDN  plan-2  C10  0.020
 SDN  plan-2  C9   0.020
 SDN  plan-2  C8   0.020
 SDN  plan-2  C7   0.020
 SDN  plan-2  C6   0.020
 SDN  plan-2  C5   0.020
 SDN  plan-2  C4   0.020
 SDN  plan-2  H10  0.020
 SDN  plan-2  H9   0.020
 SDN  plan-2  H8   0.020
 SDN  plan-2  H6   0.020

