# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:16:52 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C(=O)c2cccc3cccc(C1=O)c23
#
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
 ALR  ALR  '(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)acetic acid'  ligand  27  19  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ALR
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
 ALR  C1   C  CR66   0  -0.149  -1.2321  -0.1750  -0.8092
 ALR  C2   C  CR66   0  -0.150   1.2099  -0.1600  -0.8148
 ALR  C3   C  CR6    0   0.562   1.2180  -0.4407   0.6327
 ALR  C4   C  CR6    0   0.561  -1.2301  -0.4460   0.6400
 ALR  O5   O  O      0  -0.439   2.2523  -0.5177   1.2648
 ALR  O6   O  O      0  -0.439  -2.2598  -0.5196   1.2801
 ALR  C8   C  C      0   0.291  -0.0135  -0.0413  -1.5015
 ALR  C9   C  CR66   0   0.118  -0.0182   0.2198  -2.8913
 ALR  C10  C  CR16   0  -0.303   1.2173   0.3574  -3.5611
 ALR  C11  C  CR16   0  -0.249   2.3985   0.2454  -2.8751
 ALR  C12  C  CR16   0  -0.294   2.3964  -0.0146  -1.4948
 ALR  C16  C  CR16   0  -0.294  -2.4236  -0.0497  -1.4849
 ALR  C17  C  CR16   0  -0.249  -2.4350   0.2048  -2.8660
 ALR  C18  C  CR16   0  -0.303  -1.2583   0.3353  -3.5566
 ALR  N22  N  NR6    0  -0.582  -0.0037  -0.6485   1.2461
 ALR  C23  C  C      0   0.418   0.0098   0.4897   3.4655
 ALR  O24  O  O      0  -0.591   0.0227   1.5387   2.8026
 ALR  O27  O  OC    -1  -0.616   0.0034   0.3615   4.7036
 ALR  H71  H  HCH2   0   0.269   0.8742  -1.4357   2.9557
 ALR  H72  H  HCH2   0   0.269  -0.8727  -1.4300   2.9630
 ALR  H10  H  HCR6   0   0.274   1.2198   0.5533  -4.6261
 ALR  H11  H  HCR6   0   0.273   3.3408   0.3563  -3.3938
 ALR  H12  H  HCR6   0   0.273   3.3363  -0.1047  -0.9672
 ALR  H16  H  HCR6   0   0.273  -3.3598  -0.1515  -0.9529
 ALR  H17  H  HCR6   0   0.273  -3.3805   0.2985  -3.3820
 ALR  H18  H  HCR6   0   0.274  -1.2686   0.5280  -4.6221
 ALR  C7   C  CH2    0  -0.471   0.0014  -0.8440   2.6860

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
 ALR  C1   C4   single    1.474  0.020  1.474
 ALR  C1   C8   aromatic  1.408  0.020  1.408
 ALR  C1   C16  aromatic  1.375  0.020  1.375
 ALR  C2   C3   single    1.474  0.020  1.474
 ALR  C2   C8   aromatic  1.408  0.020  1.408
 ALR  C2   C12  aromatic  1.375  0.020  1.375
 ALR  C3   O5   double    1.215  0.020  1.215
 ALR  C3   N22  single    1.383  0.020  1.383
 ALR  C4   O6   double    1.215  0.020  1.215
 ALR  C4   N22  single    1.383  0.020  1.383
 ALR  C7   N22  single    1.453  0.020  1.453
 ALR  C7   C23  single    1.545  0.020  1.545
 ALR  C7   H71  single    0.970  0.020  1.090
 ALR  C7   H72  single    0.970  0.020  1.090
 ALR  C8   C9   aromatic  1.414  0.020  1.414
 ALR  C9   C10  aromatic  1.412  0.020  1.412
 ALR  C9   C18  aromatic  1.412  0.020  1.412
 ALR  C10  C11  aromatic  1.371  0.020  1.371
 ALR  C10  H10  single    0.930  0.020  1.080
 ALR  C11  C12  aromatic  1.405  0.020  1.405
 ALR  C11  H11  single    0.930  0.020  1.080
 ALR  C12  H12  single    0.930  0.020  1.080
 ALR  C16  C17  aromatic  1.404  0.020  1.404
 ALR  C16  H16  single    0.930  0.020  1.080
 ALR  C17  C18  aromatic  1.371  0.020  1.371
 ALR  C17  H17  single    0.930  0.020  1.080
 ALR  C18  H18  single    0.930  0.020  1.080
 ALR  C23  O24  deloc     1.241  0.020  1.241
 ALR  C23  O27  deloc     1.245  0.020  1.245

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
 ALR  C16  C1   C8   119.97  3.000
 ALR  C16  C1   C4   120.05  3.000
 ALR  C8   C1   C4   119.97  3.000
 ALR  C12  C2   C8   119.97  3.000
 ALR  C12  C2   C3   120.05  3.000
 ALR  C8   C2   C3   119.98  3.000
 ALR  N22  C3   O5   120.79  3.000
 ALR  N22  C3   C2   117.34  3.000
 ALR  O5   C3   C2   121.85  3.000
 ALR  N22  C4   O6   120.80  3.000
 ALR  N22  C4   C1   117.32  3.000
 ALR  O6   C4   C1   121.86  3.000
 ALR  C9   C8   C2   119.85  3.000
 ALR  C9   C8   C1   119.86  3.000
 ALR  C2   C8   C1   120.28  3.000
 ALR  C18  C9   C10  122.48  3.000
 ALR  C18  C9   C8   118.76  3.000
 ALR  C10  C9   C8   118.77  3.000
 ALR  H10  C10  C11  120.34  3.000
 ALR  H10  C10  C9   119.08  3.000
 ALR  C11  C10  C9   120.58  3.000
 ALR  H11  C11  C12  119.45  3.000
 ALR  H11  C11  C10  120.17  3.000
 ALR  C12  C11  C10  120.38  3.000
 ALR  H12  C12  C11  119.57  3.000
 ALR  H12  C12  C2   119.98  3.000
 ALR  C11  C12  C2   120.45  3.000
 ALR  H16  C16  C17  119.58  3.000
 ALR  H16  C16  C1   119.98  3.000
 ALR  C17  C16  C1   120.44  3.000
 ALR  H17  C17  C18  120.13  3.000
 ALR  H17  C17  C16  119.48  3.000
 ALR  C18  C17  C16  120.38  3.000
 ALR  H18  C18  C17  120.30  3.000
 ALR  H18  C18  C9   119.11  3.000
 ALR  C17  C18  C9   120.58  3.000
 ALR  C7   N22  C4   117.20  3.000
 ALR  C7   N22  C3   117.17  3.000
 ALR  C4   N22  C3   124.55  3.000
 ALR  O27  C23  O24  128.20  3.000
 ALR  O27  C23  C7   114.39  3.000
 ALR  O24  C23  C7   117.41  3.000
 ALR  H72  C7   H71  106.76  3.000
 ALR  H72  C7   C23  109.93  3.000
 ALR  H71  C7   C23  109.88  3.000
 ALR  H72  C7   N22  108.77  3.000
 ALR  H71  C7   N22  108.75  3.000
 ALR  C23  C7   N22  112.57  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
 ALR  CONST_01  C12  C2   C8   C1   180.00   0.0  0
 ALR  CONST_02  C10  C9   C8   C1   180.00   0.0  0
 ALR  CONST_03  C18  C9   C8   C1     0.00   0.0  0
 ALR  CONST_04  C18  C17  C16  C1     0.00   0.0  0
 ALR  CONST_05  C16  C1   C8   C2   180.00   0.0  0
 ALR  CONST_06  C10  C9   C8   C2     0.00   0.0  0
 ALR  CONST_07  C18  C9   C8   C2   180.00   0.0  0
 ALR  CONST_08  C10  C11  C12  C2     0.00   0.0  0
 ALR  CONST_09  C17  C16  C1   C8     0.00   0.0  0
 ALR  CONST_10  C11  C12  C2   C8     0.00   0.0  0
 ALR  CONST_11  C11  C10  C9   C8     0.00   0.0  0
 ALR  CONST_12  C17  C18  C9   C8     0.00   0.0  0
 ALR  CONST_13  C16  C1   C8   C9     0.00   0.0  0
 ALR  CONST_14  C12  C2   C8   C9     0.00   0.0  0
 ALR  CONST_15  C12  C11  C10  C9     0.00   0.0  0
 ALR  CONST_16  C16  C17  C18  C9     0.00   0.0  0
 ALR  CONST_17  C17  C18  C9   C10  180.00   0.0  0
 ALR  CONST_18  C18  C9   C10  C11  180.00   0.0  0
 ALR  CONST_19  C4   N22  C3   C2     0.00   0.0  0
 ALR  CONST_20  C7   N22  C3   C2   180.00   0.0  0
 ALR  CONST_21  O5   C3   N22  C4   180.00   0.0  0
 ALR  CONST_22  H17  C17  C16  C1   180.00   0.0  0
 ALR  CONST_23  H11  C11  C12  C2   180.00   0.0  0
 ALR  CONST_24  H12  C12  C2   C3     0.00   0.0  0
 ALR  CONST_25  H16  C16  C1   C4     0.00   0.0  0
 ALR  CONST_26  H10  C10  C9   C8   180.00   0.0  0
 ALR  CONST_27  H18  C18  C9   C8   180.00   0.0  0
 ALR  CONST_28  C7   N22  C3   O5     0.00   0.0  0
 ALR  Var_01    C23  C7   N22  C3    83.99  30.0  2
 ALR  Var_02    O24  C23  C7   N22   -0.60  30.0  3

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
 ALR  plan-1  C1   0.020
 ALR  plan-1  C2   0.020
 ALR  plan-1  C3   0.020
 ALR  plan-1  C4   0.020
 ALR  plan-1  O5   0.020
 ALR  plan-1  O6   0.020
 ALR  plan-1  C8   0.020
 ALR  plan-1  C9   0.020
 ALR  plan-1  C10  0.020
 ALR  plan-1  C11  0.020
 ALR  plan-1  C12  0.020
 ALR  plan-1  C16  0.020
 ALR  plan-1  C17  0.020
 ALR  plan-1  C18  0.020
 ALR  plan-1  N22  0.020
 ALR  plan-1  H10  0.020
 ALR  plan-1  H11  0.020
 ALR  plan-1  H12  0.020
 ALR  plan-1  H16  0.020
 ALR  plan-1  H17  0.020
 ALR  plan-1  H18  0.020
 ALR  plan-1  C7   0.020
 ALR  plan-2  C23  0.020
 ALR  plan-2  O24  0.020
 ALR  plan-2  O27  0.020
 ALR  plan-2  C7   0.020

