# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:29:14 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 3,6-dichloro-2-methoxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(Cl)ccc(Cl)c1C(O)=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
 D3M  D3M  '3,6-dichloro-2-methoxybenzoic acid'  ligand  19  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D3M
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
 D3M  CL1  CL  CL    0  -0.082  -3.3420   0.5010  -0.1549
 D3M  CL2  CL  CL    0  -0.094   2.8059   1.2972   0.1561
 D3M  C1   C   CR6   0  -0.036   0.5786  -0.1943  -0.0848
 D3M  O1   O   OH1   0  -0.567   1.8754  -1.8869   0.8579
 D3M  C2   C   CR6   0  -0.062   1.0933   1.0813   0.0911
 D3M  O2   O   O     0  -0.403   1.7773  -1.7889  -1.3765
 D3M  C3   C   CR16  0  -0.230   0.2568   2.1778   0.2121
 D3M  O3   O   O2    0  -0.473  -1.2823  -1.6259  -0.3395
 D3M  C4   C   CR16  0  -0.226  -1.1141   1.9936   0.1430
 D3M  C5   C   CR6   0  -0.134  -1.6380   0.7234  -0.0320
 D3M  C6   C   CR6   0   0.441  -0.7986  -0.3819  -0.1458
 D3M  C8   C   CH3   0  -0.415  -1.6827  -2.3152   0.8487
 D3M  HO1  H   HOH1  0   0.495   2.4599  -2.6477   0.7084
 D3M  H3   H   HCR6  0   0.297   0.6646   3.1697   0.3469
 D3M  H4   H   HCR6  0   0.300  -1.7756   2.8447   0.2263
 D3M  H8   H   HCH3  0   0.254  -1.9902  -3.3111   0.5412
 D3M  H8A  H   HCH3  0   0.232  -0.8547  -2.3988   1.5547
 D3M  H8B  H   HCH3  0   0.233  -2.5220  -1.8196   1.3386
 D3M  C7   C   C     0   0.471   1.4744  -1.3767  -0.2903

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
 D3M  C5   CL1  single    1.723  0.020  1.723
 D3M  CL2  C2   single    1.727  0.020  1.727
 D3M  C7   C1   single    1.498  0.020  1.498
 D3M  C2   C1   aromatic  1.387  0.020  1.387
 D3M  C1   C6   aromatic  1.391  0.020  1.391
 D3M  C7   O1   single    1.319  0.020  1.319
 D3M  O1   HO1  single    0.850  0.020  0.980
 D3M  C2   C3   aromatic  1.384  0.020  1.384
 D3M  O2   C7   double    1.201  0.020  1.201
 D3M  C3   C4   aromatic  1.385  0.020  1.385
 D3M  C3   H3   single    0.930  0.020  1.080
 D3M  C6   O3   single    1.349  0.020  1.349
 D3M  O3   C8   single    1.431  0.020  1.431
 D3M  C4   C5   aromatic  1.385  0.020  1.385
 D3M  C4   H4   single    0.930  0.020  1.080
 D3M  C6   C5   aromatic  1.393  0.020  1.393
 D3M  C8   H8   single    0.970  0.020  1.090
 D3M  C8   H8A  single    0.970  0.020  1.090
 D3M  C8   H8B  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
 D3M  C7   C1  C6   118.67  3.000
 D3M  C6   C1  C2   119.80  3.000
 D3M  C7   C1  C2   121.44  3.000
 D3M  HO1  O1  C7   110.62  3.000
 D3M  C3   C2  C1   121.02  3.000
 D3M  C3   C2  CL2  119.79  3.000
 D3M  C1   C2  CL2  119.19  3.000
 D3M  H3   C3  C4   120.11  3.000
 D3M  H3   C3  C2   120.65  3.000
 D3M  C4   C3  C2   119.23  3.000
 D3M  C8   O3  C6   115.17  3.000
 D3M  H4   C4  C5   120.02  3.000
 D3M  H4   C4  C3   119.81  3.000
 D3M  C5   C4  C3   120.18  3.000
 D3M  C6   C5  C4   120.68  3.000
 D3M  C6   C5  CL1  119.20  3.000
 D3M  C4   C5  CL1  120.10  3.000
 D3M  C5   C6  O3   121.85  3.000
 D3M  C5   C6  C1   119.09  3.000
 D3M  O3   C6  C1   119.05  3.000
 D3M  H8B  C8  H8A  109.15  3.000
 D3M  H8B  C8  H8   109.01  3.000
 D3M  H8A  C8  H8   109.12  3.000
 D3M  H8B  C8  O3   111.68  3.000
 D3M  H8A  C8  O3   111.21  3.000
 D3M  H8   C8  O3   106.59  3.000
 D3M  O2   C7  O1   125.32  3.000
 D3M  O2   C7  C1   123.10  3.000
 D3M  O1   C7  C1   111.58  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
 D3M  CONST_01  C4   C3  C2  C1      0.00   0.0  0
 D3M  CONST_02  C4   C5  C6  C1      0.00   0.0  0
 D3M  CONST_03  C5   C6  C1  C2      0.00   0.0  0
 D3M  CONST_04  C5   C4  C3  C2      0.00   0.0  0
 D3M  CONST_05  C6   C1  C2  C3      0.00   0.0  0
 D3M  CONST_06  C6   C5  C4  C3      0.00   0.0  0
 D3M  CONST_07  C3   C4  C5  CL1   180.00   0.0  0
 D3M  CONST_08  C1   C6  C5  CL1   180.00   0.0  0
 D3M  CONST_09  C6   C1  C2  CL2   180.00   0.0  0
 D3M  CONST_10  C4   C3  C2  CL2   180.00   0.0  0
 D3M  CONST_11  O3   C6  C1  C2    180.00   0.0  0
 D3M  CONST_12  C7   C1  C2  C3    180.00   0.0  0
 D3M  CONST_13  C4   C5  C6  O3    180.00   0.0  0
 D3M  CONST_14  C7   C1  C6  C5    180.00   0.0  0
 D3M  CONST_15  H3   C3  C2  C1    180.00   0.0  0
 D3M  CONST_16  H4   C4  C3  C2    180.00   0.0  0
 D3M  CONST_17  HO1  O1  C7  C1    180.00   0.0  0
 D3M  Var_01    C2   C1  C7  O1     85.71  30.0  2
 D3M  Var_02    H8   C8  O3  C6   -176.74  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
 D3M  plan-1  CL1  0.020
 D3M  plan-1  CL2  0.020
 D3M  plan-1  C1   0.020
 D3M  plan-1  C2   0.020
 D3M  plan-1  C3   0.020
 D3M  plan-1  O3   0.020
 D3M  plan-1  C4   0.020
 D3M  plan-1  C5   0.020
 D3M  plan-1  C6   0.020
 D3M  plan-1  H3   0.020
 D3M  plan-1  H4   0.020
 D3M  plan-1  C7   0.020
 D3M  plan-2  C1   0.020
 D3M  plan-2  O1   0.020
 D3M  plan-2  O2   0.020
 D3M  plan-2  HO1  0.020
 D3M  plan-2  C7   0.020

