# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 06:16:24 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1oc(COc2cccc(Cl)c2Cl)cc1
#
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
 2JY  2JY  '5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid'  ligand  25  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2JY
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
 2JY  C01  C   CR16   0  -0.241   3.2523   2.3148  -0.5283
 2JY  C02  C   CR16   0  -0.252   4.1098   1.2368  -0.6487
 2JY  C03  C   CR6    0   0.008   3.6132  -0.0404  -0.4269
 2JY  C04  C   CR6    0  -0.127   2.2817  -0.2370  -0.0928
 2JY  C05  C   CR6    0   0.478   1.4171   0.8602   0.0263
 2JY  C06  C   CR16   0  -0.387   1.9170   2.1396  -0.1933
 2JY  CL1  CL  CL     0  -0.095   4.6704  -1.3925  -0.5754
 2JY  CL2  CL  CL     0  -0.077   1.6574  -1.8144   0.1811
 2JY  O09  O   O2     0  -0.454   0.1514   0.5773   0.3531
 2JY  C10  C   CH2    0  -0.305  -0.7986   1.6408   0.3864
 2JY  C11  C   CR5    0   0.346  -2.1264   1.0597   0.6716
 2JY  O12  O   O      0  -0.419  -2.7173   0.3310  -0.2945
 2JY  C13  C   CR5    0   0.173  -3.9111  -0.0970   0.1747
 2JY  C14  C   CR15   0  -0.335  -4.0888   0.3625   1.4424
 2JY  C15  C   CR15   0  -0.364  -2.9259   1.1152   1.7670
 2JY  C16  C   C      0   0.337  -4.7774  -0.9434  -0.7130
 2JY  O17  O   OC    -1  -0.596  -4.3322  -1.2065  -1.8428
 2JY  O18  O   O      0  -0.592  -5.8601  -1.2901  -0.2072
 2JY  H1   H   HCR6   0   0.278   3.6272   3.3150  -0.6975
 2JY  H2   H   HCR6   0   0.285   5.1494   1.3773  -0.9081
 2JY  H3   H   HCR6   0   0.299   1.2809   3.0089  -0.1042
 2JY  H4   H   HCH2   0   0.262  -0.5526   2.3601   1.1726
 2JY  H5   H   HCH2   0   0.258  -0.7992   2.1714  -0.5719
 2JY  H6   H   HCR5   0   0.258  -4.9460   0.1853   2.0708
 2JY  H7   H   HCR5   0   0.264  -2.7072   1.6307   2.6888

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
 2JY  CL1  C03  single    1.723  0.020  1.723
 2JY  C03  C02  aromatic  1.388  0.020  1.388
 2JY  C03  C04  aromatic  1.387  0.020  1.387
 2JY  C02  C01  aromatic  1.383  0.020  1.383
 2JY  CL2  C04  single    1.718  0.020  1.718
 2JY  C04  C05  aromatic  1.402  0.020  1.402
 2JY  C01  C06  aromatic  1.388  0.020  1.388
 2JY  C05  C06  aromatic  1.391  0.020  1.391
 2JY  C05  O09  single    1.337  0.020  1.337
 2JY  O09  C10  single    1.426  0.020  1.426
 2JY  O18  C16  deloc     1.244  0.020  1.244
 2JY  O12  C11  aromatic  1.347  0.020  1.347
 2JY  O12  C13  aromatic  1.352  0.020  1.352
 2JY  C10  C11  single    1.477  0.020  1.477
 2JY  C16  O17  deloc     1.243  0.020  1.243
 2JY  C16  C13  single    1.502  0.020  1.502
 2JY  C11  C15  aromatic  1.357  0.020  1.357
 2JY  C13  C14  aromatic  1.360  0.020  1.360
 2JY  C15  C14  aromatic  1.423  0.020  1.423
 2JY  C01  H1   single    0.930  0.020  1.080
 2JY  C02  H2   single    0.930  0.020  1.080
 2JY  C06  H3   single    0.930  0.020  1.080
 2JY  C10  H4   single    0.970  0.020  1.090
 2JY  C10  H5   single    0.970  0.020  1.090
 2JY  C14  H6   single    0.930  0.020  1.080
 2JY  C15  H7   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
 2JY  H1   C01  C06  119.21  3.000
 2JY  H1   C01  C02  119.50  3.000
 2JY  C06  C01  C02  121.28  3.000
 2JY  H2   C02  C03  120.14  3.000
 2JY  H2   C02  C01  121.07  3.000
 2JY  C03  C02  C01  118.79  3.000
 2JY  CL1  C03  C04  119.91  3.000
 2JY  C04  C03  C02  120.83  3.000
 2JY  CL1  C03  C02  119.26  3.000
 2JY  CL2  C04  C05  118.74  3.000
 2JY  C05  C04  C03  120.11  3.000
 2JY  CL2  C04  C03  121.16  3.000
 2JY  O09  C05  C06  124.97  3.000
 2JY  O09  C05  C04  116.03  3.000
 2JY  C06  C05  C04  119.00  3.000
 2JY  H3   C06  C05  121.02  3.000
 2JY  H3   C06  C01  118.99  3.000
 2JY  C05  C06  C01  120.00  3.000
 2JY  C10  O09  C05  118.58  3.000
 2JY  H5   C10  H4   108.09  3.000
 2JY  H5   C10  C11  111.04  3.000
 2JY  H4   C10  C11  108.79  3.000
 2JY  H5   C10  O09  109.94  3.000
 2JY  H4   C10  O09  110.94  3.000
 2JY  C11  C10  O09  108.05  3.000
 2JY  C15  C11  O12  110.04  3.000
 2JY  C15  C11  C10  132.00  3.000
 2JY  O12  C11  C10  117.95  3.000
 2JY  C13  O12  C11  108.04  3.000
 2JY  C16  C13  C14  131.76  3.000
 2JY  C14  C13  O12  109.38  3.000
 2JY  C16  C13  O12  118.85  3.000
 2JY  H6   C14  C15  127.17  3.000
 2JY  H6   C14  C13  126.30  3.000
 2JY  C15  C14  C13  106.53  3.000
 2JY  H7   C15  C14  127.85  3.000
 2JY  H7   C15  C11  126.14  3.000
 2JY  C14  C15  C11  106.00  3.000
 2JY  O18  C16  O17  128.49  3.000
 2JY  O17  C16  C13  116.76  3.000
 2JY  O18  C16  C13  114.76  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
 2JY  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 2JY  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 2JY  CONST_03  C05  C04  C03  C02     0.00   0.0  0
 2JY  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 2JY  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 2JY  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 2JY  CONST_07  C14  C13  O12  C11     0.00   0.0  0
 2JY  CONST_08  C13  C14  C15  C11     0.00   0.0  0
 2JY  CONST_09  C14  C15  C11  O12     0.00   0.0  0
 2JY  CONST_10  C15  C14  C13  O12     0.00   0.0  0
 2JY  CONST_11  C15  C11  O12  C13     0.00   0.0  0
 2JY  CONST_12  CL1  C03  C02  C01   180.00   0.0  0
 2JY  CONST_13  O09  C05  C06  C01   180.00   0.0  0
 2JY  CONST_14  CL2  C04  C03  C02   180.00   0.0  0
 2JY  CONST_15  O09  C05  C04  C03   180.00   0.0  0
 2JY  CONST_16  CL1  C03  C04  C05   180.00   0.0  0
 2JY  CONST_17  CL2  C04  C05  C06   180.00   0.0  0
 2JY  CONST_18  C13  O12  C11  C10   180.00   0.0  0
 2JY  CONST_19  C14  C15  C11  C10   180.00   0.0  0
 2JY  CONST_20  C16  C13  O12  C11   180.00   0.0  0
 2JY  CONST_21  C16  C13  C14  C15   180.00   0.0  0
 2JY  CONST_22  H3   C06  C01  C02   180.00   0.0  0
 2JY  CONST_23  H1   C01  C02  C03   180.00   0.0  0
 2JY  CONST_24  H2   C02  C03  C04   180.00   0.0  0
 2JY  CONST_25  H6   C14  C15  C11   180.00   0.0  0
 2JY  CONST_26  H7   C15  C11  O12   180.00   0.0  0
 2JY  Var_01    C11  C10  O09  C05   175.87  30.0  3
 2JY  Var_02    O12  C11  C10  O09   -71.01  30.0  2
 2JY  Var_03    O18  C16  C13  O12  -179.73  30.0  2

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
 2JY  plan-1  C10  0.020
 2JY  plan-1  C11  0.020
 2JY  plan-1  O12  0.020
 2JY  plan-1  C13  0.020
 2JY  plan-1  C14  0.020
 2JY  plan-1  C15  0.020
 2JY  plan-1  C16  0.020
 2JY  plan-1  H6   0.020
 2JY  plan-1  H7   0.020
 2JY  plan-2  C01  0.020
 2JY  plan-2  C02  0.020
 2JY  plan-2  C03  0.020
 2JY  plan-2  C04  0.020
 2JY  plan-2  C05  0.020
 2JY  plan-2  C06  0.020
 2JY  plan-2  CL1  0.020
 2JY  plan-2  CL2  0.020
 2JY  plan-2  O09  0.020
 2JY  plan-2  H1   0.020
 2JY  plan-2  H2   0.020
 2JY  plan-2  H3   0.020
 2JY  plan-3  C13  0.020
 2JY  plan-3  C16  0.020
 2JY  plan-3  O17  0.020
 2JY  plan-3  O18  0.020

