# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:59:24 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [1-(3-chlorobenzyl)-1H-indol-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cn(Cc2cccc(Cl)c2)c3ccccc13
#
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
 2SY  2SY  '[1-(3-chlorobenzyl)-1H-indol-3-yl]acetic acid'  ligand  35  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2SY
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
 2SY  CL2  CL  CL    0  -0.129  -3.4951  -0.6746  -2.5627
 2SY  C16  C   CR6   0  -0.022  -3.3597   0.1309  -1.0319
 2SY  C13  C   CR16  0  -0.240  -2.1939  -0.0143  -0.2972
 2SY  C20  C   CR16  0  -0.228  -4.4171   0.9023  -0.5767
 2SY  C17  C   CR16  0  -0.247  -4.2889   1.5441   0.6467
 2SY  C14  C   CR16  0  -0.293  -3.1266   1.4140   1.3924
 2SY  C10  C   CR6   0   0.083  -2.0752   0.6310   0.9284
 2SY  C6   C   CH2   0  -0.366  -0.8370   0.4691   1.7780
 2SY  N2   N   NR5   0  -0.533   0.3556   0.2112   1.0160
 2SY  C5   C   CR15  0  -0.079   1.0057  -0.9925   0.9252
 2SY  C7   C   CR5   0   0.032   2.0552  -0.9041   0.0594
 2SY  C11  C   CH2   0  -0.725   2.9990  -1.9887  -0.3169
 2SY  C15  C   C     0   0.551   4.3899  -1.7955   0.2380
 2SY  O19  O   O     0  -0.433   4.7233  -0.9191   0.9930
 2SY  O18  O   OH1   0  -0.595   5.2223  -2.7310  -0.2085
 2SY  C3   C   CR56  0   0.053   2.0548   0.4402  -0.4323
 2SY  C1   C   CR56  0   0.371   0.9749   1.1053   0.1850
 2SY  C8   C   CR16  0  -0.376   2.8620   1.1397  -1.3347
 2SY  C12  C   CR16  0  -0.268   2.5709   2.4636  -1.6013
 2SY  C9   C   CR16  0  -0.283   1.4890   3.1068  -0.9781
 2SY  C4   C   CR16  0  -0.300   0.6764   2.4406  -0.0799
 2SY  H1   H   HCR6  0   0.275  -1.3855  -0.6227  -0.6824
 2SY  H2   H   HCR6  0   0.280  -5.3195   1.0053  -1.1635
 2SY  H3   H   HCR6  0   0.270  -5.1015   2.1565   1.0141
 2SY  H4   H   HCR6  0   0.261  -3.0355   1.9300   2.3405
 2SY  H5   H   HCH2  0   0.279  -0.6954   1.3599   2.3947
 2SY  H6   H   HCH2  0   0.295  -0.9719  -0.3626   2.4716
 2SY  H7   H   HCR5  0   0.291   0.6633  -1.8391   1.5019
 2SY  H8   H   HCH2  0   0.306   2.6312  -2.9579   0.0336
 2SY  H9   H   HCH2  0   0.292   3.0768  -2.0851  -1.4048
 2SY  H10  H   HOH1  0   0.480   6.1056  -2.5941   0.1649
 2SY  H11  H   HCR6  0   0.241   3.6980   0.6525  -1.8221
 2SY  H12  H   HCR6  0   0.248   3.1832   3.0188  -2.3001
 2SY  H13  H   HCR6  0   0.251   1.2850   4.1444  -1.2085
 2SY  H14  H   HCR6  0   0.260  -0.1593   2.9435   0.3903

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
 2SY  C20  C17  aromatic  1.387  0.020  1.387
 2SY  C20  C16  aromatic  1.386  0.020  1.386
 2SY  C17  C14  aromatic  1.387  0.020  1.387
 2SY  CL2  C16  single    1.735  0.020  1.735
 2SY  C16  C13  aromatic  1.386  0.020  1.386
 2SY  C14  C10  aromatic  1.391  0.020  1.391
 2SY  C13  C10  aromatic  1.390  0.020  1.390
 2SY  C10  C6   single    1.510  0.020  1.510
 2SY  C6   N2   single    1.439  0.020  1.439
 2SY  N2   C5   aromatic  1.371  0.020  1.371
 2SY  N2   C1   aromatic  1.369  0.020  1.369
 2SY  C5   C7   aromatic  1.363  0.020  1.363
 2SY  C1   C4   aromatic  1.394  0.020  1.394
 2SY  C1   C3   aromatic  1.411  0.020  1.411
 2SY  C4   C9   aromatic  1.382  0.020  1.382
 2SY  C7   C3   aromatic  1.431  0.020  1.431
 2SY  C7   C11  single    1.486  0.020  1.486
 2SY  C3   C8   aromatic  1.398  0.020  1.398
 2SY  C9   C12  aromatic  1.404  0.020  1.404
 2SY  C11  C15  single    1.510  0.020  1.510
 2SY  C8   C12  aromatic  1.381  0.020  1.381
 2SY  O19  C15  double    1.204  0.020  1.204
 2SY  C15  O18  single    1.329  0.020  1.329
 2SY  C13  H1   single    0.930  0.020  1.080
 2SY  C20  H2   single    0.930  0.020  1.080
 2SY  C17  H3   single    0.930  0.020  1.080
 2SY  C14  H4   single    0.930  0.020  1.080
 2SY  C6   H5   single    0.970  0.020  1.090
 2SY  C6   H6   single    0.970  0.020  1.090
 2SY  C5   H7   single    0.930  0.020  1.080
 2SY  C11  H8   single    0.970  0.020  1.090
 2SY  C11  H9   single    0.970  0.020  1.090
 2SY  O18  H10  single    0.850  0.020  0.980
 2SY  C8   H11  single    0.930  0.020  1.080
 2SY  C12  H12  single    0.930  0.020  1.080
 2SY  C9   H13  single    0.930  0.020  1.080
 2SY  C4   H14  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
 2SY  C20  C16  C13  121.74  3.000
 2SY  C13  C16  CL2  119.00  3.000
 2SY  C20  C16  CL2  119.25  3.000
 2SY  H1   C13  C10  120.71  3.000
 2SY  H1   C13  C16  119.90  3.000
 2SY  C10  C13  C16  119.39  3.000
 2SY  H2   C20  C17  120.77  3.000
 2SY  H2   C20  C16  120.77  3.000
 2SY  C17  C20  C16  118.46  3.000
 2SY  H3   C17  C14  120.00  3.000
 2SY  H3   C17  C20  119.46  3.000
 2SY  C14  C17  C20  120.54  3.000
 2SY  H4   C14  C10  119.78  3.000
 2SY  H4   C14  C17  119.76  3.000
 2SY  C10  C14  C17  120.46  3.000
 2SY  C6   C10  C14  119.50  3.000
 2SY  C6   C10  C13  121.08  3.000
 2SY  C14  C10  C13  119.40  3.000
 2SY  H6   C6   H5   106.18  3.000
 2SY  H6   C6   N2   107.60  3.000
 2SY  H5   C6   N2   109.74  3.000
 2SY  H6   C6   C10  109.75  3.000
 2SY  H5   C6   C10  109.65  3.000
 2SY  N2   C6   C10  113.63  3.000
 2SY  C1   N2   C5   108.59  3.000
 2SY  C1   N2   C6   125.42  3.000
 2SY  C5   N2   C6   125.85  3.000
 2SY  H7   C5   C7   129.34  3.000
 2SY  H7   C5   N2   120.16  3.000
 2SY  C7   C5   N2   110.50  3.000
 2SY  C3   C7   C11  126.77  3.000
 2SY  C11  C7   C5   127.03  3.000
 2SY  C3   C7   C5   106.19  3.000
 2SY  H9   C11  H8   105.32  3.000
 2SY  H9   C11  C15  108.12  3.000
 2SY  H8   C11  C15  107.77  3.000
 2SY  H9   C11  C7   111.16  3.000
 2SY  H8   C11  C7   110.60  3.000
 2SY  C15  C11  C7   113.48  3.000
 2SY  O18  C15  O19  123.33  3.000
 2SY  O18  C15  C11  111.30  3.000
 2SY  O19  C15  C11  125.37  3.000
 2SY  H10  O18  C15  110.00  3.000
 2SY  C8   C3   C1   119.24  3.000
 2SY  C8   C3   C7   133.74  3.000
 2SY  C1   C3   C7   107.02  3.000
 2SY  C4   C1   C3   122.18  3.000
 2SY  C3   C1   N2   107.70  3.000
 2SY  C4   C1   N2   130.12  3.000
 2SY  H11  C8   C12  120.45  3.000
 2SY  H11  C8   C3   120.71  3.000
 2SY  C12  C8   C3   118.84  3.000
 2SY  H12  C12  C9   119.17  3.000
 2SY  H12  C12  C8   119.80  3.000
 2SY  C9   C12  C8   121.03  3.000
 2SY  H13  C9   C4   119.31  3.000
 2SY  H13  C9   C12  119.33  3.000
 2SY  C4   C9   C12  121.37  3.000
 2SY  H14  C4   C9   120.80  3.000
 2SY  H14  C4   C1   121.86  3.000
 2SY  C9   C4   C1   117.34  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
 2SY  CONST_01  C14  C17  C20  C16     0.00   0.0  0
 2SY  CONST_02  C14  C10  C13  C16     0.00   0.0  0
 2SY  CONST_03  C17  C20  C16  C13     0.00   0.0  0
 2SY  CONST_04  C17  C14  C10  C13     0.00   0.0  0
 2SY  CONST_05  C10  C14  C17  C20     0.00   0.0  0
 2SY  CONST_06  C10  C13  C16  C20     0.00   0.0  0
 2SY  CONST_07  C3   C7   C5   N2      0.00   0.0  0
 2SY  CONST_08  C9   C4   C1   N2    180.00   0.0  0
 2SY  CONST_09  C7   C3   C1   N2      0.00   0.0  0
 2SY  CONST_10  C8   C3   C1   N2    180.00   0.0  0
 2SY  CONST_11  C4   C1   N2   C5    180.00   0.0  0
 2SY  CONST_12  C3   C1   N2   C5      0.00   0.0  0
 2SY  CONST_13  C1   C3   C7   C5      0.00   0.0  0
 2SY  CONST_14  C8   C3   C7   C5    180.00   0.0  0
 2SY  CONST_15  C1   N2   C5   C7      0.00   0.0  0
 2SY  CONST_16  C4   C1   C3   C7    180.00   0.0  0
 2SY  CONST_17  C12  C8   C3   C7    180.00   0.0  0
 2SY  CONST_18  C9   C4   C1   C3      0.00   0.0  0
 2SY  CONST_19  C9   C12  C8   C3      0.00   0.0  0
 2SY  CONST_20  C12  C9   C4   C1      0.00   0.0  0
 2SY  CONST_21  C12  C8   C3   C1      0.00   0.0  0
 2SY  CONST_22  C4   C1   C3   C8      0.00   0.0  0
 2SY  CONST_23  C4   C9   C12  C8      0.00   0.0  0
 2SY  CONST_24  C17  C20  C16  CL2   180.00   0.0  0
 2SY  CONST_25  C10  C13  C16  CL2   180.00   0.0  0
 2SY  CONST_26  C6   C10  C13  C16   180.00   0.0  0
 2SY  CONST_27  C6   C10  C14  C17   180.00   0.0  0
 2SY  CONST_28  C7   C5   N2   C6    180.00   0.0  0
 2SY  CONST_29  C4   C1   N2   C6      0.00   0.0  0
 2SY  CONST_30  C3   C1   N2   C6    180.00   0.0  0
 2SY  CONST_31  C11  C7   C5   N2    180.00   0.0  0
 2SY  CONST_32  C1   C3   C7   C11   180.00   0.0  0
 2SY  CONST_33  C8   C3   C7   C11     0.00   0.0  0
 2SY  CONST_34  H3   C17  C20  C16   180.00   0.0  0
 2SY  CONST_35  H2   C20  C16  C13   180.00   0.0  0
 2SY  CONST_36  H4   C14  C10  C13   180.00   0.0  0
 2SY  CONST_37  H1   C13  C16  C20   180.00   0.0  0
 2SY  CONST_38  H14  C4   C1   N2      0.00   0.0  0
 2SY  CONST_39  H11  C8   C3   C7      0.00   0.0  0
 2SY  CONST_40  H7   C5   C7   C3    180.00   0.0  0
 2SY  CONST_41  H12  C12  C8   C3    180.00   0.0  0
 2SY  CONST_42  H13  C9   C4   C1    180.00   0.0  0
 2SY  CONST_43  H10  O18  C15  C11   180.00   0.0  0
 2SY  Var_01    N2   C6   C10  C13    28.98  30.0  2
 2SY  Var_02    C5   N2   C6   C10  -106.49  30.0  2
 2SY  Var_03    C15  C11  C7   C5   -109.46  30.0  2
 2SY  Var_04    O19  C15  C11  C7      5.18  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
 2SY  plan-1  CL2  0.020
 2SY  plan-1  C16  0.020
 2SY  plan-1  C13  0.020
 2SY  plan-1  C20  0.020
 2SY  plan-1  C17  0.020
 2SY  plan-1  C14  0.020
 2SY  plan-1  C10  0.020
 2SY  plan-1  C6   0.020
 2SY  plan-1  H1   0.020
 2SY  plan-1  H2   0.020
 2SY  plan-1  H3   0.020
 2SY  plan-1  H4   0.020
 2SY  plan-2  C6   0.020
 2SY  plan-2  N2   0.020
 2SY  plan-2  C5   0.020
 2SY  plan-2  C7   0.020
 2SY  plan-2  C11  0.020
 2SY  plan-2  C3   0.020
 2SY  plan-2  C1   0.020
 2SY  plan-2  C8   0.020
 2SY  plan-2  C12  0.020
 2SY  plan-2  C9   0.020
 2SY  plan-2  C4   0.020
 2SY  plan-2  H7   0.020
 2SY  plan-2  H11  0.020
 2SY  plan-2  H12  0.020
 2SY  plan-2  H13  0.020
 2SY  plan-2  H14  0.020
 2SY  plan-3  C11  0.020
 2SY  plan-3  C15  0.020
 2SY  plan-3  O19  0.020
 2SY  plan-3  O18  0.020
 2SY  plan-3  H10  0.020

