# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:23:53 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2,2'-{5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]benzene-1,3-diyl}diacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC#Cc1sc(cc1)c2cc(CC(O)=O)cc(CC(O)=O)c2
#
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
 LNY  LNY  '2,2'-{5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]benzene-1,3-diyl}diacetic acid'  ligand  35  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LNY
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
 LNY  C1   C  CH2    0  -0.610   3.6940   2.3084   0.5780
 LNY  C2   C  C      0   0.178   2.6930   1.1979   0.6235
 LNY  C3   C  C1     0  -0.377   3.1073  -0.1266   0.7489
 LNY  O1   O  O      0  -0.505   4.0009   1.8062  -1.7447
 LNY  O2   O  OC    -1  -0.720   3.5627  -4.3200  -0.4198
 LNY  O3   O  O      0  -0.521   1.9322  -3.0607  -1.2711
 LNY  C11  C  CR15   0  -0.282  -3.0531   1.8631   0.7731
 LNY  C12  C  CR5    0  -0.280  -3.5033   0.6628   0.2860
 LNY  C13  C  CSP    0   0.330  -4.8242   0.2577   0.0288
 LNY  C14  C  CSP    0  -0.145  -5.9572  -0.0925  -0.1912
 LNY  C15  C  CH2    0  -0.263  -7.3269  -0.5347  -0.4080
 LNY  C16  C  C1     0  -0.421   1.3331   1.4559   0.5439
 LNY  O    O  OC    -1  -0.783   5.1652   3.4854  -0.8482
 LNY  C    C  C      0   0.422   4.3419   2.5487  -0.8106
 LNY  C8   C  C      0   0.154   0.3966   0.4191   0.6004
 LNY  C7   C  C1     0  -0.397   0.8460  -0.8920   0.7199
 LNY  C4   C  C      0   0.137   2.2039  -1.1810   0.7993
 LNY  C5   C  CH2    0  -0.670   2.6827  -2.5904   0.9464
 LNY  C6   C  C      0   0.402   2.7344  -3.3886  -0.3787
 LNY  C9   C  CR5    0  -0.210  -1.0302   0.7328   0.5585
 LNY  C10  C  CR15   0  -0.136  -1.6524   1.8999   0.9249
 LNY  S    S  S2     0   0.158  -2.1885  -0.4204   0.0115
 LNY  O4   O  OH1    0  -0.678  -7.7557  -0.1353  -1.6868
 LNY  H1   H  HCH2   0   0.240   3.2354   3.2455   0.9080
 LNY  H2   H  HCH2   0   0.300   4.4994   2.1111   1.2929
 LNY  H3   H  H      0   0.213   4.1692  -0.3386   0.8244
 LNY  H5   H  HCR5   0   0.240  -3.7142   2.6803   1.0221
 LNY  H6   H  HCH2   0   0.219  -7.3602  -1.6247  -0.2813
 LNY  H7   H  HCH2   0   0.233  -7.9547  -0.1138   0.3878
 LNY  H8   H  H      0   0.233   0.9950   2.4795   0.4292
 LNY  H10  H  H      0   0.237   0.1354  -1.7059   0.7998
 LNY  H11  H  HCH2   0   0.282   3.6659  -2.6064   1.4210
 LNY  H12  H  HCH2   0   0.275   2.0129  -3.1353   1.6201
 LNY  H13  H  HCR5   0   0.277  -1.1221   2.7533   1.3215
 LNY  H14  H  HOH1   0   0.468  -8.6715  -0.4121  -1.7797

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
 LNY  O4   C15  single    1.407  0.020  1.407
 LNY  C15  C14  single    1.456  0.020  1.456
 LNY  C14  C13  triple    1.206  0.020  1.206
 LNY  C13  C12  single    1.405  0.020  1.405
 LNY  C11  C12  aromatic  1.371  0.020  1.371
 LNY  C11  C10  aromatic  1.409  0.020  1.409
 LNY  C12  S    aromatic  1.726  0.020  1.726
 LNY  C10  C9   aromatic  1.372  0.020  1.372
 LNY  S    C9   aromatic  1.724  0.020  1.724
 LNY  C9   C8   single    1.462  0.020  1.462
 LNY  C8   C7   aromatic  1.391  0.020  1.391
 LNY  C8   C16  aromatic  1.398  0.020  1.398
 LNY  C7   C4   aromatic  1.391  0.020  1.391
 LNY  C16  C2   aromatic  1.386  0.020  1.386
 LNY  C4   C5   single    1.496  0.020  1.496
 LNY  C4   C3   aromatic  1.389  0.020  1.389
 LNY  C2   C3   aromatic  1.393  0.020  1.393
 LNY  C2   C1   single    1.496  0.020  1.496
 LNY  C5   C6   single    1.548  0.020  1.548
 LNY  O3   C6   deloc     1.244  0.020  1.244
 LNY  C6   O2   deloc     1.247  0.020  1.247
 LNY  C1   C    single    1.551  0.020  1.551
 LNY  O1   C    deloc     1.241  0.020  1.241
 LNY  C    O    deloc     1.248  0.020  1.248
 LNY  C1   H1   single    0.970  0.020  1.090
 LNY  C1   H2   single    0.970  0.020  1.090
 LNY  C3   H3   single    0.930  0.020  1.080
 LNY  C11  H5   single    0.930  0.020  1.080
 LNY  C15  H6   single    0.970  0.020  1.090
 LNY  C15  H7   single    0.970  0.020  1.090
 LNY  C16  H8   single    0.930  0.020  1.080
 LNY  C7   H10  single    0.930  0.020  1.080
 LNY  C5   H11  single    0.970  0.020  1.090
 LNY  C5   H12  single    0.970  0.020  1.090
 LNY  C10  H13  single    0.930  0.020  1.080
 LNY  O4   H14  single    0.850  0.020  0.980

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
 LNY  H2   C1   H1   105.41  3.000
 LNY  H2   C1   C    107.77  3.000
 LNY  H1   C1   C    108.20  3.000
 LNY  H2   C1   C2   109.80  3.000
 LNY  H1   C1   C2   110.25  3.000
 LNY  C    C1   C2   114.95  3.000
 LNY  C16  C2   C3   118.27  3.000
 LNY  C3   C2   C1   120.63  3.000
 LNY  C16  C2   C1   121.10  3.000
 LNY  H3   C3   C4   119.03  3.000
 LNY  H3   C3   C2   118.87  3.000
 LNY  C4   C3   C2   122.10  3.000
 LNY  H5   C11  C10  124.31  3.000
 LNY  H5   C11  C12  122.90  3.000
 LNY  C10  C11  C12  112.79  3.000
 LNY  S    C12  C13  120.41  3.000
 LNY  S    C12  C11  110.84  3.000
 LNY  C13  C12  C11  128.75  3.000
 LNY  C14  C13  C12  180.00  3.000
 LNY  C15  C14  C13  180.00  3.000
 LNY  H7   C15  H6   106.25  3.000
 LNY  H7   C15  O4   112.08  3.000
 LNY  H6   C15  O4   112.19  3.000
 LNY  H7   C15  C14  108.29  3.000
 LNY  H6   C15  C14  108.24  3.000
 LNY  O4   C15  C14  109.63  3.000
 LNY  H8   C16  C8   119.70  3.000
 LNY  H8   C16  C2   119.19  3.000
 LNY  C8   C16  C2   121.11  3.000
 LNY  O    C    O1   127.43  3.000
 LNY  O    C    C1   114.77  3.000
 LNY  O1   C    C1   117.80  3.000
 LNY  C9   C8   C7   121.34  3.000
 LNY  C7   C8   C16  119.07  3.000
 LNY  C9   C8   C16  119.58  3.000
 LNY  H10  C7   C4   118.69  3.000
 LNY  H10  C7   C8   120.16  3.000
 LNY  C4   C7   C8   121.08  3.000
 LNY  C5   C4   C7   120.93  3.000
 LNY  C5   C4   C3   120.70  3.000
 LNY  C7   C4   C3   118.37  3.000
 LNY  H12  C5   H11  106.03  3.000
 LNY  H12  C5   C6   106.89  3.000
 LNY  H11  C5   C6   109.55  3.000
 LNY  H12  C5   C4   109.48  3.000
 LNY  H11  C5   C4   110.17  3.000
 LNY  C6   C5   C4   114.35  3.000
 LNY  C5   C6   O3   117.18  3.000
 LNY  O3   C6   O2   126.98  3.000
 LNY  C5   C6   O2   115.82  3.000
 LNY  S    C9   C10  110.43  3.000
 LNY  S    C9   C8   121.44  3.000
 LNY  C10  C9   C8   128.13  3.000
 LNY  H13  C10  C9   123.18  3.000
 LNY  H13  C10  C11  123.23  3.000
 LNY  C9   C10  C11  113.55  3.000
 LNY  C9   S    C12   92.38  3.000
 LNY  H14  O4   C15  107.25  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
 LNY  CONST_01  C9   C8   C16  C2   180.00   0.0  0
 LNY  CONST_02  C7   C8   C16  C2     0.00   0.0  0
 LNY  CONST_03  C7   C4   C3   C2     0.00   0.0  0
 LNY  CONST_04  C8   C7   C4   C3     0.00   0.0  0
 LNY  CONST_05  C8   C16  C2   C3     0.00   0.0  0
 LNY  CONST_06  C9   S    C12  C11    0.00   0.0  0
 LNY  CONST_07  S    C9   C10  C11    0.00   0.0  0
 LNY  CONST_08  C8   C9   C10  C11  180.00   0.0  0
 LNY  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 LNY  CONST_10  C10  C9   S    C12    0.00   0.0  0
 LNY  CONST_11  C8   C9   S    C12  180.00   0.0  0
 LNY  CONST_14  C4   C7   C8   C16    0.00   0.0  0
 LNY  CONST_15  C4   C3   C2   C16    0.00   0.0  0
 LNY  CONST_18  C9   C8   C7   C4   180.00   0.0  0
 LNY  CONST_19  S    C12  C11  C10    0.00   0.0  0
 LNY  CONST_20  C8   C16  C2   C1   180.00   0.0  0
 LNY  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 LNY  CONST_22  C5   C4   C3   C2   180.00   0.0  0
 LNY  CONST_23  C10  C11  C12  C13  180.00   0.0  0
 LNY  CONST_24  C9   S    C12  C13  180.00   0.0  0
 LNY  CONST_25  C5   C4   C7   C8   180.00   0.0  0
 LNY  CONST_26  H10  C7   C4   C3   180.00   0.0  0
 LNY  CONST_27  H8   C16  C2   C3   180.00   0.0  0
 LNY  CONST_28  H13  C10  C11  C12  180.00   0.0  0
 LNY  CONST_29  H3   C3   C2   C16  180.00   0.0  0
 LNY  CONST_30  H5   C11  C10  C9   180.00   0.0  0
 LNY  Var_01    C6   C5   C4   C3   -99.41  30.0  2
 LNY  Var_02    C    C1   C2   C3    81.81  30.0  2
 LNY  Var_03    O1   C    C1   C2    -1.01  30.0  3
 LNY  Var_04    C4   C5   C6   O2   153.43  30.0  2
 LNY  Var_05    O4   C15  C14  C13  177.23  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
 LNY  plan-1  C11  0.020
 LNY  plan-1  C12  0.020
 LNY  plan-1  C13  0.020
 LNY  plan-1  C14  0.020
 LNY  plan-1  C8   0.020
 LNY  plan-1  C9   0.020
 LNY  plan-1  C10  0.020
 LNY  plan-1  S    0.020
 LNY  plan-1  H5   0.020
 LNY  plan-1  H13  0.020
 LNY  plan-2  C1   0.020
 LNY  plan-2  C2   0.020
 LNY  plan-2  C3   0.020
 LNY  plan-2  C16  0.020
 LNY  plan-2  C8   0.020
 LNY  plan-2  C7   0.020
 LNY  plan-2  C4   0.020
 LNY  plan-2  C5   0.020
 LNY  plan-2  C9   0.020
 LNY  plan-2  H3   0.020
 LNY  plan-2  H8   0.020
 LNY  plan-2  H10  0.020
 LNY  plan-3  C1   0.020
 LNY  plan-3  O1   0.020
 LNY  plan-3  O    0.020
 LNY  plan-3  C    0.020
 LNY  plan-4  O2   0.020
 LNY  plan-4  O3   0.020
 LNY  plan-4  C5   0.020
 LNY  plan-4  C6   0.020

