# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 00:38:24 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-[(4-methylphenyl)sulfanyl]-1-(piperidin-1-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(SCC(=O)N2CCCCC2)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
 L2S  L2S  2-[(4-methylphenyl)sulfanyl]-1-(piperidin-1-yl)ethanone  ligand  36  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L2S
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
 L2S  C1    C  CH2   0  -0.447  -5.0039   1.4919   0.5017
 L2S  N1    N  NT    0  -0.446  -2.8934  -0.1457  -0.5680
 L2S  O1    O  O     0  -0.494  -1.8818  -2.0483   0.1216
 L2S  S1    S  S2    0   0.073   0.7707  -1.3794   0.2528
 L2S  C2    C  CH2   0  -0.433  -4.9949  -0.0239   0.6765
 L2S  C3    C  CH2   0  -0.316  -4.2368  -0.6978  -0.4614
 L2S  C4    C  CH2   0  -0.326  -2.8831   1.2862  -0.8245
 L2S  C5    C  CH2   0  -0.427  -3.5932   2.0345   0.2965
 L2S  C6    C  C     0   0.595  -1.8221  -0.8695  -0.2025
 L2S  C7    C  CH2   0  -0.755  -0.4779  -0.1598  -0.2104
 L2S  C8    C  CR6   0  -0.118   2.2648  -0.4462   0.1459
 L2S  C9    C  CR16  0  -0.256   3.4534  -1.1751   0.2357
 L2S  C10   C  CR16  0  -0.282   4.6784  -0.5328   0.1996
 L2S  C11   C  CR6   0   0.084   4.7689   0.8527   0.0637
 L2S  C12   C  CR16  0  -0.284   3.5803   1.5670  -0.0273
 L2S  C13   C  CR16  0  -0.244   2.3418   0.9368   0.0142
 L2S  C14   C  CH3   0  -0.722   6.1014   1.5395  -0.0059
 L2S  H11   H  HCH2  0   0.219  -5.6162   1.7481  -0.3697
 L2S  H21   H  HCH2  0   0.241  -5.4724   1.9727   1.3626
 L2S  H12   H  HCH2  0   0.227  -4.5258  -0.2919   1.6276
 L2S  H22   H  HCH2  0   0.240  -6.0157  -0.4107   0.7053
 L2S  H13   H  HCH2  0   0.241  -4.7520  -0.5172  -1.4102
 L2S  H23   H  HCH2  0   0.265  -4.1800  -1.7734  -0.3201
 L2S  H14   H  HCH2  0   0.272  -1.8674   1.6502  -0.9554
 L2S  H24   H  HCH2  0   0.250  -3.3980   1.4624  -1.7739
 L2S  H15   H  HCH2  0   0.242  -3.6216   3.0985   0.0529
 L2S  H25   H  HCH2  0   0.225  -3.0108   1.9356   1.2180
 L2S  H17   H  HCH2  0   0.307  -0.4893   0.6687   0.5010
 L2S  H27   H  HCH2  0   0.315  -0.2508   0.2509  -1.1963
 L2S  H9    H  HCR6  0   0.261   3.4230  -2.2540   0.3330
 L2S  H10   H  HCR6  0   0.251   5.5819  -1.1265   0.2763
 L2S  H112  H  HCR6  0   0.251   3.6109   2.6457  -0.1268
 L2S  H113  H  HCR6  0   0.259   1.4524   1.5477  -0.0529
 L2S  H114  H  HCH3  0   0.247   6.5277   1.4709  -1.0091
 L2S  H214  H  HCH3  0   0.243   6.0174   2.5975   0.2398
 L2S  H314  H  HCH3  0   0.243   6.8201   1.0899   0.6795

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
 L2S  C1   C2    single    1.526  0.020  1.526
 L2S  C1   C5    single    1.525  0.020  1.525
 L2S  C1   H11   single    0.970  0.020  1.090
 L2S  C1   H21   single    0.970  0.020  1.090
 L2S  N1   C3    single    1.456  0.020  1.456
 L2S  N1   C4    single    1.455  0.020  1.455
 L2S  N1   C6    single    1.344  0.020  1.344
 L2S  O1   C6    double    1.224  0.020  1.224
 L2S  S1   C7    single    1.806  0.020  1.806
 L2S  S1   C8    single    1.765  0.020  1.765
 L2S  C2   C3    single    1.524  0.020  1.524
 L2S  C2   H12   single    0.970  0.020  1.090
 L2S  C2   H22   single    0.970  0.020  1.090
 L2S  C3   H13   single    0.970  0.020  1.090
 L2S  C3   H23   single    0.970  0.020  1.090
 L2S  C4   C5    single    1.523  0.020  1.523
 L2S  C4   H14   single    0.970  0.020  1.090
 L2S  C4   H24   single    0.970  0.020  1.090
 L2S  C5   H15   single    0.970  0.020  1.090
 L2S  C5   H25   single    0.970  0.020  1.090
 L2S  C6   C7    single    1.520  0.020  1.520
 L2S  C7   H17   single    0.970  0.020  1.090
 L2S  C7   H27   single    0.970  0.020  1.090
 L2S  C8   C9    aromatic  1.397  0.020  1.397
 L2S  C8   C13   aromatic  1.391  0.020  1.391
 L2S  C9   C10   aromatic  1.384  0.020  1.384
 L2S  C9   H9    single    0.930  0.020  1.080
 L2S  C10  C11   aromatic  1.395  0.020  1.395
 L2S  C10  H10   single    0.930  0.020  1.080
 L2S  C11  C12   aromatic  1.390  0.020  1.390
 L2S  C11  C14   single    1.501  0.020  1.501
 L2S  C12  C13   aromatic  1.390  0.020  1.390
 L2S  C12  H112  single    0.930  0.020  1.080
 L2S  C13  H113  single    0.930  0.020  1.080
 L2S  C14  H114  single    0.970  0.020  1.090
 L2S  C14  H214  single    0.970  0.020  1.090
 L2S  C14  H314  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
 L2S  H21   C1   H11   106.52  3.000
 L2S  H21   C1   C5    110.26  3.000
 L2S  H11   C1   C5    109.07  3.000
 L2S  H21   C1   C2    110.47  3.000
 L2S  H11   C1   C2    109.07  3.000
 L2S  C5    C1   C2    111.30  3.000
 L2S  C6    N1   C4    124.93  3.000
 L2S  C6    N1   C3    120.76  3.000
 L2S  C4    N1   C3    113.12  3.000
 L2S  C8    S1   C7    102.28  3.000
 L2S  H22   C2   H12   106.93  3.000
 L2S  H22   C2   C3    109.15  3.000
 L2S  H12   C2   C3    109.12  3.000
 L2S  H22   C2   C1    110.45  3.000
 L2S  H12   C2   C1    110.21  3.000
 L2S  C3    C2   C1    110.89  3.000
 L2S  H23   C3   H13   107.50  3.000
 L2S  H23   C3   C2    111.51  3.000
 L2S  H13   C3   C2    109.88  3.000
 L2S  H23   C3   N1    109.67  3.000
 L2S  H13   C3   N1    107.95  3.000
 L2S  C2    C3   N1    110.23  3.000
 L2S  H24   C4   H14   106.34  3.000
 L2S  H24   C4   C5    109.87  3.000
 L2S  H14   C4   C5    111.08  3.000
 L2S  H24   C4   N1    107.95  3.000
 L2S  H14   C4   N1    110.95  3.000
 L2S  C5    C4   N1    110.51  3.000
 L2S  H25   C5   H15   106.84  3.000
 L2S  H25   C5   C4    109.09  3.000
 L2S  H15   C5   C4    109.06  3.000
 L2S  H25   C5   C1    110.29  3.000
 L2S  H15   C5   C1    110.64  3.000
 L2S  C4    C5   C1    110.82  3.000
 L2S  C7    C6   O1    119.61  3.000
 L2S  C7    C6   N1    116.89  3.000
 L2S  O1    C6   N1    123.50  3.000
 L2S  H27   C7   H17   107.76  3.000
 L2S  H27   C7   C6    111.37  3.000
 L2S  H17   C7   C6    109.97  3.000
 L2S  H27   C7   S1    109.99  3.000
 L2S  H17   C7   S1    110.63  3.000
 L2S  C6    C7   S1    107.15  3.000
 L2S  C13   C8   C9    118.52  3.000
 L2S  C13   C8   S1    125.33  3.000
 L2S  C9    C8   S1    116.13  3.000
 L2S  H9    C9   C10   119.30  3.000
 L2S  H9    C9   C8    120.08  3.000
 L2S  C10   C9   C8    120.62  3.000
 L2S  H10   C10  C11   119.79  3.000
 L2S  H10   C10  C9    118.81  3.000
 L2S  C11   C10  C9    121.40  3.000
 L2S  C14   C11  C12   121.41  3.000
 L2S  C14   C11  C10   121.10  3.000
 L2S  C12   C11  C10   117.48  3.000
 L2S  H112  C12  C13   118.63  3.000
 L2S  H112  C12  C11   119.57  3.000
 L2S  C13   C12  C11   121.80  3.000
 L2S  H113  C13  C12   118.35  3.000
 L2S  H113  C13  C8    121.47  3.000
 L2S  C12   C13  C8    120.18  3.000
 L2S  H314  C14  H214  108.03  3.000
 L2S  H314  C14  H114  107.12  3.000
 L2S  H214  C14  H114  107.35  3.000
 L2S  H314  C14  C11   111.56  3.000
 L2S  H214  C14  C11   111.44  3.000
 L2S  H114  C14  C11   111.13  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
 L2S  CONST_01  C11   C10  C9   C8      0.00   0.0  0
 L2S  CONST_02  C11   C12  C13  C8      0.00   0.0  0
 L2S  CONST_03  C12   C13  C8   C9      0.00   0.0  0
 L2S  CONST_04  C12   C11  C10  C9      0.00   0.0  0
 L2S  CONST_05  C13   C8   C9   C10     0.00   0.0  0
 L2S  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 L2S  CONST_07  C10   C9   C8   S1    180.00   0.0  0
 L2S  CONST_08  C12   C13  C8   S1    180.00   0.0  0
 L2S  CONST_09  C14   C11  C10  C9    180.00   0.0  0
 L2S  CONST_10  C14   C11  C12  C13   180.00   0.0  0
 L2S  CONST_11  H10   C10  C9   C8    180.00   0.0  0
 L2S  CONST_12  H112  C12  C13  C8    180.00   0.0  0
 L2S  CONST_13  H113  C13  C8   C9    180.00   0.0  0
 L2S  CONST_14  H9    C9   C10  C11   180.00   0.0  0
 L2S  CONST_15  C3    N1   C6   O1      0.00   0.0  0
 L2S  CONST_16  C4    N1   C6   O1    180.00   0.0  0
 L2S  CONST_17  C7    C6   N1   C3    180.00   0.0  0
 L2S  CONST_18  C7    C6   N1   C4      0.00   0.0  0
 L2S  Var_01    N1    C3   C2   C1     55.00  30.0  1
 L2S  Var_02    N1    C4   C5   C1    -54.78  30.0  1
 L2S  Var_03    C4    C5   C1   C2     52.05  30.0  1
 L2S  Var_04    C4    N1   C3   C2    -59.67  30.0  1
 L2S  Var_05    C5    C4   N1   C3     59.65  30.0  1
 L2S  Var_06    C5    C1   C2   C3    -52.26  30.0  1
 L2S  Var_07    C9    C8   S1   C7   -169.79  30.0  2
 L2S  Var_08    H114  C14  C11  C10    80.36  30.0  2
 L2S  Var_09    S1    C7   C6   N1   -177.75  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
 L2S  plan-1  S1    0.020
 L2S  plan-1  C8    0.020
 L2S  plan-1  C9    0.020
 L2S  plan-1  C10   0.020
 L2S  plan-1  C11   0.020
 L2S  plan-1  C12   0.020
 L2S  plan-1  C13   0.020
 L2S  plan-1  C14   0.020
 L2S  plan-1  H9    0.020
 L2S  plan-1  H10   0.020
 L2S  plan-1  H112  0.020
 L2S  plan-1  H113  0.020
 L2S  plan-2  N1    0.020
 L2S  plan-2  O1    0.020
 L2S  plan-2  C3    0.020
 L2S  plan-2  C4    0.020
 L2S  plan-2  C6    0.020
 L2S  plan-2  C7    0.020

