# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:49:45 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 1-[4-(naphthalen-1-ylmethyl)piperazin-1-yl]-4-sulfanylbutan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCC(=O)N1CCN(CC1)Cc2cccc3ccccc23
#
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
 J30  J30  1-[4-(naphthalen-1-ylmethyl)piperazin-1-yl]-4-sulfanylbutan-1-one  ligand  47  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_J30
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
 J30  SD    S  S2    0  -0.257   7.6581   1.2082  -0.5715
 J30  CE    C  CH2   0  -0.553   5.8511   1.3125  -0.8003
 J30  CH    C  CH2   0  -0.601   3.6962   0.1135  -0.4012
 J30  CZ    C  CH2   0  -0.406   5.2089   0.0484  -0.2489
 J30  C12   C  C     0   0.574   2.9949  -1.1164   0.1472
 J30  O13   O  O     0  -0.505   3.6337  -2.0261   0.6617
 J30  N14   N  NT    0  -0.466   1.6494  -1.1596   0.0381
 J30  C15   C  CH2   0  -0.311   0.8840  -2.2802   0.5512
 J30  C16   C  CH2   0  -0.279  -0.1643  -1.7962   1.5372
 J30  N17   N  NT    0  -0.413  -1.0190  -0.7968   0.9291
 J30  C18   C  CH2   0  -0.267  -0.2376   0.3299   0.4634
 J30  C19   C  CH2   0  -0.315   0.8080  -0.1289  -0.5386
 J30  C40   C  CR6   0   0.092  -3.0878   0.5251   1.1772
 J30  C41   C  CR66  0   0.079  -3.8606   0.1267   0.0466
 J30  C42   C  CR66  0   0.110  -4.7920   1.0432  -0.5127
 J30  C43   C  CR16  0  -0.333  -4.9318   2.3322   0.0548
 J30  C44   C  CR16  0  -0.245  -4.1833   2.6934   1.1380
 J30  C45   C  CR16  0  -0.328  -3.2626   1.7826   1.6952
 J30  C46   C  CR16  0  -0.320  -3.7487  -1.1583  -0.5396
 J30  C47   C  CR16  0  -0.254  -4.5216  -1.5124  -1.6130
 J30  C48   C  CR16  0  -0.260  -5.4410  -0.5993  -2.1671
 J30  C49   C  CR16  0  -0.313  -5.5705   0.6504  -1.6269
 J30  HSD   H  HSH1  0   0.222   7.9786   2.3904  -1.1078
 J30  HE    H  HCH2  0   0.264   5.4722   2.1927  -0.2797
 J30  HEA   H  HCH2  0   0.264   5.6291   1.4249  -1.8619
 J30  HH    H  HCH2  0   0.269   3.3167   1.0050   0.1081
 J30  HHA   H  HCH2  0   0.270   3.4359   0.2407  -1.4566
 J30  HZ    H  HCH2  0   0.240   5.6043  -0.8233  -0.7741
 J30  HZA   H  HCH2  0   0.239   5.4745  -0.0667   0.8039
 J30  H15   H  HCH2  0   0.239   0.3922  -2.7916  -0.2828
 J30  H15A  H  HCH2  0   0.263   1.5492  -2.9903   1.0341
 J30  H16   H  HCH2  0   0.243  -0.7728  -2.6498   1.8453
 J30  H16A  H  HCH2  0   0.200   0.3388  -1.4124   2.4421
 J30  H17   H  HCH2  0   0.251  -2.6104  -1.3282   2.1310
 J30  H17A  H  HCH2  0   0.229  -1.7214   0.0595   2.7408
 J30  H18   H  HCH2  0   0.250  -0.8929   1.0488  -0.0316
 J30  H18A  H  HCH2  0   0.197   0.2590   0.8618   1.2944
 J30  H19   H  HCH2  0   0.273   1.3947   0.7260  -0.8611
 J30  H19A  H  HCH2  0   0.243   0.3054  -0.5319  -1.4240
 J30  H43   H  HCR6  0   0.254  -5.6413   3.0242  -0.3829
 J30  H44   H  HCR6  0   0.256  -4.2886   3.6790   1.5722
 J30  H45   H  HCR6  0   0.252  -2.6781   2.0881   2.5552
 J30  H46   H  HCR6  0   0.257  -3.0306  -1.8607  -0.1422
 J30  H47   H  HCR6  0   0.256  -4.4236  -2.5006  -2.0435
 J30  H48   H  HCR6  0   0.256  -6.0417  -0.8904  -3.0191
 J30  H49   H  HCR6  0   0.254  -6.2759   1.3577  -2.0465
 J30  C17   C  CH2   0  -0.369  -2.0983  -0.4118   1.8181

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
 J30  SD   CE    single    1.824  0.020  1.824
 J30  SD   HSD   single    1.200  0.020  1.300
 J30  CZ   CE    single    1.521  0.020  1.521
 J30  CE   HE    single    0.970  0.020  1.090
 J30  CE   HEA   single    0.970  0.020  1.090
 J30  C12  CH    single    1.518  0.020  1.518
 J30  CH   CZ    single    1.522  0.020  1.522
 J30  CH   HH    single    0.970  0.020  1.090
 J30  CH   HHA   single    0.970  0.020  1.090
 J30  CZ   HZ    single    0.970  0.020  1.090
 J30  CZ   HZA   single    0.970  0.020  1.090
 J30  N14  C12   single    1.351  0.020  1.351
 J30  C12  O13   double    1.225  0.020  1.225
 J30  C19  N14   single    1.450  0.020  1.450
 J30  C15  N14   single    1.451  0.020  1.451
 J30  C16  C15   single    1.518  0.020  1.518
 J30  C15  H15   single    0.970  0.020  1.090
 J30  C15  H15A  single    0.970  0.020  1.090
 J30  N17  C16   single    1.449  0.020  1.449
 J30  C16  H16   single    0.970  0.020  1.090
 J30  C16  H16A  single    0.970  0.020  1.090
 J30  C40  C17   single    1.506  0.020  1.506
 J30  C17  N17   single    1.450  0.020  1.450
 J30  C17  H17   single    0.970  0.020  1.090
 J30  C17  H17A  single    0.970  0.020  1.090
 J30  N17  C18   single    1.448  0.020  1.448
 J30  C18  C19   single    1.519  0.020  1.519
 J30  C18  H18   single    0.970  0.020  1.090
 J30  C18  H18A  single    0.970  0.020  1.090
 J30  C19  H19   single    0.970  0.020  1.090
 J30  C19  H19A  single    0.970  0.020  1.090
 J30  C45  C40   aromatic  1.371  0.020  1.371
 J30  C41  C40   aromatic  1.426  0.020  1.426
 J30  C42  C41   aromatic  1.421  0.020  1.421
 J30  C41  C46   aromatic  1.417  0.020  1.417
 J30  C43  C42   aromatic  1.415  0.020  1.415
 J30  C49  C42   aromatic  1.415  0.020  1.415
 J30  C43  C44   aromatic  1.365  0.020  1.365
 J30  C43  H43   single    0.930  0.020  1.080
 J30  C44  C45   aromatic  1.410  0.020  1.410
 J30  C44  H44   single    0.930  0.020  1.080
 J30  C45  H45   single    0.930  0.020  1.080
 J30  C47  C46   aromatic  1.369  0.020  1.369
 J30  C46  H46   single    0.930  0.020  1.080
 J30  C48  C47   aromatic  1.409  0.020  1.409
 J30  C47  H47   single    0.930  0.020  1.080
 J30  C49  C48   aromatic  1.368  0.020  1.368
 J30  C48  H48   single    0.930  0.020  1.080
 J30  C49  H49   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
 J30  HSD   SD   CE    97.85  3.000
 J30  HEA   CE   HE   108.11  3.000
 J30  HEA   CE   CZ   110.65  3.000
 J30  HE    CE   CZ   110.55  3.000
 J30  HEA   CE   SD   109.24  3.000
 J30  HE    CE   SD   109.29  3.000
 J30  CZ    CE   SD   108.98  3.000
 J30  HHA   CH   HH   105.76  3.000
 J30  HHA   CH   C12  109.43  3.000
 J30  HH    CH   C12  109.36  3.000
 J30  HHA   CH   CZ   109.75  3.000
 J30  HH    CH   CZ   109.44  3.000
 J30  C12   CH   CZ   112.85  3.000
 J30  HZA   CZ   HZ   106.95  3.000
 J30  HZA   CZ   CH   110.05  3.000
 J30  HZ    CZ   CH   110.24  3.000
 J30  HZA   CZ   CE   109.54  3.000
 J30  HZ    CZ   CE   109.64  3.000
 J30  CH    CZ   CE   110.35  3.000
 J30  N14   C12  O13  121.98  3.000
 J30  O13   C12  CH   120.83  3.000
 J30  N14   C12  CH   117.18  3.000
 J30  C19   N14  C15  112.55  3.000
 J30  C15   N14  C12  121.45  3.000
 J30  C19   N14  C12  125.97  3.000
 J30  H15A  C15  H15  107.96  3.000
 J30  H15A  C15  C16  110.02  3.000
 J30  H15   C15  C16  109.48  3.000
 J30  H15A  C15  N14  109.82  3.000
 J30  H15   C15  N14  109.16  3.000
 J30  C16   C15  N14  110.35  3.000
 J30  H16A  C16  H16  107.11  3.000
 J30  H16A  C16  N17  111.90  3.000
 J30  H16   C16  N17  109.19  3.000
 J30  H16A  C16  C15  109.18  3.000
 J30  H16   C16  C15  108.58  3.000
 J30  N17   C16  C15  110.77  3.000
 J30  C18   N17  C17  113.09  3.000
 J30  C18   N17  C16  110.69  3.000
 J30  C17   N17  C16  111.40  3.000
 J30  H18A  C18  H18  107.09  3.000
 J30  H18A  C18  C19  109.40  3.000
 J30  H18   C18  C19  108.24  3.000
 J30  H18A  C18  N17  112.04  3.000
 J30  H18   C18  N17  109.54  3.000
 J30  C19   C18  N17  110.40  3.000
 J30  H19A  C19  H19  107.31  3.000
 J30  H19A  C19  C18  109.18  3.000
 J30  H19   C19  C18  109.27  3.000
 J30  H19A  C19  N14  109.05  3.000
 J30  H19   C19  N14  111.36  3.000
 J30  C18   C19  N14  110.59  3.000
 J30  C45   C40  C41  119.11  3.000
 J30  C41   C40  C17  121.31  3.000
 J30  C45   C40  C17  119.57  3.000
 J30  C46   C41  C42  118.28  3.000
 J30  C46   C41  C40  122.58  3.000
 J30  C42   C41  C40  119.14  3.000
 J30  C49   C42  C43  120.95  3.000
 J30  C49   C42  C41  119.43  3.000
 J30  C43   C42  C41  119.62  3.000
 J30  H43   C43  C44  120.70  3.000
 J30  H43   C43  C42  118.98  3.000
 J30  C44   C43  C42  120.33  3.000
 J30  H44   C44  C45  119.56  3.000
 J30  H44   C44  C43  120.40  3.000
 J30  C45   C44  C43  120.04  3.000
 J30  H45   C45  C44  118.93  3.000
 J30  H45   C45  C40  119.31  3.000
 J30  C44   C45  C40  121.76  3.000
 J30  H46   C46  C47  119.70  3.000
 J30  H46   C46  C41  119.34  3.000
 J30  C47   C46  C41  120.95  3.000
 J30  H47   C47  C48  119.62  3.000
 J30  H47   C47  C46  119.79  3.000
 J30  C48   C47  C46  120.59  3.000
 J30  H48   C48  C49  120.27  3.000
 J30  H48   C48  C47  119.82  3.000
 J30  C49   C48  C47  119.90  3.000
 J30  H49   C49  C48  120.35  3.000
 J30  H49   C49  C42  118.81  3.000
 J30  C48   C49  C42  120.84  3.000
 J30  H17A  C17  H17  106.16  3.000
 J30  H17A  C17  C40  108.36  3.000
 J30  H17   C17  C40  109.56  3.000
 J30  H17A  C17  N17  111.84  3.000
 J30  H17   C17  N17  107.51  3.000
 J30  C40   C17  N17  113.16  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
 J30  CONST_01  C43  C44  C45  C40     0.00   0.0  0
 J30  CONST_02  C43  C42  C41  C40     0.00   0.0  0
 J30  CONST_03  C49  C42  C41  C40   180.00   0.0  0
 J30  CONST_04  C47  C46  C41  C40   180.00   0.0  0
 J30  CONST_05  C44  C45  C40  C41     0.00   0.0  0
 J30  CONST_06  C44  C43  C42  C41     0.00   0.0  0
 J30  CONST_07  C48  C49  C42  C41     0.00   0.0  0
 J30  CONST_08  C48  C47  C46  C41     0.00   0.0  0
 J30  CONST_09  C45  C40  C41  C42     0.00   0.0  0
 J30  CONST_10  C47  C46  C41  C42     0.00   0.0  0
 J30  CONST_11  C45  C44  C43  C42     0.00   0.0  0
 J30  CONST_12  C47  C48  C49  C42     0.00   0.0  0
 J30  CONST_13  C46  C41  C42  C43   180.00   0.0  0
 J30  CONST_14  C48  C49  C42  C43   180.00   0.0  0
 J30  CONST_15  C49  C42  C43  C44   180.00   0.0  0
 J30  CONST_16  C46  C41  C40  C45   180.00   0.0  0
 J30  CONST_17  C49  C42  C41  C46     0.00   0.0  0
 J30  CONST_18  C49  C48  C47  C46     0.00   0.0  0
 J30  CONST_19  C44  C45  C40  C17   180.00   0.0  0
 J30  CONST_20  C42  C41  C40  C17   180.00   0.0  0
 J30  CONST_21  C46  C41  C40  C17     0.00   0.0  0
 J30  CONST_22  H44  C44  C45  C40   180.00   0.0  0
 J30  CONST_23  H46  C46  C41  C40     0.00   0.0  0
 J30  CONST_24  H45  C45  C40  C41   180.00   0.0  0
 J30  CONST_25  H43  C43  C42  C41   180.00   0.0  0
 J30  CONST_26  H49  C49  C42  C41   180.00   0.0  0
 J30  CONST_27  H47  C47  C46  C41   180.00   0.0  0
 J30  CONST_28  H48  C48  C49  C42   180.00   0.0  0
 J30  CONST_29  C19  N14  C12  CH      0.00   0.0  0
 J30  CONST_30  C15  N14  C12  CH    180.00   0.0  0
 J30  CONST_31  C19  N14  C12  O13   180.00   0.0  0
 J30  CONST_32  C15  N14  C12  O13     0.00   0.0  0
 J30  Var_01    N17  C18  C19  N14   -56.02  30.0  1
 J30  Var_02    N17  C16  C15  N14    55.76  30.0  1
 J30  Var_03    C18  C19  N14  C15    54.82  30.0  1
 J30  Var_04    C18  N17  C16  C15   -58.37  30.0  1
 J30  Var_05    C19  N14  C15  C16   -54.55  30.0  1
 J30  Var_06    C19  C18  N17  C16    58.30  30.0  1
 J30  Var_07    C40  C17  N17  C16  -174.40  30.0  2
 J30  Var_08    C45  C40  C17  N17  -118.03  30.0  2
 J30  Var_09    N14  C12  CH   CZ   -179.00  30.0  2
 J30  Var_10    CH   CZ   CE   SD    178.98  30.0  1
 J30  Var_11    C12  CH   CZ   CE   -179.33  30.0  1

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
 J30  plan-1  C40  0.020
 J30  plan-1  C41  0.020
 J30  plan-1  C42  0.020
 J30  plan-1  C43  0.020
 J30  plan-1  C44  0.020
 J30  plan-1  C45  0.020
 J30  plan-1  C46  0.020
 J30  plan-1  C47  0.020
 J30  plan-1  C48  0.020
 J30  plan-1  C49  0.020
 J30  plan-1  H43  0.020
 J30  plan-1  H44  0.020
 J30  plan-1  H45  0.020
 J30  plan-1  H46  0.020
 J30  plan-1  H47  0.020
 J30  plan-1  H48  0.020
 J30  plan-1  H49  0.020
 J30  plan-1  C17  0.020
 J30  plan-2  CH   0.020
 J30  plan-2  C12  0.020
 J30  plan-2  O13  0.020
 J30  plan-2  N14  0.020
 J30  plan-2  C15  0.020
 J30  plan-2  C19  0.020

