# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:58:04 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl)naphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C2=C(Sc3ccccc3)C(=O)c4ccccc4C2=O
#
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
 9SV  9SV  2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl)naphthalene-1,4-dione  ligand  46  26  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9SV
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
 9SV  C1   C  CH2   0  -0.269   4.0946  -0.6305  -0.9265
 9SV  C2   C  CH2   0  -0.320   2.6685  -1.1019  -0.6802
 9SV  C3   C  CH2   0  -0.316   2.7628  -0.0136   1.4800
 9SV  C4   C  CH2   0  -0.281   4.1920   0.4119   1.2082
 9SV  C6   C  CR6   0  -0.464  -0.2498  -0.2310  -0.5920
 9SV  C13  C  CR16  0  -0.275  -2.9003   2.4819  -0.5513
 9SV  C14  C  CR6   0   0.311   0.6965   1.8565   0.3392
 9SV  O1   O  O     0  -0.351   1.6797   2.4997   0.6252
 9SV  C5   C  CR6   0   0.352   0.8116   0.3834   0.0131
 9SV  N1   N  NT    0  -0.478   2.0126  -0.1921   0.2439
 9SV  N    N  NT    0  -0.417   4.8342  -0.5297   0.3131
 9SV  C    C  CH3   0  -0.516   6.2196  -0.1893   0.0856
 9SV  C9   C  CR66  0  -0.007  -0.6333   2.4911   0.2583
 9SV  C10  C  CR16  0  -0.270  -0.8304   3.7544   0.8057
 9SV  C11  C  CR16  0  -0.237  -2.0665   4.3697   0.6885
 9SV  C12  C  CR16  0  -0.232  -3.0988   3.7350   0.0081
 9SV  C8   C  CR66  0  -0.029  -1.6684   1.8522  -0.4199
 9SV  C7   C  CR6   0   0.439  -1.4631   0.4959  -0.9866
 9SV  O    O  O     0  -0.383  -2.3111  -0.0133  -1.6929
 9SV  H1   H  HCH2  0   0.246   4.5835  -1.3584  -1.5790
 9SV  H2   H  HCH2  0   0.198   4.0674   0.3284  -1.4734
 9SV  H3   H  HCH2  0   0.263   2.1422  -1.1079  -1.6333
 9SV  H4   H  HCH2  0   0.242   2.6767  -2.1222  -0.2875
 9SV  H5   H  HCH2  0   0.251   2.7690  -0.9786   2.0010
 9SV  H6   H  HCH2  0   0.268   2.2682   0.6933   2.1389
 9SV  H7   H  HCH2  0   0.204   4.1974   1.4354   0.8020
 9SV  H8   H  HCH2  0   0.240   4.7373   0.4335   2.1550
 9SV  H10  H  HCR6  0   0.273  -3.7039   1.9909  -1.0827
 9SV  H12  H  HCH3  0   0.194   6.3557   0.8031  -0.3717
 9SV  H13  H  HCH3  0   0.234   6.7664  -0.1967   1.0298
 9SV  H14  H  HCH3  0   0.234   6.6816  -0.9259  -0.5731
 9SV  H15  H  HCR6  0   0.274  -0.0246   4.2521   1.3278
 9SV  H16  H  HCR6  0   0.276  -2.2253   5.3476   1.1224
 9SV  H17  H  HCR6  0   0.276  -4.0620   4.2183  -0.0859
 9SV  C16  C  CR6   0  -0.100  -1.6966  -2.4805  -0.0709
 9SV  C15  C  CR16  0  -0.261  -2.5014  -3.4498  -0.6595
 9SV  C17  C  CR16  0  -0.246  -3.6032  -3.9431   0.0263
 9SV  C18  C  CR16  0  -0.262  -3.9179  -3.4573   1.2883
 9SV  C19  C  CR16  0  -0.244  -3.1152  -2.4830   1.8691
 9SV  C20  C  CR16  0  -0.223  -1.9990  -2.0022   1.2002
 9SV  H9   H  HCR6  0   0.266  -2.2746  -3.8143  -1.6535
 9SV  H11  H  HCR6  0   0.262  -4.2246  -4.6986  -0.4370
 9SV  H18  H  HCR6  0   0.259  -4.7827  -3.8361   1.8172
 9SV  H19  H  HCR6  0   0.262  -3.3503  -2.1017   2.8543
 9SV  H20  H  HCR6  0   0.265  -1.3691  -1.2561   1.6684
 9SV  S1   S  S2    0   0.096  -0.2478  -1.9577  -0.9461

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
 9SV  C    N    single    1.445  0.020  1.445
 9SV  C1   N    single    1.447  0.020  1.447
 9SV  C1   C2   single    1.522  0.020  1.522
 9SV  N    C4   single    1.449  0.020  1.449
 9SV  C4   C3   single    1.516  0.020  1.516
 9SV  C2   N1   single    1.453  0.020  1.453
 9SV  O1   C14  double    1.209  0.020  1.209
 9SV  N1   C3   single    1.457  0.020  1.457
 9SV  N1   C5   single    1.352  0.020  1.352
 9SV  C14  C5   single    1.513  0.020  1.513
 9SV  C14  C9   single    1.476  0.020  1.476
 9SV  C5   C6   double    1.368  0.020  1.368
 9SV  C10  C9   aromatic  1.391  0.020  1.391
 9SV  C10  C11  aromatic  1.386  0.020  1.386
 9SV  C9   C8   aromatic  1.393  0.020  1.393
 9SV  C6   C7   single    1.468  0.020  1.468
 9SV  C11  C12  aromatic  1.390  0.020  1.390
 9SV  C8   C7   single    1.484  0.020  1.484
 9SV  C8   C13  aromatic  1.390  0.020  1.390
 9SV  C7   O    double    1.215  0.020  1.215
 9SV  C12  C13  aromatic  1.387  0.020  1.387
 9SV  C1   H1   single    0.970  0.020  1.090
 9SV  C1   H2   single    0.970  0.020  1.090
 9SV  C2   H3   single    0.970  0.020  1.090
 9SV  C2   H4   single    0.970  0.020  1.090
 9SV  C3   H5   single    0.970  0.020  1.090
 9SV  C3   H6   single    0.970  0.020  1.090
 9SV  C4   H7   single    0.970  0.020  1.090
 9SV  C4   H8   single    0.970  0.020  1.090
 9SV  C13  H10  single    0.930  0.020  1.080
 9SV  C    H12  single    0.970  0.020  1.090
 9SV  C    H13  single    0.970  0.020  1.090
 9SV  C    H14  single    0.970  0.020  1.090
 9SV  C10  H15  single    0.930  0.020  1.080
 9SV  C11  H16  single    0.930  0.020  1.080
 9SV  C12  H17  single    0.930  0.020  1.080
 9SV  C6   S1   single    1.763  0.020  1.763
 9SV  S1   C16  single    1.772  0.020  1.772
 9SV  C16  C15  aromatic  1.391  0.020  1.391
 9SV  C15  C17  aromatic  1.388  0.020  1.388
 9SV  C17  C18  aromatic  1.388  0.020  1.388
 9SV  C18  C19  aromatic  1.390  0.020  1.390
 9SV  C19  C20  aromatic  1.387  0.020  1.387
 9SV  C20  C16  aromatic  1.391  0.020  1.391
 9SV  C15  H9   single    0.930  0.020  1.080
 9SV  C17  H11  single    0.930  0.020  1.080
 9SV  C18  H18  single    0.930  0.020  1.080
 9SV  C19  H19  single    0.930  0.020  1.080
 9SV  C20  H20  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
 9SV  H2   C1   H1   107.07  3.000
 9SV  H2   C1   N    112.11  3.000
 9SV  H1   C1   N    109.22  3.000
 9SV  H2   C1   C2   109.03  3.000
 9SV  H1   C1   C2   108.03  3.000
 9SV  N    C1   C2   111.22  3.000
 9SV  H4   C2   H3   108.23  3.000
 9SV  H4   C2   N1   111.05  3.000
 9SV  H3   C2   N1   110.00  3.000
 9SV  H4   C2   C1   109.88  3.000
 9SV  H3   C2   C1   108.24  3.000
 9SV  N1   C2   C1   109.38  3.000
 9SV  H6   C3   H5   106.69  3.000
 9SV  H6   C3   N1   111.11  3.000
 9SV  H5   C3   N1   107.35  3.000
 9SV  H6   C3   C4   110.83  3.000
 9SV  H5   C3   C4   109.07  3.000
 9SV  N1   C3   C4   111.58  3.000
 9SV  H8   C4   H7   107.38  3.000
 9SV  H8   C4   N    109.08  3.000
 9SV  H7   C4   N    111.95  3.000
 9SV  H8   C4   C3   108.71  3.000
 9SV  H7   C4   C3   109.37  3.000
 9SV  N    C4   C3   110.26  3.000
 9SV  S1   C6   C7   115.59  3.000
 9SV  S1   C6   C5   121.88  3.000
 9SV  C7   C6   C5   122.53  3.000
 9SV  H10  C13  C8   119.97  3.000
 9SV  H10  C13  C12  120.15  3.000
 9SV  C8   C13  C12  119.88  3.000
 9SV  C9   C14  C5   118.39  3.000
 9SV  C9   C14  O1   121.12  3.000
 9SV  C5   C14  O1   120.46  3.000
 9SV  N1   C5   C14  116.44  3.000
 9SV  C14  C5   C6   118.27  3.000
 9SV  N1   C5   C6   125.02  3.000
 9SV  C5   N1   C3   123.39  3.000
 9SV  C5   N1   C2   123.98  3.000
 9SV  C3   N1   C2   112.57  3.000
 9SV  C    N    C4   111.66  3.000
 9SV  C4   N    C1   110.36  3.000
 9SV  C    N    C1   111.82  3.000
 9SV  H14  C    H13  107.80  3.000
 9SV  H14  C    H12  107.79  3.000
 9SV  H13  C    H12  107.67  3.000
 9SV  H14  C    N    110.00  3.000
 9SV  H13  C    N    110.04  3.000
 9SV  H12  C    N    113.35  3.000
 9SV  C8   C9   C10  120.20  3.000
 9SV  C8   C9   C14  119.94  3.000
 9SV  C10  C9   C14  119.79  3.000
 9SV  H15  C10  C11  120.07  3.000
 9SV  H15  C10  C9   120.16  3.000
 9SV  C11  C10  C9   119.77  3.000
 9SV  H16  C11  C12  120.02  3.000
 9SV  H16  C11  C10  119.90  3.000
 9SV  C12  C11  C10  120.08  3.000
 9SV  H17  C12  C11  119.99  3.000
 9SV  H17  C12  C13  119.75  3.000
 9SV  C11  C12  C13  120.26  3.000
 9SV  C7   C8   C9   120.15  3.000
 9SV  C7   C8   C13  120.04  3.000
 9SV  C9   C8   C13  119.80  3.000
 9SV  O    C7   C8   120.54  3.000
 9SV  O    C7   C6   121.68  3.000
 9SV  C8   C7   C6   117.66  3.000
 9SV  C20  C16  C15  120.04  3.000
 9SV  C20  C16  S1   121.85  3.000
 9SV  C15  C16  S1   118.03  3.000
 9SV  H9   C15  C17  120.00  3.000
 9SV  H9   C15  C16  120.14  3.000
 9SV  C17  C15  C16  119.86  3.000
 9SV  H11  C17  C18  120.20  3.000
 9SV  H11  C17  C15  119.48  3.000
 9SV  C18  C17  C15  120.30  3.000
 9SV  H18  C18  C19  120.18  3.000
 9SV  H18  C18  C17  120.20  3.000
 9SV  C19  C18  C17  119.62  3.000
 9SV  H19  C19  C20  119.44  3.000
 9SV  H19  C19  C18  120.13  3.000
 9SV  C20  C19  C18  120.42  3.000
 9SV  H20  C20  C19  119.90  3.000
 9SV  H20  C20  C16  120.36  3.000
 9SV  C19  C20  C16  119.75  3.000
 9SV  C16  S1   C6   100.89  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
 9SV  CONST_01  C10  C9   C8   C13     0.00   0.0  0
 9SV  CONST_02  C10  C11  C12  C13     0.00   0.0  0
 9SV  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 9SV  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 9SV  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 9SV  CONST_06  C8   C13  C12  C11     0.00   0.0  0
 9SV  CONST_07  C18  C17  C15  C16     0.00   0.0  0
 9SV  CONST_08  C18  C19  C20  C16     0.00   0.0  0
 9SV  CONST_09  C19  C20  C16  C15     0.00   0.0  0
 9SV  CONST_10  C19  C18  C17  C15     0.00   0.0  0
 9SV  CONST_11  C20  C16  C15  C17     0.00   0.0  0
 9SV  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 9SV  CONST_13  C17  C15  C16  S1    180.00   0.0  0
 9SV  CONST_14  C19  C20  C16  S1    180.00   0.0  0
 9SV  CONST_15  H16  C11  C12  C13   180.00   0.0  0
 9SV  CONST_16  H15  C10  C9   C14     0.00   0.0  0
 9SV  CONST_17  H10  C13  C8   C9    180.00   0.0  0
 9SV  CONST_18  H17  C12  C11  C10   180.00   0.0  0
 9SV  CONST_19  H11  C17  C15  C16   180.00   0.0  0
 9SV  CONST_20  H19  C19  C20  C16   180.00   0.0  0
 9SV  CONST_21  H20  C20  C16  C15   180.00   0.0  0
 9SV  CONST_22  H18  C18  C17  C15   180.00   0.0  0
 9SV  CONST_23  H9   C15  C17  C18   180.00   0.0  0
 9SV  Var_01    C3   C4   N    C1     57.82  30.0  1
 9SV  Var_02    C3   N1   C2   C1    -54.12  30.0  1
 9SV  Var_03    C4   N    C1   C2    -59.78  30.0  1
 9SV  Var_04    C4   C3   N1   C2     53.97  30.0  1
 9SV  Var_05    C14  C5   N1   C2   -135.77  30.0  2
 9SV  Var_06    N    C1   C2   N1     57.09  30.0  1
 9SV  Var_07    N    C4   C3   N1    -54.81  30.0  1
 9SV  Var_08    C15  C16  S1   C6    141.51  30.0  2
 9SV  Var_09    H12  C    N    C1     63.74  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
 9SV  plan-1  C16  0.020
 9SV  plan-1  C15  0.020
 9SV  plan-1  C17  0.020
 9SV  plan-1  C18  0.020
 9SV  plan-1  C19  0.020
 9SV  plan-1  C20  0.020
 9SV  plan-1  H9   0.020
 9SV  plan-1  H11  0.020
 9SV  plan-1  H18  0.020
 9SV  plan-1  H19  0.020
 9SV  plan-1  H20  0.020
 9SV  plan-1  S1   0.020
 9SV  plan-2  C6   0.020
 9SV  plan-2  C13  0.020
 9SV  plan-2  C14  0.020
 9SV  plan-2  O1   0.020
 9SV  plan-2  C5   0.020
 9SV  plan-2  N1   0.020
 9SV  plan-2  C9   0.020
 9SV  plan-2  C10  0.020
 9SV  plan-2  C11  0.020
 9SV  plan-2  C12  0.020
 9SV  plan-2  C8   0.020
 9SV  plan-2  C7   0.020
 9SV  plan-2  O    0.020
 9SV  plan-2  H10  0.020
 9SV  plan-2  H15  0.020
 9SV  plan-2  H16  0.020
 9SV  plan-2  H17  0.020
 9SV  plan-2  S1   0.020
 9SV  plan-3  C2   0.020
 9SV  plan-3  C3   0.020
 9SV  plan-3  C5   0.020
 9SV  plan-3  N1   0.020

