# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:57:47 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: 7-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butoxy]-3,4-dihydro-1~{H}-quinolin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(N2CCN(CCCCOc3ccc4CCC(=O)Nc4c3)CC2)c1Cl
#
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
 9SC  9SC  7-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butoxy]-3,4-dihydro-1~{H}-quinolin-2-one  ligand  57  30  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9SC
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
 9SC  N1   N   NT    0  -0.502  -4.6616  -0.9688   0.0855
 9SC  N3   N   NH1   0  -0.735   8.9508  -0.3449  -0.8124
 9SC  C4   C   CR16  0  -0.325  -6.6478  -1.3865   1.4566
 9SC  C5   C   CR16  0  -0.251  -7.9795  -1.1358   1.7464
 9SC  C6   C   CR16  0  -0.243  -8.6972  -0.2031   1.0182
 9SC  C7   C   CH2   0  -0.319  -4.1243  -2.2734   0.4232
 9SC  C8   C   CH2   0  -0.277  -2.8084  -2.4789  -0.3039
 9SC  C10  C   CH2   0  -0.305  -3.7163   0.0842   0.4405
 9SC  C13  C   CH2   0  -0.458   1.9265  -1.2395  -0.4527
 9SC  C15  C   CR6   0   0.385   5.3655  -0.0947  -0.0067
 9SC  C17  C   CR16  0  -0.319   6.5747   1.6300   1.1427
 9SC  C20  C   CR16  0  -0.433   6.5661  -0.5471  -0.5551
 9SC  C21  C   CH2   0  -0.486   9.0874   1.8962   0.8261
 9SC  C22  C   CH2   0  -0.592  10.2167   0.8748   0.8517
 9SC  C1   C   CR6   0  -0.003  -8.0690   0.4586  -0.0260
 9SC  C12  C   CH2   0  -0.455   0.5494  -0.8327   0.0597
 9SC  C14  C   CH2   0  -0.169   3.0036  -0.3515   0.1334
 9SC  C16  C   CR16  0  -0.387   5.3688   0.9977   0.8565
 9SC  C18  C   CR6   0   0.040   7.7739   1.2111   0.5966
 9SC  C19  C   CR6   0   0.395   7.7530   0.1001  -0.2518
 9SC  C2   C   CR6   0  -0.069  -6.7413   0.1949  -0.3405
 9SC  C23  C   C     0   0.506  10.1918  -0.0385  -0.3478
 9SC  C3   C   CR6   0   0.397  -5.9963  -0.7261   0.4147
 9SC  C9   C   CH2   0  -0.290  -2.3992  -0.1410  -0.2733
 9SC  N2   N   NT    0  -0.428  -1.8558  -1.4458   0.0518
 9SC  O1   O   O2    0  -0.480   4.2622  -0.7804  -0.3620
 9SC  O2A  O   O     0  -0.469  11.1945  -0.5050  -0.8592
 9SC  CL2  CL  CL    0  -0.080  -6.0206   0.9551  -1.7081
 9SC  H2   H   HCR6  0   0.277  -6.1033  -2.1032   2.0560
 9SC  H3   H   HCR6  0   0.272  -8.4603  -1.6607   2.5608
 9SC  H4   H   HCR6  0   0.284  -9.7330   0.0055   1.2463
 9SC  H5   H   HCH2  0   0.213  -3.9557  -2.3894   1.5046
 9SC  H6   H   HCH2  0   0.254  -4.8291  -3.0463   0.1124
 9SC  H7   H   HCH2  0   0.240  -2.4028  -3.4522  -0.0183
 9SC  H8   H   HCH2  0   0.194  -3.0002  -2.5092  -1.3900
 9SC  H9   H   HCH2  0   0.249  -4.1105   1.0592   0.1585
 9SC  H10  H   HCH2  0   0.218  -3.5474   0.0997   1.5273
 9SC  H11  H   HCH2  0   0.233   2.1247  -2.2825  -0.1907
 9SC  H12  H   HCH2  0   0.232   1.9533  -1.1707  -1.5443
 9SC  H13  H   HCR6  0   0.255   6.5708   2.4833   1.8104
 9SC  H14  H   HCR6  0   0.271   6.5608  -1.4071  -1.2147
 9SC  H15  H   HCH2  0   0.266   9.0728   2.4609   1.7587
 9SC  H16  H   HCH2  0   0.257   9.2706   2.6213   0.0260
 9SC  H17  H   HCH2  0   0.277  11.1919   1.3573   0.9009
 9SC  H18  H   HCH2  0   0.281  10.1260   0.2420   1.7417
 9SC  H21  H   HCH2  0   0.224   0.5118  -0.9369   1.1480
 9SC  H22  H   HCH2  0   0.229   0.3886   0.2263  -0.1592
 9SC  H23  H   HCH2  0   0.221   2.8227   0.6930  -0.1459
 9SC  H24  H   HCH2  0   0.220   2.9867  -0.4065   1.2284
 9SC  H25  H   HCR6  0   0.276   4.4611   1.3685   1.3110
 9SC  H26  H   HCH2  0   0.194  -2.5557  -0.0238  -1.3599
 9SC  H27  H   HCH2  0   0.244  -1.7034   0.6390   0.0392
 9SC  C11  C   CH2   0  -0.249  -0.5571  -1.6829  -0.5505
 9SC  CL1  CL  CL    0  -0.101  -8.9741   1.5952  -0.9563
 9SC  H1   H   HNH1  0   0.406   8.9002  -1.0260  -1.5578
 9SC  H19  H   HCH2  0   0.191  -0.5805  -1.5307  -1.6437
 9SC  H20  H   HCH2  0   0.227  -0.3093  -2.7370  -0.3926

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
 9SC  C16  C17  aromatic  1.391  0.020  1.391
 9SC  C16  C15  aromatic  1.392  0.020  1.392
 9SC  C17  C18  aromatic  1.383  0.020  1.383
 9SC  O1   C15  single    1.347  0.020  1.347
 9SC  O1   C14  single    1.419  0.020  1.419
 9SC  C15  C20  aromatic  1.395  0.020  1.395
 9SC  C13  C12  single    1.525  0.020  1.525
 9SC  C13  C14  single    1.514  0.020  1.514
 9SC  C7   C8   single    1.517  0.020  1.517
 9SC  C7   N1   single    1.451  0.020  1.451
 9SC  C8   N2   single    1.450  0.020  1.450
 9SC  C12  C11  single    1.523  0.020  1.523
 9SC  C18  C21  single    1.499  0.020  1.499
 9SC  C18  C19  aromatic  1.398  0.020  1.398
 9SC  C21  C22  single    1.523  0.020  1.523
 9SC  C11  N2   single    1.451  0.020  1.451
 9SC  C20  C19  aromatic  1.386  0.020  1.386
 9SC  N2   C9   single    1.450  0.020  1.450
 9SC  C19  N3   single    1.395  0.020  1.395
 9SC  N1   C3   single    1.396  0.020  1.396
 9SC  N1   C10  single    1.459  0.020  1.459
 9SC  C3   C4   aromatic  1.395  0.020  1.395
 9SC  C3   C2   aromatic  1.405  0.020  1.405
 9SC  CL2  C2   single    1.723  0.020  1.723
 9SC  C4   C5   aromatic  1.386  0.020  1.386
 9SC  C22  C23  single    1.508  0.020  1.508
 9SC  C9   C10  single    1.515  0.020  1.515
 9SC  C2   C1   aromatic  1.390  0.020  1.390
 9SC  N3   C23  single    1.360  0.020  1.360
 9SC  C5   C6   aromatic  1.384  0.020  1.384
 9SC  C1   C6   aromatic  1.387  0.020  1.387
 9SC  C1   CL1  single    1.725  0.020  1.725
 9SC  C23  O2A  double    1.218  0.020  1.218
 9SC  N3   H1   single    0.860  0.020  1.020
 9SC  C4   H2   single    0.930  0.020  1.080
 9SC  C5   H3   single    0.930  0.020  1.080
 9SC  C6   H4   single    0.930  0.020  1.080
 9SC  C7   H5   single    0.970  0.020  1.090
 9SC  C7   H6   single    0.970  0.020  1.090
 9SC  C8   H7   single    0.970  0.020  1.090
 9SC  C8   H8   single    0.970  0.020  1.090
 9SC  C10  H9   single    0.970  0.020  1.090
 9SC  C10  H10  single    0.970  0.020  1.090
 9SC  C13  H11  single    0.970  0.020  1.090
 9SC  C13  H12  single    0.970  0.020  1.090
 9SC  C17  H13  single    0.930  0.020  1.080
 9SC  C20  H14  single    0.930  0.020  1.080
 9SC  C21  H15  single    0.970  0.020  1.090
 9SC  C21  H16  single    0.970  0.020  1.090
 9SC  C22  H17  single    0.970  0.020  1.090
 9SC  C22  H18  single    0.970  0.020  1.090
 9SC  C11  H19  single    0.970  0.020  1.090
 9SC  C11  H20  single    0.970  0.020  1.090
 9SC  C12  H21  single    0.970  0.020  1.090
 9SC  C12  H22  single    0.970  0.020  1.090
 9SC  C14  H23  single    0.970  0.020  1.090
 9SC  C14  H24  single    0.970  0.020  1.090
 9SC  C16  H25  single    0.930  0.020  1.080
 9SC  C9   H26  single    0.970  0.020  1.090
 9SC  C9   H27  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
 9SC  C3   N1   C10  115.89  3.000
 9SC  C10  N1   C7   110.64  3.000
 9SC  C3   N1   C7   117.10  3.000
 9SC  H1   N3   C23  116.70  3.000
 9SC  H1   N3   C19  117.92  3.000
 9SC  C23  N3   C19  125.04  3.000
 9SC  H2   C4   C3   119.51  3.000
 9SC  H2   C4   C5   119.20  3.000
 9SC  C3   C4   C5   121.29  3.000
 9SC  H3   C5   C6   119.52  3.000
 9SC  H3   C5   C4   119.79  3.000
 9SC  C6   C5   C4   120.68  3.000
 9SC  H4   C6   C1   120.06  3.000
 9SC  H4   C6   C5   121.06  3.000
 9SC  C1   C6   C5   118.87  3.000
 9SC  H6   C7   H5   107.71  3.000
 9SC  H6   C7   C8   109.13  3.000
 9SC  H5   C7   C8   108.89  3.000
 9SC  H6   C7   N1   109.36  3.000
 9SC  H5   C7   N1   112.34  3.000
 9SC  C8   C7   N1   109.36  3.000
 9SC  H8   C8   H7   107.31  3.000
 9SC  H8   C8   N2   112.05  3.000
 9SC  H7   C8   N2   109.07  3.000
 9SC  H8   C8   C7   108.94  3.000
 9SC  H7   C8   C7   108.50  3.000
 9SC  N2   C8   C7   110.84  3.000
 9SC  H10  C10  H9   107.39  3.000
 9SC  H10  C10  C9   109.52  3.000
 9SC  H9   C10  C9   109.01  3.000
 9SC  H10  C10  N1   110.49  3.000
 9SC  H9   C10  N1   110.41  3.000
 9SC  C9   C10  N1   109.96  3.000
 9SC  H12  C13  H11  107.13  3.000
 9SC  H12  C13  C14  109.39  3.000
 9SC  H11  C13  C14  109.74  3.000
 9SC  H12  C13  C12  109.92  3.000
 9SC  H11  C13  C12  109.73  3.000
 9SC  C14  C13  C12  110.85  3.000
 9SC  O1   C15  C16  124.40  3.000
 9SC  O1   C15  C20  115.86  3.000
 9SC  C16  C15  C20  119.73  3.000
 9SC  H13  C17  C18  119.02  3.000
 9SC  H13  C17  C16  118.79  3.000
 9SC  C18  C17  C16  122.19  3.000
 9SC  H14  C20  C19  120.54  3.000
 9SC  H14  C20  C15  119.49  3.000
 9SC  C19  C20  C15  119.98  3.000
 9SC  H16  C21  H15  106.51  3.000
 9SC  H16  C21  C18  109.71  3.000
 9SC  H15  C21  C18  110.85  3.000
 9SC  H16  C21  C22  109.41  3.000
 9SC  H15  C21  C22  110.05  3.000
 9SC  C18  C21  C22  110.23  3.000
 9SC  H18  C22  H17  107.05  3.000
 9SC  H18  C22  C23  107.15  3.000
 9SC  H17  C22  C23  108.60  3.000
 9SC  H18  C22  C21  109.85  3.000
 9SC  H17  C22  C21  111.57  3.000
 9SC  C23  C22  C21  112.37  3.000
 9SC  CL1  C1   C2   120.28  3.000
 9SC  CL1  C1   C6   118.87  3.000
 9SC  C2   C1   C6   120.85  3.000
 9SC  H22  C12  H21  106.64  3.000
 9SC  H22  C12  C11  110.71  3.000
 9SC  H21  C12  C11  108.69  3.000
 9SC  H22  C12  C13  108.91  3.000
 9SC  H21  C12  C13  109.88  3.000
 9SC  C11  C12  C13  111.88  3.000
 9SC  H24  C14  H23  107.44  3.000
 9SC  H24  C14  O1   110.31  3.000
 9SC  H23  C14  O1   110.21  3.000
 9SC  H24  C14  C13  110.26  3.000
 9SC  H23  C14  C13  110.05  3.000
 9SC  O1   C14  C13  108.57  3.000
 9SC  H25  C16  C17  119.05  3.000
 9SC  H25  C16  C15  121.86  3.000
 9SC  C17  C16  C15  119.09  3.000
 9SC  C19  C18  C21  117.98  3.000
 9SC  C19  C18  C17  117.87  3.000
 9SC  C21  C18  C17  124.13  3.000
 9SC  C18  C19  C20  121.12  3.000
 9SC  C20  C19  N3   119.89  3.000
 9SC  C18  C19  N3   118.98  3.000
 9SC  CL2  C2   C3   119.62  3.000
 9SC  CL2  C2   C1   119.71  3.000
 9SC  C3   C2   C1   120.62  3.000
 9SC  O2A  C23  C22  123.52  3.000
 9SC  O2A  C23  N3   121.42  3.000
 9SC  C22  C23  N3   115.04  3.000
 9SC  C2   C3   C4   117.66  3.000
 9SC  C2   C3   N1   119.62  3.000
 9SC  C4   C3   N1   122.70  3.000
 9SC  H27  C9   H26  107.25  3.000
 9SC  H27  C9   N2   109.87  3.000
 9SC  H26  C9   N2   111.67  3.000
 9SC  H27  C9   C10  108.26  3.000
 9SC  H26  C9   C10  108.95  3.000
 9SC  N2   C9   C10  110.72  3.000
 9SC  C9   N2   C11  112.91  3.000
 9SC  C9   N2   C8   109.87  3.000
 9SC  C11  N2   C8   111.71  3.000
 9SC  C14  O1   C15  118.73  3.000
 9SC  H20  C11  H19  106.29  3.000
 9SC  H20  C11  N2   107.47  3.000
 9SC  H19  C11  N2   111.69  3.000
 9SC  H20  C11  C12  108.38  3.000
 9SC  H19  C11  C12  109.58  3.000
 9SC  N2   C11  C12  113.12  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
 9SC  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 9SC  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 9SC  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 9SC  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 9SC  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 9SC  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 9SC  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 9SC  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 9SC  CONST_09  C20  C15  C16  C17     0.00   0.0  0
 9SC  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 9SC  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 9SC  CONST_12  C19  C20  C15  C16     0.00   0.0  0
 9SC  CONST_13  C5   C4   C3   N1    180.00   0.0  0
 9SC  CONST_14  C1   C2   C3   N1    180.00   0.0  0
 9SC  CONST_15  C19  N3   C23  C22     0.00   0.0  0
 9SC  CONST_16  CL2  C2   C3   N1      0.00   0.0  0
 9SC  CONST_17  CL2  C2   C3   C4    180.00   0.0  0
 9SC  CONST_18  CL1  C1   C6   C5    180.00   0.0  0
 9SC  CONST_19  CL2  C2   C1   C6    180.00   0.0  0
 9SC  CONST_20  O1   C15  C16  C17   180.00   0.0  0
 9SC  CONST_21  O1   C15  C20  C19   180.00   0.0  0
 9SC  CONST_22  CL1  C1   C2   C3    180.00   0.0  0
 9SC  CONST_23  O2A  C23  N3   C19   180.00   0.0  0
 9SC  CONST_24  H2   C4   C3   N1      0.00   0.0  0
 9SC  CONST_25  H14  C20  C19  N3      0.00   0.0  0
 9SC  CONST_26  H4   C6   C5   C4    180.00   0.0  0
 9SC  CONST_27  H13  C17  C16  C15   180.00   0.0  0
 9SC  CONST_28  H25  C16  C15  C20   180.00   0.0  0
 9SC  CONST_29  H3   C5   C6   C1    180.00   0.0  0
 9SC  CONST_30  H1   N3   C23  C22   180.00   0.0  0
 9SC  Var_01    N2   C8   C7   N1     58.69  30.0  1
 9SC  Var_02    N2   C9   C10  N1    -57.46  30.0  1
 9SC  Var_03    C21  C22  C23  N3    -34.27  30.0  1
 9SC  Var_04    C7   N1   C3   C4     26.10  30.0  2
 9SC  Var_05    C9   N2   C8   C7    -58.42  30.0  1
 9SC  Var_06    C9   C10  N1   C7     57.98  30.0  1
 9SC  Var_07    C3   N1   C7   C8    165.93  30.0  1
 9SC  Var_08    C10  C9   N2   C8     57.70  30.0  1
 9SC  Var_09    C22  C21  C18  C17   146.23  30.0  1
 9SC  Var_10    C23  N3   C19  C20  -162.12  30.0  1
 9SC  Var_11    C23  C22  C21  C18    51.12  30.0  1
 9SC  Var_12    C12  C11  N2   C8   -165.81  30.0  1
 9SC  Var_13    C16  C15  O1   C14     2.04  30.0  2
 9SC  Var_14    N2   C11  C12  C13   172.02  30.0  3
 9SC  Var_15    H23  C14  O1   C15    56.96  30.0  3
 9SC  Var_16    C14  C13  C12  C11   178.16  30.0  2
 9SC  Var_17    O1   C14  C13  C12   179.35  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
 9SC  plan-1  N1   0.020
 9SC  plan-1  C4   0.020
 9SC  plan-1  C5   0.020
 9SC  plan-1  C6   0.020
 9SC  plan-1  C1   0.020
 9SC  plan-1  C2   0.020
 9SC  plan-1  C3   0.020
 9SC  plan-1  CL2  0.020
 9SC  plan-1  H2   0.020
 9SC  plan-1  H3   0.020
 9SC  plan-1  H4   0.020
 9SC  plan-1  CL1  0.020
 9SC  plan-2  N3   0.020
 9SC  plan-2  C15  0.020
 9SC  plan-2  C17  0.020
 9SC  plan-2  C20  0.020
 9SC  plan-2  C21  0.020
 9SC  plan-2  C16  0.020
 9SC  plan-2  C18  0.020
 9SC  plan-2  C19  0.020
 9SC  plan-2  O1   0.020
 9SC  plan-2  H13  0.020
 9SC  plan-2  H14  0.020
 9SC  plan-2  H25  0.020
 9SC  plan-3  N3   0.020
 9SC  plan-3  C22  0.020
 9SC  plan-3  C19  0.020
 9SC  plan-3  C23  0.020
 9SC  plan-3  O2A  0.020
 9SC  plan-3  H1   0.020

