# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:07:13 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: ~{N}-[(3~{S})-1-(4-chlorophenyl)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-~{N}-oxidanyl-hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)N(O)[C@H]1CC(=O)N(C1=O)c2ccc(Cl)cc2
#
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
 E7Q  E7Q  ~{N}-[(3~{S})-1-(4-chlorophenyl)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-~{N}-oxidanyl-hexanamide  ligand  42  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E7Q
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
 E7Q  C01  C   CH3   0  -0.662   7.1886   3.5991  -0.0482
 E7Q  C02  C   CH2   0  -0.419   5.7427   3.1946   0.2032
 E7Q  C03  C   CH2   0  -0.410   5.4627   1.7414  -0.1614
 E7Q  C04  C   CH2   0  -0.414   4.0117   1.3375   0.0669
 E7Q  C05  C   CH2   0  -0.569   3.7722  -0.1187  -0.3043
 E7Q  C06  C   C     0   0.583   2.3437  -0.5518  -0.1100
 E7Q  C10  C   CH1   0  -0.221   0.7197  -2.3550  -0.2085
 E7Q  C11  C   CH2   0  -0.602   0.4005  -2.5653   1.2733
 E7Q  C12  C   C     0   0.552  -0.8907  -1.8310   1.5084
 E7Q  C15  C   CR6   0   0.330  -2.4609  -0.4783   0.1715
 E7Q  C16  C   CR16  0  -0.270  -3.5568  -0.9845  -0.5103
 E7Q  C17  C   CR16  0  -0.215  -4.6968  -0.2105  -0.6585
 E7Q  C18  C   CR6   0  -0.033  -4.7235   1.0630  -0.1106
 E7Q  C20  C   CR16  0  -0.215  -3.6331   1.5763   0.5756
 E7Q  C21  C   CR16  0  -0.263  -2.4939   0.7992   0.7105
 E7Q  C22  C   C     0   0.557  -0.3904  -1.4432  -0.7172
 E7Q  N08  N   NT    0  -0.221   2.0102  -1.8017  -0.5218
 E7Q  N14  N   NT    0  -0.648  -1.2945  -1.2692   0.3084
 E7Q  O07  O   O     0  -0.482   1.4708   0.1535   0.3735
 E7Q  O09  O   OH1   0  -0.540   2.9955  -2.6922  -0.8435
 E7Q  O13  O   O     0  -0.415  -1.5054  -1.7293   2.5374
 E7Q  O23  O   O     0  -0.404  -0.5050  -0.9881  -1.8224
 E7Q  CL   CL  CL    0  -0.116  -6.1462   2.0318  -0.2884
 E7Q  H1   H   HCH3  0   0.227   7.3613   4.6451   0.2070
 E7Q  H2   H   HCH3  0   0.216   7.8785   2.9975   0.5464
 E7Q  H3   H   HCH3  0   0.216   7.4581   3.4676  -1.0980
 E7Q  H4   H   HCH2  0   0.212   5.4929   3.3580   1.2560
 E7Q  H5   H   HCH2  0   0.211   5.0770   3.8463  -0.3708
 E7Q  H6   H   HCH2  0   0.211   5.7274   1.5753  -1.2115
 E7Q  H7   H   HCH2  0   0.211   6.1202   1.0894   0.4238
 E7Q  H8   H   HCH2  0   0.224   3.7467   1.5037   1.1143
 E7Q  H9   H   HCH2  0   0.223   3.3582   1.9837  -0.5249
 E7Q  H10  H   HCH2  0   0.267   4.0626  -0.2938  -1.3445
 E7Q  H11  H   HCH2  0   0.274   4.4172  -0.7713   0.2921
 E7Q  H12  H   HCH1  0   0.347   0.6325  -3.2936  -0.7590
 E7Q  H13  H   HCH2  0   0.317   0.2623  -3.6189   1.5169
 E7Q  H14  H   HCH2  0   0.316   1.1700  -2.1757   1.9400
 E7Q  H15  H   HCR6  0   0.282  -3.5277  -1.9839  -0.9237
 E7Q  H16  H   HCR6  0   0.290  -5.5528  -0.6002  -1.1914
 E7Q  H17  H   HCR6  0   0.289  -3.6649   2.5712   0.9974
 E7Q  H18  H   HCR6  0   0.281  -1.6319   1.1952   1.2306
 E7Q  H19  H   HOH1  0   0.483   3.0082  -2.7447  -1.8093

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
 E7Q  CL   C18  single    1.730  0.020  1.730
 E7Q  C20  C18  aromatic  1.387  0.020  1.387
 E7Q  C20  C21  aromatic  1.386  0.020  1.386
 E7Q  C18  C17  aromatic  1.387  0.020  1.387
 E7Q  C21  C15  aromatic  1.387  0.020  1.387
 E7Q  C17  C16  aromatic  1.386  0.020  1.386
 E7Q  O23  C22  double    1.201  0.020  1.201
 E7Q  C01  C02  single    1.522  0.020  1.522
 E7Q  C15  C16  aromatic  1.386  0.020  1.386
 E7Q  C15  N14  single    1.416  0.020  1.416
 E7Q  C05  C04  single    1.522  0.020  1.522
 E7Q  C05  C06  single    1.505  0.020  1.505
 E7Q  C04  C03  single    1.523  0.020  1.523
 E7Q  C22  N14  single    1.378  0.020  1.378
 E7Q  C22  C10  single    1.524  0.020  1.524
 E7Q  N14  C12  single    1.385  0.020  1.385
 E7Q  C02  C03  single    1.524  0.020  1.524
 E7Q  C06  O07  double    1.222  0.020  1.222
 E7Q  C06  N08  single    1.358  0.020  1.358
 E7Q  C10  N08  single    1.439  0.020  1.439
 E7Q  C10  C11  single    1.530  0.020  1.530
 E7Q  N08  O09  single    1.366  0.020  1.366
 E7Q  C12  O13  double    1.203  0.020  1.203
 E7Q  C12  C11  single    1.504  0.020  1.504
 E7Q  C01  H1   single    0.970  0.020  1.090
 E7Q  C01  H2   single    0.970  0.020  1.090
 E7Q  C01  H3   single    0.970  0.020  1.090
 E7Q  C02  H4   single    0.970  0.020  1.090
 E7Q  C02  H5   single    0.970  0.020  1.090
 E7Q  C03  H6   single    0.970  0.020  1.090
 E7Q  C03  H7   single    0.970  0.020  1.090
 E7Q  C04  H8   single    0.970  0.020  1.090
 E7Q  C04  H9   single    0.970  0.020  1.090
 E7Q  C05  H10  single    0.970  0.020  1.090
 E7Q  C05  H11  single    0.970  0.020  1.090
 E7Q  C10  H12  single    0.970  0.020  1.090
 E7Q  C11  H13  single    0.970  0.020  1.090
 E7Q  C11  H14  single    0.970  0.020  1.090
 E7Q  C16  H15  single    0.930  0.020  1.080
 E7Q  C17  H16  single    0.930  0.020  1.080
 E7Q  C20  H17  single    0.930  0.020  1.080
 E7Q  C21  H18  single    0.930  0.020  1.080
 E7Q  O09  H19  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
 E7Q  H3   C01  H2   107.54  3.000
 E7Q  H3   C01  H1   107.54  3.000
 E7Q  H2   C01  H1   107.52  3.000
 E7Q  H3   C01  C02  111.18  3.000
 E7Q  H2   C01  C02  111.35  3.000
 E7Q  H1   C01  C02  111.51  3.000
 E7Q  H5   C02  H4   106.07  3.000
 E7Q  H5   C02  C03  109.31  3.000
 E7Q  H4   C02  C03  109.30  3.000
 E7Q  H5   C02  C01  109.45  3.000
 E7Q  H4   C02  C01  109.63  3.000
 E7Q  C03  C02  C01  112.85  3.000
 E7Q  H7   C03  H6   106.07  3.000
 E7Q  H7   C03  C04  109.50  3.000
 E7Q  H6   C03  C04  109.49  3.000
 E7Q  H7   C03  C02  109.24  3.000
 E7Q  H6   C03  C02  109.23  3.000
 E7Q  C04  C03  C02  113.07  3.000
 E7Q  H9   C04  H8   106.50  3.000
 E7Q  H9   C04  C05  109.84  3.000
 E7Q  H8   C04  C05  109.94  3.000
 E7Q  H9   C04  C03  109.37  3.000
 E7Q  H8   C04  C03  109.53  3.000
 E7Q  C05  C04  C03  111.53  3.000
 E7Q  H11  C05  H10  105.44  3.000
 E7Q  H11  C05  C06  108.51  3.000
 E7Q  H10  C05  C06  109.18  3.000
 E7Q  H11  C05  C04  110.18  3.000
 E7Q  H10  C05  C04  110.07  3.000
 E7Q  C06  C05  C04  113.15  3.000
 E7Q  O07  C06  N08  118.42  3.000
 E7Q  N08  C06  C05  117.31  3.000
 E7Q  O07  C06  C05  124.26  3.000
 E7Q  H12  C10  N08  107.01  3.000
 E7Q  H12  C10  C22  106.74  3.000
 E7Q  N08  C10  C22  110.53  3.000
 E7Q  H12  C10  C11  110.70  3.000
 E7Q  N08  C10  C11  116.79  3.000
 E7Q  C22  C10  C11  104.68  3.000
 E7Q  H14  C11  H13  107.35  3.000
 E7Q  H14  C11  C12  109.63  3.000
 E7Q  H13  C11  C12  109.15  3.000
 E7Q  H14  C11  C10  113.32  3.000
 E7Q  H13  C11  C10  112.06  3.000
 E7Q  C12  C11  C10  105.27  3.000
 E7Q  O13  C12  N14  123.90  3.000
 E7Q  O13  C12  C11  127.86  3.000
 E7Q  N14  C12  C11  108.23  3.000
 E7Q  N14  C15  C21  119.77  3.000
 E7Q  N14  C15  C16  119.66  3.000
 E7Q  C21  C15  C16  120.57  3.000
 E7Q  H15  C16  C17  119.81  3.000
 E7Q  H15  C16  C15  120.26  3.000
 E7Q  C17  C16  C15  119.93  3.000
 E7Q  H16  C17  C18  120.70  3.000
 E7Q  H16  C17  C16  120.18  3.000
 E7Q  C18  C17  C16  119.11  3.000
 E7Q  CL   C18  C20  119.34  3.000
 E7Q  C20  C18  C17  121.36  3.000
 E7Q  CL   C18  C17  119.30  3.000
 E7Q  H17  C20  C21  120.15  3.000
 E7Q  H17  C20  C18  120.71  3.000
 E7Q  C21  C20  C18  119.14  3.000
 E7Q  H18  C21  C20  119.78  3.000
 E7Q  H18  C21  C15  120.34  3.000
 E7Q  C20  C21  C15  119.89  3.000
 E7Q  O23  C22  N14  125.06  3.000
 E7Q  N14  C22  C10  107.76  3.000
 E7Q  O23  C22  C10  127.12  3.000
 E7Q  O09  N08  C10  116.57  3.000
 E7Q  O09  N08  C06  119.62  3.000
 E7Q  C10  N08  C06  120.56  3.000
 E7Q  C22  N14  C15  122.61  3.000
 E7Q  C22  N14  C12  113.72  3.000
 E7Q  C15  N14  C12  123.40  3.000
 E7Q  H19  O09  N08  106.26  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
 E7Q  CONST_01  C18  C20  C21  C15     0.00   0.0  0
 E7Q  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 E7Q  CONST_03  C20  C18  C17  C16     0.00   0.0  0
 E7Q  CONST_04  C20  C21  C15  C16     0.00   0.0  0
 E7Q  CONST_05  C21  C20  C18  C17     0.00   0.0  0
 E7Q  CONST_06  C21  C15  C16  C17     0.00   0.0  0
 E7Q  CONST_07  N14  C15  C16  C17   180.00   0.0  0
 E7Q  CONST_08  N14  C15  C21  C20   180.00   0.0  0
 E7Q  CONST_09  C15  N14  C12  C11   180.00   0.0  0
 E7Q  CONST_10  C22  N14  C12  C11     0.00   0.0  0
 E7Q  CONST_11  CL   C18  C17  C16   180.00   0.0  0
 E7Q  CONST_12  CL   C18  C20  C21   180.00   0.0  0
 E7Q  CONST_13  O13  C12  N14  C15     0.00   0.0  0
 E7Q  CONST_14  O13  C12  N14  C22   180.00   0.0  0
 E7Q  CONST_15  H17  C20  C21  C15   180.00   0.0  0
 E7Q  CONST_16  H16  C17  C16  C15   180.00   0.0  0
 E7Q  CONST_17  H18  C21  C15  C16   180.00   0.0  0
 E7Q  CONST_18  H15  C16  C17  C18   180.00   0.0  0
 E7Q  CONST_19  C10  N08  C06  C05   180.00   0.0  0
 E7Q  CONST_20  O07  C06  N08  C10     0.00   0.0  0
 E7Q  CONST_21  O09  N08  C06  C05     0.00   0.0  0
 E7Q  CONST_22  O09  N08  C06  O07   180.00   0.0  0
 E7Q  Var_01    C15  N14  C22  C10  -179.61  30.0  1
 E7Q  Var_02    N14  C12  C11  C10     0.66  30.0  1
 E7Q  Var_03    C21  C15  N14  C12    71.54  30.0  2
 E7Q  Var_04    C04  C03  C02  C01  -179.07  30.0  3
 E7Q  Var_05    C05  C04  C03  C02  -179.85  30.0  2
 E7Q  Var_06    C06  C05  C04  C03  -179.22  30.0  1
 E7Q  Var_07    O07  C06  C05  C04    -4.36  30.0  3
 E7Q  Var_08    H1   C01  C02  C03   179.23  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E7Q  chir_01  C10  C22  N08  C11  negativ

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
 E7Q  plan-1  C15  0.020
 E7Q  plan-1  C16  0.020
 E7Q  plan-1  C17  0.020
 E7Q  plan-1  C18  0.020
 E7Q  plan-1  C20  0.020
 E7Q  plan-1  C21  0.020
 E7Q  plan-1  N14  0.020
 E7Q  plan-1  CL   0.020
 E7Q  plan-1  H15  0.020
 E7Q  plan-1  H16  0.020
 E7Q  plan-1  H17  0.020
 E7Q  plan-1  H18  0.020
 E7Q  plan-2  C05  0.020
 E7Q  plan-2  C06  0.020
 E7Q  plan-2  C10  0.020
 E7Q  plan-2  N08  0.020
 E7Q  plan-2  O07  0.020
 E7Q  plan-2  O09  0.020
 E7Q  plan-3  C10  0.020
 E7Q  plan-3  C22  0.020
 E7Q  plan-3  N14  0.020
 E7Q  plan-3  O23  0.020
 E7Q  plan-4  C11  0.020
 E7Q  plan-4  C12  0.020
 E7Q  plan-4  C15  0.020
 E7Q  plan-4  C22  0.020
 E7Q  plan-4  N14  0.020
 E7Q  plan-4  O13  0.020

