# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:13:59 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 6-chloro-N-[(3S)-1-[(1R)-1-dimethylamino-2,3-dihydro-1H-inden-5-yl]-2-oxo-pyrrolidin-3-yl]naphthalene-2-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@@H]1CCc2cc(ccc12)N3CC[C@H](N[S](=O)(=O)c4ccc5cc(Cl)ccc5c4)C3=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
 439  439  6-chloro-N-[(3S)-1-[(1R)-1-dimethylamino-2,3-dihydro-1H-inden-5-yl]-2-oxo-pyrrolidin-3-yl]naphthalene-2-sulfonamide  ligand  59  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_439
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
 439  O3    O   O     0  -0.436  -0.4948   0.8429   0.3353
 439  C25   C   CR5   0   0.571  -0.1835   2.0058   0.1981
 439  N2    N   NR5   0  -0.587   1.0649   2.5460   0.2334
 439  C8    C   CR6   0   0.369   2.2761   1.8371   0.2978
 439  C7    C   CR16  0  -0.397   2.3469   0.5304   0.7976
 439  C9    C   CR16  0  -0.349   3.4496   2.4729  -0.1207
 439  C10   C   CR16  0  -0.302   4.6734   1.8191  -0.0646
 439  C11   C   CR56  0   0.089   4.7364   0.5181   0.4007
 439  C6    C   CR56  0   0.116   3.5741  -0.1059   0.8412
 439  C5    C   CH2   0  -0.485   3.8941  -1.4738   1.3715
 439  C4    C   CH2   0  -0.468   5.4027  -1.3726   1.6266
 439  C3    C   CR15  0  -0.141   5.9253  -0.4040   0.5472
 439  N1    N   NT    0  -0.402   6.2167  -1.1132  -0.7016
 439  C2    C   CH3   0  -0.525   6.3881  -0.2265  -1.8346
 439  C1    C   CH3   0  -0.530   7.3944  -1.9500  -0.5693
 439  C14   C   CR15  0  -0.238  -1.1682   3.1427  -0.0622
 439  C13   C   CH2   0  -0.464  -0.3918   4.3789   0.3615
 439  C12   C   CH2   0  -0.299   1.0427   3.9946   0.0302
 439  N3    N   NC1   0  -0.723  -2.4284   2.9813   0.6199
 439  S1    S   S     0   1.374  -3.7666   2.3921  -0.1302
 439  O1    O   OS    0  -0.652  -4.8338   2.5003   0.8496
 439  O2    O   OS    0  -0.651  -3.8687   3.0763  -1.4085
 439  C15   C   CR6   0  -0.175  -3.5004   0.6730  -0.4623
 439  C24   C   CR16  0  -0.292  -3.7658  -0.2353   0.5243
 439  C23   C   CR66  0   0.140  -3.5055  -1.6023   0.3023
 439  C18   C   CR66  0   0.125  -2.9735  -2.0130  -0.9458
 439  C17   C   CR16  0  -0.302  -2.7260  -1.0414  -1.9429
 439  C16   C   CR16  0  -0.231  -2.9832   0.2793  -1.7122
 439  C22   C   CR16  0  -0.310  -3.7633  -2.5749   1.2961
 439  C21   C   CR16  0  -0.212  -3.5024  -3.8955   1.0675
 439  C20   C   CR6   0  -0.038  -2.9719  -4.2874  -0.1786
 439  CL1   CL  CL    0  -0.115  -2.6535  -5.9675  -0.4437
 439  C19   C   CR16  0  -0.269  -2.7106  -3.3831  -1.1682
 439  H14   H   HCR5  0   0.316  -1.3496   3.1825  -1.1412
 439  H121  H   HCH2  0   0.273   1.7633   4.4825   0.6849
 439  H122  H   HCH2  0   0.260   1.2961   4.2431  -1.0034
 439  H7    H   HCR6  0   0.268   1.4675   0.0270   1.1658
 439  H9    H   HCR6  0   0.275   3.4242   3.4848  -0.5002
 439  H10   H   HCR6  0   0.252   5.5659   2.3400  -0.3900
 439  H3    H   HCR5  0   0.218   6.8170   0.1446   0.8960
 439  H51C  H   HCH2  0   0.248   3.3270  -1.7333   2.2664
 439  H52C  H   HCH2  0   0.247   3.6750  -2.2353   0.6175
 439  H41C  H   HCH2  0   0.240   5.5757  -0.9230   2.6068
 439  H42C  H   HCH2  0   0.243   5.9006  -2.3408   1.6291
 439  H21C  H   HCH3  0   0.189   7.1818   0.5231  -1.6868
 439  H22C  H   HCH3  0   0.235   6.6534  -0.8147  -2.7137
 439  H23C  H   HCH3  0   0.240   5.4655   0.3030  -2.0662
 439  H11C  H   HCH3  0   0.236   7.2766  -2.6767   0.2317
 439  H12C  H   HCH3  0   0.234   7.5515  -2.5096  -1.4925
 439  H13C  H   HCH3  0   0.191   8.3122  -1.3749  -0.3678
 439  H131  H   HCH2  0   0.276  -0.7124   5.2818  -0.1531
 439  H132  H   HCH2  0   0.263  -0.5008   4.5363   1.4362
 439  HA    H   HNC1  0   0.420  -2.3701   2.7178   1.5975
 439  H24   H   HCR6  0   0.284  -4.1694   0.0734   1.4803
 439  H16   H   HCR6  0   0.281  -2.8000   1.0095  -2.4879
 439  H22   H   HCR6  0   0.274  -4.1705  -2.2618   2.2490
 439  H17   H   HCR6  0   0.270  -2.3320  -1.3569  -2.9005
 439  H19   H   HCR6  0   0.284  -2.3066  -3.7021  -2.1201
 439  H21   H   HCR6  0   0.286  -3.6979  -4.6367   1.8300

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
 439  O3   C25   double    1.212  0.020  1.212
 439  C25  N2    single    1.361  0.020  1.361
 439  C25  C14   single    1.526  0.020  1.526
 439  N2   C8    single    1.405  0.020  1.405
 439  N2   C12   single    1.463  0.020  1.463
 439  C8   C7    aromatic  1.401  0.020  1.401
 439  C8   C9    aromatic  1.399  0.020  1.399
 439  C7   C6    aromatic  1.383  0.020  1.383
 439  C9   C10   aromatic  1.389  0.020  1.389
 439  C10  C11   aromatic  1.383  0.020  1.383
 439  C11  C6    aromatic  1.391  0.020  1.391
 439  C11  C3    single    1.512  0.020  1.512
 439  C6   C5    single    1.502  0.020  1.502
 439  C5   C4    single    1.533  0.020  1.533
 439  C4   C3    single    1.542  0.020  1.542
 439  C3   N1    single    1.465  0.020  1.465
 439  N1   C2    single    1.449  0.020  1.449
 439  N1   C1    single    1.451  0.020  1.451
 439  C14  C13   single    1.520  0.020  1.520
 439  C14  N3    single    1.442  0.020  1.442
 439  C13  C12   single    1.522  0.020  1.522
 439  N3   S1    single    1.643  0.020  1.643
 439  S1   O1    double    1.453  0.020  1.453
 439  S1   O2    double    1.454  0.020  1.454
 439  S1   C15   single    1.771  0.020  1.771
 439  C15  C24   aromatic  1.367  0.020  1.367
 439  C15  C16   aromatic  1.409  0.020  1.409
 439  C24  C23   aromatic  1.409  0.020  1.409
 439  C23  C18   aromatic  1.418  0.020  1.418
 439  C23  C22   aromatic  1.414  0.020  1.414
 439  C18  C17   aromatic  1.414  0.020  1.414
 439  C18  C19   aromatic  1.413  0.020  1.413
 439  C17  C16   aromatic  1.365  0.020  1.365
 439  C22  C21   aromatic  1.365  0.020  1.365
 439  C21  C20   aromatic  1.410  0.020  1.410
 439  C20  CL1   single    1.730  0.020  1.730
 439  C20  C19   aromatic  1.366  0.020  1.366
 439  C14  H14   single    0.970  0.020  1.090
 439  C12  H121  single    0.970  0.020  1.090
 439  C12  H122  single    0.970  0.020  1.090
 439  C7   H7    single    0.930  0.020  1.080
 439  C9   H9    single    0.930  0.020  1.080
 439  C10  H10   single    0.930  0.020  1.080
 439  C3   H3    single    0.970  0.020  1.090
 439  C5   H51C  single    0.970  0.020  1.090
 439  C5   H52C  single    0.970  0.020  1.090
 439  C4   H41C  single    0.970  0.020  1.090
 439  C4   H42C  single    0.970  0.020  1.090
 439  C2   H21C  single    0.970  0.020  1.090
 439  C2   H22C  single    0.970  0.020  1.090
 439  C2   H23C  single    0.970  0.020  1.090
 439  C1   H11C  single    0.970  0.020  1.090
 439  C1   H12C  single    0.970  0.020  1.090
 439  C1   H13C  single    0.970  0.020  1.090
 439  C13  H131  single    0.970  0.020  1.090
 439  C13  H132  single    0.970  0.020  1.090
 439  N3   HA    single    0.890  0.020  1.040
 439  C24  H24   single    0.930  0.020  1.080
 439  C16  H16   single    0.930  0.020  1.080
 439  C22  H22   single    0.930  0.020  1.080
 439  C17  H17   single    0.930  0.020  1.080
 439  C19  H19   single    0.930  0.020  1.080
 439  C21  H21   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
 439  C14   C25  N2    107.50  3.000
 439  C14   C25  O3    124.64  3.000
 439  N2    C25  O3    127.86  3.000
 439  C12   N2   C8    121.28  3.000
 439  C12   N2   C25   112.05  3.000
 439  C8    N2   C25   126.29  3.000
 439  C9    C8   C7    119.23  3.000
 439  C9    C8   N2    118.70  3.000
 439  C7    C8   N2    122.05  3.000
 439  H7    C7   C6    119.88  3.000
 439  H7    C7   C8    121.08  3.000
 439  C6    C7   C8    119.03  3.000
 439  H9    C9   C10   118.40  3.000
 439  H9    C9   C8    120.72  3.000
 439  C10   C9   C8    120.88  3.000
 439  H10   C10  C11   121.05  3.000
 439  H10   C10  C9    119.17  3.000
 439  C11   C10  C9    119.77  3.000
 439  C3    C11  C6    110.66  3.000
 439  C3    C11  C10   129.95  3.000
 439  C6    C11  C10   119.38  3.000
 439  C5    C6   C11   110.03  3.000
 439  C5    C6   C7    128.27  3.000
 439  C11   C6   C7    121.68  3.000
 439  H52C  C5   H51C  107.20  3.000
 439  H52C  C5   C4    110.96  3.000
 439  H51C  C5   C4    113.00  3.000
 439  H52C  C5   C6    110.37  3.000
 439  H51C  C5   C6    113.31  3.000
 439  C4    C5   C6    102.02  3.000
 439  H42C  C4   H41C  106.95  3.000
 439  H42C  C4   C3    113.91  3.000
 439  H41C  C4   C3    108.42  3.000
 439  H42C  C4   C5    113.06  3.000
 439  H41C  C4   C5    109.41  3.000
 439  C3    C4   C5    104.98  3.000
 439  H3    C3   N1    110.44  3.000
 439  H3    C3   C4    111.41  3.000
 439  N1    C3   C4    111.10  3.000
 439  H3    C3   C11   111.28  3.000
 439  N1    C3   C11   111.66  3.000
 439  C4    C3   C11   100.63  3.000
 439  C1    N1   C2    109.16  3.000
 439  C1    N1   C3    111.28  3.000
 439  C2    N1   C3    113.19  3.000
 439  H23C  C2   H22C  107.28  3.000
 439  H23C  C2   H21C  107.95  3.000
 439  H22C  C2   H21C  107.45  3.000
 439  H23C  C2   N1    111.33  3.000
 439  H22C  C2   N1    109.21  3.000
 439  H21C  C2   N1    113.37  3.000
 439  H13C  C1   H12C  107.62  3.000
 439  H13C  C1   H11C  107.71  3.000
 439  H12C  C1   H11C  107.21  3.000
 439  H13C  C1   N1    113.08  3.000
 439  H12C  C1   N1    109.61  3.000
 439  H11C  C1   N1    111.37  3.000
 439  H14   C14  N3    108.99  3.000
 439  H14   C14  C13   109.26  3.000
 439  N3    C14  C13   113.93  3.000
 439  H14   C14  C25   107.58  3.000
 439  N3    C14  C25   113.56  3.000
 439  C13   C14  C25   103.22  3.000
 439  H132  C13  H131  108.47  3.000
 439  H132  C13  C12   110.17  3.000
 439  H131  C13  C12   112.62  3.000
 439  H132  C13  C14   109.92  3.000
 439  H131  C13  C14   113.12  3.000
 439  C12   C13  C14   102.44  3.000
 439  H122  C12  H121  108.26  3.000
 439  H122  C12  C13   111.54  3.000
 439  H121  C12  C13   112.32  3.000
 439  H122  C12  N2    110.67  3.000
 439  H121  C12  N2    110.49  3.000
 439  C13   C12  N2    103.55  3.000
 439  HA    N3   S1    113.18  3.000
 439  HA    N3   C14   115.77  3.000
 439  S1    N3   C14   122.40  3.000
 439  C15   S1   O2    107.61  3.000
 439  C15   S1   O1    108.01  3.000
 439  O2    S1   O1    120.43  3.000
 439  C15   S1   N3    108.13  3.000
 439  O2    S1   N3    106.85  3.000
 439  O1    S1   N3    105.29  3.000
 439  C16   C15  C24   121.73  3.000
 439  C16   C15  S1    119.52  3.000
 439  C24   C15  S1    118.71  3.000
 439  H24   C24  C23   118.98  3.000
 439  H24   C24  C15   121.35  3.000
 439  C23   C24  C15   119.67  3.000
 439  C22   C23  C18   119.20  3.000
 439  C22   C23  C24   121.52  3.000
 439  C18   C23  C24   119.28  3.000
 439  C19   C18  C17   121.52  3.000
 439  C19   C18  C23   119.30  3.000
 439  C17   C18  C23   119.18  3.000
 439  H17   C17  C16   120.00  3.000
 439  H17   C17  C18   119.16  3.000
 439  C16   C17  C18   120.84  3.000
 439  H16   C16  C17   120.02  3.000
 439  H16   C16  C15   120.67  3.000
 439  C17   C16  C15   119.30  3.000
 439  H22   C22  C21   119.93  3.000
 439  H22   C22  C23   119.23  3.000
 439  C21   C22  C23   120.85  3.000
 439  H21   C21  C20   120.06  3.000
 439  H21   C21  C22   120.69  3.000
 439  C20   C21  C22   119.25  3.000
 439  C19   C20  CL1   119.78  3.000
 439  C19   C20  C21   121.90  3.000
 439  CL1   C20  C21   118.32  3.000
 439  H19   C19  C20   120.91  3.000
 439  H19   C19  C18   119.59  3.000
 439  C20   C19  C18   119.50  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
 439  CONST_01  C11   C6   C7   C8      0.00   0.0  0
 439  CONST_02  C11   C10  C9   C8      0.00   0.0  0
 439  CONST_03  C10   C9   C8   C7      0.00   0.0  0
 439  CONST_04  C10   C11  C6   C7      0.00   0.0  0
 439  CONST_05  C6    C7   C8   C9      0.00   0.0  0
 439  CONST_06  C6    C11  C10  C9      0.00   0.0  0
 439  CONST_07  C18   C23  C24  C15     0.00   0.0  0
 439  CONST_08  C22   C23  C24  C15   180.00   0.0  0
 439  CONST_09  C18   C17  C16  C15     0.00   0.0  0
 439  CONST_10  C17   C16  C15  C24     0.00   0.0  0
 439  CONST_11  C17   C18  C23  C24     0.00   0.0  0
 439  CONST_12  C19   C18  C23  C24   180.00   0.0  0
 439  CONST_13  C21   C22  C23  C24   180.00   0.0  0
 439  CONST_14  C16   C15  C24  C23     0.00   0.0  0
 439  CONST_15  C16   C17  C18  C23     0.00   0.0  0
 439  CONST_16  C20   C19  C18  C23     0.00   0.0  0
 439  CONST_17  C20   C21  C22  C23     0.00   0.0  0
 439  CONST_18  C21   C22  C23  C18     0.00   0.0  0
 439  CONST_19  C21   C20  C19  C18     0.00   0.0  0
 439  CONST_20  C22   C23  C18  C17   180.00   0.0  0
 439  CONST_21  C20   C19  C18  C17   180.00   0.0  0
 439  CONST_22  C19   C18  C17  C16   180.00   0.0  0
 439  CONST_23  C19   C18  C23  C22     0.00   0.0  0
 439  CONST_24  C19   C20  C21  C22     0.00   0.0  0
 439  CONST_25  C6    C7   C8   N2    180.00   0.0  0
 439  CONST_26  C10   C9   C8   N2    180.00   0.0  0
 439  CONST_27  C14   C25  N2   C8    180.00   0.0  0
 439  CONST_28  C12   N2   C25  C14     0.00   0.0  0
 439  CONST_29  C23   C24  C15  S1    180.00   0.0  0
 439  CONST_30  C17   C16  C15  S1    180.00   0.0  0
 439  CONST_31  CL1   C20  C19  C18   180.00   0.0  0
 439  CONST_32  CL1   C20  C21  C22   180.00   0.0  0
 439  CONST_33  C8    N2   C25  O3      0.00   0.0  0
 439  CONST_34  C12   N2   C25  O3    180.00   0.0  0
 439  CONST_35  H7    C7   C8   N2      0.00   0.0  0
 439  CONST_36  H9    C9   C8   N2      0.00   0.0  0
 439  CONST_37  H10   C10  C9   C8    180.00   0.0  0
 439  CONST_38  H17   C17  C16  C15   180.00   0.0  0
 439  CONST_39  H16   C16  C15  C24   180.00   0.0  0
 439  CONST_40  H22   C22  C23  C24     0.00   0.0  0
 439  CONST_41  H19   C19  C18  C23   180.00   0.0  0
 439  CONST_42  H21   C21  C22  C23   180.00   0.0  0
 439  CONST_43  H24   C24  C23  C18   180.00   0.0  0
 439  Var_01    C7    C8   N2   C25   -23.03  30.0  2
 439  Var_02    C13   C12  N2   C25    19.94  30.0  1
 439  Var_03    C14   C13  C12  N2    -31.52  30.0  1
 439  Var_04    C4    C5   C6   C7   -159.42  30.0  1
 439  Var_05    C3    C4   C5   C6    -32.00  30.0  1
 439  Var_06    C15   S1   N3   C14    69.71  30.0  3
 439  Var_07    C24   C15  S1   N3     84.31  30.0  2
 439  Var_08    H21C  C2   N1   C3     57.25  30.0  3
 439  Var_09    H11C  C1   N1   C3     58.15  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
 439  chir_01  C3   C11  C4   N1  negativ
 439  chir_02  C14  C25  C13  N3  positiv

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
 439  plan-1  N2   0.020
 439  plan-1  C8   0.020
 439  plan-1  C7   0.020
 439  plan-1  C9   0.020
 439  plan-1  C10  0.020
 439  plan-1  C11  0.020
 439  plan-1  C6   0.020
 439  plan-1  C5   0.020
 439  plan-1  C3   0.020
 439  plan-1  H7   0.020
 439  plan-1  H9   0.020
 439  plan-1  H10  0.020
 439  plan-2  S1   0.020
 439  plan-2  C15  0.020
 439  plan-2  C24  0.020
 439  plan-2  C23  0.020
 439  plan-2  C18  0.020
 439  plan-2  C17  0.020
 439  plan-2  C16  0.020
 439  plan-2  C22  0.020
 439  plan-2  C21  0.020
 439  plan-2  C20  0.020
 439  plan-2  CL1  0.020
 439  plan-2  C19  0.020
 439  plan-2  H24  0.020
 439  plan-2  H16  0.020
 439  plan-2  H22  0.020
 439  plan-2  H17  0.020
 439  plan-2  H19  0.020
 439  plan-2  H21  0.020
 439  plan-3  O3   0.020
 439  plan-3  C25  0.020
 439  plan-3  N2   0.020
 439  plan-3  C8   0.020
 439  plan-3  C14  0.020
 439  plan-3  C12  0.020

