# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:17:36 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: 2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCNCC(=O)Nc1cccc(c1)C#Cc2ccc(C(O)=O)c(SCc3ccc(Cl)c(Cl)c3)c2
#
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
 NXW  NXW  '2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid'  ligand  60  36  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NXW
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
 NXW  C1    C   CSP    0   0.131  -1.9855  -3.6827  -0.1315
 NXW  C2    C   CSP    0   0.139  -0.7985  -3.8474   0.0184
 NXW  C3    C   C1     0  -0.235  -5.5947  -4.3279  -0.6563
 NXW  C4    C   C1     0  -0.317  -4.2393  -4.5616  -0.4894
 NXW  C5    C   C1     0  -0.305   1.1382  -5.2498   0.5674
 NXW  C6    C   C1     0  -0.273   2.5025  -5.3554   0.7564
 NXW  C7    C   CR16   0  -0.295   4.1405   1.1413  -1.9400
 NXW  C8    C   C1     0  -0.348  -6.0972  -3.0392  -0.6348
 NXW  C9    C   CR16   0  -0.206   4.9292   2.2618  -2.1381
 NXW  C10   C   C1     0  -0.375  -3.8816  -2.1680  -0.2857
 NXW  C11   C   C1     0  -0.318   1.4481  -2.9147   0.0486
 NXW  C12   C   CR16   0  -0.254   3.7414   1.8103   0.3255
 NXW  C13   C   C      0  -0.086  -3.3833  -3.4751  -0.3053
 NXW  C14   C   C      0  -0.076   0.6014  -4.0125   0.2116
 NXW  C15   C   C      0  -0.123   3.3638  -4.2729   0.6025
 NXW  C16   C   CR6    0   0.127   3.5318   0.9086  -0.7101
 NXW  C17   C   C      0   0.393  -5.2468  -1.9448  -0.4467
 NXW  C18   C   C      0  -0.123   2.8247  -3.0254   0.2366
 NXW  C19   C   CR6    0  -0.018   5.1266   3.1630  -1.1022
 NXW  C20   C   CR6    0   0.022   4.5301   2.9340   0.1322
 NXW  C21   C   C      0   0.423   4.8476  -4.4799   0.8431
 NXW  C22   C   C      0   0.513  -5.2888   0.5331  -0.1776
 NXW  C23   C   CH3    0  -0.516  -6.5663   7.5771   1.2440
 NXW  C24   C   CH2    0  -0.682   2.7052  -0.3193  -0.4819
 NXW  C25   C   CH2    0  -0.390  -6.3023   1.6621  -0.2507
 NXW  C26   C   CH2    0  -0.280  -6.1266   5.2579   0.7553
 NXW  C27   C   CH2    0  -0.275  -6.7224   3.9806   0.1876
 NXW  N28   N   NH1    0  -0.752  -5.8423  -0.6831  -0.4328
 NXW  N29   N   NH1    0  -0.594  -7.0992   6.3305   0.7356
 NXW  N30   N   NH1    0  -0.596  -5.7552   2.9010   0.2321
 NXW  O31   O   O      0  -0.577   5.5635  -3.4677   0.7032
 NXW  O32   O   O      0  -0.452  -4.1158   0.7097   0.0817
 NXW  O33   O   OC    -1  -0.580   5.2231  -5.6217   1.1593
 NXW  S34   S   S2     0   0.099   3.8854  -1.6243   0.0203
 NXW  CL35  CL  CL     0  -0.098   6.1065   4.5564  -1.3604
 NXW  CL36  CL  CL     0  -0.098   4.7609   4.0364   1.4362
 NXW  H3    H   H      0   0.268  -6.2721  -5.1585  -0.8023
 NXW  H4    H   H      0   0.261  -3.8463  -5.5691  -0.5015
 NXW  H5    H   H      0   0.255   0.4926  -6.1079   0.6969
 NXW  H6    H   H      0   0.255   2.9297  -6.3080   1.0381
 NXW  H8    H   H      0   0.276  -7.1613  -2.8786  -0.7607
 NXW  H10   H   H      0   0.286  -3.1966  -1.3489  -0.1438
 NXW  H11   H   H      0   0.275   0.9939  -1.9761  -0.2290
 NXW  H12   H   HCR6   0   0.282   3.2838   1.6436   1.2924
 NXW  H23   H   HCH3   0   0.192  -6.1535   7.5105   2.2606
 NXW  H23A  H   HCH3   0   0.221  -5.7654   7.9311   0.5918
 NXW  H23B  H   HCH3   0   0.231  -7.3455   8.3391   1.2496
 NXW  H24   H   HCH2   0   0.288   1.9670  -0.1416   0.3011
 NXW  H24A  H   HCH2   0   0.289   2.1819  -0.6052  -1.3956
 NXW  H25   H   HCH2   0   0.275  -6.5911   1.7818  -1.3013
 NXW  H25A  H   HCH2   0   0.235  -7.2188   1.3475   0.2751
 NXW  H26   H   HCH2   0   0.188  -5.7354   5.0579   1.7678
 NXW  H26A  H   HCH2   0   0.222  -5.2670   5.5548   0.1474
 NXW  H27   H   HCH2   0   0.192  -7.6496   3.7363   0.7329
 NXW  H27A  H   HCH2   0   0.225  -7.0117   4.1516  -0.8530
 NXW  HN28  H   HNH1   0   0.416  -6.8384  -0.6869  -0.5963
 NXW  HN29  H   HNH1   0   0.341  -7.8948   6.0607   1.3011
 NXW  HN30  H   HNH1   0   0.345  -5.4389   2.7788   1.1867
 NXW  H7    H   HCR6   0   0.283   3.9958   0.4444  -2.7557
 NXW  H9    H   HCR6   0   0.295   5.3940   2.4395  -3.0984

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
 NXW  C2   C1    triple    1.208  0.020  1.208
 NXW  C1   C13   single    1.424  0.020  1.424
 NXW  C14  C2    single    1.423  0.020  1.423
 NXW  C4   C3    aromatic  1.386  0.020  1.386
 NXW  C8   C3    aromatic  1.383  0.020  1.383
 NXW  C3   H3    single    0.930  0.020  1.080
 NXW  C13  C4    aromatic  1.395  0.020  1.395
 NXW  C4   H4    single    0.930  0.020  1.080
 NXW  C6   C5    aromatic  1.381  0.020  1.381
 NXW  C5   C14   aromatic  1.395  0.020  1.395
 NXW  C5   H5    single    0.930  0.020  1.080
 NXW  C6   C15   aromatic  1.392  0.020  1.392
 NXW  C6   H6    single    0.930  0.020  1.080
 NXW  C16  C7    aromatic  1.392  0.020  1.392
 NXW  C7   C9    aromatic  1.384  0.020  1.384
 NXW  C7   H7    single    0.930  0.020  1.080
 NXW  C17  C8    aromatic  1.399  0.020  1.399
 NXW  C8   H8    single    0.930  0.020  1.080
 NXW  C9   C19   aromatic  1.387  0.020  1.387
 NXW  C9   H9    single    0.930  0.020  1.080
 NXW  C10  C13   aromatic  1.399  0.020  1.399
 NXW  C10  C17   aromatic  1.393  0.020  1.393
 NXW  C10  H10   single    0.930  0.020  1.080
 NXW  C18  C11   aromatic  1.394  0.020  1.394
 NXW  C14  C11   aromatic  1.396  0.020  1.396
 NXW  C11  H11   single    0.930  0.020  1.080
 NXW  C16  C12   aromatic  1.389  0.020  1.389
 NXW  C12  C20   aromatic  1.386  0.020  1.386
 NXW  C12  H12   single    0.930  0.020  1.080
 NXW  C21  C15   single    1.517  0.020  1.517
 NXW  C15  C18   aromatic  1.407  0.020  1.407
 NXW  C24  C16   single    1.498  0.020  1.498
 NXW  N28  C17   single    1.395  0.020  1.395
 NXW  C18  S34   single    1.771  0.020  1.771
 NXW  C20  C19   aromatic  1.390  0.020  1.390
 NXW  C19  CL35  single    1.723  0.020  1.723
 NXW  C20  CL36  single    1.723  0.020  1.723
 NXW  O31  C21   deloc     1.248  0.020  1.248
 NXW  O33  C21   deloc     1.243  0.020  1.243
 NXW  O32  C22   double    1.214  0.020  1.214
 NXW  C25  C22   single    1.519  0.020  1.519
 NXW  C22  N28   single    1.360  0.020  1.360
 NXW  N29  C23   single    1.448  0.020  1.448
 NXW  C23  H23   single    0.970  0.020  1.090
 NXW  C23  H23A  single    0.970  0.020  1.090
 NXW  C23  H23B  single    0.970  0.020  1.090
 NXW  S34  C24   single    1.830  0.020  1.830
 NXW  C24  H24   single    0.970  0.020  1.090
 NXW  C24  H24A  single    0.970  0.020  1.090
 NXW  N30  C25   single    1.438  0.020  1.438
 NXW  C25  H25   single    0.970  0.020  1.090
 NXW  C25  H25A  single    0.970  0.020  1.090
 NXW  N29  C26   single    1.448  0.020  1.448
 NXW  C26  C27   single    1.519  0.020  1.519
 NXW  C26  H26   single    0.970  0.020  1.090
 NXW  C26  H26A  single    0.970  0.020  1.090
 NXW  C27  N30   single    1.450  0.020  1.450
 NXW  C27  H27   single    0.970  0.020  1.090
 NXW  C27  H27A  single    0.970  0.020  1.090
 NXW  N28  HN28  single    0.860  0.020  1.020
 NXW  N29  HN29  single    0.890  0.020  1.040
 NXW  N30  HN30  single    0.890  0.020  1.040

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
 NXW  C13   C1   C2    180.00  3.000
 NXW  C14   C2   C1    180.00  3.000
 NXW  H3    C3   C8    119.34  3.000
 NXW  H3    C3   C4    119.95  3.000
 NXW  C8    C3   C4    120.71  3.000
 NXW  H4    C4   C13   120.25  3.000
 NXW  H4    C4   C3    120.75  3.000
 NXW  C13   C4   C3    118.99  3.000
 NXW  H5    C5   C14   120.30  3.000
 NXW  H5    C5   C6    120.83  3.000
 NXW  C14   C5   C6    118.87  3.000
 NXW  H6    C6   C15   118.00  3.000
 NXW  H6    C6   C5    119.55  3.000
 NXW  C15   C6   C5    122.45  3.000
 NXW  H7    C7   C16   119.98  3.000
 NXW  H7    C7   C9    119.29  3.000
 NXW  C16   C7   C9    120.72  3.000
 NXW  H8    C8   C17   119.79  3.000
 NXW  H8    C8   C3    119.54  3.000
 NXW  C17   C8   C3    120.67  3.000
 NXW  H9    C9   C19   119.68  3.000
 NXW  H9    C9   C7    120.32  3.000
 NXW  C19   C9   C7    120.00  3.000
 NXW  H10   C10  C17   121.12  3.000
 NXW  H10   C10  C13   119.06  3.000
 NXW  C17   C10  C13   119.82  3.000
 NXW  H11   C11  C18   121.30  3.000
 NXW  H11   C11  C14   117.31  3.000
 NXW  C18   C11  C14   121.39  3.000
 NXW  H12   C12  C20   119.33  3.000
 NXW  H12   C12  C16   120.14  3.000
 NXW  C20   C12  C16   120.53  3.000
 NXW  C10   C13  C4    120.72  3.000
 NXW  C10   C13  C1    118.96  3.000
 NXW  C4    C13  C1    120.32  3.000
 NXW  C11   C14  C5    119.60  3.000
 NXW  C11   C14  C2    119.32  3.000
 NXW  C5    C14  C2    121.08  3.000
 NXW  C21   C15  C18   122.46  3.000
 NXW  C18   C15  C6    118.76  3.000
 NXW  C21   C15  C6    118.78  3.000
 NXW  C24   C16  C12   120.13  3.000
 NXW  C24   C16  C7    120.87  3.000
 NXW  C12   C16  C7    118.97  3.000
 NXW  N28   C17  C10   124.20  3.000
 NXW  N28   C17  C8    116.71  3.000
 NXW  C10   C17  C8    119.09  3.000
 NXW  S34   C18  C15   120.25  3.000
 NXW  S34   C18  C11   120.82  3.000
 NXW  C15   C18  C11   118.93  3.000
 NXW  CL35  C19  C20   120.69  3.000
 NXW  CL35  C19  C9    119.63  3.000
 NXW  C20   C19  C9    119.68  3.000
 NXW  CL36  C20  C19   120.61  3.000
 NXW  CL36  C20  C12   119.29  3.000
 NXW  C19   C20  C12   120.10  3.000
 NXW  O33   C21  O31   126.91  3.000
 NXW  O33   C21  C15   117.46  3.000
 NXW  O31   C21  C15   115.63  3.000
 NXW  O32   C22  N28   124.28  3.000
 NXW  N28   C22  C25   112.58  3.000
 NXW  O32   C22  C25   123.14  3.000
 NXW  H23B  C23  H23A  107.51  3.000
 NXW  H23B  C23  H23   107.82  3.000
 NXW  H23A  C23  H23   107.25  3.000
 NXW  H23B  C23  N29   109.91  3.000
 NXW  H23A  C23  N29   109.84  3.000
 NXW  H23   C23  N29   114.26  3.000
 NXW  H24A  C24  H24   108.62  3.000
 NXW  H24A  C24  S34   110.62  3.000
 NXW  H24   C24  S34   110.84  3.000
 NXW  H24A  C24  C16   110.61  3.000
 NXW  H24   C24  C16   110.45  3.000
 NXW  S34   C24  C16   105.70  3.000
 NXW  H25A  C25  H25   105.62  3.000
 NXW  H25A  C25  N30   113.70  3.000
 NXW  H25   C25  N30   109.14  3.000
 NXW  H25A  C25  C22   108.64  3.000
 NXW  H25   C25  C22   107.65  3.000
 NXW  N30   C25  C22   111.74  3.000
 NXW  H26A  C26  H26   106.29  3.000
 NXW  H26A  C26  N29   108.61  3.000
 NXW  H26   C26  N29   112.63  3.000
 NXW  H26A  C26  C27   109.18  3.000
 NXW  H26   C26  C27   109.23  3.000
 NXW  N29   C26  C27   110.75  3.000
 NXW  H27A  C27  H27   106.42  3.000
 NXW  H27A  C27  N30   108.79  3.000
 NXW  H27   C27  N30   112.37  3.000
 NXW  H27A  C27  C26   109.14  3.000
 NXW  H27   C27  C26   109.33  3.000
 NXW  N30   C27  C26   110.66  3.000
 NXW  HN28  N28  C22   115.80  3.000
 NXW  HN28  N28  C17   114.59  3.000
 NXW  C22   N28  C17   129.55  3.000
 NXW  HN29  N29  C26   108.83  3.000
 NXW  HN29  N29  C23   108.81  3.000
 NXW  C26   N29  C23   112.69  3.000
 NXW  HN30  N30  C27   109.09  3.000
 NXW  HN30  N30  C25   109.35  3.000
 NXW  C27   N30  C25   112.17  3.000
 NXW  C24   S34  C18   102.21  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
 NXW  CONST_01  C10   C13  C4   C3      0.00   0.0  0
 NXW  CONST_02  C10   C17  C8   C3      0.00   0.0  0
 NXW  CONST_03  C17   C8   C3   C4      0.00   0.0  0
 NXW  CONST_04  C17   C10  C13  C4      0.00   0.0  0
 NXW  CONST_05  C18   C15  C6   C5      0.00   0.0  0
 NXW  CONST_06  C18   C11  C14  C5      0.00   0.0  0
 NXW  CONST_07  C11   C14  C5   C6      0.00   0.0  0
 NXW  CONST_08  C11   C18  C15  C6      0.00   0.0  0
 NXW  CONST_09  C20   C12  C16  C7      0.00   0.0  0
 NXW  CONST_10  C20   C19  C9   C7      0.00   0.0  0
 NXW  CONST_11  C13   C4   C3   C8      0.00   0.0  0
 NXW  CONST_12  C13   C10  C17  C8      0.00   0.0  0
 NXW  CONST_13  C12   C16  C7   C9      0.00   0.0  0
 NXW  CONST_14  C12   C20  C19  C9      0.00   0.0  0
 NXW  CONST_15  C15   C6   C5   C14     0.00   0.0  0
 NXW  CONST_16  C15   C18  C11  C14     0.00   0.0  0
 NXW  CONST_17  C19   C9   C7   C16     0.00   0.0  0
 NXW  CONST_18  C19   C20  C12  C16     0.00   0.0  0
 NXW  CONST_19  C3    C4   C13  C1    180.00   0.0  0
 NXW  CONST_20  C17   C10  C13  C1    180.00   0.0  0
 NXW  CONST_21  C6    C5   C14  C2    180.00   0.0  0
 NXW  CONST_22  C18   C11  C14  C2    180.00   0.0  0
 NXW  CONST_23  N28   C17  C8   C3    180.00   0.0  0
 NXW  CONST_24  C21   C15  C6   C5    180.00   0.0  0
 NXW  CONST_25  S34   C18  C15  C6    180.00   0.0  0
 NXW  CONST_26  CL35  C19  C9   C7    180.00   0.0  0
 NXW  CONST_27  C24   C16  C7   C9    180.00   0.0  0
 NXW  CONST_28  CL36  C20  C19  C9    180.00   0.0  0
 NXW  CONST_29  C21   C15  C18  C11   180.00   0.0  0
 NXW  CONST_30  CL35  C19  C20  C12   180.00   0.0  0
 NXW  CONST_31  N28   C17  C10  C13   180.00   0.0  0
 NXW  CONST_32  S34   C18  C11  C14   180.00   0.0  0
 NXW  CONST_33  CL36  C20  C12  C16   180.00   0.0  0
 NXW  CONST_34  C24   C16  C12  C20   180.00   0.0  0
 NXW  CONST_35  H8    C8   C3   C4    180.00   0.0  0
 NXW  CONST_36  H10   C10  C13  C4    180.00   0.0  0
 NXW  CONST_37  H11   C11  C14  C5    180.00   0.0  0
 NXW  CONST_38  H12   C12  C16  C7    180.00   0.0  0
 NXW  CONST_39  H4    C4   C3   C8    180.00   0.0  0
 NXW  CONST_40  H5    C5   C14  C11   180.00   0.0  0
 NXW  CONST_41  H7    C7   C16  C12   180.00   0.0  0
 NXW  CONST_42  H3    C3   C4   C13   180.00   0.0  0
 NXW  CONST_43  H6    C6   C5   C14   180.00   0.0  0
 NXW  CONST_44  H9    C9   C7   C16   180.00   0.0  0
 NXW  CONST_45  C22   N28  C17  C8    180.00   0.0  0
 NXW  CONST_46  C22   N28  C17  C10     0.00   0.0  0
 NXW  CONST_47  HN28  N28  C17  C8      0.00   0.0  0
 NXW  CONST_48  O32   C22  N28  C17     0.00   0.0  0
 NXW  CONST_49  C25   C22  N28  C17   180.00   0.0  0
 NXW  Var_01    O31   C21  C15  C6   -179.25  30.0  2
 NXW  Var_02    S34   C24  C16  C7     85.90  30.0  2
 NXW  Var_03    C27   N30  C25  C22  -179.03  30.0  1
 NXW  Var_04    C27   C26  N29  C23  -178.85  30.0  3
 NXW  Var_05    C26   C27  N30  C25   177.77  30.0  1
 NXW  Var_06    N30   C25  C22  N28   170.51  30.0  1
 NXW  Var_07    N30   C27  C26  N29  -178.89  30.0  3
 NXW  Var_08    H23   C23  N29  C26   -56.18  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
 NXW  plan-1  C1    0.020
 NXW  plan-1  C2    0.020
 NXW  plan-1  C3    0.020
 NXW  plan-1  C4    0.020
 NXW  plan-1  C8    0.020
 NXW  plan-1  C10   0.020
 NXW  plan-1  C13   0.020
 NXW  plan-1  C17   0.020
 NXW  plan-1  N28   0.020
 NXW  plan-1  H3    0.020
 NXW  plan-1  H4    0.020
 NXW  plan-1  H8    0.020
 NXW  plan-1  H10   0.020
 NXW  plan-2  C1    0.020
 NXW  plan-2  C2    0.020
 NXW  plan-2  C5    0.020
 NXW  plan-2  C6    0.020
 NXW  plan-2  C11   0.020
 NXW  plan-2  C14   0.020
 NXW  plan-2  C15   0.020
 NXW  plan-2  C18   0.020
 NXW  plan-2  C21   0.020
 NXW  plan-2  S34   0.020
 NXW  plan-2  H5    0.020
 NXW  plan-2  H6    0.020
 NXW  plan-2  H11   0.020
 NXW  plan-3  C7    0.020
 NXW  plan-3  C9    0.020
 NXW  plan-3  C12   0.020
 NXW  plan-3  C16   0.020
 NXW  plan-3  C19   0.020
 NXW  plan-3  C20   0.020
 NXW  plan-3  C24   0.020
 NXW  plan-3  CL35  0.020
 NXW  plan-3  CL36  0.020
 NXW  plan-3  H12   0.020
 NXW  plan-3  H7    0.020
 NXW  plan-3  H9    0.020
 NXW  plan-4  C17   0.020
 NXW  plan-4  C22   0.020
 NXW  plan-4  C25   0.020
 NXW  plan-4  N28   0.020
 NXW  plan-4  O32   0.020
 NXW  plan-4  HN28  0.020
 NXW  plan-5  C15   0.020
 NXW  plan-5  C21   0.020
 NXW  plan-5  O31   0.020
 NXW  plan-5  O33   0.020

