# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 18:36:13 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-{5-[(3-hydroxy-5-methoxyphenyl)amino]-2-(phenylcarbamoyl)phenoxy}propan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)cc(Nc2ccc(C(=O)Nc3ccccc3)c(OCCC[NH3+])c2)c1
#
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
 B5S  B5S  3-{5-[(3-hydroxy-5-methoxyphenyl)amino]-2-(phenylcarbamoyl)phenoxy}propan-1-aminium  ligand  56  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B5S
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
 B5S  C1    C  CH3   0  -0.437   6.5904  -3.0697  -1.9892
 B5S  O2    O  O2    0  -0.473   5.3700  -2.3895  -1.7730
 B5S  C3    C  CR6   0   0.411   5.3355  -1.3880  -0.8757
 B5S  C4    C  CR16  0  -0.497   6.4416  -0.9728  -0.1452
 B5S  C5    C  CR6   0   0.398   6.2900   0.0899   0.7470
 B5S  O6    O  OH1   0  -0.632   7.3878   0.4660   1.4301
 B5S  C7    C  CR16  0  -0.516   5.0634   0.7088   0.9254
 B5S  C8    C  CR6   0   0.405   3.9577   0.2775   0.1828
 B5S  N9    N  NH1   0  -0.810   2.7662   0.9648   0.3630
 B5S  C10   C  CR6   0   0.417   1.4736   0.5465   0.1436
 B5S  C11   C  CR16  0  -0.354   1.0945  -0.7966   0.0852
 B5S  C12   C  CR16  0  -0.251  -0.2374  -1.1152  -0.1080
 B5S  C13   C  CR6   0  -0.204  -1.2265  -0.1485  -0.2483
 B5S  C14   C  C     0   0.518  -2.6360  -0.5357  -0.5323
 B5S  O15   O  O     0  -0.455  -3.3037  -0.0015  -1.3992
 B5S  N16   N  NH1   0  -0.744  -3.0879  -1.5500   0.2555
 B5S  C17   C  CR6   0   0.378  -4.3097  -2.2279   0.2188
 B5S  C18   C  CR16  0  -0.319  -5.3109  -2.0112  -0.7303
 B5S  C19   C  CR16  0  -0.244  -6.4854  -2.7509  -0.6692
 B5S  C20   C  CR16  0  -0.274  -6.6896  -3.7040   0.3170
 B5S  C21   C  CR16  0  -0.243  -5.6918  -3.9188   1.2595
 B5S  C22   C  CR16  0  -0.353  -4.5162  -3.1910   1.2116
 B5S  C23   C  CR6   0   0.411  -0.8438   1.2026  -0.1679
 B5S  O24   O  O2    0  -0.456  -1.8232   2.1127  -0.2628
 B5S  C25   C  CH2   0  -0.179  -1.5125   3.4872  -0.1332
 B5S  C26   C  CH2   0  -0.484  -2.8060   4.2574  -0.3135
 B5S  C27   C  CH2   0  -0.307  -2.5491   5.7423  -0.1540
 B5S  N28   N  NT3   1  -0.776  -3.8029   6.5162  -0.3334
 B5S  C32   C  CR16  0  -0.512   0.4879   1.5367   0.0264
 B5S  C33   C  CR16  0  -0.456   4.0958  -0.7613  -0.7298
 B5S  HN28  H  HNT3  0   0.471  -4.2123   6.3735  -1.2564
 B5S  HN2A  H  HNT3  0   0.471  -4.5118   6.2609   0.3540
 B5S  HN2B  H  HNT3  0   0.481  -3.6386   7.5175  -0.2332
 B5S  H1    H  HCH3  0   0.229   7.3664  -2.4044  -2.3766
 B5S  H1A   H  HCH3  0   0.229   6.9585  -3.5484  -1.0782
 B5S  H1B   H  HCH3  0   0.261   6.3870  -3.8388  -2.7301
 B5S  H4    H  HCR6  0   0.281   7.4124  -1.4382  -0.2467
 B5S  HO6   H  HOH1  0   0.475   7.1900   1.2175   2.0003
 B5S  H7    H  HCR6  0   0.275   4.9518   1.5183   1.6382
 B5S  HN9   H  HNH1  0   0.406   2.8633   1.9087   0.7019
 B5S  H11   H  HCR6  0   0.280   1.8140  -1.5911   0.2109
 B5S  H12   H  HCR6  0   0.269  -0.5068  -2.1630  -0.1637
 B5S  HN16  H  HNH1  0   0.419  -2.4720  -1.8390   1.0003
 B5S  H18   H  HCR6  0   0.279  -5.1883  -1.2771  -1.5085
 B5S  H19   H  HCR6  0   0.258  -7.2523  -2.5698  -1.4115
 B5S  H20   H  HCR6  0   0.255  -7.6103  -4.2709   0.3520
 B5S  H21   H  HCR6  0   0.260  -5.8254  -4.6572   2.0392
 B5S  H22   H  HCR6  0   0.269  -3.7455  -3.3702   1.9523
 B5S  H25   H  HCH2  0   0.237  -1.0779   3.6914   0.8517
 B5S  H25A  H  HCH2  0   0.237  -0.7825   3.7922  -0.8907
 B5S  H26   H  HCH2  0   0.266  -3.2161   4.0541  -1.3055
 B5S  H26A  H  HCH2  0   0.266  -3.5388   3.9258   0.4262
 B5S  H27   H  HCH2  0   0.298  -2.1714   5.9838   0.8371
 B5S  H27A  H  HCH2  0   0.298  -1.8432   6.1149  -0.8930
 B5S  H32   H  HCR6  0   0.294   0.7949   2.5729   0.0896
 B5S  H33   H  HCR6  0   0.276   3.2741  -1.0786  -1.3564

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
 B5S  C1   O2    single    1.414  0.020  1.414
 B5S  C1   H1    single    0.970  0.020  1.090
 B5S  C1   H1A   single    0.970  0.020  1.090
 B5S  C1   H1B   single    0.970  0.020  1.090
 B5S  O2   C3    single    1.345  0.020  1.345
 B5S  C3   C4    aromatic  1.389  0.020  1.389
 B5S  C3   C33   aromatic  1.397  0.020  1.397
 B5S  C4   C5    aromatic  1.396  0.020  1.396
 B5S  C4   H4    single    0.930  0.020  1.080
 B5S  C5   O6    single    1.347  0.020  1.347
 B5S  C5   C7    aromatic  1.385  0.020  1.385
 B5S  O6   HO6   single    0.850  0.020  0.980
 B5S  C7   C8    aromatic  1.400  0.020  1.400
 B5S  C7   H7    single    0.930  0.020  1.080
 B5S  C8   N9    single    1.387  0.020  1.387
 B5S  C8   C33   aromatic  1.390  0.020  1.390
 B5S  N9   C10   single    1.376  0.020  1.376
 B5S  N9   HN9   single    0.860  0.020  1.020
 B5S  C10  C11   aromatic  1.397  0.020  1.397
 B5S  C10  C32   aromatic  1.402  0.020  1.402
 B5S  C11  C12   aromatic  1.383  0.020  1.383
 B5S  C11  H11   single    0.930  0.020  1.080
 B5S  C12  C13   aromatic  1.390  0.020  1.390
 B5S  C12  H12   single    0.930  0.020  1.080
 B5S  C13  C14   single    1.489  0.020  1.489
 B5S  C13  C23   aromatic  1.407  0.020  1.407
 B5S  C14  O15   double    1.218  0.020  1.218
 B5S  C14  N16   single    1.361  0.020  1.361
 B5S  N16  C17   single    1.398  0.020  1.398
 B5S  N16  HN16  single    0.860  0.020  1.020
 B5S  C17  C18   aromatic  1.396  0.020  1.396
 B5S  C17  C22   aromatic  1.398  0.020  1.398
 B5S  C18  C19   aromatic  1.389  0.020  1.389
 B5S  C18  H18   single    0.930  0.020  1.080
 B5S  C19  C20   aromatic  1.387  0.020  1.387
 B5S  C19  H19   single    0.930  0.020  1.080
 B5S  C20  C21   aromatic  1.389  0.020  1.389
 B5S  C20  H20   single    0.930  0.020  1.080
 B5S  C21  C22   aromatic  1.384  0.020  1.384
 B5S  C21  H21   single    0.930  0.020  1.080
 B5S  C22  H22   single    0.930  0.020  1.080
 B5S  C23  O24   single    1.340  0.020  1.340
 B5S  C23  C32   aromatic  1.387  0.020  1.387
 B5S  O24  C25   single    1.415  0.020  1.415
 B5S  C25  C26   single    1.516  0.020  1.516
 B5S  C25  H25   single    0.970  0.020  1.090
 B5S  C25  H25A  single    0.970  0.020  1.090
 B5S  C26  C27   single    1.515  0.020  1.515
 B5S  C26  H26   single    0.970  0.020  1.090
 B5S  C26  H26A  single    0.970  0.020  1.090
 B5S  C27  N28   single    1.484  0.020  1.484
 B5S  C27  H27   single    0.970  0.020  1.090
 B5S  C27  H27A  single    0.970  0.020  1.090
 B5S  N28  HN28  single    0.890  0.020  1.040
 B5S  N28  HN2A  single    0.890  0.020  1.040
 B5S  N28  HN2B  single    0.890  0.020  1.040
 B5S  C32  H32   single    0.930  0.020  1.080
 B5S  C33  H33   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
 B5S  H1B   C1   H1A   108.74  3.000
 B5S  H1B   C1   H1    108.77  3.000
 B5S  H1A   C1   H1    108.84  3.000
 B5S  H1B   C1   O2    106.45  3.000
 B5S  H1A   C1   O2    111.96  3.000
 B5S  H1    C1   O2    111.97  3.000
 B5S  C3    O2   C1    118.84  3.000
 B5S  C33   C3   C4    121.18  3.000
 B5S  C33   C3   O2    115.25  3.000
 B5S  C4    C3   O2    123.57  3.000
 B5S  H4    C4   C5    119.02  3.000
 B5S  H4    C4   C3    122.47  3.000
 B5S  C5    C4   C3    118.51  3.000
 B5S  C7    C5   O6    122.12  3.000
 B5S  C7    C5   C4    121.23  3.000
 B5S  O6    C5   C4    116.65  3.000
 B5S  HO6   O6   C5    110.53  3.000
 B5S  H7    C7   C8    119.82  3.000
 B5S  H7    C7   C5    120.62  3.000
 B5S  C8    C7   C5    119.56  3.000
 B5S  C33   C8   N9    122.76  3.000
 B5S  C33   C8   C7    120.01  3.000
 B5S  N9    C8   C7    117.18  3.000
 B5S  HN9   N9   C10   115.40  3.000
 B5S  HN9   N9   C8    115.15  3.000
 B5S  C10   N9   C8    129.45  3.000
 B5S  C32   C10  C11   119.00  3.000
 B5S  C32   C10  N9    117.32  3.000
 B5S  C11   C10  N9    123.63  3.000
 B5S  H11   C11  C12   119.26  3.000
 B5S  H11   C11  C10   121.47  3.000
 B5S  C12   C11  C10   119.26  3.000
 B5S  H12   C12  C13   119.37  3.000
 B5S  H12   C12  C11   118.00  3.000
 B5S  C13   C12  C11   122.62  3.000
 B5S  C23   C13  C14   121.21  3.000
 B5S  C23   C13  C12   117.94  3.000
 B5S  C14   C13  C12   120.79  3.000
 B5S  N16   C14  O15   123.83  3.000
 B5S  N16   C14  C13   113.43  3.000
 B5S  O15   C14  C13   122.73  3.000
 B5S  HN16  N16  C17   114.46  3.000
 B5S  HN16  N16  C14   115.98  3.000
 B5S  C17   N16  C14   129.52  3.000
 B5S  C22   C17  C18   118.92  3.000
 B5S  C22   C17  N16   116.39  3.000
 B5S  C18   C17  N16   124.69  3.000
 B5S  H18   C18  C19   119.40  3.000
 B5S  H18   C18  C17   121.03  3.000
 B5S  C19   C18  C17   119.57  3.000
 B5S  H19   C19  C20   119.89  3.000
 B5S  H19   C19  C18   118.66  3.000
 B5S  C20   C19  C18   121.45  3.000
 B5S  H20   C20  C21   120.55  3.000
 B5S  H20   C20  C19   120.57  3.000
 B5S  C21   C20  C19   118.88  3.000
 B5S  H21   C21  C22   119.26  3.000
 B5S  H21   C21  C20   120.38  3.000
 B5S  C22   C21  C20   120.36  3.000
 B5S  H22   C22  C21   119.58  3.000
 B5S  H22   C22  C17   119.60  3.000
 B5S  C21   C22  C17   120.82  3.000
 B5S  C32   C23  O24   123.23  3.000
 B5S  C32   C23  C13   120.05  3.000
 B5S  O24   C23  C13   116.70  3.000
 B5S  C25   O24  C23   119.51  3.000
 B5S  H25A  C25  H25   107.78  3.000
 B5S  H25A  C25  C26   110.17  3.000
 B5S  H25   C25  C26   110.52  3.000
 B5S  H25A  C25  O24   110.71  3.000
 B5S  H25   C25  O24   110.52  3.000
 B5S  C26   C25  O24   107.17  3.000
 B5S  H26A  C26  H26   107.84  3.000
 B5S  H26A  C26  C27   109.87  3.000
 B5S  H26   C26  C27   109.97  3.000
 B5S  H26A  C26  C25   109.72  3.000
 B5S  H26   C26  C25   109.49  3.000
 B5S  C27   C26  C25   109.92  3.000
 B5S  H27A  C27  H27   108.52  3.000
 B5S  H27A  C27  N28   106.71  3.000
 B5S  H27   C27  N28   106.72  3.000
 B5S  H27A  C27  C26   111.97  3.000
 B5S  H27   C27  C26   111.85  3.000
 B5S  N28   C27  C26   110.80  3.000
 B5S  HN2B  N28  HN2A  106.96  3.000
 B5S  HN2B  N28  HN28  106.92  3.000
 B5S  HN2A  N28  HN28  107.21  3.000
 B5S  HN2B  N28  C27   111.35  3.000
 B5S  HN2A  N28  C27   112.03  3.000
 B5S  HN28  N28  C27   112.06  3.000
 B5S  H32   C32  C23   120.74  3.000
 B5S  H32   C32  C10   118.15  3.000
 B5S  C23   C32  C10   121.11  3.000
 B5S  H33   C33  C8    121.64  3.000
 B5S  H33   C33  C3    118.84  3.000
 B5S  C8    C33  C3    119.49  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
 B5S  CONST_01  C7    C5   C4   C3      0.00   0.0  0
 B5S  CONST_02  C7    C8   C33  C3      0.00   0.0  0
 B5S  CONST_03  C8    C33  C3   C4      0.00   0.0  0
 B5S  CONST_04  C8    C7   C5   C4      0.00   0.0  0
 B5S  CONST_05  C33   C3   C4   C5      0.00   0.0  0
 B5S  CONST_06  C33   C8   C7   C5      0.00   0.0  0
 B5S  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 B5S  CONST_08  C13   C23  C32  C10     0.00   0.0  0
 B5S  CONST_09  C23   C32  C10  C11     0.00   0.0  0
 B5S  CONST_10  C23   C13  C12  C11     0.00   0.0  0
 B5S  CONST_11  C32   C10  C11  C12     0.00   0.0  0
 B5S  CONST_12  C32   C23  C13  C12     0.00   0.0  0
 B5S  CONST_13  C20   C19  C18  C17     0.00   0.0  0
 B5S  CONST_14  C20   C21  C22  C17     0.00   0.0  0
 B5S  CONST_15  C21   C22  C17  C18     0.00   0.0  0
 B5S  CONST_16  C21   C20  C19  C18     0.00   0.0  0
 B5S  CONST_17  C22   C17  C18  C19     0.00   0.0  0
 B5S  CONST_18  C22   C21  C20  C19     0.00   0.0  0
 B5S  CONST_19  C5    C4   C3   O2    180.00   0.0  0
 B5S  CONST_20  C8    C33  C3   O2    180.00   0.0  0
 B5S  CONST_21  O6    C5   C4   C3    180.00   0.0  0
 B5S  CONST_22  N9    C8   C33  C3    180.00   0.0  0
 B5S  CONST_23  N9    C8   C7   C5    180.00   0.0  0
 B5S  CONST_24  C8    C7   C5   O6    180.00   0.0  0
 B5S  CONST_25  C12   C11  C10  N9    180.00   0.0  0
 B5S  CONST_26  C23   C32  C10  N9    180.00   0.0  0
 B5S  CONST_27  O24   C23  C32  C10   180.00   0.0  0
 B5S  CONST_28  C14   C13  C12  C11   180.00   0.0  0
 B5S  CONST_29  O24   C23  C13  C12   180.00   0.0  0
 B5S  CONST_30  C32   C23  C13  C14   180.00   0.0  0
 B5S  CONST_31  C19   C18  C17  N16   180.00   0.0  0
 B5S  CONST_32  C21   C22  C17  N16   180.00   0.0  0
 B5S  CONST_33  H33   C33  C3   C4    180.00   0.0  0
 B5S  CONST_34  H7    C7   C5   C4    180.00   0.0  0
 B5S  CONST_35  H4    C4   C5   C7    180.00   0.0  0
 B5S  CONST_36  H12   C12  C11  C10   180.00   0.0  0
 B5S  CONST_37  H32   C32  C10  C11   180.00   0.0  0
 B5S  CONST_38  H11   C11  C12  C13   180.00   0.0  0
 B5S  CONST_39  H19   C19  C18  C17   180.00   0.0  0
 B5S  CONST_40  H21   C21  C22  C17   180.00   0.0  0
 B5S  CONST_41  H22   C22  C17  C18   180.00   0.0  0
 B5S  CONST_42  H20   C20  C19  C18   180.00   0.0  0
 B5S  CONST_43  H18   C18  C19  C20   180.00   0.0  0
 B5S  CONST_44  C17   N16  C14  C13   180.00   0.0  0
 B5S  CONST_45  C18   C17  N16  C14     0.00   0.0  0
 B5S  CONST_46  C22   C17  N16  C14   180.00   0.0  0
 B5S  CONST_47  HN16  N16  C17  C18   180.00   0.0  0
 B5S  CONST_48  C17   N16  C14  O15     0.00   0.0  0
 B5S  Var_01    C10   N9   C8   C7   -156.46  30.0  2
 B5S  Var_02    C11   C10  N9   C8     20.90  30.0  2
 B5S  Var_03    C4    C3   O2   C1      0.33  30.0  2
 B5S  Var_04    O15   C14  C13  C12  -132.72  30.0  2
 B5S  Var_05    C32   C23  O24  C25    -1.40  30.0  2
 B5S  Var_06    C26   C25  O24  C23   178.86  30.0  3
 B5S  Var_07    H1    C1   O2   C3    -62.18  30.0  3
 B5S  Var_08    C27   C26  C25  O24   178.69  30.0  3
 B5S  Var_09    N28   C27  C26  C25   179.73  30.0  3
 B5S  Var_10    HN28  N28  C27  C26   -59.96  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
 B5S  plan-1  O2    0.020
 B5S  plan-1  C3    0.020
 B5S  plan-1  C4    0.020
 B5S  plan-1  C5    0.020
 B5S  plan-1  O6    0.020
 B5S  plan-1  C7    0.020
 B5S  plan-1  C8    0.020
 B5S  plan-1  N9    0.020
 B5S  plan-1  C33   0.020
 B5S  plan-1  H4    0.020
 B5S  plan-1  H7    0.020
 B5S  plan-1  H33   0.020
 B5S  plan-2  N9    0.020
 B5S  plan-2  C10   0.020
 B5S  plan-2  C11   0.020
 B5S  plan-2  C12   0.020
 B5S  plan-2  C13   0.020
 B5S  plan-2  C14   0.020
 B5S  plan-2  C23   0.020
 B5S  plan-2  O24   0.020
 B5S  plan-2  C32   0.020
 B5S  plan-2  H11   0.020
 B5S  plan-2  H12   0.020
 B5S  plan-2  H32   0.020
 B5S  plan-3  N16   0.020
 B5S  plan-3  C17   0.020
 B5S  plan-3  C18   0.020
 B5S  plan-3  C19   0.020
 B5S  plan-3  C20   0.020
 B5S  plan-3  C21   0.020
 B5S  plan-3  C22   0.020
 B5S  plan-3  H18   0.020
 B5S  plan-3  H19   0.020
 B5S  plan-3  H20   0.020
 B5S  plan-3  H21   0.020
 B5S  plan-3  H22   0.020
 B5S  plan-4  C13   0.020
 B5S  plan-4  C14   0.020
 B5S  plan-4  O15   0.020
 B5S  plan-4  N16   0.020
 B5S  plan-4  C17   0.020
 B5S  plan-4  HN16  0.020

