# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 10:35:26 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: phenyl (3S)-3-amino-5-phenylpentane-1-sulfonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCc1ccccc1)CC[S](=O)(=O)Oc2ccccc2
#
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
 2PS  2PS  'phenyl (3S)-3-amino-5-phenylpentane-1-sulfonate'  peptide  43  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_2PS
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
 2PS  C1    C  CH2   0  -0.408   2.6269  -0.2256   0.1780
 2PS  C9    C  CH1   0  -0.097   1.2377  -0.0960   0.7991
 2PS  C32   C  CH2   0  -0.438   0.2140  -0.8237  -0.0878
 2PS  C33   C  CH2   0  -0.648  -1.2042  -0.6107   0.4243
 2PS  S34   S  S     0   1.429  -2.3924  -1.3784  -0.6584
 2PS  O37   O  OS    0  -0.633  -2.4088  -0.6922  -1.9330
 2PS  O36   O  OS    0  -0.635  -2.2531  -2.8164  -0.6167
 2PS  O35   O  OC2   0  -0.595  -3.8059  -1.1182   0.1082
 2PS  N10   N  NH2   0  -0.788   1.2639  -0.5408   2.1813
 2PS  C2    C  CH2   0  -0.499   3.6923   0.5928   0.9066
 2PS  C3    C  CR6   0   0.135   5.0329   0.4900   0.2352
 2PS  C4    C  CR16  0  -0.312   5.3757   1.3484  -0.8082
 2PS  C5    C  CR16  0  -0.240   6.5995   1.2358  -1.4544
 2PS  C6    C  CR16  0  -0.276   7.5048   0.2556  -1.0675
 2PS  C7    C  CR16  0  -0.240   7.1748  -0.6076  -0.0308
 2PS  C8    C  CR16  0  -0.316   5.9494  -0.4894   0.6125
 2PS  C36   C  CR6   0   0.314  -4.3530   0.1578   0.1225
 2PS  C37   C  CR16  0  -0.287  -5.0817   0.6086  -0.9666
 2PS  C38   C  CR16  0  -0.256  -5.6669   1.8657  -0.9036
 2PS  C39   C  CR16  0  -0.248  -5.5205   2.6545   0.2303
 2PS  C40   C  CR16  0  -0.253  -4.7897   2.1835   1.3129
 2PS  C41   C  CR16  0  -0.300  -4.1986   0.9285   1.2640
 2PS  H11   H  HCH2  0   0.224   2.9224  -1.2811   0.1605
 2PS  H12   H  HCH2  0   0.233   2.5755   0.0957  -0.8663
 2PS  H91   H  HCH1  0   0.232   0.9720   0.9678   0.8087
 2PS  H321  H  HCH2  0   0.254   0.2974  -0.4455  -1.1090
 2PS  H322  H  HCH2  0   0.252   0.4506  -1.8909  -0.1133
 2PS  H331  H  HCH2  0   0.307  -1.3583  -1.0508   1.4106
 2PS  H332  H  HCH2  0   0.310  -1.4500   0.4528   0.4689
 2PS  H10   H  HNH2  0   0.353   0.3912  -0.3346   2.6496
 2PS  H21A  H  HCH2  0   0.234   3.3777   1.6398   0.9399
 2PS  H22   H  HCH2  0   0.243   3.7652   0.2523   1.9402
 2PS  H41   H  HCR6  0   0.244   4.6768   2.1185  -1.1153
 2PS  H51   H  HCR6  0   0.252   6.8478   1.9172  -2.2584
 2PS  H61   H  HCR6  0   0.252   8.4614   0.1690  -1.5663
 2PS  H71   H  HCR6  0   0.251   7.8755  -1.3712   0.2827
 2PS  H81   H  HCR6  0   0.244   5.7062  -1.1644   1.4254
 2PS  H371  H  HCR6  0   0.280  -5.2039  -0.0144  -1.8421
 2PS  H381  H  HCR6  0   0.269  -6.2414   2.2275  -1.7458
 2PS  H391  H  HCR6  0   0.266  -5.9813   3.6322   0.2734
 2PS  H401  H  HCR6  0   0.269  -4.6789   2.7914   2.2008
 2PS  H411  H  HCR6  0   0.282  -3.6368   0.5482   2.1079
 2PS  H2    H  HNH2  0   0.340   1.3866  -1.5465   2.2230

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
 2PS  C1   C9    single    1.527  0.020  1.527
 2PS  C1   C2    single    1.528  0.020  1.528
 2PS  C1   H11   single    0.970  0.020  1.090
 2PS  C1   H12   single    0.970  0.020  1.090
 2PS  C9   C32   single    1.538  0.020  1.538
 2PS  C9   N10   single    1.452  0.020  1.452
 2PS  C9   H91   single    0.970  0.020  1.090
 2PS  C32  C33   single    1.523  0.020  1.523
 2PS  C32  H321  single    0.970  0.020  1.090
 2PS  C32  H322  single    0.970  0.020  1.090
 2PS  C33  S34   single    1.781  0.020  1.781
 2PS  C33  H331  single    0.970  0.020  1.090
 2PS  C33  H332  single    0.970  0.020  1.090
 2PS  S34  O37   deloc     1.448  0.020  1.448
 2PS  S34  O36   deloc     1.445  0.020  1.445
 2PS  S34  O35   single    1.629  0.020  1.629
 2PS  O35  C36   single    1.388  0.020  1.388
 2PS  N10  H10   single    0.890  0.020  1.040
 2PS  C2   C3    single    1.503  0.020  1.503
 2PS  C2   H21A  single    0.970  0.020  1.090
 2PS  C2   H22   single    0.970  0.020  1.090
 2PS  C3   C4    aromatic  1.394  0.020  1.394
 2PS  C3   C8    aromatic  1.393  0.020  1.393
 2PS  C4   C5    aromatic  1.388  0.020  1.388
 2PS  C4   H41   single    0.930  0.020  1.080
 2PS  C5   C6    aromatic  1.389  0.020  1.389
 2PS  C5   H51   single    0.930  0.020  1.080
 2PS  C6   C7    aromatic  1.389  0.020  1.389
 2PS  C6   H61   single    0.930  0.020  1.080
 2PS  C7   C8    aromatic  1.389  0.020  1.389
 2PS  C7   H71   single    0.930  0.020  1.080
 2PS  C8   H81   single    0.930  0.020  1.080
 2PS  C36  C37   aromatic  1.386  0.020  1.386
 2PS  C36  C41   aromatic  1.386  0.020  1.386
 2PS  C37  C38   aromatic  1.388  0.020  1.388
 2PS  C37  H371  single    0.930  0.020  1.080
 2PS  C38  C39   aromatic  1.389  0.020  1.389
 2PS  C38  H381  single    0.930  0.020  1.080
 2PS  C39  C40   aromatic  1.388  0.020  1.388
 2PS  C39  H391  single    0.930  0.020  1.080
 2PS  C40  C41   aromatic  1.388  0.020  1.388
 2PS  C40  H401  single    0.930  0.020  1.080
 2PS  C41  H411  single    0.930  0.020  1.080
 2PS  N10  H2    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
 2PS  H12   C1   H11   106.28  3.000
 2PS  H12   C1   C2    109.31  3.000
 2PS  H11   C1   C2    109.59  3.000
 2PS  H12   C1   C9    108.70  3.000
 2PS  H11   C1   C9    109.47  3.000
 2PS  C2    C1   C9    113.25  3.000
 2PS  H91   C9   N10   107.05  3.000
 2PS  H91   C9   C32   107.63  3.000
 2PS  N10   C9   C32   114.59  3.000
 2PS  H91   C9   C1    107.83  3.000
 2PS  N10   C9   C1    110.16  3.000
 2PS  C32   C9   C1    109.32  3.000
 2PS  H322  C32  H321  107.44  3.000
 2PS  H322  C32  C33   110.23  3.000
 2PS  H321  C32  C33   109.70  3.000
 2PS  H322  C32  C9    109.35  3.000
 2PS  H321  C32  C9    108.94  3.000
 2PS  C33   C32  C9    111.09  3.000
 2PS  H332  C33  H331  108.91  3.000
 2PS  H332  C33  S34   107.11  3.000
 2PS  H331  C33  S34   106.34  3.000
 2PS  H332  C33  C32   111.06  3.000
 2PS  H331  C33  C32   112.29  3.000
 2PS  S34   C33  C32   110.89  3.000
 2PS  O35   S34  O36   103.23  3.000
 2PS  O35   S34  O37   109.20  3.000
 2PS  O36   S34  O37   119.88  3.000
 2PS  O35   S34  C33   102.94  3.000
 2PS  O36   S34  C33   110.30  3.000
 2PS  O37   S34  C33   109.78  3.000
 2PS  C36   O35  S34   119.58  3.000
 2PS  H2    N10  H10   106.71  3.000
 2PS  H2    N10  C9    110.19  3.000
 2PS  H10   N10  C9    111.26  3.000
 2PS  H22   C2   H21A  106.81  3.000
 2PS  H22   C2   C3    110.03  3.000
 2PS  H21A  C2   C3    109.61  3.000
 2PS  H22   C2   C1    109.34  3.000
 2PS  H21A  C2   C1    109.06  3.000
 2PS  C3    C2   C1    111.85  3.000
 2PS  C8    C3   C4    118.28  3.000
 2PS  C8    C3   C2    120.92  3.000
 2PS  C4    C3   C2    120.78  3.000
 2PS  H41   C4   C5    119.60  3.000
 2PS  H41   C4   C3    119.40  3.000
 2PS  C5    C4   C3    121.01  3.000
 2PS  H51   C5   C6    120.09  3.000
 2PS  H51   C5   C4    119.78  3.000
 2PS  C6    C5   C4    120.13  3.000
 2PS  H61   C6   C7    120.28  3.000
 2PS  H61   C6   C5    120.27  3.000
 2PS  C7    C6   C5    119.45  3.000
 2PS  H71   C7   C8    119.79  3.000
 2PS  H71   C7   C6    120.05  3.000
 2PS  C8    C7   C6    120.16  3.000
 2PS  H81   C8   C7    119.48  3.000
 2PS  H81   C8   C3    119.54  3.000
 2PS  C7    C8   C3    120.98  3.000
 2PS  C41   C36  C37   121.67  3.000
 2PS  C41   C36  O35   118.40  3.000
 2PS  C37   C36  O35   119.87  3.000
 2PS  H371  C37  C38   120.72  3.000
 2PS  H371  C37  C36   120.55  3.000
 2PS  C38   C37  C36   118.73  3.000
 2PS  H381  C38  C39   120.11  3.000
 2PS  H381  C38  C37   119.43  3.000
 2PS  C39   C38  C37   120.46  3.000
 2PS  H391  C39  C40   119.98  3.000
 2PS  H391  C39  C38   120.06  3.000
 2PS  C40   C39  C38   119.96  3.000
 2PS  H401  C40  C41   119.56  3.000
 2PS  H401  C40  C39   120.22  3.000
 2PS  C41   C40  C39   120.22  3.000
 2PS  H411  C41  C40   120.73  3.000
 2PS  H411  C41  C36   120.29  3.000
 2PS  C40   C41  C36   118.97  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
 2PS  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 2PS  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 2PS  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 2PS  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 2PS  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 2PS  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 2PS  CONST_07  C39   C38  C37  C36     0.00   0.0  0
 2PS  CONST_08  C39   C40  C41  C36     0.00   0.0  0
 2PS  CONST_09  C40   C41  C36  C37     0.00   0.0  0
 2PS  CONST_10  C40   C39  C38  C37     0.00   0.0  0
 2PS  CONST_11  C41   C36  C37  C38     0.00   0.0  0
 2PS  CONST_12  C41   C40  C39  C38     0.00   0.0  0
 2PS  CONST_13  C38   C37  C36  O35   180.00   0.0  0
 2PS  CONST_14  C40   C41  C36  O35   180.00   0.0  0
 2PS  CONST_15  C5    C4   C3   C2    180.00   0.0  0
 2PS  CONST_16  C7    C8   C3   C2    180.00   0.0  0
 2PS  CONST_17  H51   C5   C4   C3    180.00   0.0  0
 2PS  CONST_18  H71   C7   C8   C3    180.00   0.0  0
 2PS  CONST_19  H81   C8   C3   C4    180.00   0.0  0
 2PS  CONST_20  H61   C6   C5   C4    180.00   0.0  0
 2PS  CONST_21  H41   C4   C5   C6    180.00   0.0  0
 2PS  CONST_22  H381  C38  C37  C36   180.00   0.0  0
 2PS  CONST_23  H401  C40  C41  C36   180.00   0.0  0
 2PS  CONST_24  H411  C41  C36  C37   180.00   0.0  0
 2PS  CONST_25  H391  C39  C38  C37   180.00   0.0  0
 2PS  CONST_26  H371  C37  C38  C39   180.00   0.0  0
 2PS  Var_01    C4    C3   C2   C1     86.69  30.0  2
 2PS  Var_02    C37   C36  O35  S34    81.81  30.0  2
 2PS  Var_03    C3    C2   C1   C9   -177.52  30.0  3
 2PS  Var_04    S34   C33  C32  C9    176.79  30.0  3
 2PS  Var_05    O37   S34  C33  C32   -67.25  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
 2PS  chir_01  C9  C1  C32  N10  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
 2PS  plan-1  C2    0.020
 2PS  plan-1  C3    0.020
 2PS  plan-1  C4    0.020
 2PS  plan-1  C5    0.020
 2PS  plan-1  C6    0.020
 2PS  plan-1  C7    0.020
 2PS  plan-1  C8    0.020
 2PS  plan-1  H41   0.020
 2PS  plan-1  H51   0.020
 2PS  plan-1  H61   0.020
 2PS  plan-1  H71   0.020
 2PS  plan-1  H81   0.020
 2PS  plan-2  O35   0.020
 2PS  plan-2  C36   0.020
 2PS  plan-2  C37   0.020
 2PS  plan-2  C38   0.020
 2PS  plan-2  C39   0.020
 2PS  plan-2  C40   0.020
 2PS  plan-2  C41   0.020
 2PS  plan-2  H371  0.020
 2PS  plan-2  H381  0.020
 2PS  plan-2  H391  0.020
 2PS  plan-2  H401  0.020
 2PS  plan-2  H411  0.020

