# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:31:21 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
#
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
 M31  M31  N-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide  peptide  59  32  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M31
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
 M31  C7    C   CH2   0  -0.717   -5.4042   0.4905   0.6046
 M31  S8    S   S     0   1.367   -4.8259   0.3054  -1.0916
 M31  C6    C   CR6   0   0.119   -6.8992   0.4420   0.6410
 M31  C1    C   CR16  0  -0.279   -7.5588  -0.7750   0.7885
 M31  C2    C   CR16  0  -0.242   -8.9450  -0.8226   0.8092
 M31  C30   C   CR16  0  -0.260   -9.6835   0.3459   0.6737
 M31  C4    C   CR16  0  -0.242   -9.0307   1.5621   0.5201
 M31  C5    C   CR16  0  -0.280   -7.6441   1.6094   0.4991
 M31  O13   O   OS    0  -0.664   -5.2356  -1.0088  -1.5638
 M31  O14   O   OS    0  -0.660   -5.2195   1.4930  -1.8312
 M31  N9    N   NC1   0  -0.748   -3.1894   0.3033  -1.0274
 M31  C10   C   CH2   0  -0.384   -2.4921  -0.8524  -0.5009
 M31  C11   C   C     0   0.546   -1.0976  -0.4256  -0.0730
 M31  O15   O   O     0  -0.493   -0.7591   0.7510  -0.0809
 M31  N12   N   NT    0  -0.462   -0.2898  -1.4061   0.3387
 M31  C16   C   CH1   0  -0.222    1.0479  -1.1018   0.8000
 M31  C17   C   C     0   0.570    1.9320  -0.6642  -0.3646
 M31  O18   O   O     0  -0.484    1.7303  -1.0490  -1.5044
 M31  C21   C   CH2   0  -0.472    1.5239  -2.4403   1.3835
 M31  C22   C   CH2   0  -0.474    0.7767  -3.4800   0.5568
 M31  C23   C   CH2   0  -0.276   -0.5849  -2.8365   0.3231
 M31  N19   N   NH1   0  -0.627    2.9664   0.1091  -0.0013
 M31  C20   C   CH2   0  -0.374    4.0054   0.5581  -0.9061
 M31  C24   C   CR6   0   0.062    5.3659   0.3957  -0.2783
 M31  C25   C   CR6   0   0.105    5.9895  -0.8572  -0.2086
 M31  C26   C   CH2   0  -0.391    5.3854  -2.0810  -0.8469
 M31  N32   N   NH2   0  -0.781    5.4830  -1.9927  -2.2978
 M31  C27   C   CR16  0  -0.306    7.2264  -0.9520   0.4163
 M31  C28   C   CR16  0  -0.210    7.8547   0.1551   0.9722
 M31  C29   C   CR6   0  -0.042    7.2236   1.3817   0.8900
 M31  CL3   CL  CL    0  -0.133    7.9804   2.7857   1.5717
 M31  C31   C   CR16  0  -0.246    5.9880   1.5084   0.2723
 M31  H7    H   HCH2  0   0.324   -5.0081   1.4413   0.9647
 M31  H7A   H   HCH2  0   0.319   -4.9552  -0.3162   1.1871
 M31  H1    H   HCR6  0   0.257   -6.9857  -1.6869   0.9021
 M31  H2    H   HCR6  0   0.260   -9.4490  -1.7723   0.9335
 M31  H30   H   HCR6  0   0.260  -10.7649   0.3094   0.6925
 M31  H4    H   HCR6  0   0.260   -9.6025   2.4750   0.4160
 M31  H5    H   HCR6  0   0.258   -7.1387   2.5603   0.3832
 M31  HN9   H   HNC1  0   0.417   -2.7772   1.1953  -0.7672
 M31  H10   H   HCH2  0   0.281   -2.9873  -1.2984   0.3712
 M31  H10A  H   HCH2  0   0.295   -2.4305  -1.6309  -1.2627
 M31  H16   H   HCH1  0   0.292    1.0242  -0.3251   1.5682
 M31  H21   H   HCH2  0   0.264    2.6073  -2.5539   1.3478
 M31  H21A  H   HCH2  0   0.265    1.2242  -2.4963   2.4313
 M31  H22   H   HCH2  0   0.249    1.2794  -3.6495  -0.3960
 M31  H22A  H   HCH2  0   0.262    0.6903  -4.4394   1.0639
 M31  H23   H   HCH2  0   0.253   -1.2923  -3.0896   1.1174
 M31  H23A  H   HCH2  0   0.263   -1.0211  -3.1418  -0.6282
 M31  HN19  H   HNH1  0   0.404    3.0149   0.4315   0.9528
 M31  H20   H   HCH2  0   0.277    3.9435  -0.0295  -1.8200
 M31  H20A  H   HCH2  0   0.265    3.8429   1.6052  -1.1735
 M31  H26   H   HCH2  0   0.229    5.8690  -2.9705  -0.4242
 M31  H26A  H   HCH2  0   0.238    4.3285  -2.1611  -0.5859
 M31  HN32  H   HNH2  0   0.346    6.4504  -2.1006  -2.5765
 M31  HN3A  H   HNH2  0   0.354    4.9834  -2.7682  -2.7142
 M31  H27   H   HCR6  0   0.261    7.7199  -1.9149   0.4746
 M31  H28   H   HCR6  0   0.278    8.8174   0.0559   1.4545
 M31  H31   H   HCR6  0   0.274    5.5064   2.4768   0.2164

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
 M31  C1   C2    aromatic  1.387  0.020  1.387
 M31  C1   C6    aromatic  1.392  0.020  1.392
 M31  C2   C30   aromatic  1.389  0.020  1.389
 M31  CL3  C29   single    1.735  0.020  1.735
 M31  C4   C5    aromatic  1.388  0.020  1.388
 M31  C4   C30   aromatic  1.389  0.020  1.389
 M31  C5   C6    aromatic  1.392  0.020  1.392
 M31  C6   C7    single    1.496  0.020  1.496
 M31  C7   S8    single    1.802  0.020  1.802
 M31  S8   N9    single    1.638  0.020  1.638
 M31  S8   O13   double    1.455  0.020  1.455
 M31  S8   O14   double    1.453  0.020  1.453
 M31  N9   C10   single    1.449  0.020  1.449
 M31  C10  C11   single    1.520  0.020  1.520
 M31  C11  N12   single    1.335  0.020  1.335
 M31  C11  O15   double    1.224  0.020  1.224
 M31  N12  C16   single    1.447  0.020  1.447
 M31  N12  C23   single    1.461  0.020  1.461
 M31  C16  C17   single    1.526  0.020  1.526
 M31  C16  C21   single    1.536  0.020  1.536
 M31  C17  O18   double    1.220  0.020  1.220
 M31  C17  N19   single    1.342  0.020  1.342
 M31  N19  C20   single    1.449  0.020  1.449
 M31  C20  C24   single    1.507  0.020  1.507
 M31  C21  C22   single    1.524  0.020  1.524
 M31  C22  C23   single    1.524  0.020  1.524
 M31  C24  C25   aromatic  1.401  0.020  1.401
 M31  C24  C31   aromatic  1.389  0.020  1.389
 M31  C25  C26   single    1.507  0.020  1.507
 M31  C25  C27   aromatic  1.389  0.020  1.389
 M31  C26  N32   single    1.457  0.020  1.457
 M31  C27  C28   aromatic  1.389  0.020  1.389
 M31  C28  C29   aromatic  1.382  0.020  1.382
 M31  C29  C31   aromatic  1.387  0.020  1.387
 M31  C1   H1    single    0.930  0.020  1.080
 M31  C2   H2    single    0.930  0.020  1.080
 M31  C4   H4    single    0.930  0.020  1.080
 M31  C5   H5    single    0.930  0.020  1.080
 M31  C7   H7    single    0.970  0.020  1.090
 M31  C7   H7A   single    0.970  0.020  1.090
 M31  N9   HN9   single    0.890  0.020  1.040
 M31  C10  H10   single    0.970  0.020  1.090
 M31  C10  H10A  single    0.970  0.020  1.090
 M31  C16  H16   single    0.970  0.020  1.090
 M31  N19  HN19  single    0.860  0.020  1.020
 M31  C20  H20   single    0.970  0.020  1.090
 M31  C20  H20A  single    0.970  0.020  1.090
 M31  C21  H21   single    0.970  0.020  1.090
 M31  C21  H21A  single    0.970  0.020  1.090
 M31  C22  H22   single    0.970  0.020  1.090
 M31  C22  H22A  single    0.970  0.020  1.090
 M31  C23  H23   single    0.970  0.020  1.090
 M31  C23  H23A  single    0.970  0.020  1.090
 M31  C26  H26   single    0.970  0.020  1.090
 M31  C26  H26A  single    0.970  0.020  1.090
 M31  C27  H27   single    0.930  0.020  1.080
 M31  C28  H28   single    0.930  0.020  1.080
 M31  C30  H30   single    0.930  0.020  1.080
 M31  C31  H31   single    0.930  0.020  1.080
 M31  N32  HN32  single    0.890  0.020  1.040
 M31  N32  HN3A  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
 M31  H7A   C7   H7    108.57  3.000
 M31  H7A   C7   C6    111.97  3.000
 M31  H7    C7   C6    112.52  3.000
 M31  H7A   C7   S8    107.12  3.000
 M31  H7    C7   S8    106.48  3.000
 M31  C6    C7   S8    109.90  3.000
 M31  N9    S8   O14   106.96  3.000
 M31  O14   S8   O13   119.76  3.000
 M31  N9    S8   O13   107.03  3.000
 M31  O14   S8   C7    107.95  3.000
 M31  O13   S8   C7    107.93  3.000
 M31  N9    S8   C7    106.50  3.000
 M31  C5    C6   C1    119.37  3.000
 M31  C5    C6   C7    120.33  3.000
 M31  C1    C6   C7    120.29  3.000
 M31  H1    C1   C2    119.89  3.000
 M31  H1    C1   C6    119.77  3.000
 M31  C2    C1   C6    120.34  3.000
 M31  H2    C2   C30   120.12  3.000
 M31  H2    C2   C1    119.81  3.000
 M31  C30   C2   C1    120.06  3.000
 M31  H30   C30  C4    120.08  3.000
 M31  H30   C30  C2    120.08  3.000
 M31  C4    C30  C2    119.84  3.000
 M31  H4    C4   C5    119.86  3.000
 M31  H4    C4   C30   120.06  3.000
 M31  C5    C4   C30   120.08  3.000
 M31  H5    C5   C4    119.86  3.000
 M31  H5    C5   C6    119.83  3.000
 M31  C4    C5   C6    120.31  3.000
 M31  HN9   N9   C10   114.32  3.000
 M31  HN9   N9   S8    114.46  3.000
 M31  C10   N9   S8    119.75  3.000
 M31  H10A  C10  H10   106.87  3.000
 M31  H10A  C10  C11   110.19  3.000
 M31  H10   C10  C11   107.72  3.000
 M31  H10A  C10  N9    110.04  3.000
 M31  H10   C10  N9    113.32  3.000
 M31  C11   C10  N9    108.66  3.000
 M31  N12   C11  O15   122.70  3.000
 M31  O15   C11  C10   121.45  3.000
 M31  N12   C11  C10   115.83  3.000
 M31  C23   N12  C16   113.33  3.000
 M31  C23   N12  C11   126.40  3.000
 M31  C16   N12  C11   120.20  3.000
 M31  H16   C16  C21   111.05  3.000
 M31  H16   C16  C17   110.20  3.000
 M31  C21   C16  C17   111.12  3.000
 M31  H16   C16  N12   110.69  3.000
 M31  C21   C16  N12   102.96  3.000
 M31  C17   C16  N12   110.63  3.000
 M31  N19   C17  O18   124.22  3.000
 M31  N19   C17  C16   113.90  3.000
 M31  O18   C17  C16   121.79  3.000
 M31  H21A  C21  H21   107.40  3.000
 M31  H21A  C21  C22   110.56  3.000
 M31  H21   C21  C22   113.48  3.000
 M31  H21A  C21  C16   108.93  3.000
 M31  H21   C21  C16   112.73  3.000
 M31  C22   C21  C16   103.68  3.000
 M31  H22A  C22  H22   107.85  3.000
 M31  H22A  C22  C23   111.87  3.000
 M31  H22   C22  C23   110.09  3.000
 M31  H22A  C22  C21   112.79  3.000
 M31  H22   C22  C21   110.73  3.000
 M31  C23   C22  C21   103.49  3.000
 M31  H23A  C23  H23   108.07  3.000
 M31  H23A  C23  C22   111.90  3.000
 M31  H23   C23  C22   111.66  3.000
 M31  H23A  C23  N12   111.37  3.000
 M31  H23   C23  N12   110.47  3.000
 M31  C22   C23  N12   103.37  3.000
 M31  HN19  N19  C20   117.22  3.000
 M31  HN19  N19  C17   118.53  3.000
 M31  C20   N19  C17   124.21  3.000
 M31  H20A  C20  H20   107.67  3.000
 M31  H20A  C20  C24   109.84  3.000
 M31  H20   C20  C24   110.06  3.000
 M31  H20A  C20  N19   110.06  3.000
 M31  H20   C20  N19   108.44  3.000
 M31  C24   C20  N19   110.72  3.000
 M31  C31   C24  C25   119.83  3.000
 M31  C31   C24  C20   118.90  3.000
 M31  C25   C24  C20   121.25  3.000
 M31  C27   C25  C26   119.49  3.000
 M31  C27   C25  C24   118.67  3.000
 M31  C26   C25  C24   121.79  3.000
 M31  H26A  C26  H26   105.97  3.000
 M31  H26A  C26  N32   107.91  3.000
 M31  H26   C26  N32   113.78  3.000
 M31  H26A  C26  C25   110.27  3.000
 M31  H26   C26  C25   108.58  3.000
 M31  N32   C26  C25   110.23  3.000
 M31  HN3A  N32  HN32  106.07  3.000
 M31  HN3A  N32  C26   109.28  3.000
 M31  HN32  N32  C26   109.38  3.000
 M31  H27   C27  C28   118.74  3.000
 M31  H27   C27  C25   119.36  3.000
 M31  C28   C27  C25   121.90  3.000
 M31  H28   C28  C29   120.96  3.000
 M31  H28   C28  C27   120.54  3.000
 M31  C29   C28  C27   118.50  3.000
 M31  C31   C29  CL3   119.32  3.000
 M31  C31   C29  C28   120.95  3.000
 M31  CL3   C29  C28   119.73  3.000
 M31  H31   C31  C29   120.05  3.000
 M31  H31   C31  C24   119.79  3.000
 M31  C29   C31  C24   120.16  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
 M31  CONST_01  C30   C2   C1   C6      0.00   0.0  0
 M31  CONST_02  C30   C4   C5   C6      0.00   0.0  0
 M31  CONST_03  C4    C30  C2   C1      0.00   0.0  0
 M31  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 M31  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 M31  CONST_06  C5    C4   C30  C2      0.00   0.0  0
 M31  CONST_07  C28   C27  C25  C24     0.00   0.0  0
 M31  CONST_08  C28   C29  C31  C24     0.00   0.0  0
 M31  CONST_09  C29   C31  C24  C25     0.00   0.0  0
 M31  CONST_10  C29   C28  C27  C25     0.00   0.0  0
 M31  CONST_11  C31   C24  C25  C27     0.00   0.0  0
 M31  CONST_12  C31   C29  C28  C27     0.00   0.0  0
 M31  CONST_13  C2    C1   C6   C7    180.00   0.0  0
 M31  CONST_14  C4    C5   C6   C7    180.00   0.0  0
 M31  CONST_15  C27   C25  C24  C20   180.00   0.0  0
 M31  CONST_16  C29   C31  C24  C20   180.00   0.0  0
 M31  CONST_17  CL3   C29  C31  C24   180.00   0.0  0
 M31  CONST_18  C31   C24  C25  C26   180.00   0.0  0
 M31  CONST_19  C28   C27  C25  C26   180.00   0.0  0
 M31  CONST_20  CL3   C29  C28  C27   180.00   0.0  0
 M31  CONST_21  H2    C2   C1   C6    180.00   0.0  0
 M31  CONST_22  H4    C4   C5   C6    180.00   0.0  0
 M31  CONST_23  H30   C30  C2   C1    180.00   0.0  0
 M31  CONST_24  H5    C5   C6   C1    180.00   0.0  0
 M31  CONST_25  H1    C1   C2   C30   180.00   0.0  0
 M31  CONST_26  H27   C27  C25  C24   180.00   0.0  0
 M31  CONST_27  H31   C31  C24  C25   180.00   0.0  0
 M31  CONST_28  H28   C28  C27  C25   180.00   0.0  0
 M31  CONST_29  C16   N12  C11  C10   180.00   0.0  0
 M31  CONST_30  C23   N12  C11  C10     0.00   0.0  0
 M31  CONST_31  C16   N12  C11  O15     0.00   0.0  0
 M31  CONST_32  C23   N12  C11  O15   180.00   0.0  0
 M31  CONST_33  C20   N19  C17  C16   180.00   0.0  0
 M31  CONST_34  HN19  N19  C17  C16     0.00   0.0  0
 M31  CONST_35  C20   N19  C17  O18     0.00   0.0  0
 M31  Var_01    C21   C22  C23  N12    29.07  30.0  1
 M31  Var_02    C22   C23  N12  C16   -10.82  30.0  1
 M31  Var_03    C23   C22  C21  C16   -36.63  30.0  1
 M31  Var_04    C1    C6   C7   S8     89.32  30.0  2
 M31  Var_05    C25   C24  C20  N19    77.54  30.0  2
 M31  Var_06    N32   C26  C25  C24    71.27  30.0  2
 M31  Var_07    N9    S8   C7   C6   -177.55  30.0  3
 M31  Var_08    N12   C11  C10  N9   -174.91  30.0  3
 M31  Var_09    C24   C20  N19  C17  -135.09  30.0  3
 M31  Var_10    HN32  N32  C26  C25    70.55  30.0  3
 M31  Var_11    C10   N9   S8   C7     72.76  30.0  3
 M31  Var_12    C11   C10  N9   S8   -159.16  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
 M31  chir_01  C16  N12  C17  C21  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
 M31  plan-1  C7    0.020
 M31  plan-1  C6    0.020
 M31  plan-1  C1    0.020
 M31  plan-1  C2    0.020
 M31  plan-1  C30   0.020
 M31  plan-1  C4    0.020
 M31  plan-1  C5    0.020
 M31  plan-1  H1    0.020
 M31  plan-1  H2    0.020
 M31  plan-1  H30   0.020
 M31  plan-1  H4    0.020
 M31  plan-1  H5    0.020
 M31  plan-2  C20   0.020
 M31  plan-2  C24   0.020
 M31  plan-2  C25   0.020
 M31  plan-2  C26   0.020
 M31  plan-2  C27   0.020
 M31  plan-2  C28   0.020
 M31  plan-2  C29   0.020
 M31  plan-2  CL3   0.020
 M31  plan-2  C31   0.020
 M31  plan-2  H27   0.020
 M31  plan-2  H28   0.020
 M31  plan-2  H31   0.020
 M31  plan-3  C16   0.020
 M31  plan-3  C17   0.020
 M31  plan-3  O18   0.020
 M31  plan-3  N19   0.020
 M31  plan-3  C20   0.020
 M31  plan-3  HN19  0.020
 M31  plan-4  C10   0.020
 M31  plan-4  C11   0.020
 M31  plan-4  O15   0.020
 M31  plan-4  N12   0.020
 M31  plan-4  C16   0.020
 M31  plan-4  C23   0.020

