# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:41:19 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-(benzylsulfonyl)-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
#
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
 S29  S29  N-(benzylsulfonyl)-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  peptide  62  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S29
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
 S29  C7    C  CH2   0  -0.718   -5.3397   0.2271   0.9964
 S29  S8    S  S     0   1.371   -4.0343   0.6404  -0.1762
 S29  C6    C  CR6   0   0.123   -6.6592   0.7039   0.4767
 S29  C1    C  CR16  0  -0.279   -7.4224  -0.1077  -0.3579
 S29  C2    C  CR16  0  -0.243   -8.6370   0.3435  -0.8546
 S29  C3    C  CR16  0  -0.260   -9.0958   1.6125  -0.5262
 S29  C4    C  CR16  0  -0.243   -8.3368   2.4276   0.3037
 S29  C5    C  CR16  0  -0.280   -7.1218   1.9766   0.7990
 S29  O13   O  OS    0  -0.663   -4.2396  -0.1653  -1.3710
 S29  O14   O  OS    0  -0.663   -3.9935   2.0898  -0.2842
 S29  N9    N  NC1   0  -0.741   -2.6119   0.1869   0.4860
 S29  C10   C  CH1   0  -0.215   -2.1282  -1.1801   0.5028
 S29  C33   C  CH3   0  -0.658   -2.5119  -1.9466   1.7694
 S29  C11   C  C     0   0.580   -0.6049  -1.1289   0.4035
 S29  O15   O  O     0  -0.492    0.0161  -0.1558   0.8082
 S29  N12   N  NT    0  -0.463    0.0127  -2.2226  -0.0618
 S29  C16   C  CH1   0  -0.222    1.4604  -2.2752  -0.0643
 S29  C17   C  C     0   0.582    2.0333  -1.3018  -1.0904
 S29  O18   O  O     0  -0.492    1.4371  -1.0090  -2.1148
 S29  C21   C  CH2   0  -0.470    1.7562  -3.7292  -0.4553
 S29  C22   C  CH2   0  -0.473    0.5739  -4.1074  -1.3397
 S29  C23   C  CH2   0  -0.282   -0.6011  -3.3974  -0.6775
 S29  N19   N  NH1   0  -0.636    3.2598  -0.8510  -0.7989
 S29  C20   C  CH2   0  -0.315    4.0191  -0.0056  -1.7025
 S29  C24   C  CR6   0   0.043    5.2801   0.4522  -1.0257
 S29  C31   C  CR16  0  -0.268    5.2727   1.5678  -0.1957
 S29  C29   C  CR16  0  -0.280    6.4239   1.9671   0.4667
 S29  C28   C  CR6   0   0.040    7.6123   1.2552   0.3127
 S29  C26   C  C     0   0.335    8.8670   1.6570   1.0081
 S29  N30   N  N     0  -0.651    9.9862   1.3157   0.4948
 S29  N32   N  NH2   0  -0.823    8.6966   2.4123   2.1328
 S29  C27   C  CR16  0  -0.260    7.6223   0.1446  -0.5282
 S29  C25   C  CR16  0  -0.275    6.4692  -0.2543  -1.1832
 S29  H7    H  HCH2  0   0.321   -5.0698   0.6998   1.9416
 S29  H7A   H  HCH2  0   0.318   -5.3179  -0.8548   1.1310
 S29  H1    H  HCR6  0   0.257   -7.0735  -1.1010  -0.6118
 S29  H2    H  HCR6  0   0.260   -9.2247  -0.2961  -1.4999
 S29  H3    H  HCR6  0   0.260  -10.0441   1.9627  -0.9126
 S29  H4    H  HCR6  0   0.260   -8.6897   3.4165   0.5654
 S29  H5    H  HCR6  0   0.258   -6.5361   2.6135   1.4499
 S29  HN9   H  HNC1  0   0.417   -2.2746   0.7961   1.2219
 S29  H10   H  HCH1  0   0.288   -2.5444  -1.6862  -0.3684
 S29  H33   H  HCH3  0   0.245   -2.1122  -1.4542   2.6561
 S29  H33A  H  HCH3  0   0.254   -3.5941  -2.0103   1.8710
 S29  H33B  H  HCH3  0   0.251   -2.1281  -2.9659   1.7450
 S29  H16   H  HCH1  0   0.289    1.8562  -2.0437   0.9278
 S29  H21   H  HCH2  0   0.266    2.7231  -3.8448  -0.9439
 S29  H21A  H  HCH2  0   0.261    1.7671  -4.3432   0.4470
 S29  H22   H  HCH2  0   0.249    0.7174  -3.7374  -2.3551
 S29  H22A  H  HCH2  0   0.260    0.4154  -5.1832  -1.3948
 S29  H23   H  HCH2  0   0.247   -1.0649  -4.0340   0.0806
 S29  H23A  H  HCH2  0   0.263   -1.3692  -3.1205  -1.3993
 S29  HN19  H  HNH1  0   0.406    3.6919  -1.1295   0.0676
 S29  H20   H  HCH2  0   0.256    4.2608  -0.5519  -2.6178
 S29  H20A  H  HCH2  0   0.259    3.4134   0.8556  -1.9927
 S29  H31   H  HCR6  0   0.258    4.3608   2.1388  -0.0700
 S29  H29   H  HCR6  0   0.260    6.3857   2.8530   1.0873
 S29  HN30  H  H     0   0.324   10.7634   1.6168   1.0766
 S29  HN32  H  HNH2  0   0.395    7.8486   2.3018   2.6638
 S29  HN3A  H  HNH2  0   0.392    9.5101   2.5750   2.7049
 S29  H27   H  HCR6  0   0.257    8.5401  -0.4122  -0.6602
 S29  H25   H  HCR6  0   0.258    6.4955  -1.1262  -1.8258

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
 S29  C1   C2    aromatic  1.388  0.020  1.388
 S29  C1   C6    aromatic  1.392  0.020  1.392
 S29  C2   C3    aromatic  1.389  0.020  1.389
 S29  C3   C4    aromatic  1.389  0.020  1.389
 S29  C4   C5    aromatic  1.387  0.020  1.387
 S29  C5   C6    aromatic  1.392  0.020  1.392
 S29  C6   C7    single    1.496  0.020  1.496
 S29  C7   S8    single    1.803  0.020  1.803
 S29  S8   N9    single    1.633  0.020  1.633
 S29  S8   O13   double    1.456  0.020  1.456
 S29  S8   O14   double    1.454  0.020  1.454
 S29  N9   C10   single    1.450  0.020  1.450
 S29  C10  C11   single    1.527  0.020  1.527
 S29  C10  C33   single    1.529  0.020  1.529
 S29  C11  N12   single    1.339  0.020  1.339
 S29  C11  O15   double    1.223  0.020  1.223
 S29  N12  C16   single    1.449  0.020  1.449
 S29  N12  C23   single    1.461  0.020  1.461
 S29  C16  C17   single    1.526  0.020  1.526
 S29  C16  C21   single    1.534  0.020  1.534
 S29  C17  O18   double    1.221  0.020  1.221
 S29  C17  N19   single    1.339  0.020  1.339
 S29  N19  C20   single    1.452  0.020  1.452
 S29  C20  C24   single    1.503  0.020  1.503
 S29  C21  C22   single    1.524  0.020  1.524
 S29  C22  C23   single    1.524  0.020  1.524
 S29  C24  C25   aromatic  1.392  0.020  1.392
 S29  C24  C31   aromatic  1.391  0.020  1.391
 S29  C25  C27   aromatic  1.385  0.020  1.385
 S29  C26  C28   single    1.490  0.020  1.490
 S29  C26  N30   double    1.278  0.020  1.278
 S29  C26  N32   single    1.365  0.020  1.365
 S29  C27  C28   aromatic  1.393  0.020  1.393
 S29  C28  C29   aromatic  1.394  0.020  1.394
 S29  C29  C31   aromatic  1.387  0.020  1.387
 S29  C1   H1    single    0.930  0.020  1.080
 S29  C2   H2    single    0.930  0.020  1.080
 S29  C3   H3    single    0.930  0.020  1.080
 S29  C4   H4    single    0.930  0.020  1.080
 S29  C5   H5    single    0.930  0.020  1.080
 S29  C7   H7    single    0.970  0.020  1.090
 S29  C7   H7A   single    0.970  0.020  1.090
 S29  N9   HN9   single    0.890  0.020  1.040
 S29  C10  H10   single    0.970  0.020  1.090
 S29  C16  H16   single    0.970  0.020  1.090
 S29  N19  HN19  single    0.860  0.020  1.020
 S29  C20  H20   single    0.970  0.020  1.090
 S29  C20  H20A  single    0.970  0.020  1.090
 S29  C21  H21   single    0.970  0.020  1.090
 S29  C21  H21A  single    0.970  0.020  1.090
 S29  C22  H22   single    0.970  0.020  1.090
 S29  C22  H22A  single    0.970  0.020  1.090
 S29  C23  H23   single    0.970  0.020  1.090
 S29  C23  H23A  single    0.970  0.020  1.090
 S29  C25  H25   single    0.930  0.020  1.080
 S29  C27  H27   single    0.930  0.020  1.080
 S29  C29  H29   single    0.930  0.020  1.080
 S29  N30  HN30  single    0.890  0.020  1.040
 S29  C31  H31   single    0.930  0.020  1.080
 S29  N32  HN32  single    0.890  0.020  1.040
 S29  N32  HN3A  single    0.890  0.020  1.040
 S29  C33  H33   single    0.970  0.020  1.090
 S29  C33  H33A  single    0.970  0.020  1.090
 S29  C33  H33B  single    0.970  0.020  1.090

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
 S29  H7A   C7   H7    108.55  3.000
 S29  H7A   C7   C6    112.13  3.000
 S29  H7    C7   C6    112.40  3.000
 S29  H7A   C7   S8    107.06  3.000
 S29  H7    C7   S8    106.57  3.000
 S29  C6    C7   S8    109.85  3.000
 S29  N9    S8   O14   106.41  3.000
 S29  O14   S8   O13   119.65  3.000
 S29  N9    S8   O13   107.58  3.000
 S29  O14   S8   C7    107.29  3.000
 S29  O13   S8   C7    107.75  3.000
 S29  N9    S8   C7    107.65  3.000
 S29  C5    C6   C1    119.32  3.000
 S29  C5    C6   C7    120.27  3.000
 S29  C1    C6   C7    120.39  3.000
 S29  H1    C1   C2    119.76  3.000
 S29  H1    C1   C6    119.91  3.000
 S29  C2    C1   C6    120.32  3.000
 S29  H2    C2   C3    120.11  3.000
 S29  H2    C2   C1    119.78  3.000
 S29  C3    C2   C1    120.11  3.000
 S29  H3    C3   C4    120.15  3.000
 S29  H3    C3   C2    120.05  3.000
 S29  C4    C3   C2    119.80  3.000
 S29  H4    C4   C5    119.75  3.000
 S29  H4    C4   C3    120.17  3.000
 S29  C5    C4   C3    120.07  3.000
 S29  H5    C5   C4    119.81  3.000
 S29  H5    C5   C6    119.82  3.000
 S29  C4    C5   C6    120.37  3.000
 S29  HN9   N9   C10   116.57  3.000
 S29  HN9   N9   S8    114.68  3.000
 S29  C10   N9   S8    123.85  3.000
 S29  H10   C10  C11   110.15  3.000
 S29  H10   C10  C33   109.48  3.000
 S29  C11   C10  C33   108.71  3.000
 S29  H10   C10  N9    107.52  3.000
 S29  C33   C10  N9    113.47  3.000
 S29  C11   C10  N9    107.48  3.000
 S29  H33B  C33  H33A  107.31  3.000
 S29  H33B  C33  H33   108.16  3.000
 S29  H33A  C33  H33   108.35  3.000
 S29  H33B  C33  C10   111.22  3.000
 S29  H33A  C33  C10   110.85  3.000
 S29  H33   C33  C10   110.81  3.000
 S29  N12   C11  O15   122.04  3.000
 S29  O15   C11  C10   120.76  3.000
 S29  N12   C11  C10   117.07  3.000
 S29  C23   N12  C16   112.95  3.000
 S29  C23   N12  C11   127.52  3.000
 S29  C16   N12  C11   119.41  3.000
 S29  H16   C16  C21   111.24  3.000
 S29  H16   C16  C17   109.84  3.000
 S29  C21   C16  C17   111.15  3.000
 S29  H16   C16  N12   110.65  3.000
 S29  C21   C16  N12   103.15  3.000
 S29  C17   C16  N12   110.68  3.000
 S29  N19   C17  O18   123.32  3.000
 S29  N19   C17  C16   114.35  3.000
 S29  O18   C17  C16   122.27  3.000
 S29  H21A  C21  H21   107.58  3.000
 S29  H21A  C21  C22   110.36  3.000
 S29  H21   C21  C22   113.69  3.000
 S29  H21A  C21  C16   108.93  3.000
 S29  H21   C21  C16   112.70  3.000
 S29  C22   C21  C16   103.50  3.000
 S29  H22A  C22  H22   107.90  3.000
 S29  H22A  C22  C23   111.71  3.000
 S29  H22   C22  C23   110.37  3.000
 S29  H22A  C22  C21   112.80  3.000
 S29  H22   C22  C21   110.74  3.000
 S29  C23   C22  C21   103.31  3.000
 S29  H23A  C23  H23   107.96  3.000
 S29  H23A  C23  C22   111.95  3.000
 S29  H23   C23  C22   110.92  3.000
 S29  H23A  C23  N12   111.77  3.000
 S29  H23   C23  N12   110.74  3.000
 S29  C22   C23  N12   103.51  3.000
 S29  HN19  N19  C20   118.16  3.000
 S29  HN19  N19  C17   119.15  3.000
 S29  C20   N19  C17   122.66  3.000
 S29  H20A  C20  H20   107.11  3.000
 S29  H20A  C20  C24   110.17  3.000
 S29  H20   C20  C24   110.11  3.000
 S29  H20A  C20  N19   109.55  3.000
 S29  H20   C20  N19   110.23  3.000
 S29  C24   C20  N19   109.63  3.000
 S29  C25   C24  C31   118.63  3.000
 S29  C31   C24  C20   120.59  3.000
 S29  C25   C24  C20   120.75  3.000
 S29  H31   C31  C29   119.45  3.000
 S29  H31   C31  C24   119.77  3.000
 S29  C29   C31  C24   120.77  3.000
 S29  H29   C29  C28   120.76  3.000
 S29  H29   C29  C31   118.70  3.000
 S29  C28   C29  C31   120.53  3.000
 S29  C27   C28  C26   119.39  3.000
 S29  C27   C28  C29   118.68  3.000
 S29  C26   C28  C29   121.93  3.000
 S29  N32   C26  N30   126.01  3.000
 S29  N32   C26  C28   115.38  3.000
 S29  N30   C26  C28   118.57  3.000
 S29  HN30  N30  C26   111.15  3.000
 S29  HN3A  N32  HN32  113.47  3.000
 S29  HN3A  N32  C26   117.14  3.000
 S29  HN32  N32  C26   118.62  3.000
 S29  H27   C27  C25   120.04  3.000
 S29  H27   C27  C28   119.35  3.000
 S29  C25   C27  C28   120.61  3.000
 S29  H25   C25  C27   119.48  3.000
 S29  H25   C25  C24   119.75  3.000
 S29  C27   C25  C24   120.77  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
 S29  CONST_01  C3    C2   C1   C6      0.00   0.0  0
 S29  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 S29  CONST_03  C4    C3   C2   C1      0.00   0.0  0
 S29  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 S29  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 S29  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 S29  CONST_07  C28   C27  C25  C24     0.00   0.0  0
 S29  CONST_08  C28   C29  C31  C24     0.00   0.0  0
 S29  CONST_09  C27   C25  C24  C31     0.00   0.0  0
 S29  CONST_10  C27   C28  C29  C31     0.00   0.0  0
 S29  CONST_11  C25   C27  C28  C29     0.00   0.0  0
 S29  CONST_12  C25   C24  C31  C29     0.00   0.0  0
 S29  CONST_13  C2    C1   C6   C7    180.00   0.0  0
 S29  CONST_14  C4    C5   C6   C7    180.00   0.0  0
 S29  CONST_15  C27   C25  C24  C20   180.00   0.0  0
 S29  CONST_16  C29   C31  C24  C20   180.00   0.0  0
 S29  CONST_17  C26   C28  C29  C31   180.00   0.0  0
 S29  CONST_18  C25   C27  C28  C26   180.00   0.0  0
 S29  CONST_19  H2    C2   C1   C6    180.00   0.0  0
 S29  CONST_20  H4    C4   C5   C6    180.00   0.0  0
 S29  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 S29  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 S29  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 S29  CONST_24  H27   C27  C25  C24   180.00   0.0  0
 S29  CONST_25  H29   C29  C31  C24   180.00   0.0  0
 S29  CONST_26  H25   C25  C24  C31   180.00   0.0  0
 S29  CONST_27  H31   C31  C29  C28   180.00   0.0  0
 S29  CONST_28  C16   N12  C11  C10   180.00   0.0  0
 S29  CONST_29  C23   N12  C11  C10     0.00   0.0  0
 S29  CONST_30  C16   N12  C11  O15     0.00   0.0  0
 S29  CONST_31  C23   N12  C11  O15   180.00   0.0  0
 S29  CONST_32  C20   N19  C17  C16   180.00   0.0  0
 S29  CONST_33  HN19  N19  C17  C16     0.00   0.0  0
 S29  CONST_34  HN30  N30  C26  C28   180.00   0.0  0
 S29  CONST_36  HN3A  N32  C26  C28   180.00   0.0  0
 S29  CONST_37  C20   N19  C17  O18     0.00   0.0  0
 S29  Var_01    C21   C22  C23  N12    29.50  30.0  1
 S29  Var_02    C22   C23  N12  C16   -10.94  30.0  1
 S29  Var_03    C23   C22  C21  C16   -37.13  30.0  1
 S29  Var_04    C1    C6   C7   S8     87.81  30.0  2
 S29  Var_05    C25   C24  C20  N19    93.53  30.0  2
 S29  Var_06    N30   C26  C28  C29  -154.86  30.0  3
 S29  Var_07    N9    S8   C7   C6    176.31  30.0  3
 S29  Var_08    C24   C20  N19  C17   173.69  30.0  3
 S29  Var_09    C10   N9   S8   C7     79.00  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
 S29  chir_01  C10  N9   C11  C33  negativ
 S29  chir_02  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
 S29  plan-1  C7    0.020
 S29  plan-1  C6    0.020
 S29  plan-1  C1    0.020
 S29  plan-1  C2    0.020
 S29  plan-1  C3    0.020
 S29  plan-1  C4    0.020
 S29  plan-1  C5    0.020
 S29  plan-1  H1    0.020
 S29  plan-1  H2    0.020
 S29  plan-1  H3    0.020
 S29  plan-1  H4    0.020
 S29  plan-1  H5    0.020
 S29  plan-2  C20   0.020
 S29  plan-2  C24   0.020
 S29  plan-2  C31   0.020
 S29  plan-2  C29   0.020
 S29  plan-2  C28   0.020
 S29  plan-2  C26   0.020
 S29  plan-2  C27   0.020
 S29  plan-2  C25   0.020
 S29  plan-2  H31   0.020
 S29  plan-2  H29   0.020
 S29  plan-2  H27   0.020
 S29  plan-2  H25   0.020
 S29  plan-3  C16   0.020
 S29  plan-3  C17   0.020
 S29  plan-3  O18   0.020
 S29  plan-3  N19   0.020
 S29  plan-3  C20   0.020
 S29  plan-3  HN19  0.020
 S29  plan-4  C10   0.020
 S29  plan-4  C11   0.020
 S29  plan-4  O15   0.020
 S29  plan-4  N12   0.020
 S29  plan-4  C16   0.020
 S29  plan-4  C23   0.020
 S29  plan-5  C28   0.020
 S29  plan-5  C26   0.020
 S29  plan-5  N30   0.020
 S29  plan-5  N32   0.020
 S29  plan-5  HN30  0.020
 S29  plan-5  HN32  0.020
 S29  plan-5  HN3A  0.020

