# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:07:04 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@@H](CO)N[S](=O)(=O)Cc1ccccc1)C(=O)NCc2ccc(cc2)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
 SK1  SK1  N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-alaninamide  ligand  59  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SK1
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
 SK1  N3    N  NH1   0  -0.633  -3.1779   0.5241  -1.1989
 SK1  N5    N  NH2   0  -0.823  -8.2525  -3.1416   2.4590
 SK1  N4    N  N     0  -0.651  -8.6185  -0.8652   2.9392
 SK1  C14   C  CR6   0   0.040  -7.0674  -1.4391   1.2250
 SK1  C13   C  CR16  0  -0.260  -7.1227  -0.1767   0.6364
 SK1  C12   C  CR16  0  -0.268  -6.2141   0.1850  -0.3431
 SK1  C17   C  CR6   0   0.043  -5.2187  -0.7003  -0.7521
 SK1  C16   C  CR16  0  -0.278  -5.1541  -1.9527  -0.1548
 SK1  C15   C  CR16  0  -0.278  -6.0696  -2.3225   0.8202
 SK1  C11   C  CH2   0  -0.317  -4.2179  -0.2967  -1.7973
 SK1  C10   C  C     0   0.560  -2.1171   0.9449  -1.8926
 SK1  O5    O  O     0  -0.496  -1.9160   0.6411  -3.0607
 SK1  C8    C  CH1   0  -0.193  -1.1836   1.8902  -1.1449
 SK1  N2    N  NH1   0  -0.643   0.1482   1.7027  -1.6685
 SK1  C7    C  C     0   0.570   1.2570   2.0191  -0.9878
 SK1  O4    O  O     0  -0.482   1.2578   2.4289   0.1604
 SK1  C5    C  CH1   0  -0.254   2.5572   1.8315  -1.7796
 SK1  C6    C  CH2   0  -0.155   2.6874   2.9034  -2.8535
 SK1  O3    O  OH1   0  -0.664   2.6410   4.1570  -2.2215
 SK1  N1    N  NC1   0  -0.732   3.7196   1.8902  -0.9187
 SK1  S1    S  S     0   1.374   3.9672   0.6896   0.1923
 SK1  O1    O  OS    0  -0.661   2.8867  -0.2825   0.0834
 SK1  O2    O  OS    0  -0.661   4.2657   1.2921   1.4831
 SK1  C1    C  CH2   0  -0.691   5.4684  -0.0931  -0.4114
 SK1  C4    C  CR6   0   0.106   5.8305  -1.2433   0.4740
 SK1  C19   C  CR16  0  -0.278   5.3247  -2.5143   0.2142
 SK1  C20   C  CR16  0  -0.242   5.6413  -3.5792   1.0452
 SK1  C21   C  CR16  0  -0.261   6.4610  -3.3810   2.1489
 SK1  C2    C  CR16  0  -0.242   6.9646  -2.1145   2.4163
 SK1  C3    C  CR16  0  -0.279   6.6468  -1.0498   1.5851
 SK1  C22   C  CH3   0  -0.649  -1.6734   3.3290  -1.3184
 SK1  H3    H  HNH1  0   0.410  -3.2745   0.7865  -0.2306
 SK1  H5N1  H  HNH2  0   0.395  -8.0976  -3.7622   1.6818
 SK1  H5N2  H  HNH2  0   0.392  -9.0195  -3.4213   3.0502
 SK1  H4    H  H     0   0.324  -9.2937  -1.2403   3.5998
 SK1  H13   H  HCR6  0   0.257  -7.8916   0.5190   0.9434
 SK1  H12   H  HCR6  0   0.259  -6.2847   1.1651  -0.7994
 SK1  H16   H  HCR6  0   0.259  -4.3830  -2.6523  -0.4538
 SK1  H15   H  HCR6  0   0.260  -5.9810  -3.3028   1.2703
 SK1  H111  H  HCH2  0   0.261  -4.7128   0.2575  -2.5987
 SK1  H112  H  HCH2  0   0.261  -3.7699  -1.1847  -2.2468
 SK1  H8    H  HCH1  0   0.277  -1.1769   1.6394  -0.0820
 SK1  H2    H  HNH1  0   0.401   0.2180   1.3844  -2.6243
 SK1  H5    H  HCH1  0   0.306   2.5386   0.8675  -2.2938
 SK1  H6C1  H  HCH2  0   0.237   3.6287   2.7427  -3.3900
 SK1  H6C2  H  HCH2  0   0.220   1.8762   2.7766  -3.5794
 SK1  HA    H  HOH1  0   0.466   2.8341   4.8370  -2.8735
 SK1  H1    H  HNC1  0   0.414   3.9039   2.8076  -0.5274
 SK1  H1C1  H  HCH2  0   0.319   5.2651  -0.4048  -1.4367
 SK1  H1C2  H  HCH2  0   0.320   6.2359   0.6814  -0.4309
 SK1  H19   H  HCR6  0   0.257   4.6877  -2.6747  -0.6467
 SK1  H20   H  HCR6  0   0.260   5.2476  -4.5643   0.8312
 SK1  H21   H  HCR6  0   0.260   6.7099  -4.2120   2.7962
 SK1  HC    H  HCR6  0   0.260   7.6055  -1.9553   3.2736
 SK1  HB    H  HCR6  0   0.257   7.0446  -0.0649   1.7963
 SK1  H221  H  HCH3  0   0.252  -1.0183   4.0142  -0.7828
 SK1  H222  H  HCH3  0   0.236  -1.6799   3.6100  -2.3718
 SK1  H223  H  HCH3  0   0.241  -2.6819   3.4502  -0.9232
 SK1  C18   C  C     0   0.336  -8.0622  -1.8026   2.2726

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
 SK1  N3   C11   single    1.454  0.020  1.454
 SK1  N3   C10   single    1.336  0.020  1.336
 SK1  N3   H3    single    0.860  0.020  1.020
 SK1  N5   C18   single    1.365  0.020  1.365
 SK1  N5   H5N1  single    0.890  0.020  1.040
 SK1  N5   H5N2  single    0.890  0.020  1.040
 SK1  C18  N4    double    1.278  0.020  1.278
 SK1  C18  C14   single    1.490  0.020  1.490
 SK1  N4   H4    single    0.890  0.020  1.040
 SK1  C14  C13   aromatic  1.394  0.020  1.394
 SK1  C14  C15   aromatic  1.393  0.020  1.393
 SK1  C13  C12   aromatic  1.384  0.020  1.384
 SK1  C13  H13   single    0.930  0.020  1.080
 SK1  C12  C17   aromatic  1.393  0.020  1.393
 SK1  C12  H12   single    0.930  0.020  1.080
 SK1  C17  C16   aromatic  1.389  0.020  1.389
 SK1  C17  C11   single    1.502  0.020  1.502
 SK1  C16  C15   aromatic  1.388  0.020  1.388
 SK1  C16  H16   single    0.930  0.020  1.080
 SK1  C15  H15   single    0.930  0.020  1.080
 SK1  C11  H111  single    0.970  0.020  1.090
 SK1  C11  H112  single    0.970  0.020  1.090
 SK1  C10  O5    double    1.224  0.020  1.224
 SK1  C10  C8    single    1.524  0.020  1.524
 SK1  C8   N2    single    1.443  0.020  1.443
 SK1  C8   C22   single    1.530  0.020  1.530
 SK1  C8   H8    single    0.970  0.020  1.090
 SK1  N2   C7    single    1.339  0.020  1.339
 SK1  N2   H2    single    0.860  0.020  1.020
 SK1  C7   O4    double    1.219  0.020  1.219
 SK1  C7   C5    single    1.534  0.020  1.534
 SK1  C5   C6    single    1.523  0.020  1.523
 SK1  C5   N1    single    1.448  0.020  1.448
 SK1  C5   H5    single    0.970  0.020  1.090
 SK1  C6   O3    single    1.405  0.020  1.405
 SK1  C6   H6C1  single    0.970  0.020  1.090
 SK1  C6   H6C2  single    0.970  0.020  1.090
 SK1  O3   HA    single    0.850  0.020  0.980
 SK1  N1   S1    single    1.654  0.020  1.654
 SK1  N1   H1    single    0.890  0.020  1.040
 SK1  S1   O1    double    1.457  0.020  1.457
 SK1  S1   O2    double    1.455  0.020  1.455
 SK1  S1   C1    single    1.797  0.020  1.797
 SK1  C1   C4    single    1.496  0.020  1.496
 SK1  C1   H1C1  single    0.970  0.020  1.090
 SK1  C1   H1C2  single    0.970  0.020  1.090
 SK1  C4   C19   aromatic  1.392  0.020  1.392
 SK1  C4   C3    aromatic  1.392  0.020  1.392
 SK1  C19  C20   aromatic  1.387  0.020  1.387
 SK1  C19  H19   single    0.930  0.020  1.080
 SK1  C20  C21   aromatic  1.389  0.020  1.389
 SK1  C20  H20   single    0.930  0.020  1.080
 SK1  C21  C2    aromatic  1.389  0.020  1.389
 SK1  C21  H21   single    0.930  0.020  1.080
 SK1  C2   C3    aromatic  1.388  0.020  1.388
 SK1  C2   HC    single    0.930  0.020  1.080
 SK1  C3   HB    single    0.930  0.020  1.080
 SK1  C22  H221  single    0.970  0.020  1.090
 SK1  C22  H222  single    0.970  0.020  1.090
 SK1  C22  H223  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
 SK1  H3    N3   C10   119.55  3.000
 SK1  H3    N3   C11   118.29  3.000
 SK1  C10   N3   C11   122.17  3.000
 SK1  H5N2  N5   H5N1  113.51  3.000
 SK1  H5N2  N5   C18   117.28  3.000
 SK1  H5N1  N5   C18   118.55  3.000
 SK1  H4    N4   C18   110.95  3.000
 SK1  C15   C14  C13   118.69  3.000
 SK1  C15   C14  C18   121.87  3.000
 SK1  C13   C14  C18   119.43  3.000
 SK1  H13   C13  C12   119.97  3.000
 SK1  H13   C13  C14   119.40  3.000
 SK1  C12   C13  C14   120.62  3.000
 SK1  H12   C12  C17   119.84  3.000
 SK1  H12   C12  C13   119.45  3.000
 SK1  C17   C12  C13   120.71  3.000
 SK1  C11   C17  C16   120.69  3.000
 SK1  C11   C17  C12   120.63  3.000
 SK1  C16   C17  C12   118.67  3.000
 SK1  H16   C16  C15   119.44  3.000
 SK1  H16   C16  C17   119.78  3.000
 SK1  C15   C16  C17   120.78  3.000
 SK1  H15   C15  C16   118.66  3.000
 SK1  H15   C15  C14   120.82  3.000
 SK1  C16   C15  C14   120.52  3.000
 SK1  H112  C11  H111  107.24  3.000
 SK1  H112  C11  C17   109.97  3.000
 SK1  H111  C11  C17   110.16  3.000
 SK1  H112  C11  N3    109.59  3.000
 SK1  H111  C11  N3    109.84  3.000
 SK1  C17   C11  N3    109.99  3.000
 SK1  C8    C10  O5    121.44  3.000
 SK1  C8    C10  N3    115.28  3.000
 SK1  O5    C10  N3    123.24  3.000
 SK1  H8    C8   C22   109.17  3.000
 SK1  H8    C8   N2    108.52  3.000
 SK1  C22   C8   N2    112.11  3.000
 SK1  H8    C8   C10   109.80  3.000
 SK1  C22   C8   C10   109.36  3.000
 SK1  N2    C8   C10   107.85  3.000
 SK1  H2    N2   C7    119.89  3.000
 SK1  H2    N2   C8    116.63  3.000
 SK1  C7    N2   C8    123.30  3.000
 SK1  C5    C7   O4    121.78  3.000
 SK1  C5    C7   N2    114.24  3.000
 SK1  O4    C7   N2    123.97  3.000
 SK1  H5    C5   N1    109.22  3.000
 SK1  H5    C5   C6    106.89  3.000
 SK1  N1    C5   C6    108.80  3.000
 SK1  H5    C5   C7    109.66  3.000
 SK1  N1    C5   C7    111.64  3.000
 SK1  C6    C5   C7    110.51  3.000
 SK1  H6C2  C6   H6C1  107.14  3.000
 SK1  H6C2  C6   O3    112.14  3.000
 SK1  H6C1  C6   O3    112.31  3.000
 SK1  H6C2  C6   C5    108.81  3.000
 SK1  H6C1  C6   C5    108.40  3.000
 SK1  O3    C6   C5    107.94  3.000
 SK1  HA    O3   C6    108.62  3.000
 SK1  H1    N1   S1    111.72  3.000
 SK1  H1    N1   C5    114.33  3.000
 SK1  S1    N1   C5    119.35  3.000
 SK1  C1    S1   O2    107.87  3.000
 SK1  C1    S1   O1    107.68  3.000
 SK1  O2    S1   O1    119.63  3.000
 SK1  C1    S1   N1    102.44  3.000
 SK1  O2    S1   N1    109.02  3.000
 SK1  O1    S1   N1    108.83  3.000
 SK1  H1C2  C1   H1C1  108.50  3.000
 SK1  H1C2  C1   C4    112.72  3.000
 SK1  H1C1  C1   C4    112.44  3.000
 SK1  H1C2  C1   S1    106.53  3.000
 SK1  H1C1  C1   S1    106.53  3.000
 SK1  C4    C1   S1    109.76  3.000
 SK1  C3    C4   C19   119.25  3.000
 SK1  C3    C4   C1    120.49  3.000
 SK1  C19   C4   C1    120.23  3.000
 SK1  H19   C19  C20   119.78  3.000
 SK1  H19   C19  C4    119.81  3.000
 SK1  C20   C19  C4    120.40  3.000
 SK1  H20   C20  C21   120.11  3.000
 SK1  H20   C20  C19   119.82  3.000
 SK1  C21   C20  C19   120.07  3.000
 SK1  H21   C21  C2    120.10  3.000
 SK1  H21   C21  C20   120.09  3.000
 SK1  C2    C21  C20   119.80  3.000
 SK1  HC    C2   C3    119.82  3.000
 SK1  HC    C2   C21   120.09  3.000
 SK1  C3    C2   C21   120.09  3.000
 SK1  HB    C3   C2    119.80  3.000
 SK1  HB    C3   C4    119.82  3.000
 SK1  C2    C3   C4    120.37  3.000
 SK1  H223  C22  H222  108.43  3.000
 SK1  H223  C22  H221  107.96  3.000
 SK1  H222  C22  H221  108.46  3.000
 SK1  H223  C22  C8    111.08  3.000
 SK1  H222  C22  C8    110.73  3.000
 SK1  H221  C22  C8    110.09  3.000
 SK1  C14   C18  N4    118.59  3.000
 SK1  C14   C18  N5    115.37  3.000
 SK1  N4    C18  N5    125.99  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
 SK1  CONST_01  C17   C12  C13  C14     0.00   0.0  0
 SK1  CONST_02  C17   C16  C15  C14     0.00   0.0  0
 SK1  CONST_03  C16   C15  C14  C13     0.00   0.0  0
 SK1  CONST_04  C16   C17  C12  C13     0.00   0.0  0
 SK1  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 SK1  CONST_06  C15   C16  C17  C12     0.00   0.0  0
 SK1  CONST_07  C21   C20  C19  C4      0.00   0.0  0
 SK1  CONST_08  C21   C2   C3   C4      0.00   0.0  0
 SK1  CONST_09  C2    C3   C4   C19     0.00   0.0  0
 SK1  CONST_10  C2    C21  C20  C19     0.00   0.0  0
 SK1  CONST_11  C3    C4   C19  C20     0.00   0.0  0
 SK1  CONST_12  C3    C2   C21  C20     0.00   0.0  0
 SK1  CONST_13  C12   C13  C14  C18   180.00   0.0  0
 SK1  CONST_14  C16   C15  C14  C18   180.00   0.0  0
 SK1  CONST_15  C11   C17  C12  C13   180.00   0.0  0
 SK1  CONST_16  C11   C17  C16  C15   180.00   0.0  0
 SK1  CONST_17  C20   C19  C4   C1    180.00   0.0  0
 SK1  CONST_18  C2    C3   C4   C1    180.00   0.0  0
 SK1  CONST_19  H12   C12  C13  C14   180.00   0.0  0
 SK1  CONST_20  H16   C16  C15  C14   180.00   0.0  0
 SK1  CONST_21  H15   C15  C14  C13   180.00   0.0  0
 SK1  CONST_22  H13   C13  C12  C17   180.00   0.0  0
 SK1  CONST_23  H20   C20  C19  C4    180.00   0.0  0
 SK1  CONST_24  HC    C2   C3   C4    180.00   0.0  0
 SK1  CONST_25  HB    C3   C4   C19   180.00   0.0  0
 SK1  CONST_26  H21   C21  C20  C19   180.00   0.0  0
 SK1  CONST_27  H19   C19  C20  C21   180.00   0.0  0
 SK1  CONST_29  H5N2  N5   C18  C14   180.00   0.0  0
 SK1  CONST_30  H4    N4   C18  C14   180.00   0.0  0
 SK1  CONST_31  O5    C10  N3   C11     0.00   0.0  0
 SK1  CONST_32  C8    C10  N3   C11   180.00   0.0  0
 SK1  CONST_33  O4    C7   N2   C8      0.00   0.0  0
 SK1  CONST_34  C5    C7   N2   C8    180.00   0.0  0
 SK1  CONST_35  H3    N3   C10  O5    180.00   0.0  0
 SK1  CONST_36  H2    N2   C7   O4    180.00   0.0  0
 SK1  Var_01    C12   C17  C11  N3     79.84  30.0  2
 SK1  Var_02    C13   C14  C18  N5    158.02  30.0  2
 SK1  Var_03    C19   C4   C1   S1     89.05  30.0  2
 SK1  Var_04    C10   N3   C11  C17   175.60  30.0  1
 SK1  Var_05    C4    C1   S1   N1   -178.76  30.0  3
 SK1  Var_06    O1    S1   N1   C5      0.29  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
 SK1  chir_01  C8  C10  N2  C22  negativ
 SK1  chir_02  C5  N1   C7  C6   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
 SK1  plan-1  C14   0.020
 SK1  plan-1  C13   0.020
 SK1  plan-1  C12   0.020
 SK1  plan-1  C17   0.020
 SK1  plan-1  C16   0.020
 SK1  plan-1  C15   0.020
 SK1  plan-1  C11   0.020
 SK1  plan-1  H13   0.020
 SK1  plan-1  H12   0.020
 SK1  plan-1  H16   0.020
 SK1  plan-1  H15   0.020
 SK1  plan-1  C18   0.020
 SK1  plan-2  C1    0.020
 SK1  plan-2  C4    0.020
 SK1  plan-2  C19   0.020
 SK1  plan-2  C20   0.020
 SK1  plan-2  C21   0.020
 SK1  plan-2  C2    0.020
 SK1  plan-2  C3    0.020
 SK1  plan-2  H19   0.020
 SK1  plan-2  H20   0.020
 SK1  plan-2  H21   0.020
 SK1  plan-2  HC    0.020
 SK1  plan-2  HB    0.020
 SK1  plan-3  N3    0.020
 SK1  plan-3  C11   0.020
 SK1  plan-3  C10   0.020
 SK1  plan-3  O5    0.020
 SK1  plan-3  C8    0.020
 SK1  plan-3  H3    0.020
 SK1  plan-4  C8    0.020
 SK1  plan-4  N2    0.020
 SK1  plan-4  C7    0.020
 SK1  plan-4  O4    0.020
 SK1  plan-4  C5    0.020
 SK1  plan-4  H2    0.020
 SK1  plan-5  N5    0.020
 SK1  plan-5  N4    0.020
 SK1  plan-5  C14   0.020
 SK1  plan-5  H5N1  0.020
 SK1  plan-5  H5N2  0.020
 SK1  plan-5  H4    0.020
 SK1  plan-5  C18   0.020

