# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:05:33 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidamidobenzyl)-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(NC(N)=N)cc2
#
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
 SM1  SM1  N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidamidobenzyl)-L-alaninamide  ligand  61  33  .  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_SM1
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
 SM1  N6    N  NH2   0  -0.845  -1.4665   2.0463  -10.4570
 SM1  C18   C  C     0   0.566  -0.8803   1.1778   -9.5627
 SM1  N5    N  N     0  -0.697   0.1255   0.4249   -9.7993
 SM1  N4    N  NH1   0  -0.752  -1.5498   1.1500   -8.3597
 SM1  C14   C  CR6   0   0.366  -1.2914   0.4181   -7.2115
 SM1  C13   C  CR16  0  -0.309  -0.2120  -0.4544   -7.0443
 SM1  C12   C  CR16  0  -0.276  -0.0514  -1.1333   -5.8449
 SM1  C17   C  CR6   0   0.029  -0.9411  -0.9862   -4.7879
 SM1  C16   C  CR16  0  -0.276  -2.0131  -0.1147   -4.9615
 SM1  C15   C  CR16  0  -0.346  -2.1878   0.5751   -6.1463
 SM1  C11   C  CH2   0  -0.322  -0.7377  -1.7193   -3.4943
 SM1  N3    N  NH1   0  -0.629   0.1157  -0.9484   -2.6032
 SM1  C10   C  C     0   0.558   0.6281  -1.4597   -1.4815
 SM1  O5    O  O     0  -0.496   0.4144  -2.6055   -1.1081
 SM1  C8    C  CH1   0  -0.194   1.5588  -0.5271   -0.7106
 SM1  C22   C  CH3   0  -0.648   2.9287  -0.4804   -1.3912
 SM1  N2    N  NH1   0  -0.642   1.6395  -1.0102    0.6457
 SM1  C7    C  C     0   0.577   1.9823  -0.2397    1.6845
 SM1  C5    C  CH1   0  -0.274   2.0820  -0.9926    3.0170
 SM1  C6    C  CH2   0  -0.145   3.3435  -1.8445    3.0554
 SM1  O3    O  OH1   0  -0.665   4.4456  -0.9983    2.8535
 SM1  N1    N  NC1   0  -0.724   2.0831  -0.0815    4.1435
 SM1  O4    O  O     0  -0.484   2.2208   0.9530    1.6015
 SM1  O2    O  OS    0  -0.662   0.9748   1.9078    5.1888
 SM1  S1    S  S     0   1.367   0.6527   0.6228    4.5869
 SM1  O1    O  OS    0  -0.655  -0.3109   0.5672    3.4948
 SM1  C1    C  CH2   0  -0.701   0.0711  -0.4916    5.8719
 SM1  C4    C  CR6   0   0.111  -1.2668  -0.0413    6.3672
 SM1  C19   C  CR16  0  -0.280  -2.4338  -0.4914    5.7555
 SM1  C20   C  CR16  0  -0.242  -3.6727  -0.0590    6.2053
 SM1  C21   C  CR16  0  -0.260  -3.7557   0.8329    7.2671
 SM1  C2    C  CR16  0  -0.242  -2.5951   1.2885    7.8784
 SM1  C3    C  CR16  0  -0.279  -1.3558   0.8568    7.4270
 SM1  H6N1  H  HNH2  0   0.392  -0.9063   2.2670  -11.2646
 SM1  H6N2  H  HNH2  0   0.390  -1.9193   2.8654  -10.0806
 SM1  H51   H  H     0   0.330   0.4909   0.6060  -10.7270
 SM1  H4    H  HNH1  0   0.405  -2.3883   1.7068   -8.3161
 SM1  H13   H  HCR6  0   0.288   0.4852  -0.6052   -7.8517
 SM1  H12   H  HCR6  0   0.249   0.7918  -1.8068   -5.7431
 SM1  H16   H  HCR6  0   0.254  -2.7306   0.0273   -4.1617
 SM1  H15   H  HCR6  0   0.264  -3.0340   1.2445   -6.2504
 SM1  H111  H  HCH2  0   0.255  -1.7001  -1.9133   -3.0134
 SM1  H112  H  HCH2  0   0.257  -0.2728  -2.6893   -3.6797
 SM1  H3    H  HNH1  0   0.408   0.2790   0.0210   -2.8259
 SM1  H8    H  HCH1  0   0.279   1.1317   0.4784   -0.6986
 SM1  H221  H  HCH3  0   0.236   3.3621  -1.4785   -1.4578
 SM1  H222  H  HCH3  0   0.239   2.8523  -0.0715   -2.3984
 SM1  H223  H  HCH3  0   0.251   3.6078   0.1535   -0.8231
 SM1  H2    H  HNH1  0   0.401   1.4432  -1.9911    0.7850
 SM1  H5    H  HCH1  0   0.303   1.2366  -1.6789    3.1162
 SM1  H6C1  H  HCH2  0   0.218   3.2701  -2.6191    2.2831
 SM1  H6C2  H  HCH2  0   0.233   3.3812  -2.3553    4.0241
 SM1  HA    H  HOH1  0   0.466   5.2500  -1.5175    2.9425
 SM1  H1    H  HNC1  0   0.414   2.8418   0.5924    4.1356
 SM1  H1C1  H  HCH2  0   0.324   0.8324  -0.4878    6.6521
 SM1  H1C2  H  HCH2  0   0.319   0.0337  -1.4893    5.4311
 SM1  H19   H  HCR6  0   0.258  -2.3751  -1.1929    4.9330
 SM1  H20   H  HCR6  0   0.260  -4.5744  -0.4180    5.7266
 SM1  H21   H  HCR6  0   0.261  -4.7228   1.1664    7.6201
 SM1  HC    H  HCR6  0   0.260  -2.6538   1.9807    8.7079
 SM1  HB    H  HCR6  0   0.259  -0.4538   1.2096    7.9114

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
 SM1  N6   C18   single    1.378  0.020  1.378
 SM1  N6   H6N1  single    0.890  0.020  1.040
 SM1  N6   H6N2  single    0.890  0.020  1.040
 SM1  C18  N5    double    1.278  0.020  1.278
 SM1  C18  N4    single    1.377  0.020  1.377
 SM1  N5   H51   single    0.890  0.020  1.040
 SM1  N4   C14   single    1.386  0.020  1.386
 SM1  N4   H4    single    0.860  0.020  1.020
 SM1  C14  C13   aromatic  1.398  0.020  1.398
 SM1  C14  C15   aromatic  1.401  0.020  1.401
 SM1  C13  C12   aromatic  1.387  0.020  1.387
 SM1  C13  H13   single    0.930  0.020  1.080
 SM1  C12  C17   aromatic  1.389  0.020  1.389
 SM1  C12  H12   single    0.930  0.020  1.080
 SM1  C17  C16   aromatic  1.392  0.020  1.392
 SM1  C17  C11   single    1.501  0.020  1.501
 SM1  C16  C15   aromatic  1.382  0.020  1.382
 SM1  C16  H16   single    0.930  0.020  1.080
 SM1  C15  H15   single    0.930  0.020  1.080
 SM1  C11  N3    single    1.455  0.020  1.455
 SM1  C11  H111  single    0.970  0.020  1.090
 SM1  C11  H112  single    0.970  0.020  1.090
 SM1  N3   C10   single    1.335  0.020  1.335
 SM1  N3   H3    single    0.860  0.020  1.020
 SM1  C10  O5    double    1.224  0.020  1.224
 SM1  C10  C8    single    1.527  0.020  1.527
 SM1  C8   C22   single    1.530  0.020  1.530
 SM1  C8   N2    single    1.442  0.020  1.442
 SM1  C8   H8    single    0.970  0.020  1.090
 SM1  C22  H221  single    0.970  0.020  1.090
 SM1  C22  H222  single    0.970  0.020  1.090
 SM1  C22  H223  single    0.970  0.020  1.090
 SM1  N2   C7    single    1.338  0.020  1.338
 SM1  N2   H2    single    0.860  0.020  1.020
 SM1  C7   C5    single    1.534  0.020  1.534
 SM1  C7   O4    double    1.219  0.020  1.219
 SM1  C5   C6    single    1.523  0.020  1.523
 SM1  C5   N1    single    1.449  0.020  1.449
 SM1  C5   H5    single    0.970  0.020  1.090
 SM1  C6   O3    single    1.404  0.020  1.404
 SM1  C6   H6C1  single    0.970  0.020  1.090
 SM1  C6   H6C2  single    0.970  0.020  1.090
 SM1  O3   HA    single    0.850  0.020  0.980
 SM1  N1   S1    single    1.655  0.020  1.655
 SM1  N1   H1    single    0.890  0.020  1.040
 SM1  O2   S1    double    1.455  0.020  1.455
 SM1  S1   O1    double    1.457  0.020  1.457
 SM1  S1   C1    single    1.798  0.020  1.798
 SM1  C1   C4    single    1.496  0.020  1.496
 SM1  C1   H1C1  single    0.970  0.020  1.090
 SM1  C1   H1C2  single    0.970  0.020  1.090
 SM1  C4   C19   aromatic  1.392  0.020  1.392
 SM1  C4   C3    aromatic  1.392  0.020  1.392
 SM1  C19  C20   aromatic  1.387  0.020  1.387
 SM1  C19  H19   single    0.930  0.020  1.080
 SM1  C20  C21   aromatic  1.389  0.020  1.389
 SM1  C20  H20   single    0.930  0.020  1.080
 SM1  C21  C2    aromatic  1.389  0.020  1.389
 SM1  C21  H21   single    0.930  0.020  1.080
 SM1  C2   C3    aromatic  1.388  0.020  1.388
 SM1  C2   HC    single    0.930  0.020  1.080
 SM1  C3   HB    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
 SM1  H6N2  N6   H6N1  111.77  3.000
 SM1  H6N2  N6   C18   117.43  3.000
 SM1  H6N1  N6   C18   114.95  3.000
 SM1  N4    C18  N5    122.16  3.000
 SM1  N4    C18  N6    111.90  3.000
 SM1  N5    C18  N6    125.87  3.000
 SM1  H51   N5   C18   110.36  3.000
 SM1  H4    N4   C14   114.28  3.000
 SM1  H4    N4   C18   115.55  3.000
 SM1  C14   N4   C18   130.07  3.000
 SM1  C15   C14  C13   118.23  3.000
 SM1  C15   C14  N4    116.83  3.000
 SM1  C13   C14  N4    124.94  3.000
 SM1  H13   C13  C12   120.29  3.000
 SM1  H13   C13  C14   119.83  3.000
 SM1  C12   C13  C14   119.88  3.000
 SM1  H12   C12  C17   119.50  3.000
 SM1  H12   C12  C13   118.38  3.000
 SM1  C17   C12  C13   122.12  3.000
 SM1  C11   C17  C16   121.17  3.000
 SM1  C11   C17  C12   121.15  3.000
 SM1  C16   C17  C12   117.67  3.000
 SM1  H16   C16  C15   118.92  3.000
 SM1  H16   C16  C17   119.98  3.000
 SM1  C15   C16  C17   121.10  3.000
 SM1  H15   C15  C16   119.29  3.000
 SM1  H15   C15  C14   119.71  3.000
 SM1  C16   C15  C14   120.99  3.000
 SM1  H112  C11  H111  106.98  3.000
 SM1  H112  C11  N3    108.97  3.000
 SM1  H111  C11  N3    109.93  3.000
 SM1  H112  C11  C17   110.21  3.000
 SM1  H111  C11  C17   110.28  3.000
 SM1  N3    C11  C17   110.40  3.000
 SM1  H3    N3   C10   119.46  3.000
 SM1  H3    N3   C11   117.99  3.000
 SM1  C10   N3   C11   122.47  3.000
 SM1  C8    C10  O5    121.62  3.000
 SM1  C8    C10  N3    115.11  3.000
 SM1  O5    C10  N3    123.22  3.000
 SM1  H8    C8   N2    108.66  3.000
 SM1  H8    C8   C22   109.07  3.000
 SM1  N2    C8   C22   112.23  3.000
 SM1  H8    C8   C10   109.24  3.000
 SM1  N2    C8   C10   107.72  3.000
 SM1  C22   C8   C10   109.87  3.000
 SM1  H223  C22  H222  107.91  3.000
 SM1  H223  C22  H221  108.48  3.000
 SM1  H222  C22  H221  108.35  3.000
 SM1  H223  C22  C8    110.13  3.000
 SM1  H222  C22  C8    111.08  3.000
 SM1  H221  C22  C8    110.80  3.000
 SM1  H2    N2   C7    120.13  3.000
 SM1  H2    N2   C8    116.38  3.000
 SM1  C7    N2   C8    123.48  3.000
 SM1  O4    C7   C5    121.78  3.000
 SM1  O4    C7   N2    124.10  3.000
 SM1  C5    C7   N2    114.11  3.000
 SM1  H5    C5   N1    108.95  3.000
 SM1  H5    C5   C6    106.68  3.000
 SM1  N1    C5   C6    109.37  3.000
 SM1  H5    C5   C7    109.67  3.000
 SM1  N1    C5   C7    111.52  3.000
 SM1  C6    C5   C7    110.51  3.000
 SM1  H6C2  C6   H6C1  107.20  3.000
 SM1  H6C2  C6   O3    112.40  3.000
 SM1  H6C1  C6   O3    112.15  3.000
 SM1  H6C2  C6   C5    108.16  3.000
 SM1  H6C1  C6   C5    108.79  3.000
 SM1  O3    C6   C5    108.03  3.000
 SM1  HA    O3   C6    108.54  3.000
 SM1  H1    N1   S1    111.45  3.000
 SM1  H1    N1   C5    114.34  3.000
 SM1  S1    N1   C5    118.38  3.000
 SM1  C1    S1   O1    107.34  3.000
 SM1  C1    S1   O2    108.87  3.000
 SM1  O1    S1   O2    119.34  3.000
 SM1  C1    S1   N1    101.97  3.000
 SM1  O1    S1   N1    110.76  3.000
 SM1  O2    S1   N1    107.18  3.000
 SM1  H1C2  C1   H1C1  108.43  3.000
 SM1  H1C2  C1   C4    112.22  3.000
 SM1  H1C1  C1   C4    112.74  3.000
 SM1  H1C2  C1   S1    106.80  3.000
 SM1  H1C1  C1   S1    106.47  3.000
 SM1  C4    C1   S1    109.84  3.000
 SM1  C3    C4   C19   119.31  3.000
 SM1  C3    C4   C1    120.22  3.000
 SM1  C19   C4   C1    120.46  3.000
 SM1  H19   C19  C20   119.78  3.000
 SM1  H19   C19  C4    119.86  3.000
 SM1  C20   C19  C4    120.36  3.000
 SM1  H20   C20  C21   120.09  3.000
 SM1  H20   C20  C19   119.83  3.000
 SM1  C21   C20  C19   120.08  3.000
 SM1  H21   C21  C2    120.14  3.000
 SM1  H21   C21  C20   120.04  3.000
 SM1  C2    C21  C20   119.82  3.000
 SM1  HC    C2   C3    119.79  3.000
 SM1  HC    C2   C21   120.14  3.000
 SM1  C3    C2   C21   120.07  3.000
 SM1  HB    C3   C2    119.80  3.000
 SM1  HB    C3   C4    119.83  3.000
 SM1  C2    C3   C4    120.36  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
 SM1  CONST_01  C17  C12  C13  C14     0.00   0.0  0
 SM1  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 SM1  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 SM1  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 SM1  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 SM1  CONST_06  C15  C16  C17  C12     0.00   0.0  0
 SM1  CONST_07  C21  C20  C19  C4      0.00   0.0  0
 SM1  CONST_08  C21  C2   C3   C4      0.00   0.0  0
 SM1  CONST_09  C2   C3   C4   C19     0.00   0.0  0
 SM1  CONST_10  C2   C21  C20  C19     0.00   0.0  0
 SM1  CONST_11  C3   C4   C19  C20     0.00   0.0  0
 SM1  CONST_12  C3   C2   C21  C20     0.00   0.0  0
 SM1  CONST_13  C12  C13  C14  N4    180.00   0.0  0
 SM1  CONST_14  C16  C15  C14  N4    180.00   0.0  0
 SM1  CONST_15  C11  C17  C12  C13   180.00   0.0  0
 SM1  CONST_16  C11  C17  C16  C15   180.00   0.0  0
 SM1  CONST_17  C20  C19  C4   C1    180.00   0.0  0
 SM1  CONST_18  C2   C3   C4   C1    180.00   0.0  0
 SM1  CONST_19  H12  C12  C13  C14   180.00   0.0  0
 SM1  CONST_20  H16  C16  C15  C14   180.00   0.0  0
 SM1  CONST_21  H15  C15  C14  C13   180.00   0.0  0
 SM1  CONST_22  H13  C13  C12  C17   180.00   0.0  0
 SM1  CONST_23  H20  C20  C19  C4    180.00   0.0  0
 SM1  CONST_24  HC   C2   C3   C4    180.00   0.0  0
 SM1  CONST_25  HB   C3   C4   C19   180.00   0.0  0
 SM1  CONST_26  H21  C21  C20  C19   180.00   0.0  0
 SM1  CONST_27  H19  C19  C20  C21   180.00   0.0  0
 SM1  CONST_28  C13  C14  N4   C18     0.00   0.0  0
 SM1  CONST_29  C15  C14  N4   C18   180.00   0.0  0
 SM1  CONST_30  H4   N4   C14  C13   180.00   0.0  0
 SM1  CONST_31  C14  N4   C18  N6    180.00   0.0  0
 SM1  CONST_32  C14  N4   C18  N5      0.00   0.0  0
 SM1  CONST_33  O5   C10  N3   C11     0.00   0.0  0
 SM1  CONST_34  C8   C10  N3   C11   180.00   0.0  0
 SM1  CONST_35  C5   C7   N2   C8    180.00   0.0  0
 SM1  CONST_36  O4   C7   N2   C8      0.00   0.0  0
 SM1  CONST_37  H3   N3   C10  O5    180.00   0.0  0
 SM1  CONST_38  H2   N2   C7   C5      0.00   0.0  0
 SM1  CONST_39  H51  N5   C18  N6      0.00   0.0  0
 SM1  Var_01    N3   C11  C17  C12    87.58  30.0  2
 SM1  Var_02    C19  C4   C1   S1     88.97  30.0  2
 SM1  Var_03    C10  N3   C11  C17  -169.00  30.0  3
 SM1  Var_04    C4   C1   S1   N1   -177.65  30.0  3
 SM1  Var_05    O2   S1   N1   C5   -151.22  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
 SM1  chir_01  C8  C10  C22  N2  positiv
 SM1  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
 SM1  plan-1  N4    0.020
 SM1  plan-1  C14   0.020
 SM1  plan-1  C13   0.020
 SM1  plan-1  C12   0.020
 SM1  plan-1  C17   0.020
 SM1  plan-1  C16   0.020
 SM1  plan-1  C15   0.020
 SM1  plan-1  C11   0.020
 SM1  plan-1  H13   0.020
 SM1  plan-1  H12   0.020
 SM1  plan-1  H16   0.020
 SM1  plan-1  H15   0.020
 SM1  plan-2  C1    0.020
 SM1  plan-2  C4    0.020
 SM1  plan-2  C19   0.020
 SM1  plan-2  C20   0.020
 SM1  plan-2  C21   0.020
 SM1  plan-2  C2    0.020
 SM1  plan-2  C3    0.020
 SM1  plan-2  H19   0.020
 SM1  plan-2  H20   0.020
 SM1  plan-2  H21   0.020
 SM1  plan-2  HC    0.020
 SM1  plan-2  HB    0.020
 SM1  plan-3  C11   0.020
 SM1  plan-3  N3    0.020
 SM1  plan-3  C10   0.020
 SM1  plan-3  O5    0.020
 SM1  plan-3  C8    0.020
 SM1  plan-3  H3    0.020
 SM1  plan-4  C8    0.020
 SM1  plan-4  N2    0.020
 SM1  plan-4  C7    0.020
 SM1  plan-4  C5    0.020
 SM1  plan-4  O4    0.020
 SM1  plan-4  H2    0.020
 SM1  plan-5  N6    0.020
 SM1  plan-5  C18   0.020
 SM1  plan-5  N5    0.020
 SM1  plan-5  N4    0.020
 SM1  plan-5  C14   0.020
 SM1  plan-5  H6N1  0.020
 SM1  plan-5  H6N2  0.020
 SM1  plan-5  H51   0.020
 SM1  plan-5  H4    0.020

