# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:04:25 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)CNC(=O)[C@@H](CO)N[S](=O)(=O)Cc2ccccc2)cc1
#
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
 2IN  2IN  N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)glycinamide  ligand  56  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2IN
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
 2IN  N4    N  NH2   0  -0.803   0.0393   1.3777   9.8887
 2IN  N5    N  N     0  -0.641  -1.6044  -0.2001   9.6285
 2IN  C18   C  C     0   0.329  -0.5615   0.3838   9.1754
 2IN  C14   C  CR6   0  -0.007   0.1181   0.0295   7.8977
 2IN  C13   C  CR16  0  -0.274  -0.6367  -0.3824   6.7990
 2IN  C12   C  CR16  0  -0.279  -0.0205  -0.7281   5.6096
 2IN  C17   C  CR6   0   0.120   1.3671  -0.6802   5.4873
 2IN  C16   C  CR16  0  -0.296   2.1179  -0.2741   6.5830
 2IN  C15   C  CR16  0  -0.265   1.5032   0.0817   7.7760
 2IN  C11   C  CH2   0  -0.381   2.0413  -1.0671   4.1947
 2IN  N3    N  NH1   0  -0.622   1.5851  -0.2844   3.0680
 2IN  C10   C  C     0   0.531   0.7507  -0.7366   2.1237
 2IN  O5    O  O     0  -0.492   0.3008  -1.8725   2.0894
 2IN  C8    C  CH2   0  -0.371   0.3860   0.2987   1.0719
 2IN  N2    N  NH1   0  -0.648  -0.3646  -0.3294   0.0211
 2IN  C7    C  C     0   0.567  -0.7641   0.3302  -1.0713
 2IN  O4    O  O     0  -0.483  -0.5100   1.5044  -1.2796
 2IN  C5    C  CH1   0  -0.250  -1.5910  -0.5091  -2.0519
 2IN  C6    C  CH2   0  -0.156  -2.9785  -0.7825  -1.4880
 2IN  O3    O  OH1   0  -0.666  -3.5953   0.4550  -1.2365
 2IN  N1    N  NC1   0  -0.733  -1.7312   0.1488  -3.3336
 2IN  S1    S  S     0   1.374  -0.3974   0.3574  -4.2894
 2IN  O2    O  OS    0  -0.661  -0.3420   1.7419  -4.7347
 2IN  O1    O  OS    0  -0.661   0.7534  -0.2340  -3.6188
 2IN  C1    C  CH2   0  -0.691  -0.7797  -0.6649  -5.7175
 2IN  C4    C  CR6   0   0.106   0.3423  -0.5965  -6.7046
 2IN  C3    C  CR16  0  -0.279   0.3506   0.3828  -7.6942
 2IN  C2    C  CR16  0  -0.243   1.4024   0.4605  -8.5958
 2IN  C21   C  CR16  0  -0.260   2.4605  -0.4351  -8.5102
 2IN  C20   C  CR16  0  -0.242   2.4601  -1.4114  -7.5225
 2IN  C19   C  CR16  0  -0.279   1.4076  -1.4890  -6.6216
 2IN  HN41  H  HNH2  0   0.384  -0.4715   1.7234  10.6858
 2IN  HN42  H  HNH2  0   0.393   0.5519   2.0842   9.3876
 2IN  HN5   H  H     0   0.332  -1.8640  -0.9819   9.0385
 2IN  H13   H  HCR6  0   0.262  -1.7171  -0.4156   6.8645
 2IN  H12   H  HCR6  0   0.257  -0.6297  -1.0415   4.7705
 2IN  H16   H  HCR6  0   0.260   3.1981  -0.2336   6.5098
 2IN  H15   H  HCR6  0   0.263   2.1138   0.3854   8.6165
 2IN  H111  H  HCH2  0   0.277   3.1209  -0.9449   4.2892
 2IN  H112  H  HCH2  0   0.274   1.8584  -2.1189   3.9760
 2IN  HN3   H  HNH1  0   0.411   1.8905   0.6754   3.0230
 2IN  H81   H  HCH2  0   0.284  -0.1933   1.0939   1.5524
 2IN  H82   H  HCH2  0   0.280   1.2961   0.7628   0.6824
 2IN  HN2   H  HNH1  0   0.403  -0.5871  -1.3068   0.1441
 2IN  H5    H  HCH1  0   0.305  -1.1114  -1.4796  -2.1992
 2IN  H61   H  HCH2  0   0.237  -3.5345  -1.3839  -2.2153
 2IN  H62   H  HCH2  0   0.222  -2.8793  -1.3848  -0.5780
 2IN  HO3   H  HOH1  0   0.466  -4.5044   0.2952  -0.9670
 2IN  HN1   H  HNC1  0   0.413  -2.3193   0.9752  -3.3223
 2IN  H11   H  HCH2  0   0.319  -0.9431  -1.6748  -5.3396
 2IN  H12A  H  HCH2  0   0.320  -1.7202  -0.2920  -6.1246
 2IN  H3    H  HCR6  0   0.258  -0.4737   1.0812  -7.7689
 2IN  H2    H  HCR6  0   0.260   1.3963   1.2214  -9.3651
 2IN  H21   H  HCR6  0   0.260   3.2808  -0.3747  -9.2134
 2IN  H20   H  HCR6  0   0.260   3.2809  -2.1129  -7.4521
 2IN  H19   H  HCR6  0   0.258   1.4110  -2.2555  -5.8568

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
 2IN  N4   C18   single    1.363  0.020  1.363
 2IN  N4   HN41  single    0.890  0.020  1.040
 2IN  N4   HN42  single    0.890  0.020  1.040
 2IN  N5   C18   double    1.278  0.020  1.278
 2IN  N5   HN5   single    0.890  0.020  1.040
 2IN  C18  C14   single    1.490  0.020  1.490
 2IN  C14  C13   aromatic  1.395  0.020  1.395
 2IN  C14  C15   aromatic  1.391  0.020  1.391
 2IN  C13  C12   aromatic  1.383  0.020  1.383
 2IN  C13  H13   single    0.930  0.020  1.080
 2IN  C12  C17   aromatic  1.394  0.020  1.394
 2IN  C12  H12   single    0.930  0.020  1.080
 2IN  C17  C16   aromatic  1.389  0.020  1.389
 2IN  C17  C11   single    1.508  0.020  1.508
 2IN  C16  C15   aromatic  1.388  0.020  1.388
 2IN  C16  H16   single    0.930  0.020  1.080
 2IN  C15  H15   single    0.930  0.020  1.080
 2IN  C11  N3    single    1.446  0.020  1.446
 2IN  C11  H111  single    0.970  0.020  1.090
 2IN  C11  H112  single    0.970  0.020  1.090
 2IN  N3   C10   single    1.339  0.020  1.339
 2IN  N3   HN3   single    0.860  0.020  1.020
 2IN  C10  O5    double    1.222  0.020  1.222
 2IN  C10  C8    single    1.520  0.020  1.520
 2IN  C8   N2    single    1.436  0.020  1.436
 2IN  C8   H81   single    0.970  0.020  1.090
 2IN  C8   H82   single    0.970  0.020  1.090
 2IN  N2   C7    single    1.337  0.020  1.337
 2IN  N2   HN2   single    0.860  0.020  1.020
 2IN  C7   O4    double    1.219  0.020  1.219
 2IN  C7   C5    single    1.533  0.020  1.533
 2IN  C5   C6    single    1.522  0.020  1.522
 2IN  C5   N1    single    1.447  0.020  1.447
 2IN  C5   H5    single    0.970  0.020  1.090
 2IN  C6   O3    single    1.405  0.020  1.405
 2IN  C6   H61   single    0.970  0.020  1.090
 2IN  C6   H62   single    0.970  0.020  1.090
 2IN  O3   HO3   single    0.850  0.020  0.980
 2IN  N1   S1    single    1.654  0.020  1.654
 2IN  N1   HN1   single    0.890  0.020  1.040
 2IN  S1   O2    double    1.455  0.020  1.455
 2IN  S1   O1    double    1.457  0.020  1.457
 2IN  S1   C1    single    1.797  0.020  1.797
 2IN  C1   C4    single    1.496  0.020  1.496
 2IN  C1   H11   single    0.970  0.020  1.090
 2IN  C1   H12A  single    0.970  0.020  1.090
 2IN  C4   C3    aromatic  1.392  0.020  1.392
 2IN  C4   C19   aromatic  1.392  0.020  1.392
 2IN  C3   C2    aromatic  1.388  0.020  1.388
 2IN  C3   H3    single    0.930  0.020  1.080
 2IN  C2   C21   aromatic  1.389  0.020  1.389
 2IN  C2   H2    single    0.930  0.020  1.080
 2IN  C21  C20   aromatic  1.389  0.020  1.389
 2IN  C21  H21   single    0.930  0.020  1.080
 2IN  C20  C19   aromatic  1.388  0.020  1.388
 2IN  C20  H20   single    0.930  0.020  1.080
 2IN  C19  H19   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
 2IN  HN42  N4   HN41  114.28  3.000
 2IN  HN42  N4   C18   118.42  3.000
 2IN  HN41  N4   C18   116.14  3.000
 2IN  HN5   N5   C18   110.80  3.000
 2IN  C14   C18  N5    124.57  3.000
 2IN  C14   C18  N4    114.91  3.000
 2IN  N5    C18  N4    120.48  3.000
 2IN  C15   C14  C13   118.73  3.000
 2IN  C15   C14  C18   121.34  3.000
 2IN  C13   C14  C18   119.92  3.000
 2IN  H13   C13  C12   119.25  3.000
 2IN  H13   C13  C14   120.08  3.000
 2IN  C12   C13  C14   120.66  3.000
 2IN  H12   C12  C17   120.12  3.000
 2IN  H12   C12  C13   119.20  3.000
 2IN  C17   C12  C13   120.68  3.000
 2IN  C11   C17  C16   120.63  3.000
 2IN  C11   C17  C12   120.75  3.000
 2IN  C16   C17  C12   118.62  3.000
 2IN  H16   C16  C15   119.34  3.000
 2IN  H16   C16  C17   119.77  3.000
 2IN  C15   C16  C17   120.89  3.000
 2IN  H15   C15  C16   119.29  3.000
 2IN  H15   C15  C14   120.28  3.000
 2IN  C16   C15  C14   120.42  3.000
 2IN  H112  C11  H111  106.96  3.000
 2IN  H112  C11  N3    108.25  3.000
 2IN  H111  C11  N3    108.62  3.000
 2IN  H112  C11  C17   110.15  3.000
 2IN  H111  C11  C17   109.84  3.000
 2IN  N3    C11  C17   112.83  3.000
 2IN  HN3   N3   C10   118.61  3.000
 2IN  HN3   N3   C11   117.04  3.000
 2IN  C10   N3   C11   124.30  3.000
 2IN  C8    C10  O5    121.68  3.000
 2IN  C8    C10  N3    114.05  3.000
 2IN  O5    C10  N3    124.27  3.000
 2IN  H82   C8   H81   106.77  3.000
 2IN  H82   C8   N2    111.11  3.000
 2IN  H81   C8   N2    111.24  3.000
 2IN  H82   C8   C10   109.62  3.000
 2IN  H81   C8   C10   108.53  3.000
 2IN  N2    C8   C10   109.49  3.000
 2IN  HN2   N2   C7    120.73  3.000
 2IN  HN2   N2   C8    116.71  3.000
 2IN  C7    N2   C8    122.56  3.000
 2IN  C5    C7   O4    122.03  3.000
 2IN  C5    C7   N2    114.44  3.000
 2IN  O4    C7   N2    123.53  3.000
 2IN  H5    C5   N1    109.08  3.000
 2IN  H5    C5   C6    106.88  3.000
 2IN  N1    C5   C6    108.75  3.000
 2IN  H5    C5   C7    109.62  3.000
 2IN  N1    C5   C7    111.71  3.000
 2IN  C6    C5   C7    110.67  3.000
 2IN  H62   C6   H61   107.20  3.000
 2IN  H62   C6   O3    112.03  3.000
 2IN  H61   C6   O3    112.30  3.000
 2IN  H62   C6   C5    108.90  3.000
 2IN  H61   C6   C5    108.37  3.000
 2IN  O3    C6   C5    107.94  3.000
 2IN  HO3   O3   C6    108.59  3.000
 2IN  HN1   N1   S1    111.79  3.000
 2IN  HN1   N1   C5    114.61  3.000
 2IN  S1    N1   C5    119.40  3.000
 2IN  C1    S1   O1    107.63  3.000
 2IN  C1    S1   O2    107.82  3.000
 2IN  O1    S1   O2    119.78  3.000
 2IN  C1    S1   N1    102.47  3.000
 2IN  O1    S1   N1    108.64  3.000
 2IN  O2    S1   N1    109.12  3.000
 2IN  H12A  C1   H11   108.47  3.000
 2IN  H12A  C1   C4    112.63  3.000
 2IN  H11   C1   C4    112.54  3.000
 2IN  H12A  C1   S1    106.59  3.000
 2IN  H11   C1   S1    106.45  3.000
 2IN  C4    C1   S1    109.80  3.000
 2IN  C19   C4   C3    119.25  3.000
 2IN  C19   C4   C1    120.35  3.000
 2IN  C3    C4   C1    120.37  3.000
 2IN  H3    C3   C2    119.74  3.000
 2IN  H3    C3   C4    119.87  3.000
 2IN  C2    C3   C4    120.38  3.000
 2IN  H2    C2   C21   120.11  3.000
 2IN  H2    C2   C3    119.80  3.000
 2IN  C21   C2   C3    120.09  3.000
 2IN  H21   C21  C20   120.11  3.000
 2IN  H21   C21  C2    120.09  3.000
 2IN  C20   C21  C2    119.80  3.000
 2IN  H20   C20  C19   119.79  3.000
 2IN  H20   C20  C21   120.13  3.000
 2IN  C19   C20  C21   120.09  3.000
 2IN  H19   C19  C20   119.73  3.000
 2IN  H19   C19  C4    119.88  3.000
 2IN  C20   C19  C4    120.39  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
 2IN  CONST_01  C17   C12  C13  C14     0.00   0.0  0
 2IN  CONST_02  C17   C16  C15  C14     0.00   0.0  0
 2IN  CONST_03  C16   C15  C14  C13     0.00   0.0  0
 2IN  CONST_04  C16   C17  C12  C13     0.00   0.0  0
 2IN  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 2IN  CONST_06  C15   C16  C17  C12     0.00   0.0  0
 2IN  CONST_07  C21   C2   C3   C4      0.00   0.0  0
 2IN  CONST_08  C21   C20  C19  C4      0.00   0.0  0
 2IN  CONST_09  C20   C19  C4   C3      0.00   0.0  0
 2IN  CONST_10  C20   C21  C2   C3      0.00   0.0  0
 2IN  CONST_11  C19   C4   C3   C2      0.00   0.0  0
 2IN  CONST_12  C19   C20  C21  C2      0.00   0.0  0
 2IN  CONST_13  C12   C13  C14  C18   180.00   0.0  0
 2IN  CONST_14  C16   C15  C14  C18   180.00   0.0  0
 2IN  CONST_15  C11   C17  C12  C13   180.00   0.0  0
 2IN  CONST_16  C11   C17  C16  C15   180.00   0.0  0
 2IN  CONST_17  C2    C3   C4   C1    180.00   0.0  0
 2IN  CONST_18  C20   C19  C4   C1    180.00   0.0  0
 2IN  CONST_19  H12   C12  C13  C14   180.00   0.0  0
 2IN  CONST_20  H16   C16  C15  C14   180.00   0.0  0
 2IN  CONST_21  H15   C15  C14  C13   180.00   0.0  0
 2IN  CONST_22  H13   C13  C12  C17   180.00   0.0  0
 2IN  CONST_23  H2    C2   C3   C4    180.00   0.0  0
 2IN  CONST_24  H20   C20  C19  C4    180.00   0.0  0
 2IN  CONST_25  H19   C19  C4   C3    180.00   0.0  0
 2IN  CONST_26  H21   C21  C2   C3    180.00   0.0  0
 2IN  CONST_27  H3    C3   C2   C21   180.00   0.0  0
 2IN  CONST_28  HN41  N4   C18  C14   180.00   0.0  0
 2IN  CONST_30  HN5   N5   C18  C14     0.00   0.0  0
 2IN  CONST_31  O5    C10  N3   C11     0.00   0.0  0
 2IN  CONST_32  C8    C10  N3   C11   180.00   0.0  0
 2IN  CONST_33  O4    C7   N2   C8      0.00   0.0  0
 2IN  CONST_34  C5    C7   N2   C8    180.00   0.0  0
 2IN  CONST_35  HN3   N3   C10  O5    180.00   0.0  0
 2IN  CONST_36  HN2   N2   C7   O4    180.00   0.0  0
 2IN  Var_01    C13   C14  C18  N4   -146.54  30.0  2
 2IN  Var_02    N3    C11  C17  C12    57.50  30.0  2
 2IN  Var_03    C3    C4   C1   S1    -89.44  30.0  2
 2IN  Var_04    C10   N3   C11  C17  -104.75  30.0  3
 2IN  Var_05    C4    C1   S1   N1   -179.89  30.0  3
 2IN  Var_06    N2    C8   C10  N3    172.57  30.0  3
 2IN  Var_07    C7    N2   C8   C10  -176.72  30.0  3
 2IN  Var_08    O2    S1   N1   C5   -130.88  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
 2IN  chir_01  C5  C7  C6  N1  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
 2IN  plan-1  C18   0.020
 2IN  plan-1  C14   0.020
 2IN  plan-1  C13   0.020
 2IN  plan-1  C12   0.020
 2IN  plan-1  C17   0.020
 2IN  plan-1  C16   0.020
 2IN  plan-1  C15   0.020
 2IN  plan-1  C11   0.020
 2IN  plan-1  H13   0.020
 2IN  plan-1  H12   0.020
 2IN  plan-1  H16   0.020
 2IN  plan-1  H15   0.020
 2IN  plan-2  C1    0.020
 2IN  plan-2  C4    0.020
 2IN  plan-2  C3    0.020
 2IN  plan-2  C2    0.020
 2IN  plan-2  C21   0.020
 2IN  plan-2  C20   0.020
 2IN  plan-2  C19   0.020
 2IN  plan-2  H3    0.020
 2IN  plan-2  H2    0.020
 2IN  plan-2  H21   0.020
 2IN  plan-2  H20   0.020
 2IN  plan-2  H19   0.020
 2IN  plan-3  C11   0.020
 2IN  plan-3  N3    0.020
 2IN  plan-3  C10   0.020
 2IN  plan-3  O5    0.020
 2IN  plan-3  C8    0.020
 2IN  plan-3  HN3   0.020
 2IN  plan-4  C8    0.020
 2IN  plan-4  N2    0.020
 2IN  plan-4  C7    0.020
 2IN  plan-4  O4    0.020
 2IN  plan-4  C5    0.020
 2IN  plan-4  HN2   0.020
 2IN  plan-5  N4    0.020
 2IN  plan-5  N5    0.020
 2IN  plan-5  C18   0.020
 2IN  plan-5  C14   0.020
 2IN  plan-5  HN41  0.020
 2IN  plan-5  HN42  0.020
 2IN  plan-5  HN5   0.020

