# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:21:33 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-(butylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[S](=O)(=O)N[C@H](CO)C(=O)N[C@@H](C)C(=O)NCc1ccc(cc1)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
 SI1  SI1  N-(butylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-alaninamide  ligand  58  29  .  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_SI1
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
 SI1  N4   N  NH2   0  -0.822   -8.8290  -2.6422  -1.3546
 SI1  N5   N  N     0  -0.650   -9.4727  -1.4855   0.5957
 SI1  C18  C  C     0   0.333   -8.6871  -1.6843  -0.3918
 SI1  C14  C  CR6   0   0.039   -7.4605  -0.8466  -0.5042
 SI1  C13  C  CR16  0  -0.259   -7.4411   0.4198   0.0737
 SI1  C12  C  CR16  0  -0.282   -6.3131   1.2193  -0.0179
 SI1  C17  C  CR6   0   0.049   -5.1756   0.7720  -0.6819
 SI1  C16  C  CR16  0  -0.267   -5.1894  -0.4995  -1.2475
 SI1  C15  C  CR16  0  -0.278   -6.3180  -1.2993  -1.1633
 SI1  C11  C  CH2   0  -0.319   -3.9467   1.6323  -0.7665
 SI1  N3   N  NH1   0  -0.633   -2.9261   1.1333   0.1377
 SI1  C10  C  C     0   0.560   -1.6538   1.5414   0.0839
 SI1  O5   O  O     0  -0.493   -1.2301   2.3113  -0.7665
 SI1  C8   C  CH1   0  -0.199   -0.7639   1.0103   1.2033
 SI1  N2   N  NH1   0  -0.643    0.6060   1.0727   0.7570
 SI1  C7   C  C     0   0.587    1.5761   0.2996   1.2650
 SI1  O4   O  O     0  -0.478    1.3810  -0.5803   2.0836
 SI1  C5   C  CH1   0  -0.280    2.9777   0.6278   0.7328
 SI1  C6   C  CH2   0  -0.147    3.4376   1.9817   1.2624
 SI1  O3   O  OH1   0  -0.662    3.4183   1.9147   2.6644
 SI1  N1   N  NC1   0  -0.722    3.8821  -0.4399   1.1016
 SI1  S1   S  S     0   1.361    4.9073  -1.1305   0.0280
 SI1  O2   O  OS    0  -0.673    5.4939  -2.2781   0.7049
 SI1  O1   O  OS    0  -0.673    4.1640  -1.3340  -1.2087
 SI1  C1   C  CH2   0  -0.616    6.2173   0.0432  -0.3006
 SI1  C4   C  CH2   0  -0.424    7.2336  -0.5058  -1.2916
 SI1  C3   C  CH2   0  -0.422    8.3833   0.4747  -1.5011
 SI1  C2   C  CH3   0  -0.664    9.4086  -0.0534  -2.4935
 SI1  C9   C  CH3   0  -0.650   -0.9905   1.8294   2.4764
 SI1  H41  H  HNH2  0   0.392   -9.7129  -3.1246  -1.3986
 SI1  H42  H  HNH2  0   0.395   -8.4174  -2.4765  -2.2584
 SI1  H51  H  H     0   0.324  -10.2852  -2.0946   0.5479
 SI1  H14  H  HCR6  0   0.257   -8.3193   0.7813   0.5912
 SI1  H17  H  HCR6  0   0.258   -6.3195   2.2059   0.4298
 SI1  H16  H  HCR6  0   0.260   -4.3116  -0.8721  -1.7619
 SI1  H15  H  HCR6  0   0.260   -6.2916  -2.2878  -1.6034
 SI1  H11  H  HCH2  0   0.260   -4.1978   2.6686  -0.5250
 SI1  H12  H  HCH2  0   0.264   -3.5514   1.6263  -1.7837
 SI1  H31  H  HNH1  0   0.410   -3.2141   0.5210   0.8850
 SI1  H81  H  HCH1  0   0.281   -1.0194  -0.0330   1.4020
 SI1  H21  H  HNH1  0   0.401    0.8280   1.7839   0.0754
 SI1  H52  H  HCH1  0   0.312    2.9302   0.6932  -0.3569
 SI1  H61  H  HCH2  0   0.230    4.4403   2.1920   0.8714
 SI1  H62  H  HCH2  0   0.218    2.7788   2.7676   0.8744
 SI1  H32  H  HOH1  0   0.466    3.7900   2.7282   3.0176
 SI1  H13  H  HNC1  0   0.416    4.2110  -0.4415   2.0601
 SI1  H22  H  HCH2  0   0.293    6.6775   0.2711   0.6632
 SI1  H23  H  HCH2  0   0.291    5.7462   0.9533  -0.6785
 SI1  H43  H  HCH2  0   0.243    6.7455  -0.7072  -2.2479
 SI1  H44  H  HCH2  0   0.242    7.6314  -1.4561  -0.9270
 SI1  H33  H  HCH2  0   0.224    8.8663   0.6762  -0.5408
 SI1  H34  H  HCH2  0   0.224    7.9881   1.4315  -1.8537
 SI1  H24  H  HCH3  0   0.232   10.2262   0.6541  -2.6321
 SI1  H25  H  HCH3  0   0.221    9.8407  -0.9958  -2.1520
 SI1  H26  H  HCH3  0   0.221    8.9552  -0.2324  -3.4698
 SI1  H91  H  HCH3  0   0.241   -2.0242   1.7551   2.8138
 SI1  H92  H  HCH3  0   0.252   -0.3519   1.4583   3.2765
 SI1  H93  H  HCH3  0   0.237   -0.7562   2.8807   2.3079

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
 SI1  N4   C18  single    1.366  0.020  1.366
 SI1  N4   H41  single    0.890  0.020  1.040
 SI1  N4   H42  single    0.890  0.020  1.040
 SI1  N5   C18  double    1.277  0.020  1.277
 SI1  N5   H51  single    0.890  0.020  1.040
 SI1  C18  C14  single    1.490  0.020  1.490
 SI1  C14  C13  aromatic  1.392  0.020  1.392
 SI1  C14  C15  aromatic  1.395  0.020  1.395
 SI1  C13  C12  aromatic  1.386  0.020  1.386
 SI1  C13  H14  single    0.930  0.020  1.080
 SI1  C12  C17  aromatic  1.391  0.020  1.391
 SI1  C12  H17  single    0.930  0.020  1.080
 SI1  C17  C16  aromatic  1.392  0.020  1.392
 SI1  C17  C11  single    1.503  0.020  1.503
 SI1  C16  C15  aromatic  1.386  0.020  1.386
 SI1  C16  H16  single    0.930  0.020  1.080
 SI1  C15  H15  single    0.930  0.020  1.080
 SI1  C11  N3   single    1.452  0.020  1.452
 SI1  C11  H11  single    0.970  0.020  1.090
 SI1  C11  H12  single    0.970  0.020  1.090
 SI1  N3   C10  single    1.337  0.020  1.337
 SI1  N3   H31  single    0.860  0.020  1.020
 SI1  C10  O5   double    1.223  0.020  1.223
 SI1  C10  C8   single    1.525  0.020  1.525
 SI1  C8   N2   single    1.442  0.020  1.442
 SI1  C8   C9   single    1.531  0.020  1.531
 SI1  C8   H81  single    0.970  0.020  1.090
 SI1  N2   C7   single    1.340  0.020  1.340
 SI1  N2   H21  single    0.860  0.020  1.020
 SI1  C7   O4   double    1.218  0.020  1.218
 SI1  C7   C5   single    1.535  0.020  1.535
 SI1  C5   C6   single    1.525  0.020  1.525
 SI1  C5   N1   single    1.447  0.020  1.447
 SI1  C5   H52  single    0.970  0.020  1.090
 SI1  C6   O3   single    1.404  0.020  1.404
 SI1  C6   H61  single    0.970  0.020  1.090
 SI1  C6   H62  single    0.970  0.020  1.090
 SI1  O3   H32  single    0.850  0.020  0.980
 SI1  N1   S1   single    1.637  0.020  1.637
 SI1  N1   H13  single    0.890  0.020  1.040
 SI1  S1   O2   double    1.456  0.020  1.456
 SI1  S1   O1   double    1.457  0.020  1.457
 SI1  S1   C1   single    1.789  0.020  1.789
 SI1  C1   C4   single    1.522  0.020  1.522
 SI1  C1   H22  single    0.970  0.020  1.090
 SI1  C1   H23  single    0.970  0.020  1.090
 SI1  C4   C3   single    1.525  0.020  1.525
 SI1  C4   H43  single    0.970  0.020  1.090
 SI1  C4   H44  single    0.970  0.020  1.090
 SI1  C3   C2   single    1.521  0.020  1.521
 SI1  C3   H33  single    0.970  0.020  1.090
 SI1  C3   H34  single    0.970  0.020  1.090
 SI1  C2   H24  single    0.970  0.020  1.090
 SI1  C2   H25  single    0.970  0.020  1.090
 SI1  C2   H26  single    0.970  0.020  1.090
 SI1  C9   H91  single    0.970  0.020  1.090
 SI1  C9   H92  single    0.970  0.020  1.090
 SI1  C9   H93  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
 SI1  H42  N4   H41  113.46  3.000
 SI1  H42  N4   C18  118.36  3.000
 SI1  H41  N4   C18  117.23  3.000
 SI1  H51  N5   C18  111.21  3.000
 SI1  C14  C18  N5   118.50  3.000
 SI1  C14  C18  N4   115.27  3.000
 SI1  N5   C18  N4   126.18  3.000
 SI1  C15  C14  C13  118.69  3.000
 SI1  C15  C14  C18  121.85  3.000
 SI1  C13  C14  C18  119.45  3.000
 SI1  H14  C13  C12  119.99  3.000
 SI1  H14  C13  C14  119.43  3.000
 SI1  C12  C13  C14  120.58  3.000
 SI1  H17  C12  C17  119.66  3.000
 SI1  H17  C12  C13  119.56  3.000
 SI1  C17  C12  C13  120.78  3.000
 SI1  C11  C17  C16  120.55  3.000
 SI1  C11  C17  C12  120.77  3.000
 SI1  C16  C17  C12  118.67  3.000
 SI1  H16  C16  C15  119.36  3.000
 SI1  H16  C16  C17  119.94  3.000
 SI1  C15  C16  C17  120.70  3.000
 SI1  H15  C15  C16  118.84  3.000
 SI1  H15  C15  C14  120.58  3.000
 SI1  C16  C15  C14  120.57  3.000
 SI1  H12  C11  H11  107.12  3.000
 SI1  H12  C11  N3   108.91  3.000
 SI1  H11  C11  N3   110.46  3.000
 SI1  H12  C11  C17  110.22  3.000
 SI1  H11  C11  C17  110.03  3.000
 SI1  N3   C11  C17  110.06  3.000
 SI1  H31  N3   C10  119.14  3.000
 SI1  H31  N3   C11  118.00  3.000
 SI1  C10  N3   C11  122.61  3.000
 SI1  C8   C10  O5   121.83  3.000
 SI1  C8   C10  N3   114.79  3.000
 SI1  O5   C10  N3   123.35  3.000
 SI1  H81  C8   C9   108.98  3.000
 SI1  H81  C8   N2   108.66  3.000
 SI1  C9   C8   N2   112.02  3.000
 SI1  H81  C8   C10  109.24  3.000
 SI1  C9   C8   C10  109.73  3.000
 SI1  N2   C8   C10  108.17  3.000
 SI1  H21  N2   C7   120.19  3.000
 SI1  H21  N2   C8   116.63  3.000
 SI1  C7   N2   C8   123.04  3.000
 SI1  C5   C7   O4   122.27  3.000
 SI1  C5   C7   N2   113.97  3.000
 SI1  O4   C7   N2   123.76  3.000
 SI1  H52  C5   N1   108.99  3.000
 SI1  H52  C5   C6   107.84  3.000
 SI1  N1   C5   C6   112.22  3.000
 SI1  H52  C5   C7   108.59  3.000
 SI1  N1   C5   C7   108.95  3.000
 SI1  C6   C5   C7   110.18  3.000
 SI1  H62  C6   H61  106.61  3.000
 SI1  H62  C6   O3   112.29  3.000
 SI1  H61  C6   O3   112.20  3.000
 SI1  H62  C6   C5   109.41  3.000
 SI1  H61  C6   C5   108.80  3.000
 SI1  O3   C6   C5   107.48  3.000
 SI1  H32  O3   C6   108.73  3.000
 SI1  H13  N1   S1   114.60  3.000
 SI1  H13  N1   C5   116.43  3.000
 SI1  S1   N1   C5   122.38  3.000
 SI1  C1   S1   O1   108.01  3.000
 SI1  C1   S1   O2   107.91  3.000
 SI1  O1   S1   O2   119.34  3.000
 SI1  C1   S1   N1   107.59  3.000
 SI1  O1   S1   N1   107.22  3.000
 SI1  O2   S1   N1   106.26  3.000
 SI1  H23  C1   H22  108.25  3.000
 SI1  H23  C1   C4   111.30  3.000
 SI1  H22  C1   C4   111.62  3.000
 SI1  H23  C1   S1   107.12  3.000
 SI1  H22  C1   S1   106.46  3.000
 SI1  C4   C1   S1   111.83  3.000
 SI1  H44  C4   H43  107.12  3.000
 SI1  H44  C4   C3   109.30  3.000
 SI1  H43  C4   C3   109.58  3.000
 SI1  H44  C4   C1   109.85  3.000
 SI1  H43  C4   C1   109.76  3.000
 SI1  C3   C4   C1   111.16  3.000
 SI1  H34  C3   H33  106.35  3.000
 SI1  H34  C3   C2   109.69  3.000
 SI1  H33  C3   C2   109.82  3.000
 SI1  H34  C3   C4   109.53  3.000
 SI1  H33  C3   C4   109.31  3.000
 SI1  C2   C3   C4   111.98  3.000
 SI1  H26  C2   H25  107.63  3.000
 SI1  H26  C2   H24  107.72  3.000
 SI1  H25  C2   H24  107.65  3.000
 SI1  H26  C2   C3   111.13  3.000
 SI1  H25  C2   C3   111.25  3.000
 SI1  H24  C2   C3   111.29  3.000
 SI1  H93  C9   H92  108.43  3.000
 SI1  H93  C9   H91  108.51  3.000
 SI1  H92  C9   H91  107.79  3.000
 SI1  H93  C9   C8   110.83  3.000
 SI1  H92  C9   C8   109.99  3.000
 SI1  H91  C9   C8   111.18  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
 SI1  CONST_01  C17  C12  C13  C14     0.00   0.0  0
 SI1  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 SI1  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 SI1  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 SI1  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 SI1  CONST_06  C15  C16  C17  C12     0.00   0.0  0
 SI1  CONST_07  C12  C13  C14  C18   180.00   0.0  0
 SI1  CONST_08  C16  C15  C14  C18   180.00   0.0  0
 SI1  CONST_09  C11  C17  C12  C13   180.00   0.0  0
 SI1  CONST_10  C11  C17  C16  C15   180.00   0.0  0
 SI1  CONST_11  H17  C12  C13  C14   180.00   0.0  0
 SI1  CONST_12  H16  C16  C15  C14   180.00   0.0  0
 SI1  CONST_13  H15  C15  C14  C13   180.00   0.0  0
 SI1  CONST_14  H14  C13  C12  C17   180.00   0.0  0
 SI1  CONST_15  H41  N4   C18  C14   180.00   0.0  0
 SI1  CONST_17  H51  N5   C18  C14   180.00   0.0  0
 SI1  CONST_18  O5   C10  N3   C11     0.00   0.0  0
 SI1  CONST_19  C8   C10  N3   C11   180.00   0.0  0
 SI1  CONST_20  O4   C7   N2   C8      0.00   0.0  0
 SI1  CONST_21  C5   C7   N2   C8    180.00   0.0  0
 SI1  CONST_22  H31  N3   C10  O5    180.00   0.0  0
 SI1  CONST_23  H21  N2   C7   O4    180.00   0.0  0
 SI1  Var_01    C13  C14  C18  N4    156.54  30.0  2
 SI1  Var_02    N3   C11  C17  C12   105.27  30.0  2
 SI1  Var_03    C10  N3   C11  C17   166.79  30.0  3
 SI1  Var_04    O2   S1   N1   C5   -171.60  30.0  3
 SI1  Var_05    C4   C1   S1   N1    179.86  30.0  3
 SI1  Var_06    C3   C4   C1   S1   -176.84  30.0  3
 SI1  Var_07    C2   C3   C4   C1   -179.78  30.0  3
 SI1  Var_08    H24  C2   C3   C4   -179.81  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
 SI1  chir_01  C8  C10  N2  C9  negativ
 SI1  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
 SI1  plan-1  C18  0.020
 SI1  plan-1  C14  0.020
 SI1  plan-1  C13  0.020
 SI1  plan-1  C12  0.020
 SI1  plan-1  C17  0.020
 SI1  plan-1  C16  0.020
 SI1  plan-1  C15  0.020
 SI1  plan-1  C11  0.020
 SI1  plan-1  H14  0.020
 SI1  plan-1  H17  0.020
 SI1  plan-1  H16  0.020
 SI1  plan-1  H15  0.020
 SI1  plan-2  C11  0.020
 SI1  plan-2  N3   0.020
 SI1  plan-2  C10  0.020
 SI1  plan-2  O5   0.020
 SI1  plan-2  C8   0.020
 SI1  plan-2  H31  0.020
 SI1  plan-3  C8   0.020
 SI1  plan-3  N2   0.020
 SI1  plan-3  C7   0.020
 SI1  plan-3  O4   0.020
 SI1  plan-3  C5   0.020
 SI1  plan-3  H21  0.020
 SI1  plan-4  N4   0.020
 SI1  plan-4  N5   0.020
 SI1  plan-4  C18  0.020
 SI1  plan-4  C14  0.020
 SI1  plan-4  H41  0.020
 SI1  plan-4  H42  0.020
 SI1  plan-4  H51  0.020

