# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:23:13 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-[(5-carbamimidoylthiophen-2-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1sc(CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)NCC(O)=O)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
 3SP  3SP  N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-[(5-carbamimidoylthiophen-2-yl)methyl]-L-prolinamide  peptide  64  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3SP
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
 3SP  C18   C  C      0   0.556   0.7597  -1.1979  -0.0680
 3SP  O19   O  O      0  -0.477  -0.2975  -0.8673  -0.5890
 3SP  C20   C  CH1    0  -0.205   1.9715  -0.2647  -0.0051
 3SP  C24   C  CH2    0  -0.444   2.8602  -0.5248  -1.2255
 3SP  C25   C  CH1    0  -0.221   4.1857   0.2336  -1.2382
 3SP  C26   C  CH2    0  -0.424   5.1053  -0.1769  -0.0881
 3SP  C27   C  CH2    0  -0.427   6.4571   0.5293  -0.1539
 3SP  C28   C  CH2    0  -0.427   7.1435   0.3120  -1.4977
 3SP  C29   C  CH2    0  -0.430   6.2353   0.7325  -2.6478
 3SP  C30   C  CH2    0  -0.415   4.8896   0.0185  -2.5788
 3SP  N21   N  NH1    0  -0.609   1.6263   1.1317   0.1290
 3SP  C22   C  CH2    0  -0.403   1.1316   1.8475  -1.0295
 3SP  C23   C  C      0   0.417   0.3563   3.1140  -0.6267
 3SP  O31   O  OC    -1  -0.613   0.2413   3.9919  -1.5022
 3SP  O32   O  O      0  -0.614  -0.1364   3.1409   0.5238
 3SP  N17   N  NT     0  -0.476   0.8895  -2.4213   0.4824
 3SP  C13   C  CH1    0  -0.168  -0.2621  -3.3027   0.5323
 3SP  C11   C  C      0   0.569  -1.4082  -2.6355   1.2846
 3SP  O12   O  O      0  -0.485  -1.2113  -2.0122   2.3136
 3SP  C14   C  CH2    0  -0.482   0.2513  -4.5350   1.2961
 3SP  C15   C  CH2    0  -0.467   1.7630  -4.4819   1.0976
 3SP  C16   C  CH2    0  -0.284   2.0581  -2.9905   1.1386
 3SP  C1    C  CR5    0  -0.223  -4.4528   1.2222  -0.1239
 3SP  C2    C  CR15   0  -0.195  -5.6620   0.7504   0.3014
 3SP  C3    C  CR15   0  -0.210  -5.5782  -0.5496   0.8544
 3SP  C4    C  CR5    0  -0.171  -4.3077  -1.0506   0.8437
 3SP  S5    S  S2     0   0.260  -3.2040   0.0631   0.1438
 3SP  N7    N  N      0  -0.660  -5.1873   3.1384  -1.2948
 3SP  N8    N  NH2    0  -0.845  -2.8810   2.8711  -0.8717
 3SP  C9    C  CH2    0  -0.344  -3.8401  -2.3685   1.3889
 3SP  N10   N  NH1    0  -0.639  -2.6324  -2.8564   0.7738
 3SP  H20   H  HCH1   0   0.250   2.5380  -0.5288   0.8946
 3SP  H241  H  HCH2   0   0.235   3.0715  -1.5976  -1.2953
 3SP  H242  H  HCH2   0   0.240   2.2966  -0.2779  -2.1303
 3SP  H25   H  HCH1   0   0.218   3.9774   1.3056  -1.1350
 3SP  H261  H  HCH2   0   0.228   4.6351   0.0397   0.8745
 3SP  H262  H  HCH2   0   0.203   5.2584  -1.2631  -0.1245
 3SP  H271  H  HCH2   0   0.207   6.3085   1.6030   0.0056
 3SP  H272  H  HCH2   0   0.224   7.0981   0.1824   0.6604
 3SP  H281  H  HCH2   0   0.223   8.0854   0.8652  -1.5349
 3SP  H282  H  HCH2   0   0.206   7.3993  -0.7478  -1.6076
 3SP  H291  H  HCH2   0   0.207   6.0731   1.8151  -2.6040
 3SP  H292  H  HCH2   0   0.223   6.7170   0.5299  -3.6076
 3SP  H301  H  HCH2   0   0.203   5.0425  -1.0570  -2.7330
 3SP  H302  H  HCH2   0   0.223   4.2419   0.3586  -3.3925
 3SP  HN21  H  HNH1   0   0.340   0.9615   1.2668   0.8800
 3SP  H221  H  HCH2   0   0.203   1.9625   2.1389  -1.6792
 3SP  H222  H  HCH2   0   0.216   0.4457   1.2588  -1.6527
 3SP  H13   H  HCH1   0   0.271  -0.5760  -3.5803  -0.4793
 3SP  H141  H  HCH2   0   0.251   0.0169  -4.4503   2.3590
 3SP  H142  H  HCH2   0   0.264  -0.2016  -5.4535   0.9271
 3SP  H151  H  HCH2   0   0.255   2.3094  -5.0334   1.8615
 3SP  H152  H  HCH2   0   0.244   2.0383  -4.8891   0.1227
 3SP  H161  H  HCH2   0   0.243   2.1467  -2.6339   2.1699
 3SP  H162  H  HCH2   0   0.254   2.9801  -2.7377   0.6157
 3SP  H3    H  HCR5   0   0.261  -6.4269  -1.0970   1.2419
 3SP  HN7   H  H      0   0.321  -4.8906   4.0254  -1.6929
 3SP  HN81  H  HNH2   0   0.395  -2.2164   2.5944  -0.1626
 3SP  HN82  H  HNH2   0   0.385  -2.6642   3.7687  -1.2744
 3SP  H91   H  HCH2   0   0.275  -3.6698  -2.2856   2.4631
 3SP  H92   H  HCH2   0   0.280  -4.6306  -3.1070   1.2516
 3SP  HN10  H  HNH1   0   0.405  -2.7124  -3.3132  -0.1202
 3SP  C6    C  C      0   0.347  -4.1915   2.5076  -0.7958
 3SP  H2    H  HCR5   0   0.259  -6.5784   1.3156   0.2105

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
 3SP  C1   C2    aromatic  1.366  0.020  1.366
 3SP  C1   S5    aromatic  1.725  0.020  1.725
 3SP  C1   C6    single    1.474  0.020  1.474
 3SP  C2   C3    aromatic  1.415  0.020  1.415
 3SP  C2   H2    single    0.930  0.020  1.080
 3SP  C3   C4    aromatic  1.366  0.020  1.366
 3SP  C3   H3    single    0.930  0.020  1.080
 3SP  C4   S5    aromatic  1.717  0.020  1.717
 3SP  C4   C9    single    1.501  0.020  1.501
 3SP  C6   N7    double    1.280  0.020  1.280
 3SP  C6   N8    single    1.362  0.020  1.362
 3SP  N7   HN7   single    0.890  0.020  1.040
 3SP  N8   HN81  single    0.890  0.020  1.040
 3SP  N8   HN82  single    0.890  0.020  1.040
 3SP  C9   N10   single    1.440  0.020  1.440
 3SP  C9   H91   single    0.970  0.020  1.090
 3SP  C9   H92   single    0.970  0.020  1.090
 3SP  N10  C11   single    1.345  0.020  1.345
 3SP  N10  HN10  single    0.860  0.020  1.020
 3SP  C11  O12   double    1.219  0.020  1.219
 3SP  C11  C13   single    1.525  0.020  1.525
 3SP  C13  C14   single    1.538  0.020  1.538
 3SP  C13  N17   single    1.451  0.020  1.451
 3SP  C13  H13   single    0.970  0.020  1.090
 3SP  C14  C15   single    1.526  0.020  1.526
 3SP  C14  H141  single    0.970  0.020  1.090
 3SP  C14  H142  single    0.970  0.020  1.090
 3SP  C15  C16   single    1.521  0.020  1.521
 3SP  C15  H151  single    0.970  0.020  1.090
 3SP  C15  H152  single    0.970  0.020  1.090
 3SP  C16  N17   single    1.456  0.020  1.456
 3SP  C16  H161  single    0.970  0.020  1.090
 3SP  C16  H162  single    0.970  0.020  1.090
 3SP  N17  C18   single    1.348  0.020  1.348
 3SP  C18  O19   double    1.224  0.020  1.224
 3SP  C18  C20   single    1.531  0.020  1.531
 3SP  C20  N21   single    1.445  0.020  1.445
 3SP  C20  C24   single    1.532  0.020  1.532
 3SP  C20  H20   single    0.970  0.020  1.090
 3SP  N21  C22   single    1.449  0.020  1.449
 3SP  N21  HN21  single    0.890  0.020  1.040
 3SP  C22  C23   single    1.539  0.020  1.539
 3SP  C22  H221  single    0.970  0.020  1.090
 3SP  C22  H222  single    0.970  0.020  1.090
 3SP  C23  O31   deloc     1.245  0.020  1.245
 3SP  C23  O32   deloc     1.252  0.020  1.252
 3SP  C24  C25   single    1.527  0.020  1.527
 3SP  C24  H241  single    0.970  0.020  1.090
 3SP  C24  H242  single    0.970  0.020  1.090
 3SP  C25  C26   single    1.529  0.020  1.529
 3SP  C25  C30   single    1.529  0.020  1.529
 3SP  C25  H25   single    0.970  0.020  1.090
 3SP  C26  C27   single    1.527  0.020  1.527
 3SP  C26  H261  single    0.970  0.020  1.090
 3SP  C26  H262  single    0.970  0.020  1.090
 3SP  C27  C28   single    1.525  0.020  1.525
 3SP  C27  H271  single    0.970  0.020  1.090
 3SP  C27  H272  single    0.970  0.020  1.090
 3SP  C28  C29   single    1.525  0.020  1.525
 3SP  C28  H281  single    0.970  0.020  1.090
 3SP  C28  H282  single    0.970  0.020  1.090
 3SP  C29  C30   single    1.525  0.020  1.525
 3SP  C29  H291  single    0.970  0.020  1.090
 3SP  C29  H292  single    0.970  0.020  1.090
 3SP  C30  H301  single    0.970  0.020  1.090
 3SP  C30  H302  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
 3SP  N17   C18  C20   117.41  3.000
 3SP  C20   C18  O19   122.45  3.000
 3SP  N17   C18  O19   120.14  3.000
 3SP  H20   C20  N21   106.28  3.000
 3SP  H20   C20  C24   108.26  3.000
 3SP  N21   C20  C24   112.13  3.000
 3SP  H20   C20  C18   107.23  3.000
 3SP  C24   C20  C18   108.85  3.000
 3SP  N21   C20  C18   113.82  3.000
 3SP  H242  C24  H241  105.52  3.000
 3SP  H242  C24  C25   109.16  3.000
 3SP  H241  C24  C25   108.56  3.000
 3SP  H242  C24  C20   108.76  3.000
 3SP  H241  C24  C20   109.20  3.000
 3SP  C25   C24  C20   115.20  3.000
 3SP  H25   C25  C30   107.90  3.000
 3SP  H25   C25  C26   107.81  3.000
 3SP  C30   C25  C26   110.18  3.000
 3SP  H25   C25  C24   108.64  3.000
 3SP  C30   C25  C24   109.69  3.000
 3SP  C26   C25  C24   112.49  3.000
 3SP  H262  C26  H261  106.58  3.000
 3SP  H262  C26  C27   109.44  3.000
 3SP  H261  C26  C27   109.10  3.000
 3SP  H262  C26  C25   108.95  3.000
 3SP  H261  C26  C25   110.53  3.000
 3SP  C27   C26  C25   112.09  3.000
 3SP  H272  C27  H271  106.39  3.000
 3SP  H272  C27  C28   110.33  3.000
 3SP  H271  C27  C28   109.22  3.000
 3SP  H272  C27  C26   109.90  3.000
 3SP  H271  C27  C26   109.08  3.000
 3SP  C28   C27  C26   111.76  3.000
 3SP  H282  C28  H281  106.56  3.000
 3SP  H282  C28  C29   109.28  3.000
 3SP  H281  C28  C29   110.37  3.000
 3SP  H282  C28  C27   109.35  3.000
 3SP  H281  C28  C27   110.23  3.000
 3SP  C29   C28  C27   110.94  3.000
 3SP  H292  C29  H291  106.47  3.000
 3SP  H292  C29  C30   109.99  3.000
 3SP  H291  C29  C30   109.28  3.000
 3SP  H292  C29  C28   110.42  3.000
 3SP  H291  C29  C28   109.31  3.000
 3SP  C30   C29  C28   111.25  3.000
 3SP  H302  C30  H301  106.41  3.000
 3SP  H302  C30  C29   110.07  3.000
 3SP  H301  C30  C29   109.24  3.000
 3SP  H302  C30  C25   109.62  3.000
 3SP  H301  C30  C25   108.98  3.000
 3SP  C29   C30  C25   112.33  3.000
 3SP  HN21  N21  C22   107.64  3.000
 3SP  HN21  N21  C20   110.78  3.000
 3SP  C22   N21  C20   119.00  3.000
 3SP  H222  C22  H221  106.27  3.000
 3SP  H222  C22  C23   105.97  3.000
 3SP  H221  C22  C23   108.59  3.000
 3SP  H222  C22  N21   113.72  3.000
 3SP  H221  C22  N21   110.30  3.000
 3SP  C23   C22  N21   111.68  3.000
 3SP  O32   C23  O31   126.49  3.000
 3SP  O32   C23  C22   117.17  3.000
 3SP  O31   C23  C22   116.28  3.000
 3SP  C16   N17  C13   112.58  3.000
 3SP  C16   N17  C18   128.03  3.000
 3SP  C13   N17  C18   119.27  3.000
 3SP  H13   C13  C14   110.57  3.000
 3SP  H13   C13  C11   110.57  3.000
 3SP  C14   C13  C11   110.89  3.000
 3SP  H13   C13  N17   110.47  3.000
 3SP  C14   C13  N17   103.82  3.000
 3SP  C11   C13  N17   110.35  3.000
 3SP  N10   C11  O12   123.48  3.000
 3SP  O12   C11  C13   121.25  3.000
 3SP  N10   C11  C13   115.15  3.000
 3SP  H142  C14  H141  107.83  3.000
 3SP  H142  C14  C15   113.43  3.000
 3SP  H141  C14  C15   109.68  3.000
 3SP  H142  C14  C13   111.64  3.000
 3SP  H141  C14  C13   110.46  3.000
 3SP  C15   C14  C13   103.79  3.000
 3SP  H152  C15  H151  108.11  3.000
 3SP  H152  C15  C16   109.93  3.000
 3SP  H151  C15  C16   112.35  3.000
 3SP  H152  C15  C14   110.67  3.000
 3SP  H151  C15  C14   112.84  3.000
 3SP  C16   C15  C14   102.88  3.000
 3SP  H162  C16  H161  107.94  3.000
 3SP  H162  C16  C15   112.26  3.000
 3SP  H161  C16  C15   111.13  3.000
 3SP  H162  C16  N17   111.85  3.000
 3SP  H161  C16  N17   111.23  3.000
 3SP  C15   C16  N17   102.44  3.000
 3SP  C6    C1   S5    121.91  3.000
 3SP  C6    C1   C2    126.88  3.000
 3SP  S5    C1   C2    111.13  3.000
 3SP  H2    C2   C3    124.30  3.000
 3SP  H2    C2   C1    122.96  3.000
 3SP  C3    C2   C1    112.74  3.000
 3SP  H3    C3   C4    123.17  3.000
 3SP  H3    C3   C2    123.94  3.000
 3SP  C4    C3   C2    112.89  3.000
 3SP  C9    C4   S5    121.15  3.000
 3SP  C9    C4   C3    127.52  3.000
 3SP  S5    C4   C3    111.30  3.000
 3SP  C4    S5   C1     91.94  3.000
 3SP  HN7   N7   C6    110.83  3.000
 3SP  HN82  N8   HN81  112.51  3.000
 3SP  HN82  N8   C6    117.85  3.000
 3SP  HN81  N8   C6    121.37  3.000
 3SP  H92   C9   H91   106.77  3.000
 3SP  H92   C9   N10   108.94  3.000
 3SP  H91   C9   N10   108.39  3.000
 3SP  H92   C9   C4    108.85  3.000
 3SP  H91   C9   C4    109.85  3.000
 3SP  N10   C9   C4    113.80  3.000
 3SP  HN10  N10  C9    117.78  3.000
 3SP  HN10  N10  C11   118.94  3.000
 3SP  C9    N10  C11   123.05  3.000
 3SP  N8    C6   N7    126.53  3.000
 3SP  N8    C6   C1    115.39  3.000
 3SP  N7    C6   C1    118.01  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
 3SP  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 3SP  CONST_02  C3    C4   S5   C1     0.00   0.0  0
 3SP  CONST_03  C4    S5   C1   C2     0.00   0.0  0
 3SP  CONST_04  S5    C4   C3   C2     0.00   0.0  0
 3SP  CONST_05  S5    C1   C2   C3     0.00   0.0  0
 3SP  CONST_06  C9    C4   S5   C1   180.00   0.0  0
 3SP  CONST_07  C9    C4   C3   C2   180.00   0.0  0
 3SP  CONST_08  C6    C1   C2   C3   180.00   0.0  0
 3SP  CONST_09  C6    C1   S5   C4   180.00   0.0  0
 3SP  CONST_10  H3    C3   C2   C1   180.00   0.0  0
 3SP  CONST_11  H2    C2   C3   C4   180.00   0.0  0
 3SP  CONST_12  C13   N17  C18  O19    0.00   0.0  0
 3SP  CONST_13  C16   N17  C18  O19  180.00   0.0  0
 3SP  CONST_14  C13   N17  C18  C20  180.00   0.0  0
 3SP  CONST_15  C16   N17  C18  C20    0.00   0.0  0
 3SP  CONST_16  C9    N10  C11  C13  180.00   0.0  0
 3SP  CONST_17  HN10  N10  C11  C13    0.00   0.0  0
 3SP  CONST_18  HN7   N7   C6   C1   180.00   0.0  0
 3SP  CONST_20  HN82  N8   C6   C1   180.00   0.0  0
 3SP  CONST_21  C9    N10  C11  O12    0.00   0.0  0
 3SP  Var_01    C28   C27  C26  C25  -55.01  30.0  1
 3SP  Var_02    C28   C29  C30  C25   55.69  30.0  1
 3SP  Var_03    C29   C28  C27  C26   54.81  30.0  1
 3SP  Var_04    C30   C29  C28  C27  -54.94  30.0  1
 3SP  Var_05    C14   C15  C16  N17  -35.91  30.0  1
 3SP  Var_06    C16   C15  C14  C13   36.54  30.0  1
 3SP  Var_07    C15   C16  N17  C13   22.76  30.0  1
 3SP  Var_08    N7    C6   C1   C2   -15.97  30.0  2
 3SP  Var_09    N10   C9   C4   C3   155.77  30.0  2
 3SP  Var_10    C4    C9   N10  C11   94.28  30.0  2
 3SP  Var_11    C23   C22  N21  C20  159.49  30.0  3
 3SP  Var_12    O31   C23  C22  N21  159.12  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
 3SP  chir_01  C20  C18  N21  C24  positiv
 3SP  chir_02  C25  C24  C26  C30  negativ
 3SP  chir_03  C13  N17  C11  C14  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
 3SP  plan-1  C1    0.020
 3SP  plan-1  C2    0.020
 3SP  plan-1  C3    0.020
 3SP  plan-1  C4    0.020
 3SP  plan-1  S5    0.020
 3SP  plan-1  C9    0.020
 3SP  plan-1  H3    0.020
 3SP  plan-1  C6    0.020
 3SP  plan-1  H2    0.020
 3SP  plan-2  C13   0.020
 3SP  plan-2  C11   0.020
 3SP  plan-2  O12   0.020
 3SP  plan-2  C9    0.020
 3SP  plan-2  N10   0.020
 3SP  plan-2  HN10  0.020
 3SP  plan-3  C18   0.020
 3SP  plan-3  O19   0.020
 3SP  plan-3  C20   0.020
 3SP  plan-3  N17   0.020
 3SP  plan-3  C13   0.020
 3SP  plan-3  C16   0.020
 3SP  plan-4  C1    0.020
 3SP  plan-4  N7    0.020
 3SP  plan-4  N8    0.020
 3SP  plan-4  HN7   0.020
 3SP  plan-4  HN81  0.020
 3SP  plan-4  HN82  0.020
 3SP  plan-4  C6    0.020
 3SP  plan-5  C22   0.020
 3SP  plan-5  C23   0.020
 3SP  plan-5  O31   0.020
 3SP  plan-5  O32   0.020

