# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:12:34 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  65  32  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.579   0.7952  -1.3776   0.0249
 3SP  O19   O  O     0  -0.482  -0.2116  -0.9881  -0.5545
 3SP  C20   C  CH1   0  -0.216   2.0392  -0.4920   0.1357
 3SP  C24   C  CH2   0  -0.454   2.8749  -0.6782  -1.1361
 3SP  C25   C  CH1   0  -0.216   4.0732   0.2577  -1.2667
 3SP  C26   C  CH2   0  -0.421   5.0528   0.1390  -0.1007
 3SP  C27   C  CH2   0  -0.429   6.2585   1.0574  -0.2837
 3SP  C28   C  CH2   0  -0.428   6.9673   0.7997  -1.6091
 3SP  C29   C  CH2   0  -0.431   5.9954   0.9121  -2.7793
 3SP  C30   C  CH2   0  -0.413   4.7931  -0.0060  -2.5897
 3SP  N21   N  NH1   0  -0.585   1.7406   0.8951   0.4074
 3SP  C22   C  CH2   0  -0.418   1.0025   1.6633  -0.5564
 3SP  C23   C  C     0   0.528   1.3743   3.1269  -0.4955
 3SP  O31   O  OH1   0  -0.600   0.6862   3.8271  -1.3967
 3SP  O32   O  O     0  -0.439   2.1697   3.6243   0.2579
 3SP  N17   N  NT    0  -0.480   0.8388  -2.6056   0.5684
 3SP  C13   C  CH1   0  -0.166  -0.3447  -3.4460   0.5287
 3SP  C11   C  C     0   0.572  -1.5164  -2.7510   1.2120
 3SP  O12   O  O     0  -0.487  -1.3726  -2.1593   2.2683
 3SP  C14   C  CH2   0  -0.479   0.0799  -4.7041   1.3010
 3SP  C15   C  CH2   0  -0.471   1.5964  -4.7267   1.1433
 3SP  C16   C  CH2   0  -0.280   1.9695  -3.2536   1.2212
 3SP  C1    C  CR5   0  -0.220  -4.2131   1.3901   0.0508
 3SP  C2    C  CR15  0  -0.193  -5.4841   0.9002   0.1386
 3SP  C3    C  CR15  0  -0.213  -5.5148  -0.4692   0.4996
 3SP  C4    C  CR5   0  -0.162  -4.2707  -0.9978   0.6944
 3SP  S5    S  S2    0   0.265  -3.0468   0.1770   0.4265
 3SP  N7    N  N     0  -0.643  -4.6018   3.7211  -0.0389
 3SP  N8    N  NH2   0  -0.826  -2.5481   2.8567  -0.8408
 3SP  C9    C  CH2   0  -0.355  -3.9338  -2.3852   1.1555
 3SP  N10   N  NH1   0  -0.635  -2.7070  -2.9088   0.6090
 3SP  H20   H  HCH1  0   0.263   2.6373  -0.8250   0.9876
 3SP  H241  H  HCH2  0   0.239   3.2266  -1.7156  -1.1676
 3SP  H242  H  HCH2  0   0.237   2.2364  -0.5632  -2.0180
 3SP  H25   H  HCH1  0   0.221   3.7047   1.2906  -1.2809
 3SP  H261  H  HCH2  0   0.231   4.5509   0.3789   0.8395
 3SP  H262  H  HCH2  0   0.200   5.3958  -0.9005  -0.0213
 3SP  H271  H  HCH2  0   0.207   5.9214   2.0994  -0.2512
 3SP  H272  H  HCH2  0   0.223   6.9548   0.9327   0.5495
 3SP  H281  H  HCH2  0   0.224   7.7981   1.4983  -1.7369
 3SP  H282  H  HCH2  0   0.206   7.4046  -0.2051  -1.5960
 3SP  H291  H  HCH2  0   0.207   5.6467   1.9475  -2.8619
 3SP  H292  H  HCH2  0   0.223   6.5013   0.6801  -3.7198
 3SP  H301  H  HCH2  0   0.203   5.1265  -1.0508  -2.6129
 3SP  H302  H  HCH2  0   0.222   4.0936   0.1127  -3.4228
 3SP  HN21  H  HNH1  0   0.357   1.3444   0.9967   1.3304
 3SP  H221  H  HCH2  0   0.272   1.2171   1.3175  -1.5699
 3SP  H222  H  HCH2  0   0.267  -0.0860   1.5905  -0.4525
 3SP  HO31  H  HOH1  0   0.479   0.9265   4.7636  -1.3410
 3SP  H13   H  HCH1  0   0.272  -0.5976  -3.6999  -0.5059
 3SP  H141  H  HCH2  0   0.251  -0.1808  -4.6080   2.3569
 3SP  H142  H  HCH2  0   0.265  -0.4090  -5.5969   0.9152
 3SP  H151  H  HCH2  0   0.257   2.0934  -5.3201   1.9094
 3SP  H152  H  HCH2  0   0.245   1.8751  -5.1304   0.1679
 3SP  H161  H  HCH2  0   0.245   2.0675  -2.9241   2.2600
 3SP  H162  H  HCH2  0   0.254   2.9065  -3.0387   0.7083
 3SP  H2    H  HCR5  0   0.262  -6.3615   1.4948  -0.0715
 3SP  H3    H  HCR5  0   0.263  -6.4237  -1.0452   0.6098
 3SP  HN7   H  H     0   0.326  -4.2315   4.6060  -0.3761
 3SP  HN81  H  HNH2  0   0.393  -2.2401   2.1090  -1.4424
 3SP  HN82  H  HNH2  0   0.390  -2.2582   3.7658  -1.1657
 3SP  H91   H  HCH2  0   0.275  -3.8633  -2.4071   2.2440
 3SP  H92   H  HCH2  0   0.281  -4.7518  -3.0511   0.8802
 3SP  HN10  H  HNH1  0   0.405  -2.7393  -3.3178  -0.3108
 3SP  C6    C  C     0   0.333  -3.8056   2.7593  -0.3040

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  1.365  0.020  1.365
 3SP  C1   S5    aromatic  1.724  0.020  1.724
 3SP  C1   C6    single    1.472  0.020  1.472
 3SP  C2   C3    aromatic  1.417  0.020  1.417
 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    1.500  0.020  1.500
 3SP  C6   N7    double    1.276  0.020  1.276
 3SP  C6   N8    single    1.371  0.020  1.371
 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    1.442  0.020  1.442
 3SP  C9   H91   single    0.970  0.020  1.090
 3SP  C9   H92   single    0.970  0.020  1.090
 3SP  N10  C11   single    1.344  0.020  1.344
 3SP  N10  HN10  single    0.860  0.020  1.020
 3SP  C11  O12   double    1.219  0.020  1.219
 3SP  C11  C13   single    1.524  0.020  1.524
 3SP  C13  C14   single    1.536  0.020  1.536
 3SP  C13  N17   single    1.452  0.020  1.452
 3SP  C13  H13   single    0.970  0.020  1.090
 3SP  C14  C15   single    1.525  0.020  1.525
 3SP  C14  H141  single    0.970  0.020  1.090
 3SP  C14  H142  single    0.970  0.020  1.090
 3SP  C15  C16   single    1.522  0.020  1.522
 3SP  C15  H151  single    0.970  0.020  1.090
 3SP  C15  H152  single    0.970  0.020  1.090
 3SP  C16  N17   single    1.458  0.020  1.458
 3SP  C16  H161  single    0.970  0.020  1.090
 3SP  C16  H162  single    0.970  0.020  1.090
 3SP  N17  C18   single    1.344  0.020  1.344
 3SP  C18  O19   double    1.225  0.020  1.225
 3SP  C18  C20   single    1.531  0.020  1.531
 3SP  C20  N21   single    1.445  0.020  1.445
 3SP  C20  C24   single    1.533  0.020  1.533
 3SP  C20  H20   single    0.970  0.020  1.090
 3SP  N21  C22   single    1.437  0.020  1.437
 3SP  N21  HN21  single    0.890  0.020  1.040
 3SP  C22  C23   single    1.511  0.020  1.511
 3SP  C22  H221  single    0.970  0.020  1.090
 3SP  C22  H222  single    0.970  0.020  1.090
 3SP  C23  O31   single    1.333  0.020  1.333
 3SP  C23  O32   double    1.203  0.020  1.203
 3SP  C24  C25   single    1.526  0.020  1.526
 3SP  C24  H241  single    0.970  0.020  1.090
 3SP  C24  H242  single    0.970  0.020  1.090
 3SP  C25  C26   single    1.528  0.020  1.528
 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
 3SP  O31  HO31  single    0.850  0.020  0.980

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   118.23  3.000
 3SP  C20   C18  O19   121.20  3.000
 3SP  N17   C18  O19   120.56  3.000
 3SP  H20   C20  N21   105.01  3.000
 3SP  H20   C20  C24   108.14  3.000
 3SP  N21   C20  C24   112.66  3.000
 3SP  H20   C20  C18   108.96  3.000
 3SP  C24   C20  C18   108.22  3.000
 3SP  N21   C20  C18   113.65  3.000
 3SP  H242  C24  H241  105.27  3.000
 3SP  H242  C24  C25   108.94  3.000
 3SP  H241  C24  C25   109.03  3.000
 3SP  H242  C24  C20   109.73  3.000
 3SP  H241  C24  C20   108.29  3.000
 3SP  C25   C24  C20   115.12  3.000
 3SP  H25   C25  C30   108.03  3.000
 3SP  H25   C25  C26   107.37  3.000
 3SP  C30   C25  C26   110.19  3.000
 3SP  H25   C25  C24   108.35  3.000
 3SP  C30   C25  C24   109.75  3.000
 3SP  C26   C25  C24   112.99  3.000
 3SP  H262  C26  H261  106.82  3.000
 3SP  H262  C26  C27   109.37  3.000
 3SP  H261  C26  C27   109.51  3.000
 3SP  H262  C26  C25   109.22  3.000
 3SP  H261  C26  C25   110.20  3.000
 3SP  C27   C26  C25   111.61  3.000
 3SP  H272  C27  H271  106.37  3.000
 3SP  H272  C27  C28   110.32  3.000
 3SP  H271  C27  C28   109.24  3.000
 3SP  H272  C27  C26   110.07  3.000
 3SP  H271  C27  C26   109.00  3.000
 3SP  C28   C27  C26   111.69  3.000
 3SP  H282  C28  H281  106.50  3.000
 3SP  H282  C28  C29   109.34  3.000
 3SP  H281  C28  C29   110.34  3.000
 3SP  H282  C28  C27   109.27  3.000
 3SP  H281  C28  C27   110.29  3.000
 3SP  C29   C28  C27   110.99  3.000
 3SP  H292  C29  H291  106.44  3.000
 3SP  H292  C29  C30   110.13  3.000
 3SP  H291  C29  C30   109.12  3.000
 3SP  H292  C29  C28   110.47  3.000
 3SP  H291  C29  C28   109.29  3.000
 3SP  C30   C29  C28   111.27  3.000
 3SP  H302  C30  H301  106.35  3.000
 3SP  H302  C30  C29   110.13  3.000
 3SP  H301  C30  C29   109.35  3.000
 3SP  H302  C30  C25   109.82  3.000
 3SP  H301  C30  C25   109.01  3.000
 3SP  C29   C30  C25   112.02  3.000
 3SP  HN21  N21  C22   110.97  3.000
 3SP  HN21  N21  C20   110.47  3.000
 3SP  C22   N21  C20   119.57  3.000
 3SP  H222  C22  H221  105.19  3.000
 3SP  H222  C22  C23   107.75  3.000
 3SP  H221  C22  C23   107.20  3.000
 3SP  H222  C22  N21   114.28  3.000
 3SP  H221  C22  N21   110.63  3.000
 3SP  C23   C22  N21   111.37  3.000
 3SP  O32   C23  O31   123.20  3.000
 3SP  O32   C23  C22   126.03  3.000
 3SP  O31   C23  C22   110.77  3.000
 3SP  HO31  O31  C23   109.95  3.000
 3SP  C16   N17  C13   112.78  3.000
 3SP  C16   N17  C18   127.78  3.000
 3SP  C13   N17  C18   119.44  3.000
 3SP  H13   C13  C14   110.42  3.000
 3SP  H13   C13  C11   110.59  3.000
 3SP  C14   C13  C11   111.14  3.000
 3SP  H13   C13  N17   110.38  3.000
 3SP  C14   C13  N17   103.59  3.000
 3SP  C11   C13  N17   110.52  3.000
 3SP  N10   C11  O12   123.38  3.000
 3SP  O12   C11  C13   121.27  3.000
 3SP  N10   C11  C13   115.24  3.000
 3SP  H142  C14  H141  107.93  3.000
 3SP  H142  C14  C15   113.45  3.000
 3SP  H141  C14  C15   109.80  3.000
 3SP  H142  C14  C13   111.68  3.000
 3SP  H141  C14  C13   110.37  3.000
 3SP  C15   C14  C13   103.59  3.000
 3SP  H152  C15  H151  108.09  3.000
 3SP  H152  C15  C16   109.95  3.000
 3SP  H151  C15  C16   112.31  3.000
 3SP  H152  C15  C14   110.59  3.000
 3SP  H151  C15  C14   112.90  3.000
 3SP  C16   C15  C14   102.96  3.000
 3SP  H162  C16  H161  108.09  3.000
 3SP  H162  C16  C15   112.19  3.000
 3SP  H161  C16  C15   111.23  3.000
 3SP  H162  C16  N17   111.63  3.000
 3SP  H161  C16  N17   111.15  3.000
 3SP  C15   C16  N17   102.55  3.000
 3SP  C6    C1   S5    121.31  3.000
 3SP  C6    C1   C2    127.38  3.000
 3SP  S5    C1   C2    111.31  3.000
 3SP  H2    C2   C3    124.32  3.000
 3SP  H2    C2   C1    123.10  3.000
 3SP  C3    C2   C1    112.56  3.000
 3SP  H3    C3   C4    123.01  3.000
 3SP  H3    C3   C2    123.99  3.000
 3SP  C4    C3   C2    113.00  3.000
 3SP  C9    C4   S5    121.37  3.000
 3SP  C9    C4   C3    127.32  3.000
 3SP  S5    C4   C3    111.23  3.000
 3SP  C4    S5   C1     91.90  3.000
 3SP  HN7   N7   C6    111.08  3.000
 3SP  HN82  N8   HN81  112.88  3.000
 3SP  HN82  N8   C6    117.01  3.000
 3SP  HN81  N8   C6    117.48  3.000
 3SP  H92   C9   H91   106.75  3.000
 3SP  H92   C9   N10   108.72  3.000
 3SP  H91   C9   N10   108.42  3.000
 3SP  H92   C9   C4    108.59  3.000
 3SP  H91   C9   C4    109.86  3.000
 3SP  N10   C9   C4    114.23  3.000
 3SP  HN10  N10  C9    117.81  3.000
 3SP  HN10  N10  C11   119.07  3.000
 3SP  C9    N10  C11   122.77  3.000
 3SP  N8    C6   N7    126.87  3.000
 3SP  N8    C6   C1    114.48  3.000
 3SP  N7    C6   C1    118.57  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  CONST_22  HO31  O31  C23  C22   180.00   0.0  0
 3SP  Var_01    C28   C27  C26  C25   -55.58  30.0  1
 3SP  Var_02    C28   C29  C30  C25    55.68  30.0  1
 3SP  Var_03    C29   C28  C27  C26    54.86  30.0  1
 3SP  Var_04    C30   C29  C28  C27   -54.70  30.0  1
 3SP  Var_05    C14   C15  C16  N17   -34.87  30.0  1
 3SP  Var_06    C16   C15  C14  C13    37.44  30.0  1
 3SP  Var_07    C15   C16  N17  C13    20.01  30.0  1
 3SP  Var_08    N7    C6   C1   C2     28.37  30.0  2
 3SP  Var_09    N10   C9   C4   C3    147.69  30.0  2
 3SP  Var_10    C4    C9   N10  C11    90.45  30.0  1
 3SP  Var_11    C23   C22  N21  C20  -150.76  30.0  3
 3SP  Var_12    O31   C23  C22  N21   179.80  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  H2    0.020
 3SP  plan-1  H3    0.020
 3SP  plan-1  C6    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
 3SP  plan-5  HO31  0.020

