# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:00:08 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: N-cyclooctylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CNC3CCCCCCC3)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
 13U  13U  N-cyclooctylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  ligand  65  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13U
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
 13U  C14   C  C     0   0.546  -1.5837   0.5331  -0.4854
 13U  O32   O  O     0  -0.500  -0.9424  -0.5092  -0.5244
 13U  C5    C  CH2   0  -0.398  -3.1001   0.5536  -0.4971
 13U  N21   N  NH1   0  -0.603  -3.6368  -0.7598  -0.2507
 13U  C49   C  CH1   0  -0.049  -5.0962  -0.8135  -0.1698
 13U  C48   C  CH2   0  -0.457  -5.5120  -2.2198   0.2944
 13U  C47   C  CH2   0  -0.436  -6.5531  -2.2687   1.4136
 13U  C46   C  CH2   0  -0.438  -7.9730  -1.7835   1.1181
 13U  C45   C  CH2   0  -0.449  -8.1077  -0.2891   0.7931
 13U  C44   C  CH2   0  -0.423  -8.2107   0.0442  -0.6982
 13U  C43   C  CH2   0  -0.442  -7.2608  -0.6911  -1.6369
 13U  C42   C  CH2   0  -0.444  -5.7723  -0.3962  -1.4862
 13U  N1    N  NT    0  -0.481  -0.9746   1.7298  -0.4696
 13U  C1    C  CH1   0  -0.164   0.4725   1.8195  -0.5010
 13U  C7    C  C     0   0.568   1.1084   1.0398   0.6426
 13U  O22   O  O     0  -0.496   0.6570   1.0812   1.7760
 13U  C2    C  CH2   0  -0.477   0.7379   3.3244  -0.3562
 13U  C3    C  CH2   0  -0.475  -0.5163   3.9636  -0.9408
 13U  C4    C  CH2   0  -0.274  -1.6259   3.0339  -0.4707
 13U  N23   N  NH1   0  -0.638   2.2360   0.3937   0.3158
 13U  C24   C  CH2   0  -0.317   3.0216  -0.3594   1.2698
 13U  C25   C  CR6   0   0.062   4.4326  -0.5271   0.7771
 13U  C30   C  CR16  0  -0.293   4.9908  -1.7904   0.6357
 13U  C29   C  CR16  0  -0.275   6.2967  -1.9457   0.1895
 13U  C28   C  CR6   0   0.037   7.0698  -0.8354  -0.1366
 13U  C21   C  C     0   0.332   8.4634  -0.9696  -0.6430
 13U  N46   N  N     0  -0.651   8.9335  -0.0445  -1.3885
 13U  N47   N  NH2   0  -0.822   9.1019  -2.1258  -0.2954
 13U  C27   C  CR16  0  -0.259   6.5059   0.4334  -0.0037
 13U  C26   C  CR16  0  -0.270   5.2094   0.5852   0.4525
 13U  H5    H  HCH2  0   0.257  -3.4650   1.2326   0.2810
 13U  H5A   H  HCH2  0   0.237  -3.4071   1.0103  -1.4523
 13U  HN21  H  HNH1  0   0.336  -3.3141  -1.3993  -0.9684
 13U  H49   H  HCH1  0   0.220  -5.3660  -0.0963   0.6124
 13U  H48   H  HCH2  0   0.220  -5.8464  -2.8229  -0.5563
 13U  H48A  H  HCH2  0   0.231  -4.6149  -2.7144   0.6752
 13U  H47   H  HCH2  0   0.222  -6.6194  -3.3049   1.7581
 13U  H47A  H  HCH2  0   0.211  -6.1679  -1.6974   2.2658
 13U  H46   H  HCH2  0   0.216  -8.4141  -2.3858   0.3171
 13U  H46A  H  HCH2  0   0.227  -8.5709  -2.0048   2.0060
 13U  H45   H  HCH2  0   0.230  -9.0090   0.0994   1.2741
 13U  H45A  H  HCH2  0   0.218  -7.2842   0.2609   1.2558
 13U  H44   H  HCH2  0   0.216  -9.2298  -0.1862  -1.0249
 13U  H44A  H  HCH2  0   0.213  -8.0925   1.1241  -0.8333
 13U  H43   H  HCH2  0   0.216  -7.4331  -1.7680  -1.5589
 13U  H43A  H  HCH2  0   0.228  -7.5427  -0.4330  -2.6617
 13U  H42   H  HCH2  0   0.219  -5.6077   0.6716  -1.6621
 13U  H42A  H  HCH2  0   0.214  -5.2476  -0.9182  -2.2959
 13U  H1    H  HCH1  0   0.271   0.8516   1.4592  -1.4638
 13U  H2    H  HCH2  0   0.250   0.8336   3.5899   0.6987
 13U  H2A   H  HCH2  0   0.265   1.6543   3.6233  -0.8623
 13U  H3    H  HCH2  0   0.258  -0.6669   4.9891  -0.6070
 13U  H3A   H  HCH2  0   0.245  -0.4694   3.9682  -2.0315
 13U  H4    H  HCH2  0   0.245  -1.9714   3.2993   0.5330
 13U  H4A   H  HCH2  0   0.257  -2.4871   3.0485  -1.1391
 13U  HN23  H  HNH1  0   0.403   2.4764   0.3049  -0.6587
 13U  H24   H  HCH2  0   0.264   3.0217   0.1778   2.2201
 13U  H24A  H  HCH2  0   0.257   2.5732  -1.3390   1.4596
 13U  H30   H  HCR6  0   0.259   4.4013  -2.6691   0.8671
 13U  H29   H  HCR6  0   0.259   6.6911  -2.9467   0.0712
 13U  HN46  H  H     0   0.324   9.8969  -0.2369  -1.6496
 13U  HN47  H  HNH2  0   0.395   8.8422  -2.5760   0.5668
 13U  HN4A  H  HNH2  0   0.391  10.0862  -2.1895  -0.5018
 13U  H27   H  HCR6  0   0.255   7.0957   1.3053  -0.2528
 13U  H26   H  HCR6  0   0.256   4.7973   1.5816   0.5598

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
 13U  O22  C7    double    1.221  0.020  1.221
 13U  C7   N23   single    1.340  0.020  1.340
 13U  C7   C1    single    1.523  0.020  1.523
 13U  N23  C24   single    1.447  0.020  1.447
 13U  C24  C25   single    1.504  0.020  1.504
 13U  C25  C26   aromatic  1.395  0.020  1.395
 13U  C25  C30   aromatic  1.388  0.020  1.388
 13U  C26  C27   aromatic  1.383  0.020  1.383
 13U  C27  C28   aromatic  1.395  0.020  1.395
 13U  C28  C21   single    1.489  0.020  1.489
 13U  C28  C29   aromatic  1.392  0.020  1.392
 13U  C21  N46   double    1.278  0.020  1.278
 13U  C21  N47   single    1.366  0.020  1.366
 13U  C29  C30   aromatic  1.389  0.020  1.389
 13U  C1   C2    single    1.535  0.020  1.535
 13U  C1   N1    single    1.450  0.020  1.450
 13U  C2   C3    single    1.524  0.020  1.524
 13U  C3   C4    single    1.522  0.020  1.522
 13U  C4   N1    single    1.458  0.020  1.458
 13U  N1   C14   single    1.343  0.020  1.343
 13U  C14  O32   double    1.224  0.020  1.224
 13U  C14  C5    single    1.517  0.020  1.517
 13U  C5   N21   single    1.440  0.020  1.440
 13U  N21  C49   single    1.463  0.020  1.463
 13U  C49  C48   single    1.538  0.020  1.538
 13U  C49  C42   single    1.538  0.020  1.538
 13U  C48  C47   single    1.529  0.020  1.529
 13U  C47  C46   single    1.529  0.020  1.529
 13U  C46  C45   single    1.535  0.020  1.535
 13U  C45  C44   single    1.532  0.020  1.532
 13U  C44  C43   single    1.524  0.020  1.524
 13U  C43  C42   single    1.525  0.020  1.525
 13U  N23  HN23  single    0.860  0.020  1.020
 13U  C24  H24   single    0.970  0.020  1.090
 13U  C24  H24A  single    0.970  0.020  1.090
 13U  C26  H26   single    0.930  0.020  1.080
 13U  C27  H27   single    0.930  0.020  1.080
 13U  N46  HN46  single    0.890  0.020  1.040
 13U  N47  HN47  single    0.890  0.020  1.040
 13U  N47  HN4A  single    0.890  0.020  1.040
 13U  C29  H29   single    0.930  0.020  1.080
 13U  C30  H30   single    0.930  0.020  1.080
 13U  C1   H1    single    0.970  0.020  1.090
 13U  C2   H2    single    0.970  0.020  1.090
 13U  C2   H2A   single    0.970  0.020  1.090
 13U  C3   H3    single    0.970  0.020  1.090
 13U  C3   H3A   single    0.970  0.020  1.090
 13U  C4   H4    single    0.970  0.020  1.090
 13U  C4   H4A   single    0.970  0.020  1.090
 13U  C5   H5    single    0.970  0.020  1.090
 13U  C5   H5A   single    0.970  0.020  1.090
 13U  N21  HN21  single    0.890  0.020  1.040
 13U  C49  H49   single    0.970  0.020  1.090
 13U  C48  H48   single    0.970  0.020  1.090
 13U  C48  H48A  single    0.970  0.020  1.090
 13U  C47  H47   single    0.970  0.020  1.090
 13U  C47  H47A  single    0.970  0.020  1.090
 13U  C46  H46   single    0.970  0.020  1.090
 13U  C46  H46A  single    0.970  0.020  1.090
 13U  C45  H45   single    0.970  0.020  1.090
 13U  C45  H45A  single    0.970  0.020  1.090
 13U  C44  H44   single    0.970  0.020  1.090
 13U  C44  H44A  single    0.970  0.020  1.090
 13U  C43  H43   single    0.970  0.020  1.090
 13U  C43  H43A  single    0.970  0.020  1.090
 13U  C42  H42   single    0.970  0.020  1.090
 13U  C42  H42A  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
 13U  N1    C14  C5    116.20  3.000
 13U  C5    C14  O32   122.34  3.000
 13U  N1    C14  O32   121.43  3.000
 13U  H5A   C5   H5    105.42  3.000
 13U  H5A   C5   N21   114.98  3.000
 13U  H5    C5   N21   108.65  3.000
 13U  H5A   C5   C14   106.90  3.000
 13U  H5    C5   C14   109.64  3.000
 13U  N21   C5   C14   111.04  3.000
 13U  HN21  N21  C49   109.48  3.000
 13U  HN21  N21  C5    109.61  3.000
 13U  C49   N21  C5    114.51  3.000
 13U  H49   C49  C42   108.99  3.000
 13U  H49   C49  C48   108.46  3.000
 13U  C42   C49  C48   112.81  3.000
 13U  H49   C49  N21   105.15  3.000
 13U  C42   C49  N21   112.42  3.000
 13U  C48   C49  N21   108.66  3.000
 13U  H48A  C48  H48   105.79  3.000
 13U  H48A  C48  C47   106.82  3.000
 13U  H48   C48  C47   110.06  3.000
 13U  H48A  C48  C49   107.28  3.000
 13U  H48   C48  C49   110.59  3.000
 13U  C47   C48  C49   115.73  3.000
 13U  H47A  C47  H47   105.68  3.000
 13U  H47A  C47  C46   108.13  3.000
 13U  H47   C47  C46   107.76  3.000
 13U  H47A  C47  C48   108.25  3.000
 13U  H47   C47  C48   107.58  3.000
 13U  C46   C47  C48   118.72  3.000
 13U  H46A  C46  H46   105.22  3.000
 13U  H46A  C46  C45   108.73  3.000
 13U  H46   C46  C45   110.19  3.000
 13U  H46A  C46  C47   106.66  3.000
 13U  H46   C46  C47   109.93  3.000
 13U  C45   C46  C47   115.54  3.000
 13U  H45A  C45  H45   104.84  3.000
 13U  H45A  C45  C44   110.69  3.000
 13U  H45   C45  C44   107.20  3.000
 13U  H45A  C45  C46   109.52  3.000
 13U  H45   C45  C46   108.98  3.000
 13U  C44   C45  C46   115.08  3.000
 13U  H44A  C44  H44   105.74  3.000
 13U  H44A  C44  C43   109.42  3.000
 13U  H44   C44  C43   107.14  3.000
 13U  H44A  C44  C45   109.12  3.000
 13U  H44   C44  C45   107.90  3.000
 13U  C43   C44  C45   116.92  3.000
 13U  H43A  C43  H43   105.00  3.000
 13U  H43A  C43  C42   107.37  3.000
 13U  H43   C43  C42   109.71  3.000
 13U  H43A  C43  C44   107.61  3.000
 13U  H43   C43  C44   109.44  3.000
 13U  C42   C43  C44   117.00  3.000
 13U  H42A  C42  H42   105.89  3.000
 13U  H42A  C42  C43   107.57  3.000
 13U  H42   C42  C43   108.64  3.000
 13U  H42A  C42  C49   107.00  3.000
 13U  H42   C42  C49   109.65  3.000
 13U  C43   C42  C49   117.47  3.000
 13U  C4    N1   C1    112.98  3.000
 13U  C4    N1   C14   126.48  3.000
 13U  C1    N1   C14   120.50  3.000
 13U  H1    C1   C2    110.22  3.000
 13U  H1    C1   C7    110.30  3.000
 13U  C2    C1   C7    111.03  3.000
 13U  H1    C1   N1    110.11  3.000
 13U  C2    C1   N1    103.37  3.000
 13U  C7    C1   N1    111.63  3.000
 13U  N23   C7   O22   123.64  3.000
 13U  N23   C7   C1    114.52  3.000
 13U  O22   C7   C1    121.70  3.000
 13U  H2A   C2   H2    107.98  3.000
 13U  H2A   C2   C3    113.52  3.000
 13U  H2    C2   C3    109.91  3.000
 13U  H2A   C2   C1    111.77  3.000
 13U  H2    C2   C1    110.16  3.000
 13U  C3    C2   C1    103.45  3.000
 13U  H3A   C3   H3    107.95  3.000
 13U  H3A   C3   C4    110.03  3.000
 13U  H3    C3   C4    112.32  3.000
 13U  H3A   C3   C2    110.46  3.000
 13U  H3    C3   C2    113.03  3.000
 13U  C4    C3   C2    103.02  3.000
 13U  H4A   C4   H4    108.04  3.000
 13U  H4A   C4   C3    112.24  3.000
 13U  H4    C4   C3    111.43  3.000
 13U  H4A   C4   N1    111.43  3.000
 13U  H4    C4   N1    110.94  3.000
 13U  C3    C4   N1    102.77  3.000
 13U  HN23  N23  C24   117.53  3.000
 13U  HN23  N23  C7    118.63  3.000
 13U  C24   N23  C7    123.16  3.000
 13U  H24A  C24  H24   106.84  3.000
 13U  H24A  C24  C25   109.97  3.000
 13U  H24   C24  C25   109.87  3.000
 13U  H24A  C24  N23   110.97  3.000
 13U  H24   C24  N23   108.53  3.000
 13U  C25   C24  N23   110.57  3.000
 13U  C26   C25  C30   118.55  3.000
 13U  C30   C25  C24   120.80  3.000
 13U  C26   C25  C24   120.64  3.000
 13U  H30   C30  C29   119.32  3.000
 13U  H30   C30  C25   119.84  3.000
 13U  C29   C30  C25   120.83  3.000
 13U  H29   C29  C28   120.65  3.000
 13U  H29   C29  C30   118.76  3.000
 13U  C28   C29  C30   120.56  3.000
 13U  C27   C28  C21   119.52  3.000
 13U  C21   C28  C29   121.86  3.000
 13U  C27   C28  C29   118.61  3.000
 13U  N47   C21  N46   126.12  3.000
 13U  N47   C21  C28   115.29  3.000
 13U  N46   C21  C28   118.53  3.000
 13U  HN46  N46  C21   111.20  3.000
 13U  HN4A  N47  HN47  113.52  3.000
 13U  HN4A  N47  C21   117.26  3.000
 13U  HN47  N47  C21   118.42  3.000
 13U  H27   C27  C26   119.91  3.000
 13U  H27   C27  C28   119.40  3.000
 13U  C26   C27  C28   120.69  3.000
 13U  H26   C26  C27   119.35  3.000
 13U  H26   C26  C25   119.90  3.000
 13U  C27   C26  C25   120.75  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
 13U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 13U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 13U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 13U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 13U  CONST_05  C26   C27  C28  C29     0.00   0.0  0
 13U  CONST_06  C26   C25  C30  C29     0.00   0.0  0
 13U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 13U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 13U  CONST_09  C21   C28  C29  C30   180.00   0.0  0
 13U  CONST_10  C26   C27  C28  C21   180.00   0.0  0
 13U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 13U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 13U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 13U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 13U  CONST_15  C1    N1   C14  O32     0.00   0.0  0
 13U  CONST_16  C4    N1   C14  O32   180.00   0.0  0
 13U  CONST_17  C1    N1   C14  C5    180.00   0.0  0
 13U  CONST_18  C4    N1   C14  C5      0.00   0.0  0
 13U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 13U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 13U  CONST_21  HN46  N46  C21  C28   180.00   0.0  0
 13U  CONST_23  HN4A  N47  C21  C28   180.00   0.0  0
 13U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 13U  Var_01    C2    C3   C4   N1    -33.44  30.0  1
 13U  Var_02    C4    C3   C2   C1     37.85  30.0  1
 13U  Var_03    C3    C4   N1   C1     17.08  30.0  1
 13U  Var_04    C26   C25  C24  N23    56.45  30.0  2
 13U  Var_05    N46   C21  C28  C29   153.29  30.0  2
 13U  Var_06    C49   N21  C5   C14   176.69  30.0  3
 13U  Var_07    N1    C14  C5   N21  -168.73  30.0  1
 13U  Var_08    C25   C24  N23  C7   -158.84  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
 13U  chir_01  C49  N21  C48  C42  positiv
 13U  chir_02  C1   N1   C7   C2   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
 13U  plan-1  C24   0.020
 13U  plan-1  C25   0.020
 13U  plan-1  C30   0.020
 13U  plan-1  C29   0.020
 13U  plan-1  C28   0.020
 13U  plan-1  C21   0.020
 13U  plan-1  C27   0.020
 13U  plan-1  C26   0.020
 13U  plan-1  H30   0.020
 13U  plan-1  H29   0.020
 13U  plan-1  H27   0.020
 13U  plan-1  H26   0.020
 13U  plan-2  C1    0.020
 13U  plan-2  C7    0.020
 13U  plan-2  O22   0.020
 13U  plan-2  N23   0.020
 13U  plan-2  C24   0.020
 13U  plan-2  HN23  0.020
 13U  plan-3  C14   0.020
 13U  plan-3  O32   0.020
 13U  plan-3  C5    0.020
 13U  plan-3  N1    0.020
 13U  plan-3  C1    0.020
 13U  plan-3  C4    0.020
 13U  plan-4  C28   0.020
 13U  plan-4  C21   0.020
 13U  plan-4  N46   0.020
 13U  plan-4  N47   0.020
 13U  plan-4  HN46  0.020
 13U  plan-4  HN47  0.020
 13U  plan-4  HN4A  0.020

