# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:52:03 2022
#   Inital geometry file: a 164 line input string
#   Ligand name: N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)C(=O)NCCC(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](Cc2ccccc2)C(O)=O
#
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
 5YB  5YB  N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine  ligand  61  36  .  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_5YB
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
 5YB  C26   C  C      0   0.526  53.7062  105.5692  73.6421
 5YB  O27   O  O      0  -0.482  54.5705  105.4349  72.7857
 5YB  C28   C  CR6    0  -0.032  52.7071  104.4847  73.8996
 5YB  C29   C  CR16   0  -0.279  51.4293  104.7336  74.3912
 5YB  C30   C  CR16   0  -0.273  50.5290  103.6941  74.5715
 5YB  C31   C  CR6    0   0.049  50.8888  102.3832  74.2718
 5YB  C32   C  CR16   0  -0.262  52.1712  102.1358  73.7854
 5YB  C33   C  CR16   0  -0.257  53.0619  103.1740  73.5859
 5YB  C34   C  C      0   0.335  49.9463  101.2456  74.4683
 5YB  N35   N  N      0  -0.646  50.4339  100.0900  74.7096
 5YB  N36   N  NH2    0  -0.819  48.6215  101.5726  74.4206
 5YB  N25   N  NH1    0  -0.650  53.6023  106.6709  74.4010
 5YB  C24   C  CH2    0  -0.281  54.4568  107.8250  74.2246
 5YB  C23   C  CH2    0  -0.597  54.0141  108.6881  73.0502
 5YB  C21   C  C      0   0.568  54.8384  109.9501  72.9183
 5YB  O22   O  O      0  -0.496  55.8763  110.1175  73.5453
 5YB  N20   N  NH1    0  -0.636  54.3576  110.8498  72.0422
 5YB  C15   C  CH1    0  -0.195  55.0278  112.0982  71.7201
 5YB  C13   C  C      0   0.581  54.5082  113.1982  72.6519
 5YB  O14   O  O      0  -0.511  53.5799  113.9314  72.3314
 5YB  C16   C  CH2    0  -0.594  54.8229  112.4577  70.2617
 5YB  C17   C  C      0   0.422  55.5636  113.7411  69.8364
 5YB  O18   O  O      0  -0.613  55.2873  114.1840  68.7053
 5YB  O19   O  OC    -1  -0.600  56.3890  114.2102  70.6464
 5YB  N12   N  NH1    0  -0.638  55.1117  113.2420  73.8426
 5YB  C08   C  CH1    0  -0.191  54.8098  114.1754  74.8979
 5YB  C09   C  C      0   0.423  55.9389  114.1283  75.9614
 5YB  O10   O  O      0  -0.588  56.8087  113.2455  75.8298
 5YB  C07   C  CH2    0  -0.523  53.4316  113.9357  75.5442
 5YB  C04   C  CR6    0   0.140  53.2389  112.5457  76.0795
 5YB  C03   C  CR16   0  -0.299  53.7271  112.1812  77.3343
 5YB  C05   C  CR16   0  -0.313  52.5653  111.5828  75.3301
 5YB  C02   C  CR16   0  -0.242  53.5489  110.8950  77.8257
 5YB  C06   C  CR16   0  -0.245  52.3758  110.2973  75.8211
 5YB  C01   C  CR16   0  -0.272  52.8695  109.9471  77.0708
 5YB  O11   O  OC    -1  -0.597  55.8608  114.9868  76.8581
 5YB  H291  H  HCR6   0   0.261  51.1028  105.7406  74.6192
 5YB  H301  H  HCR6   0   0.264  49.5458  103.9216  74.9622
 5YB  H321  H  HCR6   0   0.258  52.4638  101.1217  73.5497
 5YB  H331  H  HCR6   0   0.260  54.0456  102.9634  73.1881
 5YB  H351  H  H      0   0.326  49.7009   99.3910  74.7970
 5YB  H362  H  HNH2   0   0.392  47.9594  100.8125  74.4144
 5YB  H361  H  HNH2   0   0.395  48.3393  102.3548  73.8522
 5YB  H251  H  HNH1   0   0.409  52.9219  106.7087  75.1414
 5YB  H242  H  HCH2   0   0.251  55.4872  107.4967  74.0912
 5YB  H241  H  HCH2   0   0.262  54.4179  108.3977  75.1495
 5YB  H231  H  HCH2   0   0.266  52.9577  108.9490  73.1536
 5YB  H232  H  HCH2   0   0.283  54.0967  108.1194  72.1196
 5YB  H201  H  HNH1   0   0.399  53.4704  110.6664  71.5990
 5YB  H151  H  HCH1   0   0.255  56.0920  111.9520  71.9047
 5YB  H161  H  HCH2   0   0.242  55.1836  111.6273  69.6453
 5YB  H162  H  HCH2   0   0.225  53.7578  112.5593  70.0363
 5YB  H121  H  HNH1   0   0.381  55.8752  112.6106  74.0423
 5YB  H081  H  HCH1   0   0.241  54.7899  115.1901  74.4845
 5YB  H071  H  HCH2   0   0.243  53.3131  114.6691  76.3431
 5YB  H072  H  HCH2   0   0.244  52.6573  114.1485  74.8064
 5YB  H031  H  HCR6   0   0.239  54.2447  112.9176  77.9370
 5YB  H051  H  HCR6   0   0.240  52.1696  111.8472  74.3563
 5YB  H021  H  HCR6   0   0.248  53.9344  110.6350  78.8036
 5YB  H061  H  HCR6   0   0.252  51.8383  109.5679  75.2278
 5YB  H011  H  HCR6   0   0.250  52.7217  108.9457  77.4548

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
 5YB  C26  C28   single    1.497  0.020  1.497
 5YB  C26  O27   double    1.224  0.020  1.224
 5YB  C26  N25   single    1.342  0.020  1.342
 5YB  C28  C29   aromatic  1.392  0.020  1.392
 5YB  C28  C33   aromatic  1.394  0.020  1.394
 5YB  C29  C30   aromatic  1.387  0.020  1.387
 5YB  C30  C31   aromatic  1.392  0.020  1.392
 5YB  C31  C34   single    1.490  0.020  1.490
 5YB  C31  C32   aromatic  1.394  0.020  1.394
 5YB  C32  C33   aromatic  1.382  0.020  1.382
 5YB  C34  N36   single    1.365  0.020  1.365
 5YB  C34  N35   double    1.277  0.020  1.277
 5YB  N25  C24   single    1.447  0.020  1.447
 5YB  C24  C23   single    1.523  0.020  1.523
 5YB  C23  C21   single    1.513  0.020  1.513
 5YB  C21  O22   double    1.224  0.020  1.224
 5YB  C21  N20   single    1.345  0.020  1.345
 5YB  N20  C15   single    1.453  0.020  1.453
 5YB  C15  C16   single    1.516  0.020  1.516
 5YB  C15  C13   single    1.532  0.020  1.532
 5YB  C13  O14   double    1.226  0.020  1.226
 5YB  C13  N12   single    1.336  0.020  1.336
 5YB  C16  C17   single    1.542  0.020  1.542
 5YB  C17  O18   deloc     1.246  0.020  1.246
 5YB  C17  O19   deloc     1.248  0.020  1.248
 5YB  N12  C08   single    1.441  0.020  1.441
 5YB  C08  C07   single    1.541  0.020  1.541
 5YB  C08  C09   single    1.552  0.020  1.552
 5YB  C09  O10   deloc     1.246  0.020  1.246
 5YB  C09  O11   deloc     1.244  0.020  1.244
 5YB  C07  C04   single    1.502  0.020  1.502
 5YB  C04  C05   aromatic  1.394  0.020  1.394
 5YB  C04  C03   aromatic  1.395  0.020  1.395
 5YB  C03  C02   aromatic  1.388  0.020  1.388
 5YB  C05  C06   aromatic  1.389  0.020  1.389
 5YB  C02  C01   aromatic  1.389  0.020  1.389
 5YB  C06  C01   aromatic  1.388  0.020  1.388
 5YB  C29  H291  single    0.930  0.020  1.080
 5YB  C30  H301  single    0.930  0.020  1.080
 5YB  C32  H321  single    0.930  0.020  1.080
 5YB  C33  H331  single    0.930  0.020  1.080
 5YB  N35  H351  single    0.890  0.020  1.040
 5YB  N36  H362  single    0.890  0.020  1.040
 5YB  N36  H361  single    0.890  0.020  1.040
 5YB  N25  H251  single    0.860  0.020  1.020
 5YB  C24  H241  single    0.970  0.020  1.090
 5YB  C24  H242  single    0.970  0.020  1.090
 5YB  C23  H232  single    0.970  0.020  1.090
 5YB  C23  H231  single    0.970  0.020  1.090
 5YB  N20  H201  single    0.860  0.020  1.020
 5YB  C15  H151  single    0.970  0.020  1.090
 5YB  C16  H161  single    0.970  0.020  1.090
 5YB  C16  H162  single    0.970  0.020  1.090
 5YB  N12  H121  single    0.860  0.020  1.020
 5YB  C08  H081  single    0.970  0.020  1.090
 5YB  C07  H071  single    0.970  0.020  1.090
 5YB  C07  H072  single    0.970  0.020  1.090
 5YB  C03  H031  single    0.930  0.020  1.080
 5YB  C05  H051  single    0.930  0.020  1.080
 5YB  C02  H021  single    0.930  0.020  1.080
 5YB  C06  H061  single    0.930  0.020  1.080
 5YB  C01  H011  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
 5YB  N25   C26  C28   116.48  3.000
 5YB  N25   C26  O27   122.71  3.000
 5YB  C28   C26  O27   120.81  3.000
 5YB  C33   C28  C29   118.78  3.000
 5YB  C33   C28  C26   118.22  3.000
 5YB  C29   C28  C26   122.96  3.000
 5YB  H291  C29  C30   118.29  3.000
 5YB  H291  C29  C28   121.17  3.000
 5YB  C30   C29  C28   120.53  3.000
 5YB  H301  C30  C31   120.70  3.000
 5YB  H301  C30  C29   118.63  3.000
 5YB  C31   C30  C29   120.67  3.000
 5YB  C34   C31  C32   119.50  3.000
 5YB  C32   C31  C30   118.69  3.000
 5YB  C34   C31  C30   121.80  3.000
 5YB  H321  C32  C33   119.91  3.000
 5YB  H321  C32  C31   119.43  3.000
 5YB  C33   C32  C31   120.65  3.000
 5YB  H331  C33  C32   119.52  3.000
 5YB  H331  C33  C28   119.83  3.000
 5YB  C32   C33  C28   120.66  3.000
 5YB  N36   C34  N35   126.42  3.000
 5YB  N35   C34  C31   118.30  3.000
 5YB  N36   C34  C31   115.23  3.000
 5YB  H351  N35  C34   111.28  3.000
 5YB  H361  N36  H362  113.46  3.000
 5YB  H361  N36  C34   118.52  3.000
 5YB  H362  N36  C34   117.19  3.000
 5YB  H251  N25  C24   117.33  3.000
 5YB  H251  N25  C26   119.95  3.000
 5YB  C24   N25  C26   122.70  3.000
 5YB  H241  C24  H242  107.24  3.000
 5YB  H242  C24  C23   110.56  3.000
 5YB  H241  C24  C23   110.28  3.000
 5YB  H242  C24  N25   109.46  3.000
 5YB  H241  C24  N25   107.16  3.000
 5YB  C23   C24  N25   111.98  3.000
 5YB  H232  C23  H231  106.11  3.000
 5YB  H231  C23  C21   109.61  3.000
 5YB  H232  C23  C21   108.56  3.000
 5YB  H231  C23  C24   110.07  3.000
 5YB  H232  C23  C24   109.84  3.000
 5YB  C21   C23  C24   112.42  3.000
 5YB  N20   C21  O22   123.05  3.000
 5YB  N20   C21  C23   114.84  3.000
 5YB  O22   C21  C23   122.10  3.000
 5YB  H201  N20  C15   117.68  3.000
 5YB  H201  N20  C21   118.63  3.000
 5YB  C15   N20  C21   123.67  3.000
 5YB  H151  C15  C16   109.07  3.000
 5YB  H151  C15  C13   108.93  3.000
 5YB  C16   C15  C13   111.65  3.000
 5YB  H151  C15  N20   107.31  3.000
 5YB  C13   C15  N20   108.99  3.000
 5YB  C16   C15  N20   110.77  3.000
 5YB  N12   C13  O14   123.76  3.000
 5YB  N12   C13  C15   114.36  3.000
 5YB  O14   C13  C15   121.82  3.000
 5YB  H162  C16  H161  105.98  3.000
 5YB  H162  C16  C17   109.50  3.000
 5YB  H161  C16  C17   108.52  3.000
 5YB  H162  C16  C15   110.61  3.000
 5YB  H161  C16  C15   108.49  3.000
 5YB  C17   C16  C15   113.44  3.000
 5YB  O19   C17  O18   127.05  3.000
 5YB  O19   C17  C16   116.85  3.000
 5YB  O18   C17  C16   116.09  3.000
 5YB  H121  N12  C08   114.73  3.000
 5YB  H121  N12  C13   119.80  3.000
 5YB  C08   N12  C13   125.42  3.000
 5YB  H081  C08  C07   106.62  3.000
 5YB  H081  C08  C09   107.45  3.000
 5YB  C07   C08  C09   111.01  3.000
 5YB  H081  C08  N12   109.11  3.000
 5YB  C09   C08  N12   109.26  3.000
 5YB  C07   C08  N12   113.19  3.000
 5YB  O11   C09  O10   127.51  3.000
 5YB  O11   C09  C08   115.30  3.000
 5YB  O10   C09  C08   117.19  3.000
 5YB  H072  C07  H071  106.68  3.000
 5YB  H072  C07  C04   109.31  3.000
 5YB  H071  C07  C04   110.32  3.000
 5YB  H072  C07  C08   108.72  3.000
 5YB  H071  C07  C08   107.44  3.000
 5YB  C04   C07  C08   114.09  3.000
 5YB  C05   C04  C03   118.18  3.000
 5YB  C03   C04  C07   121.17  3.000
 5YB  C05   C04  C07   120.65  3.000
 5YB  H031  C03  C02   119.61  3.000
 5YB  H031  C03  C04   119.34  3.000
 5YB  C02   C03  C04   121.04  3.000
 5YB  H051  C05  C06   119.58  3.000
 5YB  H051  C05  C04   119.41  3.000
 5YB  C06   C05  C04   121.01  3.000
 5YB  H021  C02  C01   120.06  3.000
 5YB  H021  C02  C03   119.77  3.000
 5YB  C01   C02  C03   120.17  3.000
 5YB  H061  C06  C01   119.98  3.000
 5YB  H061  C06  C05   119.82  3.000
 5YB  C01   C06  C05   120.20  3.000
 5YB  H011  C01  C06   120.26  3.000
 5YB  H011  C01  C02   120.34  3.000
 5YB  C06   C01  C02   119.40  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
 5YB  CONST_01  C31   C30  C29  C28     0.00   0.0  0
 5YB  CONST_02  C31   C32  C33  C28     0.00   0.0  0
 5YB  CONST_03  C32   C33  C28  C29     0.00   0.0  0
 5YB  CONST_04  C32   C31  C30  C29     0.00   0.0  0
 5YB  CONST_05  C33   C28  C29  C30     0.00   0.0  0
 5YB  CONST_06  C33   C32  C31  C30     0.00   0.0  0
 5YB  CONST_07  C01   C06  C05  C04     0.00   0.0  0
 5YB  CONST_08  C01   C02  C03  C04     0.00   0.0  0
 5YB  CONST_09  C06   C05  C04  C03     0.00   0.0  0
 5YB  CONST_10  C06   C01  C02  C03     0.00   0.0  0
 5YB  CONST_11  C02   C03  C04  C05     0.00   0.0  0
 5YB  CONST_12  C02   C01  C06  C05     0.00   0.0  0
 5YB  CONST_13  C30   C29  C28  C26   180.00   0.0  0
 5YB  CONST_14  C32   C33  C28  C26   180.00   0.0  0
 5YB  CONST_15  C34   C31  C30  C29   180.00   0.0  0
 5YB  CONST_16  C34   C31  C32  C33   180.00   0.0  0
 5YB  CONST_17  C06   C05  C04  C07   180.00   0.0  0
 5YB  CONST_18  C02   C03  C04  C07   180.00   0.0  0
 5YB  CONST_19  H301  C30  C29  C28   180.00   0.0  0
 5YB  CONST_20  H321  C32  C33  C28   180.00   0.0  0
 5YB  CONST_21  H331  C33  C28  C29   180.00   0.0  0
 5YB  CONST_22  H291  C29  C30  C31   180.00   0.0  0
 5YB  CONST_23  H061  C06  C05  C04   180.00   0.0  0
 5YB  CONST_24  H021  C02  C03  C04   180.00   0.0  0
 5YB  CONST_25  H051  C05  C04  C03   180.00   0.0  0
 5YB  CONST_26  H011  C01  C02  C03   180.00   0.0  0
 5YB  CONST_27  H031  C03  C04  C05   180.00   0.0  0
 5YB  CONST_28  C24   N25  C26  C28   180.00   0.0  0
 5YB  CONST_29  H251  N25  C26  C28     0.00   0.0  0
 5YB  CONST_30  H362  N36  C34  C31   180.00   0.0  0
 5YB  CONST_32  H351  N35  C34  C31   180.00   0.0  0
 5YB  CONST_33  C24   N25  C26  O27     0.00   0.0  0
 5YB  CONST_34  C15   N20  C21  C23   180.00   0.0  0
 5YB  CONST_35  C15   N20  C21  O22     0.00   0.0  0
 5YB  CONST_36  C08   N12  C13  C15   180.00   0.0  0
 5YB  CONST_37  C08   N12  C13  O14     0.00   0.0  0
 5YB  CONST_38  H201  N20  C21  C23     0.00   0.0  0
 5YB  CONST_39  H121  N12  C13  C15     0.00   0.0  0
 5YB  Var_01    C29   C28  C26  O27  -152.03  30.0  2
 5YB  Var_02    N36   C34  C31  C30    25.59  30.0  2
 5YB  Var_03    C05   C04  C07  C08   -97.77  30.0  2
 5YB  Var_04    C23   C24  N25  C26    78.88  30.0  3
 5YB  Var_05    C21   C23  C24  N25   175.82  30.0  3
 5YB  Var_06    O22   C21  C23  C24    11.80  30.0  3
 5YB  Var_07    O18   C17  C16  C15  -170.56  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
 5YB  chir_01  C15  N20  C16  C13  negativ
 5YB  chir_02  C08  N12  C07  C09  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
 5YB  plan-1  C26   0.020
 5YB  plan-1  C28   0.020
 5YB  plan-1  C29   0.020
 5YB  plan-1  C30   0.020
 5YB  plan-1  C31   0.020
 5YB  plan-1  C32   0.020
 5YB  plan-1  C33   0.020
 5YB  plan-1  C34   0.020
 5YB  plan-1  H291  0.020
 5YB  plan-1  H301  0.020
 5YB  plan-1  H321  0.020
 5YB  plan-1  H331  0.020
 5YB  plan-2  C16   0.020
 5YB  plan-2  C17   0.020
 5YB  plan-2  O18   0.020
 5YB  plan-2  O19   0.020
 5YB  plan-3  C08   0.020
 5YB  plan-3  C09   0.020
 5YB  plan-3  O10   0.020
 5YB  plan-3  O11   0.020
 5YB  plan-4  C07   0.020
 5YB  plan-4  C04   0.020
 5YB  plan-4  C03   0.020
 5YB  plan-4  C05   0.020
 5YB  plan-4  C02   0.020
 5YB  plan-4  C06   0.020
 5YB  plan-4  C01   0.020
 5YB  plan-4  H031  0.020
 5YB  plan-4  H051  0.020
 5YB  plan-4  H021  0.020
 5YB  plan-4  H061  0.020
 5YB  plan-4  H011  0.020
 5YB  plan-5  C26   0.020
 5YB  plan-5  O27   0.020
 5YB  plan-5  C28   0.020
 5YB  plan-5  N25   0.020
 5YB  plan-5  C24   0.020
 5YB  plan-5  H251  0.020
 5YB  plan-6  C23   0.020
 5YB  plan-6  C21   0.020
 5YB  plan-6  O22   0.020
 5YB  plan-6  N20   0.020
 5YB  plan-6  C15   0.020
 5YB  plan-6  H201  0.020
 5YB  plan-7  C15   0.020
 5YB  plan-7  C13   0.020
 5YB  plan-7  O14   0.020
 5YB  plan-7  N12   0.020
 5YB  plan-7  C08   0.020
 5YB  plan-7  H121  0.020
 5YB  plan-8  C31   0.020
 5YB  plan-8  C34   0.020
 5YB  plan-8  N35   0.020
 5YB  plan-8  N36   0.020
 5YB  plan-8  H351  0.020
 5YB  plan-8  H362  0.020
 5YB  plan-8  H361  0.020

