# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:51:41 2021
#   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  63  36  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.534  53.8978  105.7762  73.6930
 5YB  O27   O  O     0  -0.483  54.7548  105.5564  72.8481
 5YB  C28   C  CR6   0  -0.031  52.9034  104.7273  74.0759
 5YB  C29   C  CR16  0  -0.277  51.6360  105.0319  74.5623
 5YB  C30   C  CR16  0  -0.277  50.7369  104.0221  74.8696
 5YB  C31   C  CR6   0   0.048  51.0898  102.6856  74.7044
 5YB  C32   C  CR16  0  -0.261  52.3615  102.3826  74.2213
 5YB  C33   C  CR16  0  -0.257  53.2509  103.3896  73.8964
 5YB  C34   C  C     0   0.337  50.1511  101.5785  75.0411
 5YB  N35   N  N     0  -0.647  50.6431  100.4457  75.3666
 5YB  N36   N  NH2   0  -0.822  48.8277  101.9096  75.0183
 5YB  N25   N  NH1   0  -0.654  53.7935  106.9541  74.3292
 5YB  C24   C  CH2   0  -0.280  54.6665  108.0726  74.0547
 5YB  C23   C  CH2   0  -0.587  54.3248  108.7615  72.7345
 5YB  C21   C  C     0   0.581  55.1239  110.0273  72.5638
 5YB  O22   O  O     0  -0.501  56.2731  110.1308  72.9765
 5YB  N20   N  NH1   0  -0.636  54.4913  111.0356  71.9371
 5YB  C15   C  CH1   0  -0.230  55.1046  112.3201  71.6725
 5YB  C13   C  C     0   0.603  54.8661  113.2899  72.8397
 5YB  O14   O  O     0  -0.479  54.2790  114.3489  72.6784
 5YB  C16   C  CH2   0  -0.576  54.5405  112.8879  70.3784
 5YB  C17   C  C     0   0.549  55.0748  114.2400  69.9913
 5YB  O18   O  O     0  -0.448  54.4459  115.0651  69.3782
 5YB  O19   O  OH1   0  -0.594  56.3470  114.4000  70.3357
 5YB  N12   N  NH1   0  -0.666  55.3385  112.8719  74.0200
 5YB  C08   C  CH1   0  -0.172  55.1183  113.5854  75.2505
 5YB  C09   C  C     0   0.543  56.0529  113.0121  76.2967
 5YB  O10   O  O     0  -0.423  56.7436  112.0397  76.1307
 5YB  C07   C  CH2   0  -0.556  53.6453  113.5360  75.7172
 5YB  C04   C  CR6   0   0.153  53.0831  112.1459  75.8109
 5YB  C03   C  CR16  0  -0.305  53.2568  111.3702  76.9555
 5YB  C05   C  CR16  0  -0.314  52.3613  111.6076  74.7472
 5YB  C02   C  CR16  0  -0.231  52.7160  110.0939  77.0386
 5YB  C06   C  CR16  0  -0.234  51.8116  110.3354  74.8273
 5YB  C01   C  CR16  0  -0.294  51.9865  109.5758  75.9763
 5YB  O11   O  OH1   0  -0.585  56.0090  113.7086  77.4191
 5YB  H291  H  HCR6  0   0.254  51.3136  106.0582  74.6858
 5YB  H301  H  HCR6  0   0.267  49.7628  104.2953  75.2529
 5YB  H321  H  HCR6  0   0.262  52.6465  101.3478  74.0904
 5YB  H331  H  HCR6  0   0.263  54.2263  103.1336  73.5049
 5YB  H351  H  H     0   0.327  49.9100   99.7650  75.5476
 5YB  H362  H  HNH2  0   0.393  48.1618  101.1592  75.1128
 5YB  H361  H  HNH2  0   0.397  48.5251  102.6397  74.3945
 5YB  H251  H  HNH1  0   0.402  53.1602  107.0412  75.1052
 5YB  H242  H  HCH2  0   0.259  55.7051  107.7420  74.0501
 5YB  H241  H  HCH2  0   0.263  54.5523  108.7719  74.8820
 5YB  H231  H  HCH2  0   0.260  53.2542  108.9686  72.6883
 5YB  H232  H  HCH2  0   0.294  54.5507  108.0956  71.8972
 5YB  H201  H  HNH1  0   0.409  53.5245  110.9132  71.6786
 5YB  H151  H  HCH1  0   0.304  56.1799  112.1582  71.5712
 5YB  H161  H  HCH2  0   0.310  54.7828  112.1970  69.5649
 5YB  H162  H  HCH2  0   0.281  53.4532  112.9573  70.4209
 5YB  H2    H  HOH1  0   0.483  56.6657  115.2670  70.0424
 5YB  H121  H  HNH1  0   0.415  55.8453  111.9970  74.0664
 5YB  H081  H  HCH1  0   0.311  55.3821  114.6399  75.1183
 5YB  H071  H  HCH2  0   0.278  53.5649  114.0537  76.6740
 5YB  H072  H  HCH2  0   0.279  53.0650  114.1218  75.0049
 5YB  H031  H  HCR6  0   0.248  53.7962  111.7738  77.8046
 5YB  H051  H  HCR6  0   0.245  52.2021  112.2046  73.8568
 5YB  H021  H  HCR6  0   0.259  52.8504  109.5094  77.9396
 5YB  H061  H  HCR6  0   0.260  51.2357  109.9435  73.9983
 5YB  H011  H  HCR6  0   0.258  51.5346  108.5946  76.0569
 5YB  H3    H  HOH1  0   0.491  56.5968  113.3155  78.0822

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    1.495  0.020  1.495
 5YB  C26  O27   double    1.223  0.020  1.223
 5YB  C26  N25   single    1.343  0.020  1.343
 5YB  C28  C29   aromatic  1.391  0.020  1.391
 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    1.364  0.020  1.364
 5YB  C34  N35   double    1.277  0.020  1.277
 5YB  N25  C24   single    1.445  0.020  1.445
 5YB  C24  C23   single    1.528  0.020  1.528
 5YB  C23  C21   single    1.507  0.020  1.507
 5YB  C21  O22   double    1.225  0.020  1.225
 5YB  C21  N20   single    1.345  0.020  1.345
 5YB  N20  C15   single    1.448  0.020  1.448
 5YB  C15  C16   single    1.522  0.020  1.522
 5YB  C15  C13   single    1.536  0.020  1.536
 5YB  C13  O14   double    1.222  0.020  1.222
 5YB  C13  N12   single    1.338  0.020  1.338
 5YB  C16  C17   single    1.505  0.020  1.505
 5YB  C17  O18   double    1.205  0.020  1.205
 5YB  C17  O19   single    1.328  0.020  1.328
 5YB  N12  C08   single    1.439  0.020  1.439
 5YB  C08  C07   single    1.546  0.020  1.546
 5YB  C08  C09   single    1.516  0.020  1.516
 5YB  C09  O10   double    1.204  0.020  1.204
 5YB  C09  O11   single    1.322  0.020  1.322
 5YB  C07  C04   single    1.502  0.020  1.502
 5YB  C04  C05   aromatic  1.394  0.020  1.394
 5YB  C04  C03   aromatic  1.394  0.020  1.394
 5YB  C03  C02   aromatic  1.389  0.020  1.389
 5YB  C05  C06   aromatic  1.388  0.020  1.388
 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  O19  H2    single    0.850  0.020  0.980
 5YB  N12  H121  single    0.860  0.020  1.020
 5YB  C08  H081  single    0.970  0.020  1.090
 5YB  O11  H3    single    0.850  0.020  0.980
 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   116.26  3.000
 5YB  N25   C26  O27   122.63  3.000
 5YB  C28   C26  O27   121.11  3.000
 5YB  C33   C28  C29   118.84  3.000
 5YB  C33   C28  C26   118.33  3.000
 5YB  C29   C28  C26   122.80  3.000
 5YB  H291  C29  C30   118.17  3.000
 5YB  H291  C29  C28   121.24  3.000
 5YB  C30   C29  C28   120.57  3.000
 5YB  H301  C30  C31   120.85  3.000
 5YB  H301  C30  C29   118.58  3.000
 5YB  C31   C30  C29   120.57  3.000
 5YB  C34   C31  C32   119.45  3.000
 5YB  C32   C31  C30   118.76  3.000
 5YB  C34   C31  C30   121.79  3.000
 5YB  H321  C32  C33   119.94  3.000
 5YB  H321  C32  C31   119.38  3.000
 5YB  C33   C32  C31   120.68  3.000
 5YB  H331  C33  C32   119.53  3.000
 5YB  H331  C33  C28   119.91  3.000
 5YB  C32   C33  C28   120.57  3.000
 5YB  N36   C34  N35   126.38  3.000
 5YB  N35   C34  C31   118.29  3.000
 5YB  N36   C34  C31   115.27  3.000
 5YB  H351  N35  C34   111.19  3.000
 5YB  H361  N36  H362  113.55  3.000
 5YB  H361  N36  C34   118.55  3.000
 5YB  H362  N36  C34   117.30  3.000
 5YB  H251  N25  C24   117.39  3.000
 5YB  H251  N25  C26   119.38  3.000
 5YB  C24   N25  C26   122.82  3.000
 5YB  H241  C24  H242  107.33  3.000
 5YB  H242  C24  C23   110.26  3.000
 5YB  H241  C24  C23   110.08  3.000
 5YB  H242  C24  N25   109.98  3.000
 5YB  H241  C24  N25   106.82  3.000
 5YB  C23   C24  N25   112.20  3.000
 5YB  H232  C23  H231  106.61  3.000
 5YB  H231  C23  C21   110.86  3.000
 5YB  H232  C23  C21   108.38  3.000
 5YB  H231  C23  C24   109.97  3.000
 5YB  H232  C23  C24   109.93  3.000
 5YB  C21   C23  C24   110.98  3.000
 5YB  N20   C21  O22   122.32  3.000
 5YB  N20   C21  C23   115.66  3.000
 5YB  O22   C21  C23   122.02  3.000
 5YB  H201  N20  C15   117.84  3.000
 5YB  H201  N20  C21   118.65  3.000
 5YB  C15   N20  C21   123.43  3.000
 5YB  H151  C15  C16   109.97  3.000
 5YB  H151  C15  C13   108.48  3.000
 5YB  C16   C15  C13   110.67  3.000
 5YB  H151  C15  N20   107.61  3.000
 5YB  C13   C15  N20   110.82  3.000
 5YB  C16   C15  N20   109.23  3.000
 5YB  N12   C13  O14   123.84  3.000
 5YB  N12   C13  C15   114.72  3.000
 5YB  O14   C13  C15   121.44  3.000
 5YB  H162  C16  H161  106.85  3.000
 5YB  H162  C16  C17   107.88  3.000
 5YB  H161  C16  C17   107.30  3.000
 5YB  H162  C16  C15   111.12  3.000
 5YB  H161  C16  C15   108.33  3.000
 5YB  C17   C16  C15   114.99  3.000
 5YB  O19   C17  O18   123.33  3.000
 5YB  O19   C17  C16   112.45  3.000
 5YB  O18   C17  C16   124.12  3.000
 5YB  H2    O19  C17   110.15  3.000
 5YB  H121  N12  C08   117.77  3.000
 5YB  H121  N12  C13   119.15  3.000
 5YB  C08   N12  C13   123.03  3.000
 5YB  H081  C08  C07   107.26  3.000
 5YB  H081  C08  C09   107.40  3.000
 5YB  C07   C08  C09   111.54  3.000
 5YB  H081  C08  N12   109.72  3.000
 5YB  C09   C08  N12   107.96  3.000
 5YB  C07   C08  N12   112.84  3.000
 5YB  O11   C09  O10   124.17  3.000
 5YB  O11   C09  C08   111.50  3.000
 5YB  O10   C09  C08   124.33  3.000
 5YB  H072  C07  H071  106.20  3.000
 5YB  H072  C07  C04   109.81  3.000
 5YB  H071  C07  C04   110.90  3.000
 5YB  H072  C07  C08   107.03  3.000
 5YB  H071  C07  C08   108.66  3.000
 5YB  C04   C07  C08   113.89  3.000
 5YB  C05   C04  C03   118.45  3.000
 5YB  C03   C04  C07   121.31  3.000
 5YB  C05   C04  C07   120.24  3.000
 5YB  H031  C03  C02   119.29  3.000
 5YB  H031  C03  C04   119.88  3.000
 5YB  C02   C03  C04   120.81  3.000
 5YB  H051  C05  C06   119.61  3.000
 5YB  H051  C05  C04   119.36  3.000
 5YB  C06   C05  C04   121.00  3.000
 5YB  H021  C02  C01   120.03  3.000
 5YB  H021  C02  C03   119.85  3.000
 5YB  C01   C02  C03   120.11  3.000
 5YB  H061  C06  C01   120.17  3.000
 5YB  H061  C06  C05   119.88  3.000
 5YB  C01   C06  C05   119.95  3.000
 5YB  H011  C01  C06   120.30  3.000
 5YB  H011  C01  C02   120.01  3.000
 5YB  C06   C01  C02   119.67  3.000
 5YB  H3    O11  C09   110.31  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  CONST_40  H2    O19  C17  C16   180.00   0.0  0
 5YB  CONST_41  H3    O11  C09  C08   180.00   0.0  0
 5YB  Var_01    C29   C28  C26  O27  -152.61  30.0  2
 5YB  Var_02    N36   C34  C31  C30    24.06  30.0  2
 5YB  Var_03    C05   C04  C07  C08   -95.19  30.0  2
 5YB  Var_04    C23   C24  N25  C26    75.00  30.0  3
 5YB  Var_05    C21   C23  C24  N25   172.39  30.0  3
 5YB  Var_06    O22   C21  C23  C24    34.49  30.0  3
 5YB  Var_07    O18   C17  C16  C15  -149.23  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-2  H2    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-3  H3    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

