# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:47:19 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: (2~{S})-2-[[5-[[2,4-bis(azanyl)-6-oxidanylidene-5~{H}-pyrimidin-5-yl]carbamoylamino]pyridin-2-yl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)[C@@H](NC(=O)Nc2ccc(nc2)C(=O)N[C@@H](CCc3[nH]nnn3)C(O)=O)C(=N1)N
#
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
 KUK  KUK  '(2~{S})-2-[[5-[[2,4-bis(azanyl)-6-oxidanylidene-5~{H}-pyrimidin-5-yl]carbamoylamino]pyridin-2-yl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid'  ligand  50  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KUK
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
 KUK  C15  C  CR16   0  -0.285  -52.9391  32.2803   -4.0377
 KUK  C17  C  C      0   0.532  -53.2496  30.1031   -2.8417
 KUK  C20  C  CH1    0  -0.228  -53.1323  27.9137   -1.7129
 KUK  C21  C  CH2    0  -0.421  -54.1400  26.8833   -2.2288
 KUK  C22  C  CH2    0  -0.514  -55.4656  27.4998   -2.6816
 KUK  C28  C  C      0   0.427  -51.8666  27.1723   -1.1959
 KUK  C02  C  CR6    0   0.567  -50.1252  38.8872   -7.6418
 KUK  N03  N  N      0  -0.512  -50.8014  38.2053   -8.6073
 KUK  C04  C  CR6    0   0.536  -50.4987  36.9490   -8.7566
 KUK  N05  N  NH2    0  -0.771  -51.1523  36.2020   -9.6233
 KUK  C06  C  CR16   0  -0.343  -49.3384  36.3225   -8.0275
 KUK  N07  N  NH1    0  -0.688  -49.5017  34.9177   -7.8081
 KUK  C08  C  C      0   0.770  -50.4232  34.5394   -6.8748
 KUK  O09  O  O      0  -0.494  -51.2512  35.3284   -6.4524
 KUK  N10  N  NH1    0  -0.790  -50.3486  33.2229   -6.5078
 KUK  C11  C  CR6    0   0.299  -51.1464  32.5526   -5.5948
 KUK  C12  C  CR16   0  -0.150  -50.8146  31.2181   -5.3149
 KUK  N13  N  N      0  -0.416  -51.4775  30.4653   -4.4651
 KUK  C14  C  CR6    0   0.094  -52.5256  30.9753   -3.8246
 KUK  C16  C  CR16   0  -0.206  -52.2496  33.0847   -4.9294
 KUK  O18  O  O      0  -0.493  -54.2127  30.5344   -2.2162
 KUK  N19  N  NH1    0  -0.635  -52.7538  28.8691   -2.7260
 KUK  C23  C  CR5    0   0.494  -56.4416  26.4587   -3.0844
 KUK  N24  N  NR15   0  -0.465  -56.3619  25.6947   -4.1766
 KUK  N25  N  N      0  -0.078  -57.3827  24.8545   -4.2002
 KUK  N26  N  N      0  -0.148  -58.0675  25.0975   -3.1544
 KUK  N27  N  N      0  -0.344  -57.5205  26.0813   -2.4379
 KUK  O29  O  O      0  -0.587  -50.8179  27.3303   -1.8483
 KUK  O30  O  OC    -1  -0.593  -52.0397  26.4720   -0.1844
 KUK  C31  C  CR6    0   0.452  -48.9878  37.1086   -6.7542
 KUK  O32  O  O      0  -0.466  -48.3725  36.5403   -5.8692
 KUK  N33  N  N      0  -0.529  -49.3044  38.4136   -6.7158
 KUK  H1   H  HCR6   0   0.272  -53.7946  32.6757   -3.5091
 KUK  H2   H  HCH1   0   0.239  -53.5862  28.4533   -0.8773
 KUK  H3   H  HCH2   0   0.246  -54.3315  26.1653   -1.4302
 KUK  H4   H  HCH2   0   0.234  -53.6913  26.3268   -3.0577
 KUK  H5   H  HCH2   0   0.275  -55.3032  28.1834   -3.5165
 KUK  H6   H  HCH2   0   0.269  -55.9081  28.0766   -1.8698
 KUK  H7   H  HNH2   0   0.406  -51.0221  40.6001   -8.2746
 KUK  H8   H  HNH2   0   0.405  -49.9497  40.7806   -6.9268
 KUK  H9   H  HNH2   0   0.412  -51.9118  36.5908  -10.1595
 KUK  H10  H  HNH2   0   0.422  -50.9265  35.2289   -9.7492
 KUK  H11  H  HCR6   0   0.355  -48.4774  36.4457   -8.6973
 KUK  H12  H  HNH1   0   0.413  -48.7071  34.3294   -8.0029
 KUK  H13  H  HNH1   0   0.420  -49.6102  32.6700   -6.9196
 KUK  H14  H  HCR6   0   0.278  -49.9649  30.7591   -5.8129
 KUK  H15  H  HCR6   0   0.297  -52.5705  34.0998   -5.0924
 KUK  H16  H  HNH1   0   0.384  -51.8812  28.6666   -3.1971
 KUK  H17  H  HNR5   0   0.445  -55.6704  25.6944   -4.9145
 KUK  N01  N  NH2    0  -0.784  -50.3735  40.1927   -7.6236

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
 KUK  N05  C04  single    1.318  0.020  1.318
 KUK  N03  C04  double    1.301  0.020  1.301
 KUK  N03  C02  single    1.362  0.020  1.362
 KUK  C04  C06  single    1.507  0.020  1.507
 KUK  N01  C02  single    1.329  0.020  1.329
 KUK  C02  N33  double    1.325  0.020  1.325
 KUK  C06  N07  single    1.431  0.020  1.431
 KUK  C06  C31  single    1.537  0.020  1.537
 KUK  N07  C08  single    1.365  0.020  1.365
 KUK  N33  C31  single    1.343  0.020  1.343
 KUK  C31  O32  double    1.219  0.020  1.219
 KUK  C08  N10  single    1.369  0.020  1.369
 KUK  C08  O09  double    1.219  0.020  1.219
 KUK  N10  C11  single    1.385  0.020  1.385
 KUK  N25  N24  aromatic  1.322  0.020  1.322
 KUK  N25  N26  aromatic  1.274  0.020  1.274
 KUK  C12  C11  aromatic  1.403  0.020  1.403
 KUK  C12  N13  aromatic  1.315  0.020  1.315
 KUK  C11  C16  aromatic  1.394  0.020  1.394
 KUK  N24  C23  aromatic  1.335  0.020  1.335
 KUK  N26  N27  aromatic  1.334  0.020  1.334
 KUK  N13  C14  aromatic  1.330  0.020  1.330
 KUK  C16  C15  aromatic  1.385  0.020  1.385
 KUK  C23  N27  aromatic  1.313  0.020  1.313
 KUK  C23  C22  single    1.483  0.020  1.483
 KUK  C14  C15  aromatic  1.385  0.020  1.385
 KUK  C14  C17  single    1.500  0.020  1.500
 KUK  C22  C21  single    1.530  0.020  1.530
 KUK  C21  C20  single    1.531  0.020  1.531
 KUK  N19  C17  single    1.335  0.020  1.335
 KUK  N19  C20  single    1.443  0.020  1.443
 KUK  O29  C28  deloc     1.245  0.020  1.245
 KUK  C17  O18  double    1.227  0.020  1.227
 KUK  C20  C28  single    1.555  0.020  1.555
 KUK  C28  O30  deloc     1.242  0.020  1.242
 KUK  C15  H1   single    0.930  0.020  1.080
 KUK  C20  H2   single    0.970  0.020  1.090
 KUK  C21  H3   single    0.970  0.020  1.090
 KUK  C21  H4   single    0.970  0.020  1.090
 KUK  C22  H5   single    0.970  0.020  1.090
 KUK  C22  H6   single    0.970  0.020  1.090
 KUK  N01  H7   single    0.860  0.020  1.020
 KUK  N01  H8   single    0.860  0.020  1.020
 KUK  N05  H9   single    0.860  0.020  1.020
 KUK  N05  H10  single    0.860  0.020  1.020
 KUK  C06  H11  single    0.970  0.020  1.090
 KUK  N07  H12  single    0.890  0.020  1.040
 KUK  N10  H13  single    0.860  0.020  1.020
 KUK  C12  H14  single    0.930  0.020  1.080
 KUK  C16  H15  single    0.930  0.020  1.080
 KUK  N19  H16  single    0.860  0.020  1.020
 KUK  N24  H17  single    0.860  0.020  1.020

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
 KUK  H1   C15  C16  119.78  3.000
 KUK  H1   C15  C14  120.38  3.000
 KUK  C16  C15  C14  119.84  3.000
 KUK  N19  C17  O18  124.92  3.000
 KUK  O18  C17  C14  120.56  3.000
 KUK  N19  C17  C14  114.52  3.000
 KUK  H2   C20  N19  108.59  3.000
 KUK  H2   C20  C28  108.60  3.000
 KUK  N19  C20  C28  109.60  3.000
 KUK  H2   C20  C21  108.45  3.000
 KUK  C28  C20  C21  109.08  3.000
 KUK  N19  C20  C21  112.44  3.000
 KUK  H4   C21  H3   106.96  3.000
 KUK  H4   C21  C22  109.62  3.000
 KUK  H3   C21  C22  109.25  3.000
 KUK  H4   C21  C20  109.13  3.000
 KUK  H3   C21  C20  108.17  3.000
 KUK  C22  C21  C20  113.50  3.000
 KUK  H6   C22  H5   107.39  3.000
 KUK  H6   C22  C23  107.86  3.000
 KUK  H5   C22  C23  109.27  3.000
 KUK  H6   C22  C21  110.15  3.000
 KUK  H5   C22  C21  110.47  3.000
 KUK  C23  C22  C21  111.57  3.000
 KUK  O30  C28  O29  127.99  3.000
 KUK  O30  C28  C20  115.21  3.000
 KUK  O29  C28  C20  116.79  3.000
 KUK  N33  C02  N03  128.62  3.000
 KUK  N33  C02  N01  117.21  3.000
 KUK  N03  C02  N01  114.13  3.000
 KUK  C04  N03  C02  116.71  3.000
 KUK  C06  C04  N05  117.68  3.000
 KUK  C06  C04  N03  121.68  3.000
 KUK  N05  C04  N03  120.50  3.000
 KUK  H10  N05  H9   118.38  3.000
 KUK  H10  N05  C04  121.26  3.000
 KUK  H9   N05  C04  120.33  3.000
 KUK  H11  C06  C31  105.61  3.000
 KUK  H11  C06  N07  107.05  3.000
 KUK  C31  C06  N07  113.65  3.000
 KUK  H11  C06  C04  105.19  3.000
 KUK  C31  C06  C04  111.34  3.000
 KUK  N07  C06  C04  113.23  3.000
 KUK  H12  N07  C08  120.18  3.000
 KUK  H12  N07  C06  116.96  3.000
 KUK  C08  N07  C06  116.99  3.000
 KUK  N10  C08  O09  124.51  3.000
 KUK  O09  C08  N07  121.06  3.000
 KUK  N10  C08  N07  114.40  3.000
 KUK  H13  N10  C11  115.14  3.000
 KUK  H13  N10  C08  117.19  3.000
 KUK  C11  N10  C08  127.64  3.000
 KUK  C16  C11  C12  117.07  3.000
 KUK  C16  C11  N10  125.85  3.000
 KUK  C12  C11  N10  117.08  3.000
 KUK  H14  C12  N13  116.66  3.000
 KUK  H14  C12  C11  119.69  3.000
 KUK  N13  C12  C11  123.66  3.000
 KUK  C14  N13  C12  119.28  3.000
 KUK  N13  C14  C17  118.22  3.000
 KUK  C17  C14  C15  120.29  3.000
 KUK  N13  C14  C15  121.49  3.000
 KUK  H15  C16  C11  121.56  3.000
 KUK  H15  C16  C15  119.77  3.000
 KUK  C11  C16  C15  118.66  3.000
 KUK  H16  N19  C20  114.87  3.000
 KUK  H16  N19  C17  117.70  3.000
 KUK  C20  N19  C17  125.13  3.000
 KUK  N27  C23  N24  106.69  3.000
 KUK  N27  C23  C22  127.51  3.000
 KUK  N24  C23  C22  125.78  3.000
 KUK  H17  N24  N25  120.97  3.000
 KUK  H17  N24  C23  129.63  3.000
 KUK  N25  N24  C23  109.40  3.000
 KUK  N26  N25  N24  106.22  3.000
 KUK  N27  N26  N25  111.17  3.000
 KUK  N26  N27  C23  106.52  3.000
 KUK  N33  C31  O32  123.46  3.000
 KUK  O32  C31  C06  118.58  3.000
 KUK  N33  C31  C06  117.82  3.000
 KUK  C31  N33  C02  118.25  3.000
 KUK  H8   N01  H7   118.93  3.000
 KUK  H8   N01  C02  120.34  3.000
 KUK  H7   N01  C02  120.65  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
 KUK  CONST_01  C12  C11  C16  C15     0.00   0.0  0
 KUK  CONST_02  C12  N13  C14  C15     0.00   0.0  0
 KUK  CONST_03  C14  N13  C12  C11     0.00   0.0  0
 KUK  CONST_04  C14  C15  C16  C11     0.00   0.0  0
 KUK  CONST_05  C16  C11  C12  N13     0.00   0.0  0
 KUK  CONST_06  C16  C15  C14  N13     0.00   0.0  0
 KUK  CONST_07  N26  N25  N24  C23     0.00   0.0  0
 KUK  CONST_08  N25  N26  N27  C23     0.00   0.0  0
 KUK  CONST_09  N27  N26  N25  N24     0.00   0.0  0
 KUK  CONST_10  N26  N27  C23  N24     0.00   0.0  0
 KUK  CONST_11  N27  C23  N24  N25     0.00   0.0  0
 KUK  CONST_12  C06  C04  N03  C02     0.00   0.0  0
 KUK  CONST_13  C31  N33  C02  N03     0.00   0.0  0
 KUK  CONST_14  N33  C02  N03  C04     0.00   0.0  0
 KUK  CONST_15  N10  C11  C16  C15   180.00   0.0  0
 KUK  CONST_16  C12  N13  C14  C17   180.00   0.0  0
 KUK  CONST_17  C16  C15  C14  C17   180.00   0.0  0
 KUK  CONST_18  N25  N24  C23  C22   180.00   0.0  0
 KUK  CONST_19  N26  N27  C23  C22   180.00   0.0  0
 KUK  CONST_20  N13  C12  C11  N10   180.00   0.0  0
 KUK  CONST_21  C04  N03  C02  N01   180.00   0.0  0
 KUK  CONST_22  C31  N33  C02  N01   180.00   0.0  0
 KUK  CONST_23  N05  C04  N03  C02   180.00   0.0  0
 KUK  CONST_24  H1   C15  C16  C11   180.00   0.0  0
 KUK  CONST_25  H15  C16  C11  C12   180.00   0.0  0
 KUK  CONST_26  H14  C12  N13  C14   180.00   0.0  0
 KUK  CONST_27  H17  N24  N25  N26   180.00   0.0  0
 KUK  CONST_28  C12  C11  N10  C08   180.00   0.0  0
 KUK  CONST_29  C16  C11  N10  C08     0.00   0.0  0
 KUK  CONST_30  H13  N10  C11  C12     0.00   0.0  0
 KUK  CONST_31  H9   N05  C04  N03     0.00   0.0  0
 KUK  CONST_32  H10  N05  C04  N03   180.00   0.0  0
 KUK  CONST_33  H7   N01  C02  N03     0.00   0.0  0
 KUK  CONST_34  H8   N01  C02  N03   180.00   0.0  0
 KUK  CONST_35  C14  C17  N19  C20   180.00   0.0  0
 KUK  CONST_36  O09  C08  N07  C06     0.00   0.0  0
 KUK  CONST_37  C11  N10  C08  O09     0.00   0.0  0
 KUK  CONST_38  C11  N10  C08  N07   180.00   0.0  0
 KUK  CONST_39  N10  C08  N07  C06   180.00   0.0  0
 KUK  CONST_40  H16  N19  C17  C14     0.00   0.0  0
 KUK  CONST_41  O18  C17  N19  C20     0.00   0.0  0
 KUK  CONST_42  H12  N07  C08  O09   180.00   0.0  0
 KUK  Var_01    O32  C31  N33  C02  -171.16  30.0  1
 KUK  Var_02    N19  C17  C14  C15  -179.92  30.0  2
 KUK  Var_03    N24  C23  C22  C21   -70.23  30.0  1
 KUK  Var_04    C23  C22  C21  C20  -176.08  30.0  2

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
 KUK  chir_01  C20  C21  N19  C28  positiv
 KUK  chir_02  C06  C04  N07  C31  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
 KUK  plan-1  C22  0.020
 KUK  plan-1  C23  0.020
 KUK  plan-1  N24  0.020
 KUK  plan-1  N25  0.020
 KUK  plan-1  N26  0.020
 KUK  plan-1  N27  0.020
 KUK  plan-1  H17  0.020
 KUK  plan-2  C02  0.020
 KUK  plan-2  N03  0.020
 KUK  plan-2  C04  0.020
 KUK  plan-2  N05  0.020
 KUK  plan-2  C06  0.020
 KUK  plan-2  C31  0.020
 KUK  plan-2  N33  0.020
 KUK  plan-2  H7   0.020
 KUK  plan-2  H8   0.020
 KUK  plan-2  H9   0.020
 KUK  plan-2  H10  0.020
 KUK  plan-2  N01  0.020
 KUK  plan-3  C20  0.020
 KUK  plan-3  C28  0.020
 KUK  plan-3  O29  0.020
 KUK  plan-3  O30  0.020
 KUK  plan-4  C15  0.020
 KUK  plan-4  C17  0.020
 KUK  plan-4  N10  0.020
 KUK  plan-4  C11  0.020
 KUK  plan-4  C12  0.020
 KUK  plan-4  N13  0.020
 KUK  plan-4  C14  0.020
 KUK  plan-4  C16  0.020
 KUK  plan-4  H1   0.020
 KUK  plan-4  H14  0.020
 KUK  plan-4  H15  0.020
 KUK  plan-5  C06  0.020
 KUK  plan-5  N07  0.020
 KUK  plan-5  C08  0.020
 KUK  plan-5  O09  0.020
 KUK  plan-5  N10  0.020
 KUK  plan-5  C11  0.020
 KUK  plan-5  H12  0.020
 KUK  plan-5  H13  0.020
 KUK  plan-6  C17  0.020
 KUK  plan-6  C20  0.020
 KUK  plan-6  C14  0.020
 KUK  plan-6  O18  0.020
 KUK  plan-6  N19  0.020
 KUK  plan-6  H16  0.020
 KUK  plan-7  C06  0.020
 KUK  plan-7  C31  0.020
 KUK  plan-7  O32  0.020
 KUK  plan-7  N33  0.020

