# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:29:49 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(O)=O)C(O)=O)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
 8UX  8UX  '(2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid'  ligand  40  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8UX
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
 8UX  OXT  O  OC     0  -0.628  -4.7427  -2.3321   1.5125
 8UX  C    C  C      0   0.392  -4.3771  -1.7136   0.4908
 8UX  O    O  O     -1  -0.613  -4.5857  -2.0542  -0.6915
 8UX  CA   C  CH1    0  -0.186  -3.6550  -0.3712   0.7225
 8UX  CB   C  CH3    0  -0.678  -4.7247   0.7027   0.9768
 8UX  N    N  NH1    0  -0.587  -2.7379  -0.0900  -0.3657
 8UX  CAV  C  CH1    0  -0.192  -2.0345   1.1763  -0.2806
 8UX  CAR  C  C      0   0.404  -2.7477   2.3601  -0.9748
 8UX  OAF  O  OC    -1  -0.627  -2.4384   3.5065  -0.5847
 8UX  OAC  O  O      0  -0.610  -3.5337   2.0837  -1.9042
 8UX  CAK  C  CH2    0  -0.438  -0.6303   1.0440  -0.8845
 8UX  CAJ  C  CH2    0  -0.241   0.2085  -0.0253  -0.2036
 8UX  NAN  N  NH1    0  -0.613   1.5595  -0.0516  -0.7270
 8UX  CAW  C  CH1    0  -0.144   2.3834  -1.0855  -0.1404
 8UX  CAS  C  C      0   0.389   2.0236  -2.5073  -0.6377
 8UX  OAG  O  OC    -1  -0.627   2.4421  -3.4399   0.0825
 8UX  OAD  O  O      0  -0.600   1.3949  -2.6219  -1.7044
 8UX  CAL  C  CH2    0  -0.534   3.8660  -0.8246  -0.4572
 8UX  CAT  C  CR5    0   0.147   4.4217   0.3886   0.2103
 8UX  CAI  C  CR15   0  -0.134   5.2556   0.4419   1.2940
 8UX  NAM  N  NR15   0  -0.562   5.4427   1.7701   1.5517
 8UX  CAH  C  CR15   0   0.087   4.7360   2.4631   0.6420
 8UX  NAP  N  N      0  -0.471   4.1083   1.6642  -0.1850
 8UX  H2   H  HCH1   0   0.193  -3.0591  -0.4603   1.6382
 8UX  H3   H  HCH3   0   0.210  -5.3762   0.8159   0.1082
 8UX  H4   H  HCH3   0   0.215  -5.3438   0.4361   1.8350
 8UX  H5   H  HCH3   0   0.219  -4.2784   1.6764   1.1858
 8UX  H6   H  HNH1   0   0.311  -3.2557  -0.1070  -1.2364
 8UX  H8   H  HCH1   0   0.195  -1.9034   1.4294   0.7787
 8UX  H10  H  HCH2   0   0.202  -0.7105   0.8147  -1.9529
 8UX  H11  H  HCH2   0   0.203  -0.1220   2.0112  -0.8100
 8UX  H12  H  HCH2   0   0.159   0.1848   0.1419   0.8888
 8UX  H13  H  HCH2   0   0.211  -0.2581  -0.9950  -0.3730
 8UX  H14  H  HNH1   0   0.334   1.9917   0.8485  -0.5496
 8UX  H16  H  HCH1   0   0.171   2.2933  -1.1018   0.9609
 8UX  H18  H  HCH2   0   0.240   4.4434  -1.6933  -0.1380
 8UX  H19  H  HCH2   0   0.229   3.9826  -0.7410  -1.5425
 8UX  H20  H  HCR5   0   0.280   5.7153  -0.3319   1.8856
 8UX  H21  H  HNR5   0   0.418   6.0119   2.1607   2.2854
 8UX  H22  H  HCR5   0   0.275   4.7157   3.5418   0.6219

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
 8UX  CAI  NAM  aromatic  1.366  0.020  1.366
 8UX  CAI  CAT  aromatic  1.369  0.020  1.369
 8UX  CAL  CAT  single    1.492  0.020  1.492
 8UX  CAL  CAW  single    1.538  0.020  1.538
 8UX  NAM  CAH  aromatic  1.344  0.020  1.344
 8UX  CAT  NAP  aromatic  1.372  0.020  1.372
 8UX  CAW  NAN  single    1.446  0.020  1.446
 8UX  CAW  CAS  single    1.549  0.020  1.549
 8UX  CAH  NAP  aromatic  1.310  0.020  1.310
 8UX  NAN  CAJ  single    1.449  0.020  1.449
 8UX  OAD  CAS  deloc     1.243  0.020  1.243
 8UX  CAS  OAG  deloc     1.250  0.020  1.250
 8UX  CAJ  CAK  single    1.520  0.020  1.520
 8UX  OAC  CAR  deloc     1.248  0.020  1.248
 8UX  CAK  CAV  single    1.534  0.020  1.534
 8UX  OAF  CAR  deloc     1.250  0.020  1.250
 8UX  CAR  CAV  single    1.547  0.020  1.547
 8UX  CAV  N    single    1.451  0.020  1.451
 8UX  O    C    deloc     1.248  0.020  1.248
 8UX  N    CA   single    1.451  0.020  1.451
 8UX  C    CA   single    1.542  0.020  1.542
 8UX  C    OXT  deloc     1.249  0.020  1.249
 8UX  CA   CB   single    1.537  0.020  1.537
 8UX  CA   H2   single    0.970  0.020  1.090
 8UX  CB   H3   single    0.970  0.020  1.090
 8UX  CB   H4   single    0.970  0.020  1.090
 8UX  CB   H5   single    0.970  0.020  1.090
 8UX  N    H6   single    0.890  0.020  1.040
 8UX  CAV  H8   single    0.970  0.020  1.090
 8UX  CAK  H10  single    0.970  0.020  1.090
 8UX  CAK  H11  single    0.970  0.020  1.090
 8UX  CAJ  H12  single    0.970  0.020  1.090
 8UX  CAJ  H13  single    0.970  0.020  1.090
 8UX  NAN  H14  single    0.890  0.020  1.040
 8UX  CAW  H16  single    0.970  0.020  1.090
 8UX  CAL  H18  single    0.970  0.020  1.090
 8UX  CAL  H19  single    0.970  0.020  1.090
 8UX  CAI  H20  single    0.930  0.020  1.080
 8UX  NAM  H21  single    0.860  0.020  1.020
 8UX  CAH  H22  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
 8UX  CA   C    O    117.28  3.000
 8UX  CA   C    OXT  116.44  3.000
 8UX  O    C    OXT  126.22  3.000
 8UX  H2   CA   N    107.38  3.000
 8UX  H2   CA   CB   107.27  3.000
 8UX  N    CA   CB   115.39  3.000
 8UX  H2   CA   C    108.02  3.000
 8UX  CB   CA   C    107.89  3.000
 8UX  N    CA   C    110.62  3.000
 8UX  H5   CB   H4   107.42  3.000
 8UX  H5   CB   H3   107.69  3.000
 8UX  H4   CB   H3   108.21  3.000
 8UX  H5   CB   CA   111.74  3.000
 8UX  H4   CB   CA   110.75  3.000
 8UX  H3   CB   CA   110.87  3.000
 8UX  H6   N    CAV  108.23  3.000
 8UX  H6   N    CA   108.56  3.000
 8UX  CAV  N    CA   115.57  3.000
 8UX  H8   CAV  CAK  106.89  3.000
 8UX  H8   CAV  CAR  108.17  3.000
 8UX  CAK  CAV  CAR  108.14  3.000
 8UX  H8   CAV  N    108.42  3.000
 8UX  CAR  CAV  N    114.72  3.000
 8UX  CAK  CAV  N    110.20  3.000
 8UX  OAC  CAR  OAF  126.25  3.000
 8UX  OAF  CAR  CAV  116.61  3.000
 8UX  OAC  CAR  CAV  117.07  3.000
 8UX  H11  CAK  H10  106.56  3.000
 8UX  H11  CAK  CAJ  109.55  3.000
 8UX  H10  CAK  CAJ  109.27  3.000
 8UX  H11  CAK  CAV  108.78  3.000
 8UX  H10  CAK  CAV  109.56  3.000
 8UX  CAJ  CAK  CAV  112.92  3.000
 8UX  H13  CAJ  H12  106.21  3.000
 8UX  H13  CAJ  NAN  109.09  3.000
 8UX  H12  CAJ  NAN  112.32  3.000
 8UX  H13  CAJ  CAK  108.67  3.000
 8UX  H12  CAJ  CAK  108.93  3.000
 8UX  NAN  CAJ  CAK  111.43  3.000
 8UX  H14  NAN  CAW  108.71  3.000
 8UX  H14  NAN  CAJ  108.54  3.000
 8UX  CAW  NAN  CAJ  113.42  3.000
 8UX  H16  CAW  CAL  106.64  3.000
 8UX  H16  CAW  CAS  106.71  3.000
 8UX  CAL  CAW  CAS  108.27  3.000
 8UX  H16  CAW  NAN  111.61  3.000
 8UX  CAS  CAW  NAN  113.19  3.000
 8UX  CAL  CAW  NAN  110.13  3.000
 8UX  OAD  CAS  OAG  126.48  3.000
 8UX  OAG  CAS  CAW  114.96  3.000
 8UX  OAD  CAS  CAW  118.52  3.000
 8UX  H19  CAL  H18  107.13  3.000
 8UX  H19  CAL  CAT  109.99  3.000
 8UX  H18  CAL  CAT  108.63  3.000
 8UX  H19  CAL  CAW  108.64  3.000
 8UX  H18  CAL  CAW  108.35  3.000
 8UX  CAT  CAL  CAW  113.87  3.000
 8UX  NAP  CAT  CAI  109.34  3.000
 8UX  NAP  CAT  CAL  122.83  3.000
 8UX  CAI  CAT  CAL  127.80  3.000
 8UX  H20  CAI  NAM  122.45  3.000
 8UX  H20  CAI  CAT  131.84  3.000
 8UX  NAM  CAI  CAT  105.71  3.000
 8UX  H21  NAM  CAH  126.15  3.000
 8UX  H21  NAM  CAI  126.29  3.000
 8UX  CAH  NAM  CAI  107.56  3.000
 8UX  H22  CAH  NAP  126.08  3.000
 8UX  H22  CAH  NAM  122.54  3.000
 8UX  NAP  CAH  NAM  111.39  3.000
 8UX  CAH  NAP  CAT  106.01  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
 8UX  CONST_01  CAH  NAM  CAI  CAT     0.00   0.0  0
 8UX  CONST_02  NAM  CAH  NAP  CAT     0.00   0.0  0
 8UX  CONST_03  NAP  CAH  NAM  CAI     0.00   0.0  0
 8UX  CONST_04  CAH  NAP  CAT  CAI     0.00   0.0  0
 8UX  CONST_05  NAP  CAT  CAI  NAM     0.00   0.0  0
 8UX  CONST_06  NAM  CAI  CAT  CAL   180.00   0.0  0
 8UX  CONST_07  CAH  NAP  CAT  CAL   180.00   0.0  0
 8UX  CONST_08  H21  NAM  CAI  CAT   180.00   0.0  0
 8UX  CONST_09  H22  CAH  NAP  CAT   180.00   0.0  0
 8UX  CONST_10  H20  CAI  NAM  CAH   180.00   0.0  0
 8UX  Var_01    CAI  CAT  CAL  CAW   104.65  30.0  2
 8UX  Var_02    NAN  CAJ  CAK  CAV  -175.49  30.0  2
 8UX  Var_03    CAW  NAN  CAJ  CAK  -178.01  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
 8UX  chir_01  CA   N    C    CB   positiv
 8UX  chir_02  CAV  N    CAK  CAR  negativ
 8UX  chir_03  CAW  NAN  CAL  CAS  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
 8UX  plan-1  CAL  0.020
 8UX  plan-1  CAT  0.020
 8UX  plan-1  CAI  0.020
 8UX  plan-1  NAM  0.020
 8UX  plan-1  CAH  0.020
 8UX  plan-1  NAP  0.020
 8UX  plan-1  H20  0.020
 8UX  plan-1  H21  0.020
 8UX  plan-1  H22  0.020
 8UX  plan-2  OXT  0.020
 8UX  plan-2  C    0.020
 8UX  plan-2  O    0.020
 8UX  plan-2  CA   0.020
 8UX  plan-3  CAV  0.020
 8UX  plan-3  CAR  0.020
 8UX  plan-3  OAF  0.020
 8UX  plan-3  OAC  0.020
 8UX  plan-4  CAW  0.020
 8UX  plan-4  CAS  0.020
 8UX  plan-4  OAG  0.020
 8UX  plan-4  OAD  0.020

