# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:13:18 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-alanyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](C)N[P@](O)(=O)CNC(=O)OCc1ccccc1)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
 UB2  UB2  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-alanyl-L-leucine  peptide  55  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UB2
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
 UB2  C3    C  CR16   0  -0.282   -6.9028  -1.1688   0.9255
 UB2  C2    C  CR16   0  -0.242   -8.2419  -0.8512   1.0910
 UB2  C1    C  CR16   0  -0.264   -9.0172  -0.4998  -0.0091
 UB2  H29   H  HCR6   0   0.257   -9.0408  -0.1976  -2.1339
 UB2  H28   H  HCR6   0   0.255   -6.6571  -0.7517  -2.4221
 UB2  H5    H  HCH2   0   0.243   -4.6349  -2.4360  -0.0605
 UB2  H5A   H  HCH2   0   0.245   -4.6125  -1.5266  -1.5742
 UB2  C29   C  CR16   0  -0.240   -8.4446  -0.4685  -1.2720
 UB2  C28   C  CR16   0  -0.303   -7.0999  -0.7816  -1.4335
 UB2  C4    C  CR6    0   0.074   -6.3184  -1.1360  -0.3400
 UB2  C5    C  CH2    0  -0.230   -4.8667  -1.4686  -0.5135
 UB2  O6    O  O2     0  -0.486   -4.1187  -0.4352   0.1287
 UB2  C7    C  C      0   0.748   -2.7817  -0.5651   0.1350
 UB2  O27   O  O      0  -0.526   -2.1943  -1.4616  -0.4376
 UB2  N8    N  NH1    0  -0.648   -2.2166   0.3961   0.8817
 UB2  C9    C  CH2    0  -0.560   -0.7969   0.6782   0.8523
 UB2  P10   P  P      0   1.231   -0.4337   2.0763  -0.2982
 UB2  O12   O  O      0  -0.814   -1.0046   3.3356   0.3101
 UB2  O11   O  OP    -1  -0.806   -0.8592   1.6376  -1.6783
 UB2  N13   N  NH1    0  -0.785    1.2599   2.1724  -0.1664
 UB2  C14   C  CH1    0  -0.202    2.1439   1.4227  -1.0252
 UB2  C16   C  C      0   0.570    3.4691   1.1876  -0.3106
 UB2  O26   O  O      0  -0.517    3.9914   2.0665   0.3644
 UB2  C15   C  CH3    0  -0.651    2.4331   2.1102  -2.3622
 UB2  N17   N  NH1    0  -0.621    4.0125  -0.0227  -0.4916
 UB2  C18   C  CH1    0  -0.199    5.3873  -0.3123  -0.1585
 UB2  C22   C  CH2    0  -0.443    5.6140  -1.8232  -0.1795
 UB2  C23   C  CH1    0  -0.225    4.7210  -2.6393   0.7583
 UB2  C25   C  CH3    0  -0.650    5.0273  -4.1254   0.5942
 UB2  C24   C  CH3    0  -0.659    4.8814  -2.2164   2.2141
 UB2  C19   C  C      0   0.415    6.3904   0.3912  -1.1105
 UB2  O21   O  O      0  -0.590    5.9429   0.8987  -2.1522
 UB2  O20   O  OC    -1  -0.620    7.5808   0.3560  -0.7368
 UB2  H3    H  HCR6   0   0.254   -6.3092  -1.4478   1.7882
 UB2  H2    H  HCR6   0   0.257   -8.6841  -0.8798   2.0787
 UB2  H1    H  HCR6   0   0.258  -10.0637  -0.2562   0.1209
 UB2  HN8   H  HNH1   0   0.391   -2.8149   1.1295   1.2289
 UB2  H9    H  HCH2   0   0.244   -0.4617   0.9220   1.8625
 UB2  H9A   H  HCH2   0   0.247   -0.2647  -0.2233   0.5490
 UB2  HN13  H  HNH1   0   0.358    1.6241   3.0779   0.0943
 UB2  H14   H  HCH1   0   0.237    1.6733   0.4569  -1.2318
 UB2  H15   H  HCH3   0   0.225    3.1488   1.5428  -2.9589
 UB2  H15A  H  HCH3   0   0.235    1.5060   2.2128  -2.9231
 UB2  H15B  H  HCH3   0   0.217    2.8495   3.1058  -2.1972
 UB2  HN17  H  HNH1   0   0.384    3.5640  -0.6346  -1.1556
 UB2  H18   H  HCH1   0   0.233    5.5756   0.0570   0.8524
 UB2  H22   H  HCH2   0   0.222    5.4757  -2.1857  -1.2055
 UB2  H22A  H  HCH2   0   0.228    6.6608  -2.0081   0.0740
 UB2  H23   H  HCH1   0   0.214    3.6753  -2.4805   0.4709
 UB2  H25   H  HCH3   0   0.211    6.0594  -4.3442   0.8786
 UB2  H25A  H  HCH3   0   0.224    4.3750  -4.7380   1.2190
 UB2  H25B  H  HCH3   0   0.222    4.8942  -4.4497  -0.4398
 UB2  H24   H  HCH3   0   0.211    5.9185  -2.3305   2.5412
 UB2  H24A  H  HCH3   0   0.228    4.5952  -1.1765   2.3748
 UB2  H24B  H  HCH3   0   0.226    4.2591  -2.8275   2.8701

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
 UB2  C28  C29   aromatic  1.390  0.020  1.390
 UB2  C29  C1    aromatic  1.387  0.020  1.387
 UB2  C29  H29   single    0.930  0.020  1.080
 UB2  C28  C4    aromatic  1.390  0.020  1.390
 UB2  C28  H28   single    0.930  0.020  1.080
 UB2  C5   C4    single    1.499  0.020  1.499
 UB2  C4   C3    aromatic  1.394  0.020  1.394
 UB2  O6   C5    single    1.428  0.020  1.428
 UB2  C5   H5    single    0.970  0.020  1.090
 UB2  C5   H5A   single    0.970  0.020  1.090
 UB2  C7   O6    single    1.343  0.020  1.343
 UB2  N8   C7    single    1.342  0.020  1.342
 UB2  O27  C7    double    1.215  0.020  1.215
 UB2  C9   N8    single    1.448  0.020  1.448
 UB2  N8   HN8   single    0.890  0.020  1.040
 UB2  P10  C9    single    1.847  0.020  1.847
 UB2  C9   H9    single    0.970  0.020  1.090
 UB2  C9   H9A   single    0.970  0.020  1.090
 UB2  N13  P10   single    1.701  0.020  1.701
 UB2  P10  O12   deloc     1.510  0.020  1.510
 UB2  P10  O11   deloc     1.509  0.020  1.509
 UB2  C14  N13   single    1.443  0.020  1.443
 UB2  N13  HN13  single    0.890  0.020  1.040
 UB2  C15  C14   single    1.531  0.020  1.531
 UB2  C14  C16   single    1.524  0.020  1.524
 UB2  C14  H14   single    0.970  0.020  1.090
 UB2  O26  C16   double    1.225  0.020  1.225
 UB2  C16  N17   single    1.339  0.020  1.339
 UB2  N17  C18   single    1.444  0.020  1.444
 UB2  N17  HN17  single    0.890  0.020  1.040
 UB2  C22  C18   single    1.528  0.020  1.528
 UB2  C18  C19   single    1.552  0.020  1.552
 UB2  C18  H18   single    0.970  0.020  1.090
 UB2  C23  C22   single    1.531  0.020  1.531
 UB2  C22  H22   single    0.970  0.020  1.090
 UB2  C22  H22A  single    0.970  0.020  1.090
 UB2  C24  C23   single    1.525  0.020  1.525
 UB2  C25  C23   single    1.526  0.020  1.526
 UB2  C23  H23   single    0.970  0.020  1.090
 UB2  C25  H25   single    0.970  0.020  1.090
 UB2  C25  H25A  single    0.970  0.020  1.090
 UB2  C25  H25B  single    0.970  0.020  1.090
 UB2  C24  H24   single    0.970  0.020  1.090
 UB2  C24  H24A  single    0.970  0.020  1.090
 UB2  C24  H24B  single    0.970  0.020  1.090
 UB2  C19  O21   deloc     1.242  0.020  1.242
 UB2  C19  O20   deloc     1.248  0.020  1.248
 UB2  C15  H15   single    0.970  0.020  1.090
 UB2  C15  H15A  single    0.970  0.020  1.090
 UB2  C15  H15B  single    0.970  0.020  1.090
 UB2  C3   C2    aromatic  1.386  0.020  1.386
 UB2  C3   H3    single    0.930  0.020  1.080
 UB2  C1   C2    aromatic  1.391  0.020  1.391
 UB2  C2   H2    single    0.930  0.020  1.080
 UB2  C1   H1    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
 UB2  H3    C3   C4    119.94  3.000
 UB2  H3    C3   C2    119.54  3.000
 UB2  C4    C3   C2    120.52  3.000
 UB2  H2    C2   C1    120.04  3.000
 UB2  H2    C2   C3    119.83  3.000
 UB2  C1    C2   C3    120.13  3.000
 UB2  H1    C1   C29   120.23  3.000
 UB2  H1    C1   C2    120.06  3.000
 UB2  C29   C1   C2    119.72  3.000
 UB2  C28   C29  H29   119.78  3.000
 UB2  H29   C29  C1    120.21  3.000
 UB2  C28   C29  C1    120.00  3.000
 UB2  C4    C28  C29   120.66  3.000
 UB2  C4    C28  H28   119.67  3.000
 UB2  C29   C28  H28   119.67  3.000
 UB2  C5    C4   C28   120.65  3.000
 UB2  C5    C4   C3    120.37  3.000
 UB2  C28   C4   C3    118.97  3.000
 UB2  O6    C5   C4    107.13  3.000
 UB2  O6    C5   H5A   110.68  3.000
 UB2  C4    C5   H5A   110.45  3.000
 UB2  H5A   C5   H5    107.82  3.000
 UB2  O6    C5   H5    110.06  3.000
 UB2  C4    C5   H5    110.72  3.000
 UB2  C7    O6   C5    116.97  3.000
 UB2  N8    C7   O27   125.95  3.000
 UB2  O27   C7   O6    123.38  3.000
 UB2  N8    C7   O6    110.64  3.000
 UB2  HN8   N8   C9    116.57  3.000
 UB2  HN8   N8   C7    117.56  3.000
 UB2  C9    N8   C7    122.77  3.000
 UB2  H9A   C9   H9    106.99  3.000
 UB2  H9A   C9   P10   110.91  3.000
 UB2  H9    C9   P10   110.30  3.000
 UB2  H9A   C9   N8    108.86  3.000
 UB2  H9    C9   N8    109.01  3.000
 UB2  P10   C9   N8    110.67  3.000
 UB2  N13   P10  O11   111.58  3.000
 UB2  O11   P10  O12   120.27  3.000
 UB2  N13   P10  O12   107.33  3.000
 UB2  O11   P10  C9    107.10  3.000
 UB2  O12   P10  C9    107.82  3.000
 UB2  N13   P10  C9    100.97  3.000
 UB2  HN13  N13  C14   113.49  3.000
 UB2  HN13  N13  P10   115.43  3.000
 UB2  C14   N13  P10   122.31  3.000
 UB2  H14   C14  C15   108.22  3.000
 UB2  H14   C14  C16   109.06  3.000
 UB2  C15   C14  C16   108.33  3.000
 UB2  H14   C14  N13   107.92  3.000
 UB2  C16   C14  N13   109.51  3.000
 UB2  C15   C14  N13   113.72  3.000
 UB2  N17   C16  O26   123.36  3.000
 UB2  N17   C16  C14   115.40  3.000
 UB2  O26   C16  C14   121.23  3.000
 UB2  H15B  C15  H15A  108.47  3.000
 UB2  H15B  C15  H15   107.86  3.000
 UB2  H15A  C15  H15   109.02  3.000
 UB2  H15B  C15  C14   110.46  3.000
 UB2  H15A  C15  C14   109.36  3.000
 UB2  H15   C15  C14   111.59  3.000
 UB2  HN17  N17  C18   116.98  3.000
 UB2  HN17  N17  C16   117.20  3.000
 UB2  C18   N17  C16   122.44  3.000
 UB2  H18   C18  C19   107.64  3.000
 UB2  H18   C18  C22   108.74  3.000
 UB2  C19   C18  C22   110.12  3.000
 UB2  H18   C18  N17   108.04  3.000
 UB2  C19   C18  N17   112.53  3.000
 UB2  C22   C18  N17   109.66  3.000
 UB2  H22A  C22  H22   106.36  3.000
 UB2  H22A  C22  C23   109.06  3.000
 UB2  H22   C22  C23   108.86  3.000
 UB2  H22A  C22  C18   107.84  3.000
 UB2  H22   C22  C18   108.72  3.000
 UB2  C23   C22  C18   115.61  3.000
 UB2  H23   C23  C24   108.10  3.000
 UB2  H23   C23  C25   107.72  3.000
 UB2  C24   C23  C25   110.59  3.000
 UB2  H23   C23  C22   108.59  3.000
 UB2  C25   C23  C22   109.65  3.000
 UB2  C24   C23  C22   112.07  3.000
 UB2  H25B  C25  H25A  107.61  3.000
 UB2  H25B  C25  H25   107.58  3.000
 UB2  H25A  C25  H25   107.65  3.000
 UB2  H25B  C25  C23   111.50  3.000
 UB2  H25A  C25  C23   111.42  3.000
 UB2  H25   C25  C23   110.89  3.000
 UB2  H24B  C24  H24A  107.21  3.000
 UB2  H24B  C24  H24   107.61  3.000
 UB2  H24A  C24  H24   107.72  3.000
 UB2  H24B  C24  C23   111.02  3.000
 UB2  H24A  C24  C23   112.19  3.000
 UB2  H24   C24  C23   110.89  3.000
 UB2  O20   C19  O21   127.31  3.000
 UB2  O20   C19  C18   114.84  3.000
 UB2  O21   C19  C18   117.83  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
 UB2  CONST_01  C29   C28  C4   C3      0.00   0.0  0
 UB2  CONST_02  C29   C1   C2   C3      0.00   0.0  0
 UB2  CONST_03  C28   C4   C3   C2      0.00   0.0  0
 UB2  CONST_04  C28   C29  C1   C2      0.00   0.0  0
 UB2  CONST_05  C4    C28  C29  C1      0.00   0.0  0
 UB2  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UB2  CONST_07  C5    C4   C3   C2    180.00   0.0  0
 UB2  CONST_08  C5    C4   C28  C29   180.00   0.0  0
 UB2  CONST_09  H28   C28  C4   C3    180.00   0.0  0
 UB2  CONST_10  H1    C1   C2   C3    180.00   0.0  0
 UB2  CONST_11  H29   C29  C1   C2    180.00   0.0  0
 UB2  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UB2  CONST_13  H2    C2   C1   C29   180.00   0.0  0
 UB2  CONST_14  C18   N17  C16  C14   180.00   0.0  0
 UB2  CONST_15  C18   N17  C16  O26     0.00   0.0  0
 UB2  CONST_16  HN17  N17  C16  C14     0.00   0.0  0
 UB2  Var_01    O6    C5   C4   C3    -67.12  30.0  2
 UB2  Var_02    N8    C7   O6   C5   -173.78  30.0  1
 UB2  Var_03    C9    N8   C7   O6   -166.86  30.0  2
 UB2  Var_04    P10   C9   N8   C7     96.38  30.0  1
 UB2  Var_05    N13   P10  C9   N8   -178.96  30.0  2
 UB2  Var_06    C14   N13  P10  C9     89.74  30.0  1
 UB2  Var_07    C24   C23  C22  C18   -58.70  30.0  1
 UB2  Var_08    H24   C24  C23  C22   -58.80  30.0  3
 UB2  Var_09    H25   C25  C23  C22    62.61  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
 UB2  chir_02  C14  N13  C15  C16  negativ
 UB2  chir_03  C18  N17  C22  C19  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
 UB2  plan-1  C3    0.020
 UB2  plan-1  C2    0.020
 UB2  plan-1  C1    0.020
 UB2  plan-1  H29   0.020
 UB2  plan-1  H28   0.020
 UB2  plan-1  C29   0.020
 UB2  plan-1  C28   0.020
 UB2  plan-1  C4    0.020
 UB2  plan-1  C5    0.020
 UB2  plan-1  H3    0.020
 UB2  plan-1  H2    0.020
 UB2  plan-1  H1    0.020
 UB2  plan-2  C14   0.020
 UB2  plan-2  C16   0.020
 UB2  plan-2  O26   0.020
 UB2  plan-2  N17   0.020
 UB2  plan-2  C18   0.020
 UB2  plan-2  HN17  0.020
 UB2  plan-3  C18   0.020
 UB2  plan-3  C19   0.020
 UB2  plan-3  O21   0.020
 UB2  plan-3  O20   0.020
 UB2  plan-4  O6    0.020
 UB2  plan-4  C7    0.020
 UB2  plan-4  O27   0.020
 UB2  plan-4  N8    0.020

