# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:40:41 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3-methylbutyl)-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCNC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1
#
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
 2H0  2H0  N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3-methylbutyl)-L-leucinamide  peptide  62  29  .  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_2H0
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
 2H0  C4   C  CH2    0  -0.240  -4.9235  -2.2758   0.3062
 2H0  C5   C  C      0   0.068  -5.9706  -1.3046  -0.1643
 2H0  C6   C  C1     0  -0.295  -6.8815  -0.7608   0.7337
 2H0  C7   C  C1     0  -0.244  -7.8773   0.1035   0.2963
 2H0  C8   C  C1     0  -0.266  -7.9613   0.4445  -1.0465
 2H0  C9   C  C1     0  -0.243  -7.0487  -0.0882  -1.9493
 2H0  C10  C  C1     0  -0.285  -6.0627  -0.9608  -1.5114
 2H0  C3   C  C      0   0.743  -3.0279  -0.8759   0.3454
 2H0  O21  O  O      0  -0.511  -3.4866  -0.2459   1.2752
 2H0  O4   O  O2     0  -0.489  -3.6255  -1.9590  -0.1842
 2H0  N2   N  NH1    0  -0.645  -1.8936  -0.5955  -0.3155
 2H0  C22  C  CH2    0  -0.563  -0.9220   0.3630   0.1658
 2H0  P    P  P      0   1.247   0.4178  -0.4645   1.1290
 2H0  O2   O  O      0  -0.807   1.0643  -1.4647   0.1839
 2H0  O3   O  OP    -1  -0.793  -0.1413  -0.9138   2.4518
 2H0  N    N  NH1    0  -0.787   1.5498   0.7610   1.4010
 2H0  C2   C  CH1    0  -0.210   2.4707   1.2230   0.3791
 2H0  C21  C  C      0   0.571   3.8502   0.5933   0.6288
 2H0  O1   O  O      0  -0.512   4.8271   1.2474   0.9781
 2H0  C23  C  CH2    0  -0.410   2.5062   2.7442   0.3075
 2H0  C24  C  CH1    0  -0.240   3.2767   3.3525  -0.8669
 2H0  C25  C  CH3    0  -0.664   2.7667   2.8587  -2.2183
 2H0  C26  C  CH3    0  -0.652   3.1937   4.8749  -0.7976
 2H0  C31  C  CH3    0  -0.650   7.3983  -3.3961  -1.8066
 2H0  C29  C  CH1    0  -0.237   6.8885  -2.9196  -0.4502
 2H0  C30  C  CH3    0  -0.661   8.0179  -2.2662   0.3425
 2H0  C28  C  CH2    0  -0.408   5.6974  -1.9783  -0.6343
 2H0  C27  C  CH2    0  -0.281   5.0233  -1.5671   0.6706
 2H0  N21  N  NH1    0  -0.653   3.8636  -0.7347   0.4526
 2H0  H16  H  HCH2   0   0.248  -4.9252  -2.3458   1.3956
 2H0  H17  H  HCH2   0   0.262  -5.1274  -3.2718  -0.0880
 2H0  H18  H  H      0   0.251  -6.8134  -1.0137   1.7851
 2H0  H19  H  H      0   0.255  -8.5813   0.5177   1.0065
 2H0  H20  H  H      0   0.256  -8.7335   1.1214  -1.3890
 2H0  H21  H  H      0   0.255  -7.1081   0.1731  -2.9980
 2H0  H22  H  H      0   0.253  -5.3622  -1.3753  -2.2265
 2H0  H23  H  HNH1   0   0.394  -1.5715  -1.2590  -1.0024
 2H0  H14  H  HCH2   0   0.249  -0.4992   0.8906  -0.6933
 2H0  H15  H  HCH2   0   0.252  -1.4276   1.1086   0.7778
 2H0  H1   H  HNH1   0   0.370   1.4410   1.3683   2.1986
 2H0  H2   H  HCH1   0   0.242   2.1164   0.8413  -0.5841
 2H0  H3   H  HCH2   0   0.221   1.4652   3.0812   0.2508
 2H0  H4   H  HCH2   0   0.222   2.9078   3.1414   1.2451
 2H0  H5   H  HCH1   0   0.224   4.3289   3.0707  -0.7740
 2H0  H6   H  HCH3   0   0.228   3.2766   3.3728  -3.0349
 2H0  H7   H  HCH3   0   0.225   2.9310   1.7902  -2.3637
 2H0  H8   H  HCH3   0   0.213   1.6957   3.0488  -2.3275
 2H0  H9   H  HCH3   0   0.211   2.1626   5.2171  -0.9191
 2H0  H10  H  HCH3   0   0.223   3.5567   5.2524   0.1602
 2H0  H11  H  HCH3   0   0.224   3.7899   5.3387  -1.5853
 2H0  H32  H  HCH3   0   0.212   7.7743  -2.5575  -2.3983
 2H0  H33  H  HCH3   0   0.224   8.2138  -4.1122  -1.6942
 2H0  H34  H  HCH3   0   0.223   6.6074  -3.8788  -2.3833
 2H0  H28  H  HCH1   0   0.212   6.5428  -3.7986   0.1079
 2H0  H29  H  HCH3   0   0.213   8.3516  -1.3499  -0.1507
 2H0  H30  H  HCH3   0   0.229   7.7167  -2.0053   1.3575
 2H0  H31  H  HCH3   0   0.226   8.8785  -2.9328   0.4210
 2H0  H26  H  HCH2   0   0.212   6.0254  -1.0792  -1.1683
 2H0  H27  H  HCH2   0   0.220   4.9537  -2.4652  -1.2735
 2H0  H24  H  HCH2   0   0.231   4.7097  -2.4593   1.2195
 2H0  H25  H  HCH2   0   0.233   5.7201  -1.0279   1.3112
 2H0  H12  H  HNH1   0   0.403   2.9689  -1.1824   0.2474

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
 2H0  C26  C24  single    1.526  0.020  1.526
 2H0  C24  C25  single    1.526  0.020  1.526
 2H0  C24  C23  single    1.531  0.020  1.531
 2H0  C31  C29  single    1.525  0.020  1.525
 2H0  C30  C29  single    1.527  0.020  1.527
 2H0  C23  C2   single    1.523  0.020  1.523
 2H0  C29  C28  single    1.529  0.020  1.529
 2H0  C28  C27  single    1.525  0.020  1.525
 2H0  C2   C21  single    1.537  0.020  1.537
 2H0  C2   N    single    1.451  0.020  1.451
 2H0  C21  O1   double    1.227  0.020  1.227
 2H0  C21  N21  single    1.340  0.020  1.340
 2H0  N21  C27  single    1.444  0.020  1.444
 2H0  N    P    single    1.690  0.020  1.690
 2H0  P    O2   deloc     1.520  0.020  1.520
 2H0  P    O3   deloc     1.505  0.020  1.505
 2H0  P    C22  single    1.846  0.020  1.846
 2H0  C22  N2   single    1.447  0.020  1.447
 2H0  N2   C3   single    1.342  0.020  1.342
 2H0  O21  C3   double    1.213  0.020  1.213
 2H0  C3   O4   single    1.346  0.020  1.346
 2H0  O4   C4   single    1.423  0.020  1.423
 2H0  C6   C7   aromatic  1.389  0.020  1.389
 2H0  C6   C5   aromatic  1.390  0.020  1.390
 2H0  C4   C5   single    1.504  0.020  1.504
 2H0  C7   C8   aromatic  1.388  0.020  1.388
 2H0  C5   C10  aromatic  1.393  0.020  1.393
 2H0  C8   C9   aromatic  1.390  0.020  1.390
 2H0  C10  C9   aromatic  1.388  0.020  1.388
 2H0  N    H1   single    0.860  0.020  1.020
 2H0  C2   H2   single    0.970  0.020  1.090
 2H0  C23  H3   single    0.970  0.020  1.090
 2H0  C23  H4   single    0.970  0.020  1.090
 2H0  C24  H5   single    0.970  0.020  1.090
 2H0  C25  H6   single    0.970  0.020  1.090
 2H0  C25  H7   single    0.970  0.020  1.090
 2H0  C25  H8   single    0.970  0.020  1.090
 2H0  C26  H9   single    0.970  0.020  1.090
 2H0  C26  H10  single    0.970  0.020  1.090
 2H0  C26  H11  single    0.970  0.020  1.090
 2H0  N21  H12  single    0.860  0.020  1.020
 2H0  C22  H14  single    0.970  0.020  1.090
 2H0  C22  H15  single    0.970  0.020  1.090
 2H0  C4   H16  single    0.970  0.020  1.090
 2H0  C4   H17  single    0.970  0.020  1.090
 2H0  C6   H18  single    0.930  0.020  1.080
 2H0  C7   H19  single    0.930  0.020  1.080
 2H0  C8   H20  single    0.930  0.020  1.080
 2H0  C9   H21  single    0.930  0.020  1.080
 2H0  C10  H22  single    0.930  0.020  1.080
 2H0  N2   H23  single    0.860  0.020  1.020
 2H0  C27  H24  single    0.970  0.020  1.090
 2H0  C27  H25  single    0.970  0.020  1.090
 2H0  C28  H26  single    0.970  0.020  1.090
 2H0  C28  H27  single    0.970  0.020  1.090
 2H0  C29  H28  single    0.970  0.020  1.090
 2H0  C30  H29  single    0.970  0.020  1.090
 2H0  C30  H30  single    0.970  0.020  1.090
 2H0  C30  H31  single    0.970  0.020  1.090
 2H0  C31  H32  single    0.970  0.020  1.090
 2H0  C31  H33  single    0.970  0.020  1.090
 2H0  C31  H34  single    0.970  0.020  1.090

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
 2H0  H17  C4   H16  107.57  3.000
 2H0  H17  C4   O4   104.43  3.000
 2H0  H16  C4   O4   111.07  3.000
 2H0  H17  C4   C5   110.28  3.000
 2H0  H16  C4   C5   110.65  3.000
 2H0  O4   C4   C5   112.55  3.000
 2H0  C10  C5   C6   119.00  3.000
 2H0  C10  C5   C4   120.53  3.000
 2H0  C6   C5   C4   120.46  3.000
 2H0  H18  C6   C7   119.72  3.000
 2H0  H18  C6   C5   119.63  3.000
 2H0  C7   C6   C5   120.65  3.000
 2H0  H19  C7   C8   120.09  3.000
 2H0  H19  C7   C6   119.85  3.000
 2H0  C8   C7   C6   120.06  3.000
 2H0  H20  C8   C9   120.17  3.000
 2H0  H20  C8   C7   120.19  3.000
 2H0  C9   C8   C7   119.64  3.000
 2H0  H21  C9   C10  119.77  3.000
 2H0  H21  C9   C8   120.05  3.000
 2H0  C10  C9   C8   120.18  3.000
 2H0  H22  C10  C9   119.46  3.000
 2H0  H22  C10  C5   120.06  3.000
 2H0  C9   C10  C5   120.48  3.000
 2H0  N2   C3   O4   110.46  3.000
 2H0  O4   C3   O21  123.48  3.000
 2H0  N2   C3   O21  126.04  3.000
 2H0  C3   O4   C4   116.65  3.000
 2H0  H23  N2   C22  116.62  3.000
 2H0  H23  N2   C3   117.91  3.000
 2H0  C22  N2   C3   122.81  3.000
 2H0  H15  C22  H14  106.90  3.000
 2H0  H15  C22  P    110.52  3.000
 2H0  H14  C22  P    110.23  3.000
 2H0  H15  C22  N2   109.19  3.000
 2H0  H14  C22  N2   108.54  3.000
 2H0  P    C22  N2   111.34  3.000
 2H0  N    P    O3   108.90  3.000
 2H0  O3   P    O2   120.53  3.000
 2H0  N    P    O2   106.99  3.000
 2H0  O3   P    C22  108.84  3.000
 2H0  O2   P    C22  106.21  3.000
 2H0  N    P    C22  104.18  3.000
 2H0  H1   N    C2   115.70  3.000
 2H0  H1   N    P    119.45  3.000
 2H0  C2   N    P    122.86  3.000
 2H0  H2   C2   C23  108.31  3.000
 2H0  H2   C2   C21  106.89  3.000
 2H0  C23  C2   C21  113.32  3.000
 2H0  H2   C2   N    107.64  3.000
 2H0  C21  C2   N    108.96  3.000
 2H0  C23  C2   N    111.46  3.000
 2H0  N21  C21  O1   123.93  3.000
 2H0  N21  C21  C2   113.19  3.000
 2H0  O1   C21  C2   122.87  3.000
 2H0  H4   C23  H3   106.33  3.000
 2H0  H4   C23  C24  109.17  3.000
 2H0  H3   C23  C24  108.45  3.000
 2H0  H4   C23  C2   109.30  3.000
 2H0  H3   C23  C2   106.71  3.000
 2H0  C24  C23  C2   116.40  3.000
 2H0  H5   C24  C26  107.80  3.000
 2H0  H5   C24  C25  108.26  3.000
 2H0  C26  C24  C25  110.16  3.000
 2H0  H5   C24  C23  108.48  3.000
 2H0  C25  C24  C23  112.49  3.000
 2H0  C26  C24  C23  109.52  3.000
 2H0  H8   C25  H7   107.73  3.000
 2H0  H8   C25  H6   107.52  3.000
 2H0  H7   C25  H6   106.94  3.000
 2H0  H8   C25  C24  111.07  3.000
 2H0  H7   C25  C24  112.62  3.000
 2H0  H6   C25  C24  110.73  3.000
 2H0  H11  C26  H10  107.74  3.000
 2H0  H11  C26  H9   107.58  3.000
 2H0  H10  C26  H9   107.63  3.000
 2H0  H11  C26  C24  111.19  3.000
 2H0  H10  C26  C24  111.51  3.000
 2H0  H9   C26  C24  111.01  3.000
 2H0  H34  C31  H33  107.81  3.000
 2H0  H34  C31  H32  107.62  3.000
 2H0  H33  C31  H32  107.59  3.000
 2H0  H34  C31  C29  111.46  3.000
 2H0  H33  C31  C29  111.29  3.000
 2H0  H32  C31  C29  110.90  3.000
 2H0  H28  C29  C28  108.00  3.000
 2H0  H28  C29  C30  108.17  3.000
 2H0  C28  C29  C30  112.04  3.000
 2H0  H28  C29  C31  107.90  3.000
 2H0  C28  C29  C31  110.21  3.000
 2H0  C30  C29  C31  110.38  3.000
 2H0  H31  C30  H30  107.28  3.000
 2H0  H31  C30  H29  107.69  3.000
 2H0  H30  C30  H29  107.69  3.000
 2H0  H31  C30  C29  111.05  3.000
 2H0  H30  C30  C29  112.42  3.000
 2H0  H29  C30  C29  110.51  3.000
 2H0  H27  C28  H26  106.48  3.000
 2H0  H27  C28  C27  108.61  3.000
 2H0  H26  C28  C27  109.14  3.000
 2H0  H27  C28  C29  109.01  3.000
 2H0  H26  C28  C29  109.30  3.000
 2H0  C27  C28  C29  114.03  3.000
 2H0  H25  C27  H24  106.98  3.000
 2H0  H25  C27  N21  108.50  3.000
 2H0  H24  C27  N21  108.41  3.000
 2H0  H25  C27  C28  110.72  3.000
 2H0  H24  C27  C28  109.65  3.000
 2H0  N21  C27  C28  112.41  3.000
 2H0  H12  N21  C27  118.76  3.000
 2H0  H12  N21  C21  116.89  3.000
 2H0  C27  N21  C21  124.02  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
 2H0  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 2H0  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 2H0  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 2H0  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 2H0  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 2H0  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 2H0  CONST_07  C7   C6   C5   C4    180.00   0.0  0
 2H0  CONST_08  C9   C10  C5   C4    180.00   0.0  0
 2H0  CONST_09  H19  C7   C6   C5    180.00   0.0  0
 2H0  CONST_10  H21  C9   C10  C5    180.00   0.0  0
 2H0  CONST_11  H20  C8   C7   C6    180.00   0.0  0
 2H0  CONST_12  H22  C10  C5   C6    180.00   0.0  0
 2H0  CONST_13  H18  C6   C7   C8    180.00   0.0  0
 2H0  CONST_14  C27  N21  C21  C2    180.00   0.0  0
 2H0  CONST_15  C27  N21  C21  O1      0.00   0.0  0
 2H0  CONST_16  H12  N21  C21  C2      0.00   0.0  0
 2H0  Var_01    O4   C4   C5   C6   -132.60  30.0  2
 2H0  Var_02    N2   C3   O4   C4   -172.36  30.0  1
 2H0  Var_03    P    C22  N2   C3     94.80  30.0  1
 2H0  Var_04    C22  N2   C3   O21    12.38  30.0  2
 2H0  Var_05    N    P    C22  N2    171.95  30.0  2
 2H0  Var_06    C2   N    P    C22   -77.05  30.0  1
 2H0  Var_07    C26  C24  C23  C2    179.16  30.0  3
 2H0  Var_08    C28  C27  N21  C21  -102.89  30.0  3
 2H0  Var_09    C27  C28  C29  C31   173.76  30.0  3
 2H0  Var_10    N21  C27  C28  C29  -177.04  30.0  3
 2H0  Var_11    H9   C26  C24  C23   -64.06  30.0  3
 2H0  Var_12    H6   C25  C24  C23   175.16  30.0  3
 2H0  Var_13    H29  C30  C29  C31    65.54  30.0  3
 2H0  Var_14    H32  C31  C29  C30   -60.90  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
 2H0  chir_02  C2  C23  C21  N  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
 2H0  plan-1  C4   0.020
 2H0  plan-1  C5   0.020
 2H0  plan-1  C6   0.020
 2H0  plan-1  C7   0.020
 2H0  plan-1  C8   0.020
 2H0  plan-1  C9   0.020
 2H0  plan-1  C10  0.020
 2H0  plan-1  H18  0.020
 2H0  plan-1  H19  0.020
 2H0  plan-1  H20  0.020
 2H0  plan-1  H21  0.020
 2H0  plan-1  H22  0.020
 2H0  plan-2  C2   0.020
 2H0  plan-2  C21  0.020
 2H0  plan-2  O1   0.020
 2H0  plan-2  C27  0.020
 2H0  plan-2  N21  0.020
 2H0  plan-2  H12  0.020
 2H0  plan-3  C3   0.020
 2H0  plan-3  O21  0.020
 2H0  plan-3  O4   0.020
 2H0  plan-3  N2   0.020

