# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 10:31:22 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-phenylalanyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)N[P](O)(=O)CNC(=O)OCc2ccccc2)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
 1U4  1U4  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-phenylalanyl-L-leucine  ligand  65  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1U4
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
 1U4  C9    C  C      0   0.748   2.1564   1.2810  -0.0590
 1U4  O10   O  O      0  -0.512   1.4320   1.7348  -0.9214
 1U4  O8    O  O2     0  -0.487   3.4933   1.4272  -0.0644
 1U4  C7    C  CH2    0  -0.234   4.0572   2.1599  -1.1543
 1U4  C6    C  CR6    0   0.077   5.5472   2.0789  -1.0118
 1U4  C4    C  CR16   0  -0.296   6.2618   3.1143  -0.4185
 1U4  C2    C  CR16   0  -0.242   7.6405   3.0286  -0.2711
 1U4  C1    C  CR16   0  -0.262   8.3169   1.8999  -0.7131
 1U4  C63   C  CR16   0  -0.243   7.6103   0.8595  -1.3049
 1U4  C61   C  CR16   0  -0.288   6.2339   0.9501  -1.4524
 1U4  N11   N  NH1    0  -0.649   1.7616   0.6093   1.0350
 1U4  C12   C  CH2    0  -0.571   0.4186   0.0933   1.1945
 1U4  P13   P  P      0   1.222   0.3495  -1.7030   0.7524
 1U4  O54   O  O      0  -0.816   1.2274  -2.4346   1.7395
 1U4  O55   O  OP    -1  -0.806   0.5985  -1.8159  -0.7293
 1U4  N14   N  NH1    0  -0.749  -1.2589  -2.1671   1.0657
 1U4  C15   C  CH1    0  -0.201  -2.3482  -1.6762   0.2625
 1U4  C16   C  C      0   0.563  -2.9438  -0.3920   0.8322
 1U4  O17   O  O      0  -0.520  -3.2215  -0.3063   2.0239
 1U4  C38   C  CH2    0  -0.522  -3.4886  -2.7056   0.1548
 1U4  C41   C  CR6    0   0.167  -3.0594  -3.9480  -0.5658
 1U4  C42   C  CR16   0  -0.315  -3.1798  -4.0387  -1.9507
 1U4  C50   C  CR16   0  -0.295  -2.5015  -5.0224   0.1226
 1U4  C44   C  CR16   0  -0.242  -2.7567  -5.1715  -2.6331
 1U4  C48   C  CR16   0  -0.247  -2.0804  -6.1596  -0.5534
 1U4  C46   C  CR16   0  -0.276  -2.2045  -6.2377  -1.9348
 1U4  N18   N  NH1    0  -0.611  -3.1270   0.5953  -0.0485
 1U4  C19   C  CH1    0  -0.220  -3.8799   1.7921   0.2372
 1U4  C33   C  C      0   0.419  -5.4088   1.5755   0.0867
 1U4  O34   O  O      0  -0.590  -5.8040   0.4442  -0.2428
 1U4  C20   C  CH2    0  -0.431  -3.3808   2.9417  -0.6371
 1U4  C21   C  CH1    0  -0.227  -1.8790   3.2171  -0.5419
 1U4  C26   C  CH3    0  -0.651  -1.4949   4.3566  -1.4803
 1U4  C22   C  CH3    0  -0.661  -1.4341   3.5293   0.8820
 1U4  O35   O  OC    -1  -0.617  -6.1089   2.5806   0.3244
 1U4  H7    H  HCH2   0   0.242   3.7230   3.1999  -1.1265
 1U4  H7A   H  HCH2   0   0.243   3.7390   1.7281  -2.1054
 1U4  H4    H  HCR6   0   0.255   5.7384   3.9971  -0.0711
 1U4  H2    H  HCR6   0   0.258   8.1843   3.8440   0.1879
 1U4  H1    H  HCR6   0   0.258   9.3912   1.8313  -0.6008
 1U4  H63   H  HCR6   0   0.258   8.1328  -0.0209  -1.6561
 1U4  H61   H  HCR6   0   0.254   5.6899   0.1382  -1.9208
 1U4  HN11  H  HNH1   0   0.389   2.4773   0.1896   1.6079
 1U4  H12   H  HCH2   0   0.239   0.0979   0.2470   2.2282
 1U4  H12A  H  HCH2   0   0.262  -0.2536   0.6763   0.5663
 1U4  HN14  H  HNH1   0   0.352  -1.5016  -2.2394   2.0452
 1U4  H15   H  HCH1   0   0.253  -1.9585  -1.4945  -0.7428
 1U4  H38   H  HCH2   0   0.245  -3.8364  -2.9497   1.1621
 1U4  H38A  H  HCH2   0   0.253  -4.3303  -2.2377  -0.3644
 1U4  H42   H  HCR6   0   0.240  -3.6138  -3.2119  -2.5021
 1U4  H50   H  HCR6   0   0.236  -2.3996  -4.9693   1.1994
 1U4  H44   H  HCR6   0   0.248  -2.8622  -5.2233  -3.7095
 1U4  H48   H  HCR6   0   0.248  -1.6540  -6.9880  -0.0015
 1U4  H46   H  HCR6   0   0.249  -1.8759  -7.1241  -2.4621
 1U4  HN18  H  HNH1   0   0.384  -2.9508   0.3886  -1.0192
 1U4  H19   H  HCH1   0   0.242  -3.6960   2.0488   1.2833
 1U4  H20   H  HCH2   0   0.217  -3.6356   2.7361  -1.6842
 1U4  H20A  H  HCH2   0   0.223  -3.9341   3.8420  -0.3591
 1U4  H21   H  HCH1   0   0.225  -1.3374   2.3241  -0.8691
 1U4  H26   H  HCH3   0   0.208  -1.9668   5.2945  -1.1757
 1U4  H26A  H  HCH3   0   0.223  -0.4149   4.5138  -1.4810
 1U4  H26B  H  HCH3   0   0.219  -1.8014   4.1512  -2.5081
 1U4  H22   H  HCH3   0   0.226  -1.5999   2.6908   1.5597
 1U4  H22A  H  HCH3   0   0.225  -0.3667   3.7541   0.9083
 1U4  H22B  H  HCH3   0   0.209  -1.9705   4.3948   1.2800

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
 1U4  C63  C1    aromatic  1.390  0.020  1.390
 1U4  C1   C2    aromatic  1.388  0.020  1.388
 1U4  C1   H1    single    0.930  0.020  1.080
 1U4  C61  C63   aromatic  1.387  0.020  1.387
 1U4  C63  H63   single    0.930  0.020  1.080
 1U4  C61  C6    aromatic  1.393  0.020  1.393
 1U4  C61  H61   single    0.930  0.020  1.080
 1U4  C7   C6    single    1.499  0.020  1.499
 1U4  C6   C4    aromatic  1.391  0.020  1.391
 1U4  O8   C7    single    1.429  0.020  1.429
 1U4  C7   H7    single    0.970  0.020  1.090
 1U4  C7   H7A   single    0.970  0.020  1.090
 1U4  C9   O8    single    1.345  0.020  1.345
 1U4  N11  C9    single    1.343  0.020  1.343
 1U4  O10  C9    double    1.214  0.020  1.214
 1U4  C12  N11   single    1.448  0.020  1.448
 1U4  N11  HN11  single    0.890  0.020  1.040
 1U4  P13  C12   single    1.851  0.020  1.851
 1U4  C12  H12   single    0.970  0.020  1.090
 1U4  C12  H12A  single    0.970  0.020  1.090
 1U4  N14  P13   single    1.703  0.020  1.703
 1U4  P13  O54   deloc     1.510  0.020  1.510
 1U4  P13  O55   deloc     1.507  0.020  1.507
 1U4  C15  N14   single    1.440  0.020  1.440
 1U4  N14  HN14  single    0.890  0.020  1.040
 1U4  C38  C15   single    1.540  0.020  1.540
 1U4  C15  C16   single    1.526  0.020  1.526
 1U4  C15  H15   single    0.970  0.020  1.090
 1U4  C41  C38   single    1.499  0.020  1.499
 1U4  C38  H38   single    0.970  0.020  1.090
 1U4  C38  H38A  single    0.970  0.020  1.090
 1U4  C42  C41   aromatic  1.393  0.020  1.393
 1U4  C41  C50   aromatic  1.393  0.020  1.393
 1U4  C48  C50   aromatic  1.388  0.020  1.388
 1U4  C50  H50   single    0.930  0.020  1.080
 1U4  C46  C48   aromatic  1.389  0.020  1.389
 1U4  C48  H48   single    0.930  0.020  1.080
 1U4  C44  C46   aromatic  1.389  0.020  1.389
 1U4  C46  H46   single    0.930  0.020  1.080
 1U4  C44  C42   aromatic  1.389  0.020  1.389
 1U4  C44  H44   single    0.930  0.020  1.080
 1U4  C42  H42   single    0.930  0.020  1.080
 1U4  O17  C16   double    1.227  0.020  1.227
 1U4  C16  N18   single    1.336  0.020  1.336
 1U4  N18  C19   single    1.443  0.020  1.443
 1U4  N18  HN18  single    0.860  0.020  1.020
 1U4  C20  C19   single    1.528  0.020  1.528
 1U4  C19  C33   single    1.552  0.020  1.552
 1U4  C19  H19   single    0.970  0.020  1.090
 1U4  C33  O34   deloc     1.243  0.020  1.243
 1U4  C33  O35   deloc     1.248  0.020  1.248
 1U4  C21  C20   single    1.530  0.020  1.530
 1U4  C20  H20   single    0.970  0.020  1.090
 1U4  C20  H20A  single    0.970  0.020  1.090
 1U4  C26  C21   single    1.525  0.020  1.525
 1U4  C22  C21   single    1.524  0.020  1.524
 1U4  C21  H21   single    0.970  0.020  1.090
 1U4  C26  H26   single    0.970  0.020  1.090
 1U4  C26  H26A  single    0.970  0.020  1.090
 1U4  C26  H26B  single    0.970  0.020  1.090
 1U4  C22  H22   single    0.970  0.020  1.090
 1U4  C22  H22A  single    0.970  0.020  1.090
 1U4  C22  H22B  single    0.970  0.020  1.090
 1U4  C4   C2    aromatic  1.389  0.020  1.389
 1U4  C4   H4    single    0.930  0.020  1.080
 1U4  C2   H2    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
 1U4  N11   C9   O8    110.48  3.000
 1U4  N11   C9   O10   126.16  3.000
 1U4  O8    C9   O10   123.34  3.000
 1U4  C7    O8   C9    116.81  3.000
 1U4  H7A   C7   H7    108.02  3.000
 1U4  H7A   C7   C6    110.55  3.000
 1U4  H7    C7   C6    110.67  3.000
 1U4  H7A   C7   O8    110.27  3.000
 1U4  H7    C7   O8    110.36  3.000
 1U4  C6    C7   O8    106.98  3.000
 1U4  C61   C6   C4    119.01  3.000
 1U4  C4    C6   C7    120.73  3.000
 1U4  C61   C6   C7    120.25  3.000
 1U4  H4    C4   C2    119.71  3.000
 1U4  H4    C4   C6    119.67  3.000
 1U4  C2    C4   C6    120.61  3.000
 1U4  H2    C2   C1    120.19  3.000
 1U4  H2    C2   C4    119.81  3.000
 1U4  C1    C2   C4    120.00  3.000
 1U4  H1    C1   C63   120.09  3.000
 1U4  H1    C1   C2    120.14  3.000
 1U4  C63   C1   C2    119.77  3.000
 1U4  H63   C63  C61   119.84  3.000
 1U4  H63   C63  C1    120.11  3.000
 1U4  C61   C63  C1    120.05  3.000
 1U4  H61   C61  C63   119.67  3.000
 1U4  H61   C61  C6    119.76  3.000
 1U4  C63   C61  C6    120.56  3.000
 1U4  HN11  N11  C12   116.59  3.000
 1U4  HN11  N11  C9    117.54  3.000
 1U4  C12   N11  C9    122.73  3.000
 1U4  H12A  C12  H12   106.80  3.000
 1U4  H12A  C12  P13   111.02  3.000
 1U4  H12   C12  P13   110.57  3.000
 1U4  H12A  C12  N11   108.56  3.000
 1U4  H12   C12  N11   109.04  3.000
 1U4  P13   C12  N11   110.74  3.000
 1U4  N14   P13  O55   108.46  3.000
 1U4  O55   P13  O54   120.69  3.000
 1U4  N14   P13  O54   107.26  3.000
 1U4  O55   P13  C12   107.54  3.000
 1U4  O54   P13  C12   106.99  3.000
 1U4  N14   P13  C12   104.82  3.000
 1U4  HN14  N14  C15   112.52  3.000
 1U4  HN14  N14  P13   115.10  3.000
 1U4  C15   N14  P13   121.26  3.000
 1U4  H15   C15  C38   108.10  3.000
 1U4  H15   C15  C16   110.03  3.000
 1U4  C38   C15  C16   107.43  3.000
 1U4  H15   C15  N14   107.46  3.000
 1U4  C16   C15  N14   111.96  3.000
 1U4  C38   C15  N14   111.80  3.000
 1U4  N18   C16  O17   123.91  3.000
 1U4  N18   C16  C15   115.43  3.000
 1U4  O17   C16  C15   120.66  3.000
 1U4  H38A  C38  H38   106.74  3.000
 1U4  H38A  C38  C41   110.28  3.000
 1U4  H38   C38  C41   110.42  3.000
 1U4  H38A  C38  C15   108.49  3.000
 1U4  H38   C38  C15   108.69  3.000
 1U4  C41   C38  C15   112.06  3.000
 1U4  C50   C41  C42   118.41  3.000
 1U4  C50   C41  C38   121.10  3.000
 1U4  C42   C41  C38   120.47  3.000
 1U4  H42   C42  C44   119.61  3.000
 1U4  H42   C42  C41   119.37  3.000
 1U4  C44   C42  C41   121.02  3.000
 1U4  H50   C50  C48   119.72  3.000
 1U4  H50   C50  C41   119.43  3.000
 1U4  C48   C50  C41   120.85  3.000
 1U4  H44   C44  C46   120.12  3.000
 1U4  H44   C44  C42   119.86  3.000
 1U4  C46   C44  C42   120.02  3.000
 1U4  H48   C48  C46   119.94  3.000
 1U4  H48   C48  C50   119.86  3.000
 1U4  C46   C48  C50   120.20  3.000
 1U4  H46   C46  C48   120.21  3.000
 1U4  H46   C46  C44   120.29  3.000
 1U4  C48   C46  C44   119.49  3.000
 1U4  HN18  N18  C19   116.88  3.000
 1U4  HN18  N18  C16   117.35  3.000
 1U4  C19   N18  C16   123.66  3.000
 1U4  H19   C19  C20   108.43  3.000
 1U4  H19   C19  C33   106.95  3.000
 1U4  C20   C19  C33   111.80  3.000
 1U4  H19   C19  N18   107.26  3.000
 1U4  C33   C19  N18   112.29  3.000
 1U4  C20   C19  N18   109.90  3.000
 1U4  O35   C33  O34   127.25  3.000
 1U4  O35   C33  C19   114.96  3.000
 1U4  O34   C33  C19   117.79  3.000
 1U4  H20A  C20  H20   106.24  3.000
 1U4  H20A  C20  C21   109.45  3.000
 1U4  H20   C20  C21   108.73  3.000
 1U4  H20A  C20  C19   107.99  3.000
 1U4  H20   C20  C19   109.22  3.000
 1U4  C21   C20  C19   114.86  3.000
 1U4  H21   C21  C22   107.58  3.000
 1U4  H21   C21  C26   107.52  3.000
 1U4  C22   C21  C26   110.38  3.000
 1U4  H21   C21  C20   108.68  3.000
 1U4  C22   C21  C20   112.43  3.000
 1U4  C26   C21  C20   110.09  3.000
 1U4  H26B  C26  H26A  107.71  3.000
 1U4  H26B  C26  H26   107.60  3.000
 1U4  H26A  C26  H26   107.69  3.000
 1U4  H26B  C26  C21   111.58  3.000
 1U4  H26A  C26  C21   110.93  3.000
 1U4  H26   C26  C21   111.15  3.000
 1U4  H22B  C22  H22A  107.94  3.000
 1U4  H22B  C22  H22   107.92  3.000
 1U4  H22A  C22  H22   106.99  3.000
 1U4  H22B  C22  C21   111.04  3.000
 1U4  H22A  C22  C21   110.51  3.000
 1U4  H22   C22  C21   112.25  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
 1U4  CONST_01  C1    C63  C61  C6      0.00   0.0  0
 1U4  CONST_02  C1    C2   C4   C6      0.00   0.0  0
 1U4  CONST_03  C63   C61  C6   C4      0.00   0.0  0
 1U4  CONST_04  C63   C1   C2   C4      0.00   0.0  0
 1U4  CONST_05  C61   C63  C1   C2      0.00   0.0  0
 1U4  CONST_06  C61   C6   C4   C2      0.00   0.0  0
 1U4  CONST_07  C46   C44  C42  C41     0.00   0.0  0
 1U4  CONST_08  C46   C48  C50  C41     0.00   0.0  0
 1U4  CONST_09  C48   C50  C41  C42     0.00   0.0  0
 1U4  CONST_10  C48   C46  C44  C42     0.00   0.0  0
 1U4  CONST_11  C44   C42  C41  C50     0.00   0.0  0
 1U4  CONST_12  C44   C46  C48  C50     0.00   0.0  0
 1U4  CONST_13  C63   C61  C6   C7    180.00   0.0  0
 1U4  CONST_14  C2    C4   C6   C7    180.00   0.0  0
 1U4  CONST_15  C44   C42  C41  C38   180.00   0.0  0
 1U4  CONST_16  C48   C50  C41  C38   180.00   0.0  0
 1U4  CONST_17  H63   C63  C61  C6    180.00   0.0  0
 1U4  CONST_18  H2    C2   C4   C6    180.00   0.0  0
 1U4  CONST_19  H61   C61  C6   C4    180.00   0.0  0
 1U4  CONST_20  H1    C1   C2   C4    180.00   0.0  0
 1U4  CONST_21  H4    C4   C2   C1    180.00   0.0  0
 1U4  CONST_22  H44   C44  C42  C41   180.00   0.0  0
 1U4  CONST_23  H48   C48  C50  C41   180.00   0.0  0
 1U4  CONST_24  H50   C50  C41  C42   180.00   0.0  0
 1U4  CONST_25  H46   C46  C44  C42   180.00   0.0  0
 1U4  CONST_26  H42   C42  C41  C50   180.00   0.0  0
 1U4  CONST_27  C19   N18  C16  C15   180.00   0.0  0
 1U4  CONST_28  C19   N18  C16  O17     0.00   0.0  0
 1U4  CONST_29  HN18  N18  C16  C15     0.00   0.0  0
 1U4  Var_01    C61   C6   C7   O8     81.17  30.0  2
 1U4  Var_02    C42   C41  C38  C15   -89.03  30.0  2
 1U4  Var_03    C6    C7   O8   C9   -174.83  30.0  3
 1U4  Var_04    P13   C12  N11  C9     98.06  30.0  1
 1U4  Var_05    C12   N11  C9   O10    13.23  30.0  2
 1U4  Var_06    N11   C9   O8   C7   -178.25  30.0  1
 1U4  Var_07    N14   P13  C12  N11   177.25  30.0  1
 1U4  Var_08    C15   N14  P13  C12    68.56  30.0  1
 1U4  Var_09    C26   C21  C20  C19   178.58  30.0  1
 1U4  Var_10    H26   C26  C21  C20    64.58  30.0  3
 1U4  Var_11    H22   C22  C21  C20    62.62  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
 1U4  chir_02  C15  N14  C38  C16  negativ
 1U4  chir_03  C19  N18  C20  C33  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
 1U4  plan-1  C7    0.020
 1U4  plan-1  C6    0.020
 1U4  plan-1  C4    0.020
 1U4  plan-1  C2    0.020
 1U4  plan-1  C1    0.020
 1U4  plan-1  C63   0.020
 1U4  plan-1  C61   0.020
 1U4  plan-1  H4    0.020
 1U4  plan-1  H2    0.020
 1U4  plan-1  H1    0.020
 1U4  plan-1  H63   0.020
 1U4  plan-1  H61   0.020
 1U4  plan-2  C38   0.020
 1U4  plan-2  C41   0.020
 1U4  plan-2  C42   0.020
 1U4  plan-2  C50   0.020
 1U4  plan-2  C44   0.020
 1U4  plan-2  C48   0.020
 1U4  plan-2  C46   0.020
 1U4  plan-2  H42   0.020
 1U4  plan-2  H50   0.020
 1U4  plan-2  H44   0.020
 1U4  plan-2  H48   0.020
 1U4  plan-2  H46   0.020
 1U4  plan-3  C15   0.020
 1U4  plan-3  C16   0.020
 1U4  plan-3  O17   0.020
 1U4  plan-3  N18   0.020
 1U4  plan-3  C19   0.020
 1U4  plan-3  HN18  0.020
 1U4  plan-4  C19   0.020
 1U4  plan-4  C33   0.020
 1U4  plan-4  O34   0.020
 1U4  plan-4  O35   0.020
 1U4  plan-5  C9    0.020
 1U4  plan-5  O10   0.020
 1U4  plan-5  O8    0.020
 1U4  plan-5  N11   0.020

