# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:40:36 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: propan-2-yl hydrogen (S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}ethyl]phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[P](O)(=O)[C@H](C)NC(=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
 3UB  3UB  'propan-2-yl hydrogen (S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}ethyl]phosphonate'  ligand  39  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3UB
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
 3UB  O2P  O  O      0  -0.790  -1.6841  -1.4740   1.1611
 3UB  P    P  P      0   1.286  -2.3284  -0.5863   0.1305
 3UB  C1   C  CH1    0   0.048  -5.0030  -0.7933   0.1050
 3UB  C2   C  CH3    0  -0.668  -6.0231  -0.9249   1.2218
 3UB  C3   C  CH3    0  -0.668  -5.5403   0.0239  -1.0577
 3UB  C4   C  CH1    0  -0.347  -1.5491   1.0866   0.2173
 3UB  C5   C  CH3    0  -0.663  -2.1555   2.0868  -0.7543
 3UB  C7   C  CH2    0  -0.233   3.0610   0.2251   1.2876
 3UB  NC   N  NH1    0  -0.654  -0.1307   0.9257  -0.0507
 3UB  O1C  O  O      0  -0.523   0.6122   0.9254   2.1053
 3UB  O1P  O  O2     0  -0.636  -3.8403  -0.1736   0.6497
 3UB  O2C  O  O2     0  -0.486   1.9649   0.3909   0.3848
 3UB  O3P  O  OP    -1  -0.809  -2.3752  -1.0422  -1.3061
 3UB  C71  C  CR6    0   0.075   4.2728  -0.0610   0.4530
 3UB  C72  C  CR16   0  -0.297   5.1866   0.9472   0.1653
 3UB  C73  C  CR16   0  -0.242   6.2974   0.6897  -0.6283
 3UB  C74  C  CR16   0  -0.262   6.5006  -0.5822  -1.1458
 3UB  C75  C  CR16   0  -0.242   5.5913  -1.5952  -0.8650
 3UB  C76  C  CR16   0  -0.284   4.4849  -1.3348  -0.0694
 3UB  H1   H  HCH1   0   0.200  -4.7590  -1.7979  -0.2595
 3UB  H2   H  HCH3   0   0.221  -6.9250  -1.4180   0.8568
 3UB  H2A  H  HCH3   0   0.231  -5.6317  -1.5184   2.0491
 3UB  H2B  H  HCH3   0   0.218  -6.3113   0.0549   1.6086
 3UB  H3   H  HCH3   0   0.214  -5.7996   1.0343  -0.7343
 3UB  H3A  H  HCH3   0   0.234  -4.8002   0.0958  -1.8537
 3UB  H3B  H  HCH3   0   0.218  -6.4396  -0.4387  -1.4675
 3UB  H4   H  HCH1   0   0.256  -1.6508   1.4648   1.2354
 3UB  H5   H  HCH3   0   0.223  -2.0527   1.7460  -1.7854
 3UB  H5A  H  HCH3   0   0.236  -3.2180   2.2191  -0.5552
 3UB  H5B  H  HCH3   0   0.231  -1.6688   3.0590  -0.6654
 3UB  H7   H  HCH2   0   0.244   3.2081   1.1298   1.8812
 3UB  H7A  H  HCH2   0   0.243   2.8594  -0.5998   1.9752
 3UB  HNC  H  HNH1   0   0.391   0.1241   0.6578  -0.9896
 3UB  H72  H  HCR6   0   0.254   5.0324   1.9419   0.5667
 3UB  H73  H  HCR6   0   0.258   7.0024   1.4826  -0.8422
 3UB  H74  H  HCR6   0   0.258   7.3659  -0.7854  -1.7635
 3UB  H75  H  HCR6   0   0.258   5.7466  -2.5893  -1.2639
 3UB  H76  H  HCR6   0   0.255   3.7829  -2.1304   0.1518
 3UB  C6   C  C      0   0.753   0.7860   0.7509   0.9164

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
 3UB  P    O2P  deloc     1.505  0.020  1.505
 3UB  P    O3P  deloc     1.508  0.020  1.508
 3UB  C1   C3   single    1.519  0.020  1.519
 3UB  C2   C1   single    1.518  0.020  1.518
 3UB  C4   P    single    1.848  0.020  1.848
 3UB  C4   NC   single    1.452  0.020  1.452
 3UB  C5   C4   single    1.521  0.020  1.521
 3UB  C6   O2C  single    1.342  0.020  1.342
 3UB  NC   C6   single    1.344  0.020  1.344
 3UB  O1C  C6   double    1.214  0.020  1.214
 3UB  O1P  P    single    1.651  0.020  1.651
 3UB  O1P  C1   single    1.426  0.020  1.426
 3UB  O2C  C7   single    1.430  0.020  1.430
 3UB  C71  C7   single    1.499  0.020  1.499
 3UB  C71  C72  aromatic  1.391  0.020  1.391
 3UB  C73  C72  aromatic  1.389  0.020  1.389
 3UB  C74  C73  aromatic  1.388  0.020  1.388
 3UB  C75  C74  aromatic  1.390  0.020  1.390
 3UB  C75  C76  aromatic  1.387  0.020  1.387
 3UB  C76  C71  aromatic  1.393  0.020  1.393
 3UB  C1   H1   single    0.970  0.020  1.090
 3UB  C2   H2   single    0.970  0.020  1.090
 3UB  C2   H2A  single    0.970  0.020  1.090
 3UB  C2   H2B  single    0.970  0.020  1.090
 3UB  C3   H3   single    0.970  0.020  1.090
 3UB  C3   H3A  single    0.970  0.020  1.090
 3UB  C3   H3B  single    0.970  0.020  1.090
 3UB  C4   H4   single    0.970  0.020  1.090
 3UB  C5   H5   single    0.970  0.020  1.090
 3UB  C5   H5A  single    0.970  0.020  1.090
 3UB  C5   H5B  single    0.970  0.020  1.090
 3UB  C7   H7   single    0.970  0.020  1.090
 3UB  C7   H7A  single    0.970  0.020  1.090
 3UB  NC   HNC  single    0.860  0.020  1.020
 3UB  C72  H72  single    0.930  0.020  1.080
 3UB  C73  H73  single    0.930  0.020  1.080
 3UB  C74  H74  single    0.930  0.020  1.080
 3UB  C75  H75  single    0.930  0.020  1.080
 3UB  C76  H76  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
 3UB  O3P  P    O1P  110.29  3.000
 3UB  O1P  P    C4    98.35  3.000
 3UB  O3P  P    C4   109.37  3.000
 3UB  O1P  P    O2P  108.91  3.000
 3UB  C4   P    O2P  108.74  3.000
 3UB  O3P  P    O2P  119.16  3.000
 3UB  H1   C1   O1P  110.12  3.000
 3UB  H1   C1   C3   108.49  3.000
 3UB  O1P  C1   C3   110.30  3.000
 3UB  H1   C1   C2   108.34  3.000
 3UB  O1P  C1   C2   107.73  3.000
 3UB  C3   C1   C2   111.83  3.000
 3UB  H2B  C2   H2A  108.31  3.000
 3UB  H2B  C2   H2   107.81  3.000
 3UB  H2A  C2   H2   107.73  3.000
 3UB  H2B  C2   C1   111.11  3.000
 3UB  H2A  C2   C1   111.35  3.000
 3UB  H2   C2   C1   110.40  3.000
 3UB  H3B  C3   H3A  108.27  3.000
 3UB  H3B  C3   H3   107.92  3.000
 3UB  H3A  C3   H3   108.46  3.000
 3UB  H3B  C3   C1   110.54  3.000
 3UB  H3A  C3   C1   110.76  3.000
 3UB  H3   C3   C1   110.79  3.000
 3UB  H4   C4   NC   107.56  3.000
 3UB  H4   C4   C5   109.33  3.000
 3UB  NC   C4   C5   110.15  3.000
 3UB  H4   C4   P    108.57  3.000
 3UB  C5   C4   P    113.41  3.000
 3UB  NC   C4   P    107.64  3.000
 3UB  H5B  C5   H5A  108.19  3.000
 3UB  H5B  C5   H5   108.27  3.000
 3UB  H5A  C5   H5   107.62  3.000
 3UB  H5B  C5   C4   110.87  3.000
 3UB  H5A  C5   C4   110.62  3.000
 3UB  H5   C5   C4   111.15  3.000
 3UB  H7A  C7   H7   107.96  3.000
 3UB  H7A  C7   C71  110.82  3.000
 3UB  H7   C7   C71  110.61  3.000
 3UB  H7A  C7   O2C  110.09  3.000
 3UB  H7   C7   O2C  110.51  3.000
 3UB  C71  C7   O2C  106.88  3.000
 3UB  HNC  NC   C6   117.57  3.000
 3UB  HNC  NC   C4   116.60  3.000
 3UB  C6   NC   C4   123.21  3.000
 3UB  C1   O1P  P    121.20  3.000
 3UB  C7   O2C  C6   117.02  3.000
 3UB  C76  C71  C72  119.03  3.000
 3UB  C76  C71  C7   120.43  3.000
 3UB  C72  C71  C7   120.52  3.000
 3UB  H72  C72  C73  119.70  3.000
 3UB  H72  C72  C71  119.69  3.000
 3UB  C73  C72  C71  120.61  3.000
 3UB  H73  C73  C74  120.15  3.000
 3UB  H73  C73  C72  119.86  3.000
 3UB  C74  C73  C72  119.99  3.000
 3UB  H74  C74  C75  120.09  3.000
 3UB  H74  C74  C73  120.12  3.000
 3UB  C75  C74  C73  119.79  3.000
 3UB  H75  C75  C76  119.88  3.000
 3UB  H75  C75  C74  120.07  3.000
 3UB  C76  C75  C74  120.05  3.000
 3UB  H76  C76  C75  119.72  3.000
 3UB  H76  C76  C71  119.74  3.000
 3UB  C75  C76  C71  120.54  3.000
 3UB  O2C  C6   O1C  123.50  3.000
 3UB  O1C  C6   NC   126.04  3.000
 3UB  O2C  C6   NC   110.42  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
 3UB  CONST_01  C74  C73  C72  C71     0.00   0.0  0
 3UB  CONST_02  C74  C75  C76  C71     0.00   0.0  0
 3UB  CONST_03  C75  C76  C71  C72     0.00   0.0  0
 3UB  CONST_04  C75  C74  C73  C72     0.00   0.0  0
 3UB  CONST_05  C76  C71  C72  C73     0.00   0.0  0
 3UB  CONST_06  C76  C75  C74  C73     0.00   0.0  0
 3UB  CONST_07  C73  C72  C71  C7    180.00   0.0  0
 3UB  CONST_08  C75  C76  C71  C7    180.00   0.0  0
 3UB  CONST_09  H73  C73  C72  C71   180.00   0.0  0
 3UB  CONST_10  H75  C75  C76  C71   180.00   0.0  0
 3UB  CONST_11  H76  C76  C71  C72   180.00   0.0  0
 3UB  CONST_12  H74  C74  C73  C72   180.00   0.0  0
 3UB  CONST_13  H72  C72  C73  C74   180.00   0.0  0
 3UB  Var_01    C72  C71  C7   O2C    99.89  30.0  2
 3UB  Var_02    C71  C7   O2C  C6   -175.43  30.0  3
 3UB  Var_03    C3   C1   O1P  P     -92.71  30.0  3
 3UB  Var_04    O3P  P    O1P  C1     29.20  30.0  3
 3UB  Var_05    O2C  C6   NC   C4    168.86  30.0  2
 3UB  Var_06    NC   C6   O2C  C7    177.29  30.0  2
 3UB  Var_07    H3   C3   C1   C2     60.36  30.0  3
 3UB  Var_08    H2   C2   C1   C3     60.00  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
 3UB  chir_02  C4  P  NC  C5  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
 3UB  plan-1  C7   0.020
 3UB  plan-1  C71  0.020
 3UB  plan-1  C72  0.020
 3UB  plan-1  C73  0.020
 3UB  plan-1  C74  0.020
 3UB  plan-1  C75  0.020
 3UB  plan-1  C76  0.020
 3UB  plan-1  H72  0.020
 3UB  plan-1  H73  0.020
 3UB  plan-1  H74  0.020
 3UB  plan-1  H75  0.020
 3UB  plan-1  H76  0.020
 3UB  plan-2  NC   0.020
 3UB  plan-2  O1C  0.020
 3UB  plan-2  O2C  0.020
 3UB  plan-2  C6   0.020

