# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:43:22 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-methyl-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=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
 UBX  UBX  N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-methyl-L-leucinamide  peptide  50  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UBX
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
 UBX  C3    C  CR16   0  -0.283  -6.2025  -0.0481   0.8186
 UBX  C2    C  CR16   0  -0.243  -7.4227   0.4051   0.3394
 UBX  C1    C  CR16   0  -0.263  -7.8255   0.0878  -0.9529
 UBX  C6    C  CR16   0  -0.241  -7.0027  -0.6835  -1.7613
 UBX  C5    C  CR16   0  -0.301  -5.7797  -1.1334  -1.2787
 UBX  C4    C  CR6    0   0.075  -5.3702  -0.8227   0.0133
 UBX  C7    C  CH2    0  -0.232  -4.0460  -1.2994   0.5298
 UBX  O8    O  O2     0  -0.486  -3.1655  -0.1731   0.5320
 UBX  C9    C  C      0   0.744  -1.9156  -0.3807   0.9784
 UBX  O19   O  O      0  -0.525  -1.5028  -1.4695   1.3275
 UBX  N10   N  NH1    0  -0.649  -1.2256   0.7692   1.0062
 UBX  C11   C  CH2    0  -0.561   0.2062   0.8299   1.2143
 UBX  P12   P  P      0   1.236   1.0579   1.2190  -0.3736
 UBX  O21   O  O      0  -0.812   0.5705   2.5855  -0.8005
 UBX  O20   O  OP    -1  -0.802   0.9160   0.0301  -1.2906
 UBX  N13   N  NH1    0  -0.810   2.6928   1.3513   0.1086
 UBX  C14   C  CH1    0  -0.161   3.6561   0.3629  -0.3132
 UBX  C15   C  C      0   0.558   3.3240  -0.9914   0.3075
 UBX  N16   N  NH1    0  -0.620   3.4985  -2.0429  -0.5038
 UBX  C17   C  CH3    0  -0.512   3.2572  -3.3982  -0.0745
 UBX  C22   C  CH2    0  -0.414   5.0703   0.7422   0.1402
 UBX  O23   O  O      0  -0.505   3.0042  -1.1121   1.4820
 UBX  C27   C  CH1    0  -0.257   5.6013   2.0748  -0.3968
 UBX  C28   C  CH3    0  -0.646   7.0372   2.2775   0.0777
 UBX  C29   C  CH3    0  -0.658   5.5177   2.1639  -1.9170
 UBX  H3    H  HCR6   0   0.254  -5.8991   0.1970   1.8296
 UBX  H2    H  HCR6   0   0.258  -8.0619   1.0046   0.9745
 UBX  H1    H  HCR6   0   0.258  -8.7790   0.4397  -1.3247
 UBX  H6    H  HCR6   0   0.258  -7.3096  -0.9362  -2.7679
 UBX  H5    H  HCR6   0   0.256  -5.1412  -1.7372  -1.9126
 UBX  H7    H  HCH2   0   0.242  -4.1477  -1.6997   1.5414
 UBX  H7A   H  HCH2   0   0.244  -3.6501  -2.0934  -0.1072
 UBX  HN10  H  HNH1   0   0.389  -1.6631   1.5897   0.6160
 UBX  H11   H  HCH2   0   0.236   0.4321   1.5926   1.9643
 UBX  H11A  H  HCH2   0   0.261   0.5520  -0.1235   1.6063
 UBX  HN13  H  HNH1   0   0.368   3.0442   2.2965   0.0616
 UBX  H14   H  HCH1   0   0.226   3.6740   0.2410  -1.4048
 UBX  H17   H  HCH3   0   0.235   3.8784  -3.6613   0.7815
 UBX  H17A  H  HCH3   0   0.231   2.2132  -3.5618   0.1996
 UBX  H22   H  HCH2   0   0.231   5.0994   0.7604   1.2337
 UBX  H22A  H  HCH2   0   0.223   5.7515  -0.0532  -0.1824
 UBX  H27   H  HCH1   0   0.217   5.0061   2.8927   0.0270
 UBX  H28   H  HCH3   0   0.214   7.6967   1.5121  -0.3390
 UBX  H28A  H  HCH3   0   0.227   7.4219   3.2510  -0.2311
 UBX  H28B  H  HCH3   0   0.225   7.1116   2.2221   1.1653
 UBX  H29   H  HCH3   0   0.216   6.0517   1.3336  -2.3857
 UBX  H29A  H  HCH3   0   0.228   4.4870   2.1395  -2.2744
 UBX  H29B  H  HCH3   0   0.230   5.9645   3.0920  -2.2768
 UBX  H25   H  HNH1   0   0.396   3.6356  -1.8756  -1.4859
 UBX  H26   H  HCH3   0   0.246   3.5055  -4.0691  -0.8921

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
 UBX  C1   C2    aromatic  1.390  0.020  1.390
 UBX  C1   H1    single    0.930  0.020  1.080
 UBX  C2   H2    single    0.930  0.020  1.080
 UBX  C3   C2    aromatic  1.387  0.020  1.387
 UBX  C3   H3    single    0.930  0.020  1.080
 UBX  C4   C3    aromatic  1.393  0.020  1.393
 UBX  C5   C4    aromatic  1.390  0.020  1.390
 UBX  C5   C6    aromatic  1.390  0.020  1.390
 UBX  C5   H5    single    0.930  0.020  1.080
 UBX  C6   C1    aromatic  1.388  0.020  1.388
 UBX  C6   H6    single    0.930  0.020  1.080
 UBX  C7   C4    single    1.499  0.020  1.499
 UBX  C7   H7    single    0.970  0.020  1.090
 UBX  C7   H7A   single    0.970  0.020  1.090
 UBX  O8   C7    single    1.430  0.020  1.430
 UBX  C9   O8    single    1.343  0.020  1.343
 UBX  N10  C9    single    1.341  0.020  1.341
 UBX  N10  HN10  single    0.890  0.020  1.040
 UBX  C11  N10   single    1.448  0.020  1.448
 UBX  C11  H11   single    0.970  0.020  1.090
 UBX  C11  H11A  single    0.970  0.020  1.090
 UBX  P12  C11   single    1.843  0.020  1.843
 UBX  P12  O21   deloc     1.512  0.020  1.512
 UBX  P12  O20   deloc     1.508  0.020  1.508
 UBX  N13  P12   single    1.710  0.020  1.710
 UBX  N13  HN13  single    0.890  0.020  1.040
 UBX  C14  N13   single    1.443  0.020  1.443
 UBX  C14  C15   single    1.526  0.020  1.526
 UBX  C14  H14   single    0.970  0.020  1.090
 UBX  C15  O23   double    1.223  0.020  1.223
 UBX  C15  N16   single    1.340  0.020  1.340
 UBX  N16  C17   single    1.442  0.020  1.442
 UBX  C17  H17   single    0.970  0.020  1.090
 UBX  C17  H17A  single    0.970  0.020  1.090
 UBX  O19  C9    double    1.216  0.020  1.216
 UBX  C22  C14   single    1.533  0.020  1.533
 UBX  C22  H22   single    0.970  0.020  1.090
 UBX  C22  H22A  single    0.970  0.020  1.090
 UBX  C27  C22   single    1.532  0.020  1.532
 UBX  C27  C29   single    1.525  0.020  1.525
 UBX  C27  H27   single    0.970  0.020  1.090
 UBX  C28  C27   single    1.526  0.020  1.526
 UBX  C28  H28   single    0.970  0.020  1.090
 UBX  C28  H28A  single    0.970  0.020  1.090
 UBX  C28  H28B  single    0.970  0.020  1.090
 UBX  C29  H29   single    0.970  0.020  1.090
 UBX  C29  H29A  single    0.970  0.020  1.090
 UBX  C29  H29B  single    0.970  0.020  1.090
 UBX  N16  H25   single    0.860  0.020  1.020
 UBX  C17  H26   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
 UBX  H3    C3   C4    119.85  3.000
 UBX  C4    C3   C2    120.49  3.000
 UBX  H3    C3   C2    119.65  3.000
 UBX  H2    C2   C1    120.05  3.000
 UBX  H2    C2   C3    119.86  3.000
 UBX  C1    C2   C3    120.09  3.000
 UBX  H1    C1   C6    120.19  3.000
 UBX  C6    C1   C2    119.78  3.000
 UBX  H1    C1   C2    120.03  3.000
 UBX  H6    C6   C5    119.80  3.000
 UBX  H6    C6   C1    120.23  3.000
 UBX  C5    C6   C1    119.97  3.000
 UBX  H5    C5   C4    119.64  3.000
 UBX  H5    C5   C6    119.73  3.000
 UBX  C4    C5   C6    120.63  3.000
 UBX  C7    C4   C5    120.61  3.000
 UBX  C7    C4   C3    120.35  3.000
 UBX  C5    C4   C3    119.04  3.000
 UBX  H7A   C7   H7    107.90  3.000
 UBX  H7A   C7   O8    110.51  3.000
 UBX  H7    C7   O8    110.15  3.000
 UBX  O8    C7   C4    107.10  3.000
 UBX  H7A   C7   C4    110.51  3.000
 UBX  H7    C7   C4    110.69  3.000
 UBX  C9    O8   C7    116.86  3.000
 UBX  N10   C9   O19   125.96  3.000
 UBX  O19   C9   O8    123.35  3.000
 UBX  N10   C9   O8    110.67  3.000
 UBX  HN10  N10  C11   116.77  3.000
 UBX  C11   N10  C9    123.19  3.000
 UBX  HN10  N10  C9    117.80  3.000
 UBX  H11A  C11  H11   107.38  3.000
 UBX  H11A  C11  P12   110.41  3.000
 UBX  H11   C11  P12   110.38  3.000
 UBX  P12   C11  N10   109.99  3.000
 UBX  H11A  C11  N10   109.24  3.000
 UBX  H11   C11  N10   109.40  3.000
 UBX  N13   P12  O20   108.81  3.000
 UBX  N13   P12  O21   108.53  3.000
 UBX  O20   P12  O21   120.69  3.000
 UBX  N13   P12  C11   102.43  3.000
 UBX  O20   P12  C11   108.29  3.000
 UBX  O21   P12  C11   106.56  3.000
 UBX  HN13  N13  C14   113.28  3.000
 UBX  C14   N13  P12   120.19  3.000
 UBX  HN13  N13  P12   113.10  3.000
 UBX  H14   C14  C22   107.84  3.000
 UBX  C22   C14  C15   107.46  3.000
 UBX  H14   C14  C15   108.01  3.000
 UBX  C22   C14  N13   111.10  3.000
 UBX  H14   C14  N13   112.16  3.000
 UBX  C15   C14  N13   110.10  3.000
 UBX  O23   C15  N16   122.55  3.000
 UBX  N16   C15  C14   114.95  3.000
 UBX  O23   C15  C14   122.34  3.000
 UBX  H25   N16  C17   118.03  3.000
 UBX  H25   N16  C15   118.60  3.000
 UBX  C17   N16  C15   122.39  3.000
 UBX  H26   C17  H17A  108.36  3.000
 UBX  H26   C17  H17   108.16  3.000
 UBX  H17A  C17  H17   108.16  3.000
 UBX  H26   C17  N16   108.54  3.000
 UBX  H17A  C17  N16   112.07  3.000
 UBX  H17   C17  N16   111.43  3.000
 UBX  H22A  C22  H22   106.85  3.000
 UBX  H22A  C22  C27   108.23  3.000
 UBX  H22   C22  C27   109.07  3.000
 UBX  C27   C22  C14   115.55  3.000
 UBX  H22A  C22  C14   107.87  3.000
 UBX  H22   C22  C14   108.93  3.000
 UBX  H27   C27  C29   108.18  3.000
 UBX  H27   C27  C28   106.95  3.000
 UBX  C29   C27  C28   110.72  3.000
 UBX  C28   C27  C22   109.43  3.000
 UBX  H27   C27  C22   108.98  3.000
 UBX  C29   C27  C22   112.41  3.000
 UBX  H28B  C28  H28A  107.64  3.000
 UBX  H28B  C28  H28   107.65  3.000
 UBX  H28A  C28  H28   107.71  3.000
 UBX  H28B  C28  C27   111.54  3.000
 UBX  H28A  C28  C27   111.24  3.000
 UBX  H28   C28  C27   110.88  3.000
 UBX  H29B  C29  H29A  107.33  3.000
 UBX  H29B  C29  H29   107.75  3.000
 UBX  H29A  C29  H29   107.70  3.000
 UBX  H29B  C29  C27   110.85  3.000
 UBX  H29A  C29  C27   112.14  3.000
 UBX  H29   C29  C27   110.87  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
 UBX  CONST_01  C6   C1   C2   C3      0.00   0.0  0
 UBX  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 UBX  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 UBX  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 UBX  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 UBX  CONST_06  C4   C5   C6   C1      0.00   0.0  0
 UBX  CONST_07  C7   C4   C3   C2    180.00   0.0  0
 UBX  CONST_08  C7   C4   C5   C6    180.00   0.0  0
 UBX  CONST_09  H1   C1   C2   C3    180.00   0.0  0
 UBX  CONST_10  H5   C5   C4   C3    180.00   0.0  0
 UBX  CONST_11  H6   C6   C1   C2    180.00   0.0  0
 UBX  CONST_12  H3   C3   C2   C1    180.00   0.0  0
 UBX  CONST_13  H2   C2   C1   C6    180.00   0.0  0
 UBX  CONST_14  C17  N16  C15  C14   180.00   0.0  0
 UBX  CONST_15  O23  C15  N16  C17     0.00   0.0  0
 UBX  CONST_16  H25  N16  C15  C14     0.00   0.0  0
 UBX  Var_01    O8   C7   C4   C3    -74.56  30.0  2
 UBX  Var_02    N10  C9   O8   C7   -176.11  30.0  1
 UBX  Var_03    C11  N10  C9   O8   -168.77  30.0  2
 UBX  Var_04    P12  C11  N10  C9    105.76  30.0  1
 UBX  Var_05    O21  P12  C11  N10    62.30  30.0  1
 UBX  Var_06    C14  N13  P12  C11   111.35  30.0  1
 UBX  Var_07    C29  C27  C22  C14   -53.56  30.0  1
 UBX  Var_08    H17  C17  N16  C15   -58.76  30.0  3
 UBX  Var_09    H29  C29  C27  C22   -56.46  30.0  3
 UBX  Var_10    H28  C28  C27  C22    64.09  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
 UBX  chir_02  C14  N13  C15  C22  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
 UBX  plan-1  C3   0.020
 UBX  plan-1  C2   0.020
 UBX  plan-1  C1   0.020
 UBX  plan-1  C6   0.020
 UBX  plan-1  C5   0.020
 UBX  plan-1  C4   0.020
 UBX  plan-1  C7   0.020
 UBX  plan-1  H3   0.020
 UBX  plan-1  H2   0.020
 UBX  plan-1  H1   0.020
 UBX  plan-1  H6   0.020
 UBX  plan-1  H5   0.020
 UBX  plan-2  C14  0.020
 UBX  plan-2  C15  0.020
 UBX  plan-2  N16  0.020
 UBX  plan-2  C17  0.020
 UBX  plan-2  O23  0.020
 UBX  plan-2  H25  0.020
 UBX  plan-3  O8   0.020
 UBX  plan-3  C9   0.020
 UBX  plan-3  O19  0.020
 UBX  plan-3  N10  0.020

