# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:12:19 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: [(1~{R})-1-[[(2~{S})-2-[[(2~{S})-1-azaniumyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]pent-4-ynyl]-oxidanyl-phosphoryl]-3-phenyl-propyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H](CCc1ccccc1)[P](O)(=O)C[C@@H](CC#C)C(=O)N[C@@H](Cc2ccccc2)C([NH3+])=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
 HJ5  HJ5  '[(1~{R})-1-[[(2~{S})-2-[[(2~{S})-1-azaniumyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]pent-4-ynyl]-oxidanyl-phosphoryl]-3-phenyl-propyl]azanium'  ligand  63  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJ5
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
 HJ5  C1    C  CH1    0  -0.376  -2.6348  -1.4516  -0.8416
 HJ5  C2    C  CH2    0  -0.442  -3.9682  -0.7598  -0.5701
 HJ5  C3    C  CH2    0  -0.519  -3.8593   0.7630  -0.6572
 HJ5  C14   C  CH2    0  -0.723   0.1126  -1.8397  -0.0600
 HJ5  C15   C  CH1    0  -0.407   1.2220  -1.8717   1.0010
 HJ5  C16   C  CH2    0  -0.563   1.2292  -3.1906   1.7819
 HJ5  C17   C  CSP    0   0.279   2.2890  -3.2254   2.7802
 HJ5  C20   C  C      0   0.629   2.5548  -1.6670   0.3189
 HJ5  C21   C  CSP1   0  -0.552   3.1847  -3.2279   3.5824
 HJ5  C24   C  CH1    0  -0.169   4.3175  -0.1651  -0.2778
 HJ5  C25   C  CH2    0  -0.563   4.8489   1.2300   0.0811
 HJ5  C26   C  CR6    0   0.123   3.8766   2.3002  -0.3351
 HJ5  C27   C  CR16   0  -0.323   3.0751   2.9328   0.6107
 HJ5  C28   C  CR16   0  -0.239   2.1505   3.8958   0.2244
 HJ5  C29   C  CR16   0  -0.263   2.0213   4.2373  -1.1139
 HJ5  C30   C  CR16   0  -0.238   2.8205   3.6128  -2.0644
 HJ5  C31   C  CR16   0  -0.292   3.7400   2.6498  -1.6769
 HJ5  C32   C  C      0   0.529   5.3212  -1.2153   0.1561
 HJ5  C4    C  C      0   0.132  -5.1910   1.4191  -0.4244
 HJ5  C5    C  C1     0  -0.310  -5.5971   1.7669   0.8622
 HJ5  C6    C  C1     0  -0.240  -6.8446   2.3343   1.0860
 HJ5  C7    C  C1     0  -0.273  -7.7072   2.5652   0.0220
 HJ5  C8    C  C1     0  -0.240  -7.3140   2.2215  -1.2651
 HJ5  C9    C  C1     0  -0.310  -6.0663   1.6520  -1.4829
 HJ5  N10   N  NT3    1  -0.786  -2.8933  -2.8533  -1.2879
 HJ5  N23   N  NH1    0  -0.639   3.0778  -0.4326   0.3939
 HJ5  O22   O  O      0  -0.492   3.1471  -2.5529  -0.2868
 HJ5  P11   P  P      0   1.208  -1.5482  -1.5546   0.6822
 HJ5  H1    H  HCH1   0   0.306  -2.1184  -0.9617  -1.6693
 HJ5  H22   H  HCH2   0   0.257  -4.7047  -1.0941  -1.3092
 HJ5  H2    H  HCH2   0   0.254  -4.3608  -1.0551   0.4071
 HJ5  H32   H  HCH2   0   0.265  -3.1322   1.1132   0.0738
 HJ5  H3    H  HCH2   0   0.244  -3.4803   1.0344  -1.6462
 HJ5  H141  H  HCH2   0   0.279   0.2861  -1.0091  -0.7508
 HJ5  H14   H  HCH2   0   0.264   0.1466  -2.7562  -0.6571
 HJ5  H15   H  HCH1   0   0.283   1.0600  -1.0514   1.7064
 HJ5  H16   H  HCH2   0   0.293   0.2595  -3.3214   2.2635
 HJ5  H161  H  HCH2   0   0.274   1.3502  -4.0286   1.0918
 HJ5  H21   H  H      0   0.277   3.9711  -3.2398   4.3018
 HJ5  H24   H  HCH1   0   0.322   4.1758  -0.2304  -1.3617
 HJ5  H251  H  HCH2   0   0.293   5.0267   1.2779   1.1575
 HJ5  H25   H  HCH2   0   0.298   5.8146   1.3809  -0.4062
 HJ5  H27   H  HCR6   0   0.262   3.1772   2.6791   1.6601
 HJ5  H28   H  HCR6   0   0.261   1.5334   4.3792   0.9705
 HJ5  H29   H  HCR6   0   0.260   1.3035   4.9886  -1.4168
 HJ5  H30   H  HCR6   0   0.260   2.7291   3.8790  -3.1094
 HJ5  H31   H  HCR6   0   0.255   4.3602   2.1685  -2.4244
 HJ5  H5    H  H      0   0.246  -4.9291   1.5932   1.6982
 HJ5  H6    H  H      0   0.254  -7.1435   2.5975   2.0927
 HJ5  H7    H  H      0   0.253  -8.6772   3.0134   0.1953
 HJ5  H8    H  H      0   0.253  -7.9770   2.4007  -2.1020
 HJ5  H9    H  H      0   0.246  -5.7646   1.3900  -2.4906
 HJ5  HN12  H  HNT3   0   0.468  -3.5771  -2.8994  -2.0438
 HJ5  HN10  H  HNT3   0   0.469  -2.0526  -3.3131  -1.6348
 HJ5  HN11  H  HNT3   0   0.456  -3.2366  -3.4196  -0.5085
 HJ5  HN23  H  HNH1   0   0.420   2.6392   0.2845   0.9507
 HJ5  HN31  H  HNT3   0   0.495   6.5311  -1.1913  -1.5704
 HJ5  HN32  H  HNT3   0   0.491   6.7262  -2.5458  -0.6468
 HJ5  HN33  H  HNT3   0   0.492   5.3729  -2.3601  -1.5843
 HJ5  N34   N  NT3    1  -0.861   6.0372  -1.8669  -0.9794
 HJ5  O12   O  O      0  -0.783  -2.0409  -2.7868   1.4127
 HJ5  O13   O  OP    -1  -0.763  -1.5286  -0.2135   1.3668
 HJ5  O33   O  O      0  -0.281   5.6208  -1.5084   1.2617

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
 HJ5  N10   C1    single    1.494  0.020  1.494
 HJ5  C3    C4    single    1.503  0.020  1.503
 HJ5  C3    C2    single    1.529  0.020  1.529
 HJ5  C1    C2    single    1.526  0.020  1.526
 HJ5  C1    P11   single    1.874  0.020  1.874
 HJ5  C4    C5    aromatic  1.393  0.020  1.393
 HJ5  C4    C9    aromatic  1.393  0.020  1.393
 HJ5  O12   P11   deloc     1.515  0.020  1.515
 HJ5  C5    C6    aromatic  1.389  0.020  1.389
 HJ5  C9    C8    aromatic  1.389  0.020  1.389
 HJ5  C6    C7    aromatic  1.389  0.020  1.389
 HJ5  P11   O13   deloc     1.506  0.020  1.506
 HJ5  P11   C14   single    1.841  0.020  1.841
 HJ5  C8    C7    aromatic  1.389  0.020  1.389
 HJ5  C14   C15   single    1.535  0.020  1.535
 HJ5  C16   C15   single    1.533  0.020  1.533
 HJ5  C16   C17   single    1.456  0.020  1.456
 HJ5  C15   C20   single    1.511  0.020  1.511
 HJ5  C17   C21   triple    1.202  0.020  1.202
 HJ5  O22   C20   double    1.226  0.020  1.226
 HJ5  C29   C28   aromatic  1.387  0.020  1.387
 HJ5  C29   C30   aromatic  1.390  0.020  1.390
 HJ5  C20   N23   single    1.343  0.020  1.343
 HJ5  C28   C27   aromatic  1.390  0.020  1.390
 HJ5  C30   C31   aromatic  1.387  0.020  1.387
 HJ5  C27   C26   aromatic  1.392  0.020  1.392
 HJ5  N23   C24   single    1.435  0.020  1.435
 HJ5  C31   C26   aromatic  1.393  0.020  1.393
 HJ5  C26   C25   single    1.505  0.020  1.505
 HJ5  C24   C25   single    1.535  0.020  1.535
 HJ5  C24   C32   single    1.516  0.020  1.516
 HJ5  C32   O33   double    1.182  0.020  1.182
 HJ5  C32   N34   single    1.492  0.020  1.492
 HJ5  C1    H1    single    0.939  0.020  1.096
 HJ5  C2    H22   single    0.939  0.020  1.096
 HJ5  C2    H2    single    0.939  0.020  1.096
 HJ5  C3    H32   single    0.939  0.020  1.096
 HJ5  C3    H3    single    0.939  0.020  1.096
 HJ5  C14   H141  single    0.939  0.020  1.096
 HJ5  C14   H14   single    0.939  0.020  1.096
 HJ5  C15   H15   single    0.939  0.020  1.096
 HJ5  C16   H16   single    0.939  0.020  1.096
 HJ5  C16   H161  single    0.939  0.020  1.096
 HJ5  C21   H21   single    0.913  0.020  1.066
 HJ5  C24   H24   single    0.939  0.020  1.096
 HJ5  C25   H251  single    0.939  0.020  1.096
 HJ5  C25   H25   single    0.939  0.020  1.096
 HJ5  C27   H27   single    0.929  0.020  1.085
 HJ5  C28   H28   single    0.929  0.020  1.085
 HJ5  C29   H29   single    0.929  0.020  1.085
 HJ5  C30   H30   single    0.929  0.020  1.085
 HJ5  C31   H31   single    0.929  0.020  1.085
 HJ5  C5    H5    single    0.929  0.020  1.085
 HJ5  C6    H6    single    0.929  0.020  1.085
 HJ5  C7    H7    single    0.929  0.020  1.085
 HJ5  C8    H8    single    0.929  0.020  1.085
 HJ5  C9    H9    single    0.929  0.020  1.085
 HJ5  N10   HN10  single    0.874  0.020  1.020
 HJ5  N10   HN11  single    0.874  0.020  1.020
 HJ5  N23   HN23  single    0.868  0.020  1.013
 HJ5  N34   HN31  single    0.874  0.020  1.020
 HJ5  N34   HN32  single    0.874  0.020  1.020
 HJ5  N34   HN33  single    0.874  0.020  1.020
 HJ5  HN12  N10   single    0.874  0.020  1.020

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
 HJ5  H1    C1   P11   111.51  3.000
 HJ5  H1    C1   N10   106.05  3.000
 HJ5  P11   C1   N10   106.96  3.000
 HJ5  H1    C1   C2    110.17  3.000
 HJ5  P11   C1   C2    112.75  3.000
 HJ5  N10   C1   C2    109.10  3.000
 HJ5  H2    C2   H22   106.20  3.000
 HJ5  H2    C2   C3    110.20  3.000
 HJ5  H22   C2   C3    108.26  3.000
 HJ5  H2    C2   C1    110.49  3.000
 HJ5  H22   C2   C1    109.20  3.000
 HJ5  C3    C2   C1    112.27  3.000
 HJ5  H3    C3   H32   107.21  3.000
 HJ5  H3    C3   C4    109.82  3.000
 HJ5  H32   C3   C4    110.32  3.000
 HJ5  H3    C3   C2    108.87  3.000
 HJ5  H32   C3   C2    109.24  3.000
 HJ5  C4    C3   C2    111.28  3.000
 HJ5  H14   C14  H141  106.64  3.000
 HJ5  H14   C14  P11   112.19  3.000
 HJ5  H141  C14  P11   106.26  3.000
 HJ5  H14   C14  C15   109.70  3.000
 HJ5  H141  C14  C15   109.73  3.000
 HJ5  P11   C14  C15   112.11  3.000
 HJ5  H15   C15  C20   108.67  3.000
 HJ5  H15   C15  C16   108.51  3.000
 HJ5  C20   C15  C16   110.02  3.000
 HJ5  H15   C15  C14   108.84  3.000
 HJ5  C20   C15  C14   108.82  3.000
 HJ5  C16   C15  C14   111.92  3.000
 HJ5  H161  C16  H16   106.59  3.000
 HJ5  H161  C16  C17   109.52  3.000
 HJ5  H16   C16  C17   109.96  3.000
 HJ5  H161  C16  C15   109.81  3.000
 HJ5  H16   C16  C15   108.90  3.000
 HJ5  C17   C16  C15   111.91  3.000
 HJ5  C21   C17  C16   180.00  3.000
 HJ5  O22   C20  N23   120.25  3.000
 HJ5  N23   C20  C15   116.29  3.000
 HJ5  O22   C20  C15   123.46  3.000
 HJ5  H21   C21  C17   180.00  3.000
 HJ5  H24   C24  N23   109.90  3.000
 HJ5  H24   C24  C32   109.12  3.000
 HJ5  N23   C24  C32   107.99  3.000
 HJ5  H24   C24  C25   109.29  3.000
 HJ5  C32   C24  C25   109.47  3.000
 HJ5  N23   C24  C25   111.03  3.000
 HJ5  H25   C25  H251  106.84  3.000
 HJ5  H25   C25  C26   110.47  3.000
 HJ5  H251  C25  C26   110.28  3.000
 HJ5  H25   C25  C24   109.10  3.000
 HJ5  H251  C25  C24   109.06  3.000
 HJ5  C26   C25  C24   110.98  3.000
 HJ5  C31   C26  C27   118.94  3.000
 HJ5  C31   C26  C25   120.54  3.000
 HJ5  C27   C26  C25   120.49  3.000
 HJ5  H27   C27  C28   119.59  3.000
 HJ5  H27   C27  C26   119.80  3.000
 HJ5  C28   C27  C26   120.61  3.000
 HJ5  H28   C28  C29   120.14  3.000
 HJ5  H28   C28  C27   119.82  3.000
 HJ5  C29   C28  C27   120.05  3.000
 HJ5  H29   C29  C30   120.12  3.000
 HJ5  H29   C29  C28   120.17  3.000
 HJ5  C30   C29  C28   119.70  3.000
 HJ5  H30   C30  C31   119.77  3.000
 HJ5  H30   C30  C29   120.08  3.000
 HJ5  C31   C30  C29   120.14  3.000
 HJ5  H31   C31  C30   119.67  3.000
 HJ5  H31   C31  C26   119.78  3.000
 HJ5  C30   C31  C26   120.55  3.000
 HJ5  O33   C32  N34   118.80  3.000
 HJ5  N34   C32  C24   113.73  3.000
 HJ5  O33   C32  C24   127.37  3.000
 HJ5  C9    C4   C5    118.47  3.000
 HJ5  C9    C4   C3    120.80  3.000
 HJ5  C5    C4   C3    120.69  3.000
 HJ5  H5    C5   C6    119.65  3.000
 HJ5  H5    C5   C4    119.50  3.000
 HJ5  C6    C5   C4    120.85  3.000
 HJ5  H6    C6   C7    120.03  3.000
 HJ5  H6    C6   C5    119.82  3.000
 HJ5  C7    C6   C5    120.15  3.000
 HJ5  H7    C7   C8    120.29  3.000
 HJ5  H7    C7   C6    120.18  3.000
 HJ5  C8    C7   C6    119.53  3.000
 HJ5  H8    C8   C9    119.79  3.000
 HJ5  H8    C8   C7    120.13  3.000
 HJ5  C9    C8   C7    120.08  3.000
 HJ5  H9    C9   C8    119.67  3.000
 HJ5  H9    C9   C4    119.41  3.000
 HJ5  C8    C9   C4    120.92  3.000
 HJ5  HN11  N10  HN10  106.64  3.000
 HJ5  HN11  N10  HN12  108.34  3.000
 HJ5  HN10  N10  HN12  106.28  3.000
 HJ5  HN12  N10  C1    112.32  3.000
 HJ5  HN11  N10  C1    110.49  3.000
 HJ5  HN10  N10  C1    112.48  3.000
 HJ5  HN23  N23  C24   120.11  3.000
 HJ5  HN23  N23  C20   121.01  3.000
 HJ5  C24   N23  C20   118.80  3.000
 HJ5  O13   P11  O12   120.63  3.000
 HJ5  O13   P11  C14   108.03  3.000
 HJ5  O12   P11  C14   111.21  3.000
 HJ5  C14   P11  C1    101.75  3.000
 HJ5  O13   P11  C1    109.16  3.000
 HJ5  O12   P11  C1    104.37  3.000
 HJ5  HN33  N34  HN32  108.01  3.000
 HJ5  HN33  N34  HN31  106.82  3.000
 HJ5  HN32  N34  HN31  107.49  3.000
 HJ5  HN33  N34  C32   110.38  3.000
 HJ5  HN32  N34  C32   111.44  3.000
 HJ5  HN31  N34  C32   112.47  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
 HJ5  CONST_01  C29   C28  C27  C26     0.00   0.0  0
 HJ5  CONST_02  C29   C30  C31  C26     0.00   0.0  0
 HJ5  CONST_03  C30   C29  C28  C27     0.00   0.0  0
 HJ5  CONST_04  C30   C31  C26  C27     0.00   0.0  0
 HJ5  CONST_05  C31   C30  C29  C28     0.00   0.0  0
 HJ5  CONST_06  C31   C26  C27  C28     0.00   0.0  0
 HJ5  CONST_07  C7    C6   C5   C4      0.00   0.0  0
 HJ5  CONST_08  C7    C8   C9   C4      0.00   0.0  0
 HJ5  CONST_09  C8    C9   C4   C5      0.00   0.0  0
 HJ5  CONST_10  C8    C7   C6   C5      0.00   0.0  0
 HJ5  CONST_11  C9    C4   C5   C6      0.00   0.0  0
 HJ5  CONST_12  C9    C8   C7   C6      0.00   0.0  0
 HJ5  CONST_13  C6    C5   C4   C3    180.00   0.0  0
 HJ5  CONST_14  C8    C9   C4   C3    180.00   0.0  0
 HJ5  CONST_15  C28   C27  C26  C25   180.00   0.0  0
 HJ5  CONST_16  C30   C31  C26  C25   180.00   0.0  0
 HJ5  CONST_17  H28   C28  C27  C26   180.00   0.0  0
 HJ5  CONST_18  H30   C30  C31  C26   180.00   0.0  0
 HJ5  CONST_19  H29   C29  C28  C27   180.00   0.0  0
 HJ5  CONST_20  H31   C31  C26  C27   180.00   0.0  0
 HJ5  CONST_21  H27   C27  C28  C29   180.00   0.0  0
 HJ5  CONST_22  H6    C6   C5   C4    180.00   0.0  0
 HJ5  CONST_23  H8    C8   C9   C4    180.00   0.0  0
 HJ5  CONST_24  H9    C9   C4   C5    180.00   0.0  0
 HJ5  CONST_25  H7    C7   C6   C5    180.00   0.0  0
 HJ5  CONST_26  H5    C5   C6   C7    180.00   0.0  0
 HJ5  CONST_27  C24   N23  C20  C15   180.00   0.0  0
 HJ5  CONST_28  O22   C20  N23  C24     0.00   0.0  0
 HJ5  CONST_29  HN23  N23  C20  C15     0.00   0.0  0
 HJ5  CONST_31  HN32  N34  C32  O33     0.00   0.0  0
 HJ5  Var_01    C5    C4   C3   C2     89.29  30.0  2
 HJ5  Var_02    C27   C26  C25  C24   103.72  30.0  3
 HJ5  Var_03    C4    C3   C2   C1    178.41  30.0  1
 HJ5  Var_04    C15   C14  P11  C1    176.27  30.0  3
 HJ5  Var_05    H16   C16  C17  C21  -146.95  30.0  2

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
 HJ5  chir_01  C1   N10  C2   P11  negativ
 HJ5  chir_02  C15  C20  C16  C14  positiv
 HJ5  chir_03  C24  N23  C25  C32  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
 HJ5  plan-1  C25   0.020
 HJ5  plan-1  C26   0.020
 HJ5  plan-1  C27   0.020
 HJ5  plan-1  C28   0.020
 HJ5  plan-1  C29   0.020
 HJ5  plan-1  C30   0.020
 HJ5  plan-1  C31   0.020
 HJ5  plan-1  H27   0.020
 HJ5  plan-1  H28   0.020
 HJ5  plan-1  H29   0.020
 HJ5  plan-1  H30   0.020
 HJ5  plan-1  H31   0.020
 HJ5  plan-2  C3    0.020
 HJ5  plan-2  C4    0.020
 HJ5  plan-2  C5    0.020
 HJ5  plan-2  C6    0.020
 HJ5  plan-2  C7    0.020
 HJ5  plan-2  C8    0.020
 HJ5  plan-2  C9    0.020
 HJ5  plan-2  H5    0.020
 HJ5  plan-2  H6    0.020
 HJ5  plan-2  H7    0.020
 HJ5  plan-2  H8    0.020
 HJ5  plan-2  H9    0.020
 HJ5  plan-3  C15   0.020
 HJ5  plan-3  C20   0.020
 HJ5  plan-3  C24   0.020
 HJ5  plan-3  N23   0.020
 HJ5  plan-3  O22   0.020
 HJ5  plan-3  HN23  0.020
 HJ5  plan-4  C24   0.020
 HJ5  plan-4  C32   0.020
 HJ5  plan-4  HN31  0.020
 HJ5  plan-4  HN32  0.020
 HJ5  plan-4  HN33  0.020
 HJ5  plan-4  N34   0.020
 HJ5  plan-4  O33   0.020

