# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 21:09:38 2021
#   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  64  32  .  2021-08-11  2022-11-17
;
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  -0.397  -618.3629  377.8463  453.2786
 HJ5  C2    C  CH2   0  -0.443  -619.5534  377.1048  453.8642
 HJ5  C3    C  CH2   0  -0.529  -620.7219  376.9646  452.8838
 HJ5  C14   C  CH2   0  -0.744  -617.6501  379.5033  455.5310
 HJ5  C15   C  CH1   0  -0.416  -616.6866  379.9469  456.6461
 HJ5  C16   C  CH2   0  -0.559  -615.5511  380.8259  456.1137
 HJ5  C17   C  CSP   0   0.282  -614.6933  381.2999  457.1908
 HJ5  C20   C  C     0   0.594  -617.5238  380.7155  457.6552
 HJ5  C21   C  CSP1  0  -0.547  -614.0080  381.6743  458.1044
 HJ5  C24   C  CH1   0  -0.207  -618.8980  380.4853  459.6398
 HJ5  C25   C  CH2   0  -0.571  -619.6475  379.3180  460.3192
 HJ5  C26   C  CR6   0   0.148  -620.2502  378.4203  459.2729
 HJ5  C27   C  CR16  0  -0.323  -619.6442  377.2121  458.9430
 HJ5  C28   C  CR16  0  -0.234  -620.1675  376.4096  457.9373
 HJ5  C29   C  CR16  0  -0.254  -621.3079  376.8067  457.2542
 HJ5  C30   C  CR16  0  -0.243  -621.9190  378.0120  457.5781
 HJ5  C31   C  CR16  0  -0.293  -621.3925  378.8135  458.5803
 HJ5  C32   C  C     0   0.546  -618.2174  381.3501  460.6737
 HJ5  C4    C  CR6   0   0.124  -621.9183  376.3606  453.5642
 HJ5  C5    C  CR16  0  -0.304  -622.9533  377.1689  454.0257
 HJ5  C6    C  CR16  0  -0.243  -624.0327  376.6215  454.7070
 HJ5  C7    C  CR16  0  -0.269  -624.0879  375.2537  454.9386
 HJ5  C8    C  CR16  0  -0.244  -623.0616  374.4373  454.4791
 HJ5  C9    C  CR16  0  -0.298  -621.9865  374.9881  453.7950
 HJ5  N10   N  NT3   1  -0.790  -617.7824  377.1276  452.1100
 HJ5  N23   N  NH1   0  -0.628  -617.9371  379.9862  458.7096
 HJ5  O22   O  O     0  -0.460  -617.8568  381.8737  457.4877
 HJ5  O33   O  O     0  -0.268  -617.0711  381.3835  460.9555
 HJ5  P11   P  P     0   1.292  -616.9886  378.2049  454.4674
 HJ5  H1    H  HCH1  0   0.352  -618.6799  378.8183  452.8909
 HJ5  H22   H  HCH2  0   0.278  -619.8950  377.6627  454.7394
 HJ5  H2    H  HCH2  0   0.273  -619.2465  376.1226  454.2305
 HJ5  H32   H  HCH2  0   0.260  -620.4319  376.3409  452.0336
 HJ5  H3    H  HCH2  0   0.265  -620.9803  377.9480  452.4841
 HJ5  H141  H  HCH2  0   0.321  -617.9193  380.3520  454.8973
 HJ5  H14   H  HCH2  0   0.311  -618.5820  379.1266  455.9647
 HJ5  H15   H  HCH1  0   0.302  -616.2555  379.0661  457.1291
 HJ5  H16   H  HCH2  0   0.297  -614.9537  380.2601  455.3977
 HJ5  H161  H  HCH2  0   0.282  -615.9650  381.6789  455.5712
 HJ5  H21   H  H     0   0.279  -613.3970  382.0088  458.9110
 HJ5  H24   H  HCH1  0   0.334  -619.6297  381.1049  459.1108
 HJ5  H251  H  HCH2  0   0.293  -620.4278  379.7164  460.9701
 HJ5  H25   H  HCH2  0   0.301  -618.9557  378.7588  460.9526
 HJ5  H27   H  HCR6  0   0.257  -618.7581  376.8893  459.4777
 HJ5  H28   H  HCR6  0   0.256  -619.6852  375.4726  457.6909
 HJ5  H29   H  HCR6  0   0.265  -621.7233  376.1816  456.4745
 HJ5  H30   H  HCR6  0   0.254  -622.8108  378.3249  457.0508
 HJ5  H31   H  HCR6  0   0.255  -621.8742  379.7529  458.8273
 HJ5  H5    H  HCR6  0   0.250  -622.9129  378.2379  453.8515
 HJ5  H6    H  HCR6  0   0.256  -624.8300  377.2640  455.0586
 HJ5  H7    H  HCR6  0   0.256  -624.9272  374.8244  455.4701
 HJ5  H8    H  HCR6  0   0.256  -623.0997  373.3694  454.6518
 HJ5  H9    H  HCR6  0   0.249  -621.1919  374.3438  453.4354
 HJ5  HN12  H  HNT3  0   0.489  -618.4230  377.1207  451.3154
 HJ5  HN10  H  HNT3  0   0.478  -616.9209  377.5762  451.7883
 HJ5  HN11  H  HNT3  0   0.475  -617.5537  376.1535  452.3141
 HJ5  HN23  H  HNH1  0   0.420  -617.5581  379.0640  458.8588
 HJ5  HN31  H  HNT3  0   0.496  -618.7399  382.5939  462.2764
 HJ5  HN32  H  HNT3  0   0.503  -619.3591  383.0945  460.8343
 HJ5  H4    H  HOH1  0   0.500  -616.3252  376.2517  455.2247
 HJ5  HN33  H  HNT3  0   0.495  -620.0569  381.8371  461.6247
 HJ5  N34   N  NT3   1  -0.865  -619.1542  382.2643  461.4007
 HJ5  O12   O  O     0  -0.685  -615.7413  378.4894  453.7011
 HJ5  O13   O  OH1   0  -0.731  -616.9231  376.9661  455.4863

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    1.490  0.020  1.490
 HJ5  C3    C4    single    1.503  0.020  1.503
 HJ5  C3    C2    single    1.532  0.020  1.532
 HJ5  C1    C2    single    1.520  0.020  1.520
 HJ5  C1    P11   single    1.852  0.020  1.852
 HJ5  C4    C5    aromatic  1.392  0.020  1.392
 HJ5  C4    C9    aromatic  1.393  0.020  1.393
 HJ5  O12   P11   double    1.491  0.020  1.491
 HJ5  C5    C6    aromatic  1.389  0.020  1.389
 HJ5  C9    C8    aromatic  1.388  0.020  1.388
 HJ5  C6    C7    aromatic  1.388  0.020  1.388
 HJ5  P11   O13   single    1.605  0.020  1.605
 HJ5  P11   C14   single    1.804  0.020  1.804
 HJ5  C8    C7    aromatic  1.390  0.020  1.390
 HJ5  C14   C15   single    1.539  0.020  1.539
 HJ5  C16   C15   single    1.531  0.020  1.531
 HJ5  C16   C17   single    1.456  0.020  1.456
 HJ5  C15   C20   single    1.520  0.020  1.520
 HJ5  C17   C21   triple    1.202  0.020  1.202
 HJ5  O22   C20   double    1.217  0.020  1.217
 HJ5  C29   C28   aromatic  1.387  0.020  1.387
 HJ5  C29   C30   aromatic  1.390  0.020  1.390
 HJ5  C20   N23   single    1.347  0.020  1.347
 HJ5  C28   C27   aromatic  1.389  0.020  1.389
 HJ5  C30   C31   aromatic  1.387  0.020  1.387
 HJ5  C27   C26   aromatic  1.391  0.020  1.391
 HJ5  N23   C24   single    1.428  0.020  1.428
 HJ5  C31   C26   aromatic  1.393  0.020  1.393
 HJ5  C26   C25   single    1.505  0.020  1.505
 HJ5  C24   C25   single    1.545  0.020  1.545
 HJ5  C24   C32   single    1.510  0.020  1.510
 HJ5  C32   O33   double    1.181  0.020  1.181
 HJ5  C32   N34   single    1.497  0.020  1.497
 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  O13   H4    single    0.832  0.020  0.971
 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   105.71  3.000
 HJ5  H1    C1   N10   105.29  3.000
 HJ5  P11   C1   N10   107.92  3.000
 HJ5  H1    C1   C2    110.07  3.000
 HJ5  P11   C1   C2    115.36  3.000
 HJ5  N10   C1   C2    111.84  3.000
 HJ5  H2    C2   H22   106.16  3.000
 HJ5  H2    C2   C3    110.29  3.000
 HJ5  H22   C2   C3    108.72  3.000
 HJ5  H2    C2   C1    110.36  3.000
 HJ5  H22   C2   C1    107.72  3.000
 HJ5  C3    C2   C1    113.30  3.000
 HJ5  H3    C3   H32   106.96  3.000
 HJ5  H3    C3   C4    109.82  3.000
 HJ5  H32   C3   C4    109.50  3.000
 HJ5  H3    C3   C2    109.41  3.000
 HJ5  H32   C3   C2    110.33  3.000
 HJ5  C4    C3   C2    110.74  3.000
 HJ5  H14   C14  H141  106.69  3.000
 HJ5  H14   C14  P11   107.34  3.000
 HJ5  H141  C14  P11   107.90  3.000
 HJ5  H14   C14  C15   110.18  3.000
 HJ5  H141  C14  C15   110.52  3.000
 HJ5  P11   C14  C15   113.90  3.000
 HJ5  H15   C15  C20   109.35  3.000
 HJ5  H15   C15  C16   108.89  3.000
 HJ5  C20   C15  C16   110.43  3.000
 HJ5  H15   C15  C14   109.56  3.000
 HJ5  C20   C15  C14   106.38  3.000
 HJ5  C16   C15  C14   112.19  3.000
 HJ5  H161  C16  H16   106.65  3.000
 HJ5  H161  C16  C17   109.65  3.000
 HJ5  H16   C16  C17   109.37  3.000
 HJ5  H161  C16  C15   109.88  3.000
 HJ5  H16   C16  C15   109.67  3.000
 HJ5  C17   C16  C15   111.50  3.000
 HJ5  C21   C17  C16   180.00  3.000
 HJ5  O22   C20  N23   122.63  3.000
 HJ5  N23   C20  C15   114.52  3.000
 HJ5  O22   C20  C15   122.73  3.000
 HJ5  H21   C21  C17   180.00  3.000
 HJ5  H24   C24  N23   109.44  3.000
 HJ5  H24   C24  C32   107.93  3.000
 HJ5  N23   C24  C32   110.06  3.000
 HJ5  H24   C24  C25   108.41  3.000
 HJ5  C32   C24  C25   110.51  3.000
 HJ5  N23   C24  C25   110.42  3.000
 HJ5  H25   C25  H251  107.09  3.000
 HJ5  H25   C25  C26   110.59  3.000
 HJ5  H251  C25  C26   110.25  3.000
 HJ5  H25   C25  C24   109.55  3.000
 HJ5  H251  C25  C24   109.47  3.000
 HJ5  C26   C25  C24   109.84  3.000
 HJ5  C31   C26  C27   118.98  3.000
 HJ5  C31   C26  C25   120.40  3.000
 HJ5  C27   C26  C25   120.57  3.000
 HJ5  H27   C27  C28   119.54  3.000
 HJ5  H27   C27  C26   119.84  3.000
 HJ5  C28   C27  C26   120.62  3.000
 HJ5  H28   C28  C29   120.14  3.000
 HJ5  H28   C28  C27   119.81  3.000
 HJ5  C29   C28  C27   120.05  3.000
 HJ5  H29   C29  C30   120.01  3.000
 HJ5  H29   C29  C28   120.32  3.000
 HJ5  C30   C29  C28   119.67  3.000
 HJ5  H30   C30  C31   119.85  3.000
 HJ5  H30   C30  C29   119.97  3.000
 HJ5  C31   C30  C29   120.18  3.000
 HJ5  H31   C31  C30   119.78  3.000
 HJ5  H31   C31  C26   119.72  3.000
 HJ5  C30   C31  C26   120.50  3.000
 HJ5  O33   C32  N34   118.31  3.000
 HJ5  N34   C32  C24   113.58  3.000
 HJ5  O33   C32  C24   128.11  3.000
 HJ5  C9    C4   C5    118.73  3.000
 HJ5  C9    C4   C3    120.65  3.000
 HJ5  C5    C4   C3    120.57  3.000
 HJ5  H5    C5   C6    119.77  3.000
 HJ5  H5    C5   C4    119.46  3.000
 HJ5  C6    C5   C4    120.77  3.000
 HJ5  H6    C6   C7    120.08  3.000
 HJ5  H6    C6   C5    119.85  3.000
 HJ5  C7    C6   C5    120.07  3.000
 HJ5  H7    C7   C8    120.15  3.000
 HJ5  H7    C7   C6    120.24  3.000
 HJ5  C8    C7   C6    119.62  3.000
 HJ5  H8    C8   C9    119.83  3.000
 HJ5  H8    C8   C7    120.05  3.000
 HJ5  C9    C8   C7    120.12  3.000
 HJ5  H9    C9   C8    119.68  3.000
 HJ5  H9    C9   C4    119.63  3.000
 HJ5  C8    C9   C4    120.69  3.000
 HJ5  HN11  N10  HN10  107.01  3.000
 HJ5  HN11  N10  HN12  106.84  3.000
 HJ5  HN10  N10  HN12  106.66  3.000
 HJ5  HN12  N10  C1    111.68  3.000
 HJ5  HN11  N10  C1    113.00  3.000
 HJ5  HN10  N10  C1    111.30  3.000
 HJ5  HN23  N23  C24   118.45  3.000
 HJ5  HN23  N23  C20   119.72  3.000
 HJ5  C24   N23  C20   121.82  3.000
 HJ5  O13   P11  O12   116.05  3.000
 HJ5  O13   P11  C14   101.31  3.000
 HJ5  O12   P11  C14   118.18  3.000
 HJ5  C14   P11  C1    104.22  3.000
 HJ5  O13   P11  C1    106.76  3.000
 HJ5  O12   P11  C1    109.13  3.000
 HJ5  HN33  N34  HN32  106.41  3.000
 HJ5  HN33  N34  HN31  107.71  3.000
 HJ5  HN32  N34  HN31  107.03  3.000
 HJ5  HN33  N34  C32   113.78  3.000
 HJ5  HN32  N34  C32   110.55  3.000
 HJ5  HN31  N34  C32   111.03  3.000
 HJ5  H4    O13  P11   115.04  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  Var_01    C5    C4   C3   C2     98.70  30.0  2
 HJ5  Var_02    C27   C26  C25  C24   101.98  30.0  2
 HJ5  Var_03    C4    C3   C2   C1   -173.78  30.0  2
 HJ5  Var_04    C15   C14  P11  C1    178.27  30.0  3
 HJ5  Var_05    H16   C16  C17  C21  -124.71  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
 HJ5  chir_04  P11  O12  O13  C14  both

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  O33   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

