# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 18:36:56 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1n(Cc2ccccc2)c3ccc(OCCC[P](O)(O)=O)cc3c1CC(N)=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
 U8D  U8D  '(3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid'  ligand  55  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U8D
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
 U8D  N1    N  NR5    0  -0.586   3.3019   0.1571   0.6725
 U8D  C2    C  CR5    0   0.325   3.7960  -0.9906   0.0910
 U8D  C3    C  CR5    0  -0.026   2.7578  -1.7298  -0.4139
 U8D  C4    C  CR56   0   0.108   1.5565  -1.0040  -0.1415
 U8D  C5    C  CR16   0  -0.500   0.2089  -1.2481  -0.4060
 U8D  C6    C  CR6    0   0.391  -0.7371  -0.3121  -0.0086
 U8D  C7    C  CR16   0  -0.410  -0.3413   0.8610   0.6593
 U8D  C8    C  CR16   0  -0.289   0.9955   1.1112   0.9309
 U8D  C9    C  CR56   0   0.332   1.9356   0.1728   0.5319
 U8D  C10   C  CH2    0  -0.542   5.2460  -1.3324   0.1176
 U8D  C11   C  CH2    0  -0.719   2.8192  -3.0587  -1.0825
 U8D  O12   O  O2     0  -0.490  -2.0265  -0.6018  -0.3052
 U8D  C13   C  CH2    0  -0.391   4.0566   1.2363   1.2549
 U8D  C14   C  CR16   0  -0.268   4.0641   4.8735  -1.0454
 U8D  C15   C  CR16   0  -0.241   4.1174   4.9159   0.3414
 U8D  C16   C  CR16   0  -0.308   4.0983   3.7366   1.0739
 U8D  C17   C  CR6    0   0.104   4.0332   2.5031   0.4335
 U8D  C18   C  CR16   0  -0.285   3.9774   2.4675  -0.9560
 U8D  C19   C  CR16   0  -0.240   3.9927   3.6455  -1.6906
 U8D  C20   C  CH3    0  -0.663   5.6983  -1.9001   1.4636
 U8D  C21   C  C      0   0.525   2.4120  -4.1913  -0.1508
 U8D  O22   O  O      0  -0.481   2.8557  -4.2831   0.9839
 U8D  N23   N  NH2    0  -0.800   1.5548  -5.0790  -0.6757
 U8D  C24   C  CH2    0  -0.161  -3.0505   0.2750   0.1413
 U8D  C25   C  CH2    0  -0.448  -4.3936  -0.2529  -0.3143
 U8D  P26   P  P      0   1.170  -7.2117   0.0448  -0.4205
 U8D  O27   O  O      0  -0.916  -7.3627  -1.3853   0.1194
 U8D  O28   O  OP    -1  -0.916  -7.1297   0.1166  -1.9528
 U8D  O29   O  OP    -1  -0.915  -8.2085   1.0423   0.1886
 U8D  C30   C  CH2    0  -0.723  -5.5427   0.6161   0.1787
 U8D  H5    H  HCR6   0   0.237  -0.1092  -2.1525  -0.9118
 U8D  H7    H  HCR6   0   0.271  -1.0726   1.5937   0.9705
 U8D  H8    H  HCR6   0   0.260   1.2778   2.0249   1.4386
 U8D  H10   H  HCH2   0   0.259   5.4352  -2.0728  -0.6610
 U8D  H10A  H  HCH2   0   0.250   5.8540  -0.4642  -0.1506
 U8D  H11   H  HCH2   0   0.264   2.2000  -3.0603  -1.9834
 U8D  H11A  H  HCH2   0   0.286   3.8380  -3.2786  -1.4142
 U8D  H13   H  HCH2   0   0.274   3.6810   1.4406   2.2613
 U8D  H13A  H  HCH2   0   0.291   5.0874   0.9056   1.3857
 U8D  H14   H  HCR6   0   0.256   4.0720   5.7903  -1.6205
 U8D  H15   H  HCR6   0   0.256   4.1663   5.8673   0.8556
 U8D  H16   H  HCR6   0   0.252   4.1286   3.7775   2.1567
 U8D  H18   H  HCR6   0   0.253   3.9112   1.5189  -1.4758
 U8D  H19   H  HCR6   0   0.256   3.9465   3.6035  -2.7712
 U8D  H20   H  HCH3   0   0.238   5.1120  -2.7830   1.7161
 U8D  H20A  H  HCH3   0   0.235   6.7500  -2.1842   1.4256
 U8D  H20B  H  HCH3   0   0.226   5.5805  -1.1767   2.2713
 U8D  HN23  H  HNH2   0   0.407   1.1883  -4.9786  -1.6061
 U8D  HN2A  H  HNH2   0   0.399   1.2495  -5.8764  -0.1415
 U8D  H24   H  HCH2   0   0.204  -3.0256   0.3567   1.2356
 U8D  H24A  H  HCH2   0   0.204  -2.8934   1.2828  -0.2626
 U8D  H25   H  HCH2   0   0.208  -4.4205  -0.2976  -1.4064
 U8D  H25A  H  HCH2   0   0.209  -4.5342  -1.2751   0.0475
 U8D  H30   H  HCH2   0   0.185  -5.5356   0.6384   1.2751
 U8D  H30A  H  HCH2   0   0.184  -5.3813   1.6528  -0.1415

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
 U8D  C2   N1    aromatic  1.378  0.020  1.378
 U8D  N1   C9    aromatic  1.374  0.020  1.374
 U8D  N1   C13   single    1.440  0.020  1.440
 U8D  C3   C2    aromatic  1.371  0.020  1.371
 U8D  C10  C2    single    1.490  0.020  1.490
 U8D  C11  C3    single    1.489  0.020  1.489
 U8D  C3   C4    aromatic  1.430  0.020  1.430
 U8D  C5   C4    aromatic  1.395  0.020  1.395
 U8D  C4   C9    aromatic  1.408  0.020  1.408
 U8D  C5   C6    aromatic  1.389  0.020  1.389
 U8D  C5   H5    single    0.930  0.020  1.080
 U8D  O12  C6    single    1.354  0.020  1.354
 U8D  C6   C7    aromatic  1.407  0.020  1.407
 U8D  C7   C8    aromatic  1.387  0.020  1.387
 U8D  C7   H7    single    0.930  0.020  1.080
 U8D  C9   C8    aromatic  1.387  0.020  1.387
 U8D  C8   H8    single    0.930  0.020  1.080
 U8D  C20  C10   single    1.529  0.020  1.529
 U8D  C10  H10   single    0.970  0.020  1.090
 U8D  C10  H10A  single    0.970  0.020  1.090
 U8D  C21  C11   single    1.522  0.020  1.522
 U8D  C11  H11   single    0.970  0.020  1.090
 U8D  C11  H11A  single    0.970  0.020  1.090
 U8D  C24  O12   single    1.420  0.020  1.420
 U8D  C13  C17   single    1.510  0.020  1.510
 U8D  C13  H13   single    0.970  0.020  1.090
 U8D  C13  H13A  single    0.970  0.020  1.090
 U8D  C15  C14   aromatic  1.388  0.020  1.388
 U8D  C14  C19   aromatic  1.389  0.020  1.389
 U8D  C14  H14   single    0.930  0.020  1.080
 U8D  C16  C15   aromatic  1.388  0.020  1.388
 U8D  C15  H15   single    0.930  0.020  1.080
 U8D  C16  C17   aromatic  1.391  0.020  1.391
 U8D  C16  H16   single    0.930  0.020  1.080
 U8D  C17  C18   aromatic  1.391  0.020  1.391
 U8D  C18  C19   aromatic  1.388  0.020  1.388
 U8D  C18  H18   single    0.930  0.020  1.080
 U8D  C19  H19   single    0.930  0.020  1.080
 U8D  C20  H20   single    0.970  0.020  1.090
 U8D  C20  H20A  single    0.970  0.020  1.090
 U8D  C20  H20B  single    0.970  0.020  1.090
 U8D  N23  C21   single    1.341  0.020  1.341
 U8D  C21  O22   double    1.222  0.020  1.222
 U8D  N23  HN23  single    0.860  0.020  1.020
 U8D  N23  HN2A  single    0.860  0.020  1.020
 U8D  C25  C24   single    1.513  0.020  1.513
 U8D  C24  H24   single    0.970  0.020  1.090
 U8D  C24  H24A  single    0.970  0.020  1.090
 U8D  C30  C25   single    1.523  0.020  1.523
 U8D  C25  H25   single    0.970  0.020  1.090
 U8D  C25  H25A  single    0.970  0.020  1.090
 U8D  O27  P26   deloc     1.536  0.020  1.536
 U8D  C30  P26   single    1.863  0.020  1.863
 U8D  P26  O29   deloc     1.536  0.020  1.536
 U8D  P26  O28   deloc     1.536  0.020  1.536
 U8D  C30  H30   single    0.970  0.020  1.090
 U8D  C30  H30A  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
 U8D  C13   N1   C9    123.65  3.000
 U8D  C13   N1   C2    127.37  3.000
 U8D  C9    N1   C2    108.84  3.000
 U8D  C10   C2   C3    128.31  3.000
 U8D  C10   C2   N1    122.17  3.000
 U8D  C3    C2   N1    109.45  3.000
 U8D  C11   C3   C4    124.99  3.000
 U8D  C4    C3   C2    107.00  3.000
 U8D  C11   C3   C2    127.99  3.000
 U8D  C9    C4   C5    119.81  3.000
 U8D  C9    C4   C3    106.82  3.000
 U8D  C5    C4   C3    133.37  3.000
 U8D  H5    C5   C6    119.73  3.000
 U8D  H5    C5   C4    121.20  3.000
 U8D  C6    C5   C4    119.07  3.000
 U8D  O12   C6   C7    123.38  3.000
 U8D  C7    C6   C5    120.41  3.000
 U8D  O12   C6   C5    116.21  3.000
 U8D  H7    C7   C8    118.25  3.000
 U8D  H7    C7   C6    120.77  3.000
 U8D  C8    C7   C6    120.98  3.000
 U8D  H8    C8   C9    121.95  3.000
 U8D  H8    C8   C7    119.70  3.000
 U8D  C9    C8   C7    118.35  3.000
 U8D  C8    C9   C4    121.38  3.000
 U8D  C8    C9   N1    130.73  3.000
 U8D  C4    C9   N1    107.89  3.000
 U8D  H10A  C10  H10   105.51  3.000
 U8D  H10A  C10  C20   110.26  3.000
 U8D  H10   C10  C20   108.96  3.000
 U8D  H10A  C10  C2    110.77  3.000
 U8D  H10   C10  C2    108.17  3.000
 U8D  C20   C10  C2    112.87  3.000
 U8D  H11A  C11  H11   106.11  3.000
 U8D  H11A  C11  C21   106.57  3.000
 U8D  H11   C11  C21   110.61  3.000
 U8D  H11A  C11  C3    110.73  3.000
 U8D  H11   C11  C3    110.37  3.000
 U8D  C21   C11  C3    112.22  3.000
 U8D  C24   O12  C6    119.05  3.000
 U8D  H13A  C13  H13   105.72  3.000
 U8D  H13A  C13  C17   109.54  3.000
 U8D  H13   C13  C17   109.79  3.000
 U8D  H13A  C13  N1    108.46  3.000
 U8D  H13   C13  N1    109.40  3.000
 U8D  C17   C13  N1    113.62  3.000
 U8D  H14   C14  C19   120.16  3.000
 U8D  H14   C14  C15   120.30  3.000
 U8D  C19   C14  C15   119.54  3.000
 U8D  H15   C15  C16   119.77  3.000
 U8D  H15   C15  C14   120.20  3.000
 U8D  C16   C15  C14   120.03  3.000
 U8D  H16   C16  C17   119.64  3.000
 U8D  H16   C16  C15   119.64  3.000
 U8D  C17   C16  C15   120.72  3.000
 U8D  C18   C17  C16   118.97  3.000
 U8D  C18   C17  C13   121.50  3.000
 U8D  C16   C17  C13   119.52  3.000
 U8D  H18   C18  C19   119.32  3.000
 U8D  H18   C18  C17   120.26  3.000
 U8D  C19   C18  C17   120.42  3.000
 U8D  H19   C19  C18   119.66  3.000
 U8D  H19   C19  C14   120.02  3.000
 U8D  C18   C19  C14   120.33  3.000
 U8D  H20B  C20  H20A  107.63  3.000
 U8D  H20B  C20  H20   107.92  3.000
 U8D  H20A  C20  H20   108.43  3.000
 U8D  H20B  C20  C10   111.94  3.000
 U8D  H20A  C20  C10   110.57  3.000
 U8D  H20   C20  C10   110.22  3.000
 U8D  N23   C21  O22   123.08  3.000
 U8D  O22   C21  C11   121.83  3.000
 U8D  N23   C21  C11   115.08  3.000
 U8D  HN2A  N23  HN23  117.36  3.000
 U8D  HN2A  N23  C21   120.68  3.000
 U8D  HN23  N23  C21   121.96  3.000
 U8D  H24A  C24  H24   107.19  3.000
 U8D  H24A  C24  C25   109.67  3.000
 U8D  H24   C24  C25   110.25  3.000
 U8D  H24A  C24  O12   110.37  3.000
 U8D  H24   C24  O12   110.06  3.000
 U8D  C25   C24  O12   109.27  3.000
 U8D  H25A  C25  H25   106.81  3.000
 U8D  H25A  C25  C30   109.23  3.000
 U8D  H25   C25  C30   109.16  3.000
 U8D  H25A  C25  C24   109.91  3.000
 U8D  H25   C25  C24   109.68  3.000
 U8D  C30   C25  C24   111.92  3.000
 U8D  C30   P26  O29   104.75  3.000
 U8D  O29   P26  O28   113.57  3.000
 U8D  C30   P26  O28   104.99  3.000
 U8D  O28   P26  O27   113.54  3.000
 U8D  O29   P26  O27   113.67  3.000
 U8D  C30   P26  O27   105.10  3.000
 U8D  H30A  C30  H30   105.76  3.000
 U8D  H30A  C30  P26   109.13  3.000
 U8D  H30   C30  P26   109.49  3.000
 U8D  H30A  C30  C25   109.50  3.000
 U8D  H30   C30  C25   109.29  3.000
 U8D  P26   C30  C25   113.39  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
 U8D  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 U8D  CONST_02  C3    C4   C9   N1     0.00   0.0  0
 U8D  CONST_03  C5    C4   C9   N1   180.00   0.0  0
 U8D  CONST_04  C7    C8   C9   N1   180.00   0.0  0
 U8D  CONST_05  C4    C9   N1   C2     0.00   0.0  0
 U8D  CONST_06  C8    C9   N1   C2   180.00   0.0  0
 U8D  CONST_07  C5    C4   C3   C2   180.00   0.0  0
 U8D  CONST_08  C9    C4   C3   C2     0.00   0.0  0
 U8D  CONST_09  C9    N1   C2   C3     0.00   0.0  0
 U8D  CONST_10  C6    C5   C4   C3   180.00   0.0  0
 U8D  CONST_11  C8    C9   C4   C3   180.00   0.0  0
 U8D  CONST_12  C7    C6   C5   C4     0.00   0.0  0
 U8D  CONST_13  C7    C8   C9   C4     0.00   0.0  0
 U8D  CONST_14  C8    C9   C4   C5     0.00   0.0  0
 U8D  CONST_15  C8    C7   C6   C5     0.00   0.0  0
 U8D  CONST_16  C9    C4   C5   C6     0.00   0.0  0
 U8D  CONST_17  C9    C8   C7   C6     0.00   0.0  0
 U8D  CONST_18  C17   C16  C15  C14    0.00   0.0  0
 U8D  CONST_19  C17   C18  C19  C14    0.00   0.0  0
 U8D  CONST_20  C18   C19  C14  C15    0.00   0.0  0
 U8D  CONST_21  C18   C17  C16  C15    0.00   0.0  0
 U8D  CONST_22  C19   C14  C15  C16    0.00   0.0  0
 U8D  CONST_23  C19   C18  C17  C16    0.00   0.0  0
 U8D  CONST_24  C11   C3   C2   N1   180.00   0.0  0
 U8D  CONST_25  C13   N1   C2   C3   180.00   0.0  0
 U8D  CONST_26  C10   C2   C3   C4   180.00   0.0  0
 U8D  CONST_27  O12   C6   C5   C4   180.00   0.0  0
 U8D  CONST_28  C13   N1   C9   C4   180.00   0.0  0
 U8D  CONST_29  C11   C3   C4   C5     0.00   0.0  0
 U8D  CONST_30  O12   C6   C7   C8   180.00   0.0  0
 U8D  CONST_31  C13   N1   C9   C8     0.00   0.0  0
 U8D  CONST_32  C10   C2   N1   C9   180.00   0.0  0
 U8D  CONST_33  C11   C3   C4   C9   180.00   0.0  0
 U8D  CONST_34  C15   C16  C17  C13  180.00   0.0  0
 U8D  CONST_35  C19   C18  C17  C13  180.00   0.0  0
 U8D  CONST_36  H8    C8   C9   N1     0.00   0.0  0
 U8D  CONST_37  H5    C5   C4   C3     0.00   0.0  0
 U8D  CONST_38  H7    C7   C6   C5   180.00   0.0  0
 U8D  CONST_39  H16   C16  C15  C14  180.00   0.0  0
 U8D  CONST_40  H18   C18  C19  C14  180.00   0.0  0
 U8D  CONST_41  H19   C19  C14  C15  180.00   0.0  0
 U8D  CONST_42  H14   C14  C15  C16  180.00   0.0  0
 U8D  CONST_43  H15   C15  C16  C17  180.00   0.0  0
 U8D  CONST_44  HN23  N23  C21  C11    0.00   0.0  0
 U8D  CONST_45  HN2A  N23  C21  C11  180.00   0.0  0
 U8D  Var_01    C16   C17  C13  N1   148.21  30.0  2
 U8D  Var_02    C17   C13  N1   C2   108.54  30.0  2
 U8D  Var_03    C20   C10  C2   N1    77.93  30.0  2
 U8D  Var_04    C21   C11  C3   C2   101.51  30.0  2
 U8D  Var_05    N23   C21  C11  C3   133.76  30.0  1
 U8D  Var_06    C25   C24  O12  C6   179.76  30.0  1
 U8D  Var_07    H20   C20  C10  C2    57.23  30.0  3
 U8D  Var_08    C30   C25  C24  O12  177.83  30.0  1
 U8D  Var_09    P26   C30  C25  C24  177.51  30.0  1
 U8D  Var_10    O27   P26  C30  C25   59.72  30.0  3

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
 U8D  plan-1  C13   0.020
 U8D  plan-1  C14   0.020
 U8D  plan-1  C15   0.020
 U8D  plan-1  C16   0.020
 U8D  plan-1  C17   0.020
 U8D  plan-1  C18   0.020
 U8D  plan-1  C19   0.020
 U8D  plan-1  H14   0.020
 U8D  plan-1  H15   0.020
 U8D  plan-1  H16   0.020
 U8D  plan-1  H18   0.020
 U8D  plan-1  H19   0.020
 U8D  plan-2  N1    0.020
 U8D  plan-2  C2    0.020
 U8D  plan-2  C3    0.020
 U8D  plan-2  C4    0.020
 U8D  plan-2  C5    0.020
 U8D  plan-2  C6    0.020
 U8D  plan-2  C7    0.020
 U8D  plan-2  C8    0.020
 U8D  plan-2  C9    0.020
 U8D  plan-2  C10   0.020
 U8D  plan-2  C11   0.020
 U8D  plan-2  O12   0.020
 U8D  plan-2  C13   0.020
 U8D  plan-2  H5    0.020
 U8D  plan-2  H7    0.020
 U8D  plan-2  H8    0.020
 U8D  plan-3  C11   0.020
 U8D  plan-3  C21   0.020
 U8D  plan-3  O22   0.020
 U8D  plan-3  N23   0.020
 U8D  plan-3  HN23  0.020
 U8D  plan-3  HN2A  0.020

