# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:07:53 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-methyl-1H-indol-5-yl]oxy}propyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n(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
 8IN  8IN  '(3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-methyl-1H-indol-5-yl]oxy}propyl)phosphonic acid'  ligand  54  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8IN
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
 8IN  C1    C  CR16  0  -0.373  60.2162  28.3688  48.7720
 8IN  C2    C  CR16  0  -0.295  60.2096  29.7340  48.9840
 8IN  C3    C  CR56  0   0.315  59.6851  30.5495  47.9851
 8IN  C4    C  CR56  0   0.123  59.2033  30.0052  46.7849
 8IN  C5    C  CR16  0  -0.509  59.2217  28.6217  46.5774
 8IN  C6    C  CR6   0   0.384  59.7182  27.8072  47.5797
 8IN  N7    N  NR5   0  -0.580  59.5050  31.9100  47.9270
 8IN  C8    C  CR5   0   0.282  58.9418  32.2357  46.7125
 8IN  C9    C  CR5   0  -0.019  58.7345  31.0918  45.9861
 8IN  C10   C  CH2   0  -0.708  58.1241  30.9387  44.6348
 8IN  C11   C  C     0   0.511  56.8379  30.1257  44.7007
 8IN  O12   O  O     0  -0.480  55.9515  30.3915  45.4968
 8IN  N13   N  NH2   0  -0.808  56.7561  29.1134  43.8236
 8IN  C14   C  CH3   0  -0.750  58.6434  33.6488  46.3643
 8IN  C15   C  CH2   0  -0.368  59.9727  32.8484  48.9096
 8IN  C16   C  CR6   0   0.075  61.3871  33.3342  48.6846
 8IN  C17   C  CR16  0  -0.286  61.9234  34.2658  49.5719
 8IN  C18   C  CR16  0  -0.244  63.2141  34.7425  49.4037
 8IN  C19   C  CR16  0  -0.268  63.9902  34.2935  48.3410
 8IN  C20   C  CR16  0  -0.240  63.4628  33.3668  47.4545
 8IN  C21   C  CR16  0  -0.290  62.1678  32.8887  47.6249
 8IN  O22   O  O2    0  -0.492  59.7747  26.4519  47.5074
 8IN  C23   C  CH2   0  -0.190  59.2088  25.8036  46.3848
 8IN  C24   C  CH2   0  -0.496  57.6841  25.7830  46.4089
 8IN  C25   C  CH2   0  -0.755  57.1490  25.1975  45.1042
 8IN  P26   P  P     0   1.387  55.3509  25.1335  45.0771
 8IN  O27   O  O     0  -0.717  54.7184  24.3804  46.1889
 8IN  O28   O  OH1   0  -0.742  55.0800  24.5948  43.5923
 8IN  O29   O  OH1   0  -0.755  54.8573  26.6706  44.9818
 8IN  H1    H  HCR6  0   0.257  60.6114  27.7106  49.5357
 8IN  H2    H  HCR6  0   0.261  60.6031  30.1362  49.9088
 8IN  H5    H  HCR6  0   0.247  58.8368  28.2232  45.6489
 8IN  H101  H  HCH2  0   0.285  57.8720  31.9136  44.2089
 8IN  H102  H  HCH2  0   0.264  58.8343  30.4774  43.9423
 8IN  H131  H  HNH2  0   0.406  57.5086  28.8968  43.1939
 8IN  H132  H  HNH2  0   0.398  55.9646  28.4893  43.8369
 8IN  H141  H  HCH3  0   0.263  58.2297  33.7152  45.3609
 8IN  H142  H  HCH3  0   0.259  57.9157  34.0908  47.0480
 8IN  H143  H  HCH3  0   0.254  59.5392  34.2726  46.3925
 8IN  H151  H  HCH2  0   0.287  59.2916  33.7007  48.9329
 8IN  H152  H  HCH2  0   0.284  59.8938  32.3866  49.8960
 8IN  H17   H  HCR6  0   0.252  61.3242  34.6249  50.4012
 8IN  H18   H  HCR6  0   0.256  63.6156  35.4662  50.1014
 8IN  H19   H  HCR6  0   0.256  64.9978  34.6647  48.2065
 8IN  H20   H  HCR6  0   0.256  64.0588  33.0092  46.6246
 8IN  H21   H  HCR6  0   0.254  61.7746  32.1654  46.9211
 8IN  H231  H  HCH2  0   0.222  59.5749  26.2471  45.4514
 8IN  H232  H  HCH2  0   0.262  59.5871  24.7808  46.4166
 8IN  H241  H  HCH2  0   0.259  57.3443  25.1888  47.2595
 8IN  H242  H  HCH2  0   0.252  57.2923  26.7928  46.5491
 8IN  H251  H  HCH2  0   0.281  57.4968  25.7830  44.2487
 8IN  H252  H  HCH2  0   0.290  57.5174  24.1782  44.9602
 8IN  H28   H  HOH1  0   0.495  54.1539  24.3853  43.4081
 8IN  H29   H  HOH1  0   0.493  54.4949  27.0168  45.8074

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
 8IN  C1   C2    aromatic  1.382  0.020  1.382
 8IN  C1   C6    aromatic  1.409  0.020  1.409
 8IN  C1   H1    single    0.930  0.020  1.080
 8IN  C2   C3    aromatic  1.392  0.020  1.392
 8IN  C2   H2    single    0.930  0.020  1.080
 8IN  C3   C4    aromatic  1.403  0.020  1.403
 8IN  C3   N7    aromatic  1.374  0.020  1.374
 8IN  C4   C5    aromatic  1.399  0.020  1.399
 8IN  C4   C9    aromatic  1.428  0.020  1.428
 8IN  C5   C6    aromatic  1.384  0.020  1.384
 8IN  C5   H5    single    0.930  0.020  1.080
 8IN  C6   O22   single    1.358  0.020  1.358
 8IN  N7   C8    aromatic  1.378  0.020  1.378
 8IN  N7   C15   single    1.437  0.020  1.437
 8IN  C8   C9    aromatic  1.371  0.020  1.371
 8IN  C8   C14   single    1.486  0.020  1.486
 8IN  C9   C10   single    1.491  0.020  1.491
 8IN  C10  C11   single    1.523  0.020  1.523
 8IN  C10  H101  single    0.970  0.020  1.090
 8IN  C10  H102  single    0.970  0.020  1.090
 8IN  C11  O12   double    1.221  0.020  1.221
 8IN  C11  N13   single    1.342  0.020  1.342
 8IN  N13  H131  single    0.860  0.020  1.020
 8IN  N13  H132  single    0.860  0.020  1.020
 8IN  C14  H141  single    0.970  0.020  1.090
 8IN  C14  H142  single    0.970  0.020  1.090
 8IN  C14  H143  single    0.970  0.020  1.090
 8IN  C15  C16   single    1.512  0.020  1.512
 8IN  C15  H151  single    0.970  0.020  1.090
 8IN  C15  H152  single    0.970  0.020  1.090
 8IN  C16  C17   aromatic  1.394  0.020  1.394
 8IN  C16  C21   aromatic  1.390  0.020  1.390
 8IN  C17  C18   aromatic  1.386  0.020  1.386
 8IN  C17  H17   single    0.930  0.020  1.080
 8IN  C18  C19   aromatic  1.390  0.020  1.390
 8IN  C18  H18   single    0.930  0.020  1.080
 8IN  C19  C20   aromatic  1.387  0.020  1.387
 8IN  C19  H19   single    0.930  0.020  1.080
 8IN  C20  C21   aromatic  1.391  0.020  1.391
 8IN  C20  H20   single    0.930  0.020  1.080
 8IN  C21  H21   single    0.930  0.020  1.080
 8IN  O22  C23   single    1.414  0.020  1.414
 8IN  C23  C24   single    1.525  0.020  1.525
 8IN  C23  H231  single    0.970  0.020  1.090
 8IN  C23  H232  single    0.970  0.020  1.090
 8IN  C24  C25   single    1.527  0.020  1.527
 8IN  C24  H241  single    0.970  0.020  1.090
 8IN  C24  H242  single    0.970  0.020  1.090
 8IN  C25  P26   single    1.800  0.020  1.800
 8IN  C25  H251  single    0.970  0.020  1.090
 8IN  C25  H252  single    0.970  0.020  1.090
 8IN  P26  O27   double    1.484  0.020  1.484
 8IN  P26  O28   single    1.603  0.020  1.603
 8IN  P26  O29   single    1.617  0.020  1.617
 8IN  O28  H28   single    0.850  0.020  0.980
 8IN  O29  H29   single    0.850  0.020  0.980

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
 8IN  H1    C1   C6    118.91  3.000
 8IN  H1    C1   C2    119.62  3.000
 8IN  C6    C1   C2    121.47  3.000
 8IN  H2    C2   C3    122.16  3.000
 8IN  H2    C2   C1    119.77  3.000
 8IN  C3    C2   C1    118.07  3.000
 8IN  N7    C3   C4    107.64  3.000
 8IN  N7    C3   C2    131.30  3.000
 8IN  C4    C3   C2    121.05  3.000
 8IN  C9    C4   C5    132.37  3.000
 8IN  C9    C4   C3    107.22  3.000
 8IN  C5    C4   C3    120.39  3.000
 8IN  H5    C5   C6    122.20  3.000
 8IN  H5    C5   C4    119.15  3.000
 8IN  C6    C5   C4    118.65  3.000
 8IN  O22   C6   C5    124.31  3.000
 8IN  O22   C6   C1    115.35  3.000
 8IN  C5    C6   C1    120.34  3.000
 8IN  C15   N7   C8    125.55  3.000
 8IN  C15   N7   C3    125.11  3.000
 8IN  C8    N7   C3    108.97  3.000
 8IN  C14   C8   C9    129.73  3.000
 8IN  C14   C8   N7    120.90  3.000
 8IN  C9    C8   N7    109.36  3.000
 8IN  C10   C9   C8    128.90  3.000
 8IN  C10   C9   C4    124.29  3.000
 8IN  C8    C9   C4    106.80  3.000
 8IN  H102  C10  H101  106.21  3.000
 8IN  H102  C10  C11   110.52  3.000
 8IN  H101  C10  C11   107.34  3.000
 8IN  H102  C10  C9    110.57  3.000
 8IN  H101  C10  C9    110.85  3.000
 8IN  C11   C10  C9    111.19  3.000
 8IN  N13   C11  O12   123.11  3.000
 8IN  N13   C11  C10   115.21  3.000
 8IN  O12   C11  C10   121.68  3.000
 8IN  H132  N13  H131  117.57  3.000
 8IN  H132  N13  C11   120.42  3.000
 8IN  H131  N13  C11   121.77  3.000
 8IN  H143  C14  H142  107.41  3.000
 8IN  H143  C14  H141  107.52  3.000
 8IN  H142  C14  H141  107.43  3.000
 8IN  H143  C14  C8    111.87  3.000
 8IN  H142  C14  C8    111.85  3.000
 8IN  H141  C14  C8    110.54  3.000
 8IN  H152  C15  H151  105.42  3.000
 8IN  H152  C15  C16   109.75  3.000
 8IN  H151  C15  C16   109.64  3.000
 8IN  H152  C15  N7    108.54  3.000
 8IN  H151  C15  N7    108.75  3.000
 8IN  C16   C15  N7    114.36  3.000
 8IN  C21   C16  C17   118.92  3.000
 8IN  C21   C16  C15   122.41  3.000
 8IN  C17   C16  C15   118.67  3.000
 8IN  H17   C17  C18   119.57  3.000
 8IN  H17   C17  C16   119.71  3.000
 8IN  C18   C17  C16   120.72  3.000
 8IN  H18   C18  C19   120.09  3.000
 8IN  H18   C18  C17   119.81  3.000
 8IN  C19   C18  C17   120.10  3.000
 8IN  H19   C19  C20   120.26  3.000
 8IN  H19   C19  C18   120.26  3.000
 8IN  C20   C19  C18   119.48  3.000
 8IN  H20   C20  C21   119.54  3.000
 8IN  H20   C20  C19   120.10  3.000
 8IN  C21   C20  C19   120.36  3.000
 8IN  H21   C21  C20   119.21  3.000
 8IN  H21   C21  C16   120.37  3.000
 8IN  C20   C21  C16   120.42  3.000
 8IN  C23   O22  C6    118.88  3.000
 8IN  H232  C23  H231  106.75  3.000
 8IN  H232  C23  C24   109.48  3.000
 8IN  H231  C23  C24   110.65  3.000
 8IN  H232  C23  O22   105.54  3.000
 8IN  H231  C23  O22   110.90  3.000
 8IN  C24   C23  O22   113.18  3.000
 8IN  H242  C24  H241  106.95  3.000
 8IN  H242  C24  C25   109.79  3.000
 8IN  H241  C24  C25   110.37  3.000
 8IN  H242  C24  C23   110.37  3.000
 8IN  H241  C24  C23   109.32  3.000
 8IN  C25   C24  C23   110.00  3.000
 8IN  H252  C25  H251  106.80  3.000
 8IN  H252  C25  P26   107.55  3.000
 8IN  H251  C25  P26   108.97  3.000
 8IN  H252  C25  C24   110.61  3.000
 8IN  H251  C25  C24   110.59  3.000
 8IN  P26   C25  C24   112.13  3.000
 8IN  O29   P26  O28   102.31  3.000
 8IN  O29   P26  O27   113.35  3.000
 8IN  O28   P26  O27   116.84  3.000
 8IN  O29   P26  C25   105.79  3.000
 8IN  O28   P26  C25   101.23  3.000
 8IN  O27   P26  C25   115.63  3.000
 8IN  H28   O28  P26   114.27  3.000
 8IN  H29   O29  P26   113.88  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
 8IN  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 8IN  CONST_02  N7    C3   C2   C1   180.00   0.0  0
 8IN  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 8IN  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 8IN  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 8IN  CONST_06  C9    C4   C3   C2   180.00   0.0  0
 8IN  CONST_07  C8    N7   C3   C2   180.00   0.0  0
 8IN  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 8IN  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 8IN  CONST_10  C8    C9   C4   C3     0.00   0.0  0
 8IN  CONST_11  C9    C8   N7   C3     0.00   0.0  0
 8IN  CONST_12  C8    N7   C3   C4     0.00   0.0  0
 8IN  CONST_13  N7    C8   C9   C4     0.00   0.0  0
 8IN  CONST_14  N7    C3   C4   C5   180.00   0.0  0
 8IN  CONST_15  C8    C9   C4   C5   180.00   0.0  0
 8IN  CONST_16  C9    C4   C5   C6   180.00   0.0  0
 8IN  CONST_17  C9    C4   C3   N7     0.00   0.0  0
 8IN  CONST_18  C19   C18  C17  C16    0.00   0.0  0
 8IN  CONST_19  C19   C20  C21  C16    0.00   0.0  0
 8IN  CONST_20  C20   C21  C16  C17    0.00   0.0  0
 8IN  CONST_21  C20   C19  C18  C17    0.00   0.0  0
 8IN  CONST_22  C21   C16  C17  C18    0.00   0.0  0
 8IN  CONST_23  C21   C20  C19  C18    0.00   0.0  0
 8IN  CONST_24  O22   C6   C1   C2   180.00   0.0  0
 8IN  CONST_25  C15   N7   C3   C2     0.00   0.0  0
 8IN  CONST_26  C10   C9   C4   C3   180.00   0.0  0
 8IN  CONST_27  C14   C8   N7   C3   180.00   0.0  0
 8IN  CONST_28  C15   N7   C3   C4   180.00   0.0  0
 8IN  CONST_29  O22   C6   C5   C4   180.00   0.0  0
 8IN  CONST_30  C14   C8   C9   C4   180.00   0.0  0
 8IN  CONST_31  C10   C9   C4   C5     0.00   0.0  0
 8IN  CONST_32  C10   C9   C8   N7   180.00   0.0  0
 8IN  CONST_33  C15   N7   C8   C9   180.00   0.0  0
 8IN  CONST_34  C18   C17  C16  C15  180.00   0.0  0
 8IN  CONST_35  C20   C21  C16  C15  180.00   0.0  0
 8IN  CONST_36  H5    C5   C6   C1   180.00   0.0  0
 8IN  CONST_37  H1    C1   C2   C3   180.00   0.0  0
 8IN  CONST_38  H2    C2   C3   C4   180.00   0.0  0
 8IN  CONST_39  H18   C18  C17  C16  180.00   0.0  0
 8IN  CONST_40  H20   C20  C21  C16  180.00   0.0  0
 8IN  CONST_41  H21   C21  C16  C17  180.00   0.0  0
 8IN  CONST_42  H19   C19  C18  C17  180.00   0.0  0
 8IN  CONST_43  H17   C17  C18  C19  180.00   0.0  0
 8IN  CONST_44  H131  N13  C11  C10    0.00   0.0  0
 8IN  CONST_45  H132  N13  C11  C10  180.00   0.0  0
 8IN  Var_01    C16   C15  N7   C3    87.28  30.0  2
 8IN  Var_02    C17   C16  C15  N7   178.88  30.0  2
 8IN  Var_03    C11   C10  C9   C4    62.41  30.0  2
 8IN  Var_04    H141  C14  C8   N7   178.43  30.0  2
 8IN  Var_05    C24   C23  O22  C6   -74.21  30.0  3
 8IN  Var_06    O12   C11  C10  C9    50.37  30.0  3
 8IN  Var_07    C25   C24  C23  O22  174.25  30.0  3
 8IN  Var_08    P26   C25  C24  C23  179.52  30.0  3
 8IN  Var_09    O27   P26  C25  C24  -56.65  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
 8IN  plan-1  C15   0.020
 8IN  plan-1  C16   0.020
 8IN  plan-1  C17   0.020
 8IN  plan-1  C18   0.020
 8IN  plan-1  C19   0.020
 8IN  plan-1  C20   0.020
 8IN  plan-1  C21   0.020
 8IN  plan-1  H17   0.020
 8IN  plan-1  H18   0.020
 8IN  plan-1  H19   0.020
 8IN  plan-1  H20   0.020
 8IN  plan-1  H21   0.020
 8IN  plan-2  C1    0.020
 8IN  plan-2  C2    0.020
 8IN  plan-2  C3    0.020
 8IN  plan-2  C4    0.020
 8IN  plan-2  C5    0.020
 8IN  plan-2  C6    0.020
 8IN  plan-2  N7    0.020
 8IN  plan-2  C8    0.020
 8IN  plan-2  C9    0.020
 8IN  plan-2  C10   0.020
 8IN  plan-2  C14   0.020
 8IN  plan-2  C15   0.020
 8IN  plan-2  O22   0.020
 8IN  plan-2  H1    0.020
 8IN  plan-2  H2    0.020
 8IN  plan-2  H5    0.020
 8IN  plan-3  C10   0.020
 8IN  plan-3  C11   0.020
 8IN  plan-3  O12   0.020
 8IN  plan-3  N13   0.020
 8IN  plan-3  H131  0.020
 8IN  plan-3  H132  0.020

