# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 09:34:18 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  57  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 OK
;

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  -0.582   3.0250   0.3845   0.7006
 U8D  C2    C  CR5   0   0.334   3.5441  -0.6710  -0.0148
 U8D  C3    C  CR5   0  -0.025   2.5216  -1.3951  -0.5704
 U8D  C4    C  CR56  0   0.104   1.3025  -0.7547  -0.1891
 U8D  C5    C  CR16  0  -0.494  -0.0414  -1.0307  -0.4415
 U8D  C6    C  CR6   0   0.389  -1.0113  -0.1880   0.0816
 U8D  C7    C  CR16  0  -0.404  -0.6468   0.9235   0.8608
 U8D  C8    C  CR16  0  -0.300   0.6858   1.2047   1.1214
 U8D  C9    C  CR56  0   0.324   1.6543   0.3597   0.5985
 U8D  C10   C  CH2   0  -0.532   5.0082  -0.9445  -0.0616
 U8D  C11   C  CH2   0  -0.721   2.6164  -2.6424  -1.3773
 U8D  O12   O  O2    0  -0.489  -2.2982  -0.5058  -0.2108
 U8D  C13   C  CH2   0  -0.403   3.7932   1.4222   1.3444
 U8D  C14   C  CR16  0  -0.267   5.5508   4.2915  -1.3381
 U8D  C15   C  CR16  0  -0.241   4.2504   3.8487  -1.5487
 U8D  C16   C  CR16  0  -0.286   3.6812   2.9169  -0.6924
 U8D  C17   C  CR6   0   0.114   4.4052   2.4147   0.3859
 U8D  C18   C  CR16  0  -0.310   5.7077   2.8586   0.5875
 U8D  C19   C  CR16  0  -0.242   6.2786   3.7938  -0.2665
 U8D  C20   C  CH3   0  -0.663   5.5240  -1.6637   1.1859
 U8D  C21   C  C     0   0.525   2.2757  -3.8837  -0.5643
 U8D  O22   O  O     0  -0.480   2.7422  -4.0748   0.5484
 U8D  N23   N  NH2   0  -0.800   1.4471  -4.7474  -1.1693
 U8D  C24   C  CH2   0  -0.156  -3.3418   0.2324   0.3910
 U8D  C25   C  CH2   0  -0.472  -4.6593  -0.3409  -0.0911
 U8D  P26   P  P     0   1.379  -7.4172  -0.2609   0.0408
 U8D  O27   O  O     0  -0.718  -7.6134  -1.7217   0.2028
 U8D  O28   O  OH1   0  -0.752  -7.5799   0.1183  -1.5161
 U8D  O29   O  OH1   0  -0.745  -8.4280   0.6838   0.8593
 U8D  C30   C  CH2   0  -0.769  -5.8249   0.3838   0.5786
 U8D  H5    H  HCR6  0   0.239  -0.3361  -1.8906  -1.0322
 U8D  H7    H  HCR6  0   0.271  -1.3974   1.5841   1.2720
 U8D  H8    H  HCR6  0   0.266   0.9415   2.0704   1.7191
 U8D  H10   H  HCH2  0   0.256   5.2126  -1.5641  -0.9358
 U8D  H10A  H  HCH2  0   0.253   5.5650  -0.0174  -0.2175
 U8D  H11   H  HCH2  0   0.265   1.9760  -2.5771  -2.2609
 U8D  H11A  H  HCH2  0   0.287   3.6339  -2.7844  -1.7532
 U8D  H13   H  HCH2  0   0.290   3.1319   1.9396   2.0416
 U8D  H13A  H  HCH2  0   0.278   4.5720   0.9705   1.9609
 U8D  H14   H  HCR6  0   0.257   5.9946   5.0166  -2.0080
 U8D  H15   H  HCR6  0   0.257   3.6757   4.2327  -2.3818
 U8D  H16   H  HCR6  0   0.252   2.6667   2.5816  -0.8719
 U8D  H18   H  HCR6  0   0.254   6.2864   2.4637   1.4148
 U8D  H19   H  HCR6  0   0.257   7.2947   4.1261  -0.0975
 U8D  H20   H  HCH3  0   0.238   4.9713  -2.5885   1.3470
 U8D  H20A  H  HCH3  0   0.236   6.5802  -1.9095   1.0740
 U8D  H20B  H  HCH3  0   0.224   5.4243  -1.0518   2.0834
 U8D  HN23  H  HNH2  0   0.407   1.0665  -4.5678  -2.0819
 U8D  HN2A  H  HNH2  0   0.399   1.1923  -5.6138  -0.7235
 U8D  H24   H  HCH2  0   0.219  -3.2787   0.1684   1.4845
 U8D  H24A  H  HCH2  0   0.219  -3.2787   1.2931   0.1209
 U8D  H25   H  HCH2  0   0.249  -4.7230  -0.2405  -1.1769
 U8D  H25A  H  HCH2  0   0.252  -4.7026  -1.4069   0.1410
 U8D  HO28  H  HOH1  0   0.489  -7.5117   1.0597  -1.7223
 U8D  HO29  H  HOH1  0   0.494  -9.3574   0.4256   0.7874
 U8D  H30   H  HCH2  0   0.290  -5.7711   0.2662   1.6641
 U8D  H30A  H  HCH2  0   0.288  -5.7845   1.4572   0.3755

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  1.377  0.020  1.377
 U8D  N1   C9    aromatic  1.375  0.020  1.375
 U8D  N1   C13   single    1.443  0.020  1.443
 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  1.429  0.020  1.429
 U8D  C5   C4    aromatic  1.395  0.020  1.395
 U8D  C4   C9    aromatic  1.409  0.020  1.409
 U8D  C5   C6    aromatic  1.387  0.020  1.387
 U8D  C5   H5    single    0.930  0.020  1.080
 U8D  O12  C6    single    1.357  0.020  1.357
 U8D  C6   C7    aromatic  1.406  0.020  1.406
 U8D  C7   C8    aromatic  1.387  0.020  1.387
 U8D  C7   H7    single    0.930  0.020  1.080
 U8D  C9   C8    aromatic  1.388  0.020  1.388
 U8D  C8   H8    single    0.930  0.020  1.080
 U8D  C20  C10   single    1.530  0.020  1.530
 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    1.413  0.020  1.413
 U8D  C13  C17   single    1.509  0.020  1.509
 U8D  C13  H13   single    0.970  0.020  1.090
 U8D  C13  H13A  single    0.970  0.020  1.090
 U8D  C15  C14   aromatic  1.390  0.020  1.390
 U8D  C14  C19   aromatic  1.388  0.020  1.388
 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  1.393  0.020  1.393
 U8D  C16  H16   single    0.930  0.020  1.080
 U8D  C17  C18   aromatic  1.391  0.020  1.391
 U8D  C18  C19   aromatic  1.389  0.020  1.389
 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    1.516  0.020  1.516
 U8D  C24  H24   single    0.970  0.020  1.090
 U8D  C24  H24A  single    0.970  0.020  1.090
 U8D  C30  C25   single    1.527  0.020  1.527
 U8D  C25  H25   single    0.970  0.020  1.090
 U8D  C25  H25A  single    0.970  0.020  1.090
 U8D  O27  P26   double    1.483  0.020  1.483
 U8D  C30  P26   single    1.800  0.020  1.800
 U8D  P26  O29   single    1.608  0.020  1.608
 U8D  P26  O28   single    1.611  0.020  1.611
 U8D  O28  HO28  single    0.850  0.020  0.980
 U8D  O29  HO29  single    0.850  0.020  0.980
 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    125.25  3.000
 U8D  C13   N1   C2    125.63  3.000
 U8D  C9    N1   C2    108.87  3.000
 U8D  C10   C2   C3    128.56  3.000
 U8D  C10   C2   N1    121.83  3.000
 U8D  C3    C2   N1    109.54  3.000
 U8D  C11   C3   C4    125.06  3.000
 U8D  C4    C3   C2    106.95  3.000
 U8D  C11   C3   C2    127.95  3.000
 U8D  C9    C4   C5    119.87  3.000
 U8D  C9    C4   C3    106.89  3.000
 U8D  C5    C4   C3    133.24  3.000
 U8D  H5    C5   C6    119.82  3.000
 U8D  H5    C5   C4    121.16  3.000
 U8D  C6    C5   C4    119.03  3.000
 U8D  O12   C6   C7    123.40  3.000
 U8D  C7    C6   C5    120.54  3.000
 U8D  O12   C6   C5    116.07  3.000
 U8D  H7    C7   C8    118.15  3.000
 U8D  H7    C7   C6    120.93  3.000
 U8D  C8    C7   C6    120.92  3.000
 U8D  H8    C8   C9    122.02  3.000
 U8D  H8    C8   C7    119.53  3.000
 U8D  C9    C8   C7    118.45  3.000
 U8D  C8    C9   C4    121.20  3.000
 U8D  C8    C9   N1    131.06  3.000
 U8D  C4    C9   N1    107.74  3.000
 U8D  H10A  C10  H10   105.79  3.000
 U8D  H10A  C10  C20   110.09  3.000
 U8D  H10   C10  C20   108.86  3.000
 U8D  H10A  C10  C2    110.45  3.000
 U8D  H10   C10  C2    108.27  3.000
 U8D  C20   C10  C2    113.08  3.000
 U8D  H11A  C11  H11   105.96  3.000
 U8D  H11A  C11  C21   106.61  3.000
 U8D  H11   C11  C21   110.44  3.000
 U8D  H11A  C11  C3    110.74  3.000
 U8D  H11   C11  C3    110.53  3.000
 U8D  C21   C11  C3    112.30  3.000
 U8D  C24   O12  C6    119.09  3.000
 U8D  H13A  C13  H13   105.54  3.000
 U8D  H13A  C13  C17   109.97  3.000
 U8D  H13   C13  C17   109.86  3.000
 U8D  H13A  C13  N1    109.54  3.000
 U8D  H13   C13  N1    107.66  3.000
 U8D  C17   C13  N1    113.92  3.000
 U8D  H14   C14  C19   120.20  3.000
 U8D  H14   C14  C15   120.22  3.000
 U8D  C19   C14  C15   119.58  3.000
 U8D  H15   C15  C16   119.70  3.000
 U8D  H15   C15  C14   120.03  3.000
 U8D  C16   C15  C14   120.28  3.000
 U8D  H16   C16  C17   120.23  3.000
 U8D  H16   C16  C15   119.32  3.000
 U8D  C17   C16  C15   120.45  3.000
 U8D  C18   C17  C16   118.95  3.000
 U8D  C18   C17  C13   119.84  3.000
 U8D  C16   C17  C13   121.20  3.000
 U8D  H18   C18  C19   119.67  3.000
 U8D  H18   C18  C17   119.62  3.000
 U8D  C19   C18  C17   120.71  3.000
 U8D  H19   C19  C18   119.77  3.000
 U8D  H19   C19  C14   120.19  3.000
 U8D  C18   C19  C14   120.04  3.000
 U8D  H20B  C20  H20A  107.43  3.000
 U8D  H20B  C20  H20   107.95  3.000
 U8D  H20A  C20  H20   108.39  3.000
 U8D  H20B  C20  C10   112.11  3.000
 U8D  H20A  C20  C10   110.42  3.000
 U8D  H20   C20  C10   110.40  3.000
 U8D  N23   C21  O22   123.10  3.000
 U8D  O22   C21  C11   121.90  3.000
 U8D  N23   C21  C11   114.99  3.000
 U8D  HN2A  N23  HN23  117.38  3.000
 U8D  HN2A  N23  C21   120.71  3.000
 U8D  HN23  N23  C21   121.91  3.000
 U8D  H24A  C24  H24   107.39  3.000
 U8D  H24A  C24  C25   109.73  3.000
 U8D  H24   C24  C25   110.18  3.000
 U8D  H24A  C24  O12   110.97  3.000
 U8D  H24   C24  O12   110.58  3.000
 U8D  C25   C24  O12   108.00  3.000
 U8D  H25A  C25  H25   107.38  3.000
 U8D  H25A  C25  C30   109.87  3.000
 U8D  H25   C25  C30   110.35  3.000
 U8D  H25A  C25  C24   109.65  3.000
 U8D  H25   C25  C24   109.40  3.000
 U8D  C30   C25  C24   110.15  3.000
 U8D  C30   P26  O29   101.16  3.000
 U8D  O29   P26  O28   106.88  3.000
 U8D  C30   P26  O28   107.09  3.000
 U8D  O28   P26  O27   108.91  3.000
 U8D  O29   P26  O27   116.11  3.000
 U8D  C30   P26  O27   115.93  3.000
 U8D  HO28  O28  P26   115.37  3.000
 U8D  HO29  O29  P26   114.17  3.000
 U8D  H30A  C30  H30   106.76  3.000
 U8D  H30A  C30  P26   109.20  3.000
 U8D  H30   C30  P26   107.56  3.000
 U8D  H30A  C30  C25   110.87  3.000
 U8D  H30   C30  C25   110.29  3.000
 U8D  P26   C30  C25   111.97  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     42.87  30.0  2
 U8D  Var_02    C17   C13  N1   C2     73.18  30.0  2
 U8D  Var_03    C20   C10  C2   N1     79.46  30.0  2
 U8D  Var_04    C21   C11  C3   C2    101.70  30.0  2
 U8D  Var_05    N23   C21  C11  C3    134.18  30.0  1
 U8D  Var_06    C25   C24  O12  C6   -179.20  30.0  1
 U8D  Var_07    H20   C20  C10  C2     55.85  30.0  3
 U8D  Var_08    C30   C25  C24  O12   177.54  30.0  1
 U8D  Var_09    P26   C30  C25  C24  -179.95  30.0  1
 U8D  Var_10    O27   P26  C30  C25    54.68  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

