# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:21:07 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2c(cc1OCCCN3CCCC3)N=C(N)C24CCC4
#
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
 2OD  2OD  5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine  ligand  51  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2OD
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
 2OD  N1   N  NR5   0  -0.428   5.6777   0.3310  -0.2584
 2OD  N3   N  NH2   0  -0.838  -5.1369   3.0357  -0.0095
 2OD  C4   C  CR56  0   0.161  -3.1123   0.0799  -0.0148
 2OD  C5   C  CR56  0   0.234  -2.2424   1.1599  -0.0741
 2OD  C6   C  CR16  0  -0.488  -0.8673   0.9604  -0.1151
 2OD  C7   C  CR6   0   0.309  -0.3784  -0.3420  -0.0936
 2OD  C8   C  CH2   0  -0.167   1.8853   0.3858  -0.1555
 2OD  C10  C  CH2   0  -0.260   4.3360   0.8551  -0.1506
 2OD  C13  C  CH2   0  -0.462   7.9979   0.6254  -0.1953
 2OD  C15  C  CR5   0   0.474  -4.1703   2.1148  -0.0337
 2OD  C17  C  C     0  -0.415  -5.4315   0.1094   1.1404
 2OD  C16  C  C     0  -0.256  -4.4981   0.6382   0.0173
 2OD  C19  C  C     0  -0.416  -5.5048   0.0537  -1.0109
 2OD  C18  C  C     0  -0.453  -6.1314  -0.7928   0.1098
 2OD  C3   C  CR16  0  -0.487  -2.6368  -1.2198   0.0064
 2OD  N2   N  N     0  -0.522  -2.9043   2.3922  -0.0861
 2OD  C2   C  CR6   0   0.288  -1.2632  -1.4388  -0.0330
 2OD  O1   O  O2    0  -0.473  -0.6772  -2.6598  -0.0173
 2OD  C1   C  CH3   0  -0.434  -1.5121  -3.7900   0.0937
 2OD  O2   O  O2    0  -0.474   0.9327  -0.6612  -0.1262
 2OD  C9   C  CH2   0  -0.482   3.2691  -0.2305  -0.1608
 2OD  C14  C  CH2   0  -0.273   6.6818   1.3749  -0.3695
 2OD  C12  C  CH2   0  -0.468   7.6323  -0.5515   0.7321
 2OD  C11  C  CH2   0  -0.281   6.1070  -0.4718   0.8761
 2OD  H2   H  HNH2  0   0.399  -4.9146   4.0126  -0.0960
 2OD  H3   H  HNH2  0   0.406  -6.1074   2.7798  -0.0481
 2OD  H4   H  HCR6  0   0.271  -0.2038   1.8132  -0.1594
 2OD  H5   H  HCH2  0   0.218   1.7457   1.0088  -1.0476
 2OD  H6   H  HCH2  0   0.218   1.7644   1.0387   0.7178
 2OD  H7   H  HCH2  0   0.187   4.2224   1.4714   0.7603
 2OD  H8   H  HCH2  0   0.229   4.1695   1.5280  -0.9976
 2OD  H9   H  HCH2  0   0.232   8.3555   0.2586  -1.1582
 2OD  H10  H  HCH2  0   0.233   8.7776   1.2645   0.2182
 2OD  H11  H  H     0   0.249  -4.9326  -0.3678   1.9831
 2OD  H12  H  H     0   0.243  -6.0896   0.8899   1.5257
 2OD  H13  H  H     0   0.242  -6.1898   0.8143  -1.3895
 2OD  H14  H  H     0   0.250  -5.0650  -0.4656  -1.8617
 2OD  H15  H  H     0   0.240  -5.7498  -1.8139   0.1230
 2OD  H16  H  H     0   0.242  -7.2190  -0.8350   0.1479
 2OD  H17  H  HCR6  0   0.270  -3.3294  -2.0510   0.0530
 2OD  H18  H  HCH3  0   0.257  -0.8589  -4.6596   0.1099
 2OD  H19  H  HCH3  0   0.222  -2.1008  -3.7785   1.0158
 2OD  H20  H  HCH3  0   0.222  -2.1957  -3.8844  -0.7551
 2OD  H21  H  HCH2  0   0.239   3.3761  -0.8780   0.7132
 2OD  H22  H  HCH2  0   0.234   3.3951  -0.8564  -1.0482
 2OD  H23  H  HCH2  0   0.231   6.6033   1.8943  -1.3274
 2OD  H24  H  HCH2  0   0.188   6.5655   2.1327   0.4250
 2OD  H25  H  HCH2  0   0.235   7.9371  -1.5022   0.2950
 2OD  H26  H  HCH2  0   0.233   8.1181  -0.4786   1.7046
 2OD  H27  H  HCH2  0   0.190   5.8381   0.0125   1.8303
 2OD  H28  H  HCH2  0   0.232   5.6342  -1.4555   0.8718

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
 2OD  C19  C18  single    1.538  0.020  1.538
 2OD  C19  C16  single    1.553  0.020  1.553
 2OD  N3   C15  single    1.335  0.020  1.335
 2OD  C12  C13  single    1.542  0.020  1.542
 2OD  C12  C11  single    1.534  0.020  1.534
 2OD  C13  C14  single    1.525  0.020  1.525
 2OD  C15  N2   double    1.297  0.020  1.297
 2OD  C15  C16  single    1.513  0.020  1.513
 2OD  C18  C17  single    1.538  0.020  1.538
 2OD  N2   C5   single    1.399  0.020  1.399
 2OD  C16  C4   single    1.494  0.020  1.494
 2OD  C16  C17  single    1.553  0.020  1.553
 2OD  C11  N1   single    1.455  0.020  1.455
 2OD  C4   C5   aromatic  1.388  0.020  1.388
 2OD  C4   C3   aromatic  1.384  0.020  1.384
 2OD  C5   C6   aromatic  1.390  0.020  1.390
 2OD  C14  N1   single    1.453  0.020  1.453
 2OD  N1   C10  single    1.444  0.020  1.444
 2OD  C3   C2   aromatic  1.391  0.020  1.391
 2OD  C6   C7   aromatic  1.391  0.020  1.391
 2OD  C2   C7   aromatic  1.411  0.020  1.411
 2OD  C2   O1   single    1.354  0.020  1.354
 2OD  C7   O2   single    1.350  0.020  1.350
 2OD  C8   O2   single    1.416  0.020  1.416
 2OD  C8   C9   single    1.515  0.020  1.515
 2OD  O1   C1   single    1.409  0.020  1.409
 2OD  C10  C9   single    1.522  0.020  1.522
 2OD  N3   H2   single    0.860  0.020  1.020
 2OD  N3   H3   single    0.860  0.020  1.020
 2OD  C6   H4   single    0.930  0.020  1.080
 2OD  C8   H5   single    0.970  0.020  1.090
 2OD  C8   H6   single    0.970  0.020  1.090
 2OD  C10  H7   single    0.970  0.020  1.090
 2OD  C10  H8   single    0.970  0.020  1.090
 2OD  C13  H9   single    0.970  0.020  1.090
 2OD  C13  H10  single    0.970  0.020  1.090
 2OD  C17  H11  single    0.970  0.020  1.090
 2OD  C17  H12  single    0.970  0.020  1.090
 2OD  C19  H13  single    0.970  0.020  1.090
 2OD  C19  H14  single    0.970  0.020  1.090
 2OD  C18  H15  single    0.970  0.020  1.090
 2OD  C18  H16  single    0.970  0.020  1.090
 2OD  C3   H17  single    0.930  0.020  1.080
 2OD  C1   H18  single    0.970  0.020  1.090
 2OD  C1   H19  single    0.970  0.020  1.090
 2OD  C1   H20  single    0.970  0.020  1.090
 2OD  C9   H21  single    0.970  0.020  1.090
 2OD  C9   H22  single    0.970  0.020  1.090
 2OD  C14  H23  single    0.970  0.020  1.090
 2OD  C14  H24  single    0.970  0.020  1.090
 2OD  C12  H25  single    0.970  0.020  1.090
 2OD  C12  H26  single    0.970  0.020  1.090
 2OD  C11  H27  single    0.970  0.020  1.090
 2OD  C11  H28  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
 2OD  C11  N1   C14  104.61  3.000
 2OD  C14  N1   C10  112.77  3.000
 2OD  C11  N1   C10  114.59  3.000
 2OD  H3   N3   H2   117.24  3.000
 2OD  H3   N3   C15  121.54  3.000
 2OD  H2   N3   C15  120.56  3.000
 2OD  C3   C4   C16  132.00  3.000
 2OD  C3   C4   C5   121.06  3.000
 2OD  C16  C4   C5   106.94  3.000
 2OD  N2   C5   C6   126.46  3.000
 2OD  C6   C5   C4   120.63  3.000
 2OD  N2   C5   C4   112.91  3.000
 2OD  H4   C6   C7   121.55  3.000
 2OD  H4   C6   C5   119.67  3.000
 2OD  C7   C6   C5   118.79  3.000
 2OD  O2   C7   C2   115.25  3.000
 2OD  O2   C7   C6   124.22  3.000
 2OD  C2   C7   C6   120.54  3.000
 2OD  H6   C8   H5   107.18  3.000
 2OD  H6   C8   C9   110.21  3.000
 2OD  H5   C8   C9   110.15  3.000
 2OD  H6   C8   O2   110.45  3.000
 2OD  H5   C8   O2   110.56  3.000
 2OD  C9   C8   O2   108.29  3.000
 2OD  H8   C10  H7   106.21  3.000
 2OD  H8   C10  C9   109.07  3.000
 2OD  H7   C10  C9   109.33  3.000
 2OD  H8   C10  N1   107.86  3.000
 2OD  H7   C10  N1   111.05  3.000
 2OD  C9   C10  N1   113.07  3.000
 2OD  H10  C13  H9   107.32  3.000
 2OD  H10  C13  C12  112.89  3.000
 2OD  H9   C13  C12  110.61  3.000
 2OD  H10  C13  C14  111.88  3.000
 2OD  H9   C13  C14  110.34  3.000
 2OD  C12  C13  C14  103.84  3.000
 2OD  N2   C15  C16  114.92  3.000
 2OD  C16  C15  N3   121.03  3.000
 2OD  N2   C15  N3   124.04  3.000
 2OD  H12  C17  H11  108.44  3.000
 2OD  H12  C17  C18  112.44  3.000
 2OD  H11  C17  C18  118.02  3.000
 2OD  H12  C17  C16  111.98  3.000
 2OD  H11  C17  C16  115.67  3.000
 2OD  C18  C17  C16   89.35  3.000
 2OD  C19  C16  C17   87.77  3.000
 2OD  C17  C16  C15  119.13  3.000
 2OD  C19  C16  C15  119.03  3.000
 2OD  C17  C16  C4   116.47  3.000
 2OD  C15  C16  C4    99.38  3.000
 2OD  C19  C16  C4   116.50  3.000
 2OD  H14  C19  H13  108.33  3.000
 2OD  H14  C19  C18  118.11  3.000
 2OD  H13  C19  C18  112.37  3.000
 2OD  H14  C19  C16  115.77  3.000
 2OD  H13  C19  C16  111.98  3.000
 2OD  C18  C19  C16   89.36  3.000
 2OD  H16  C18  H15  108.23  3.000
 2OD  H16  C18  C19  116.99  3.000
 2OD  H15  C18  C19  112.44  3.000
 2OD  H16  C18  C17  116.98  3.000
 2OD  H15  C18  C17  112.45  3.000
 2OD  C19  C18  C17   88.85  3.000
 2OD  H17  C3   C2   120.78  3.000
 2OD  H17  C3   C4   120.11  3.000
 2OD  C2   C3   C4   119.11  3.000
 2OD  C15  N2   C5   105.85  3.000
 2OD  O1   C2   C3   124.66  3.000
 2OD  O1   C2   C7   115.47  3.000
 2OD  C3   C2   C7   119.87  3.000
 2OD  C1   O1   C2   117.87  3.000
 2OD  H20  C1   H19  108.57  3.000
 2OD  H20  C1   H18  108.53  3.000
 2OD  H19  C1   H18  108.60  3.000
 2OD  H20  C1   O1   112.23  3.000
 2OD  H19  C1   O1   112.13  3.000
 2OD  H18  C1   O1   106.65  3.000
 2OD  C8   O2   C7   118.63  3.000
 2OD  H22  C9   H21  107.37  3.000
 2OD  H22  C9   C10  109.45  3.000
 2OD  H21  C9   C10  110.40  3.000
 2OD  H22  C9   C8   109.94  3.000
 2OD  H21  C9   C8   109.13  3.000
 2OD  C10  C9   C8   110.50  3.000
 2OD  H24  C14  H23  107.28  3.000
 2OD  H24  C14  C13  110.25  3.000
 2OD  H23  C14  C13  113.32  3.000
 2OD  H24  C14  N1   111.43  3.000
 2OD  H23  C14  N1   111.05  3.000
 2OD  C13  C14  N1   103.57  3.000
 2OD  H26  C12  H25  106.96  3.000
 2OD  H26  C12  C11  110.86  3.000
 2OD  H25  C12  C11  111.17  3.000
 2OD  H26  C12  C13  112.33  3.000
 2OD  H25  C12  C13  110.99  3.000
 2OD  C11  C12  C13  104.62  3.000
 2OD  H28  C11  H27  107.07  3.000
 2OD  H28  C11  C12  112.55  3.000
 2OD  H27  C11  C12  110.26  3.000
 2OD  H28  C11  N1   111.50  3.000
 2OD  H27  C11  N1   111.13  3.000
 2OD  C12  C11  N1   104.41  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
 2OD  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 2OD  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 2OD  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 2OD  CONST_04  C2   C7   C6   C5      0.00   0.0  0
 2OD  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 2OD  CONST_06  C3   C2   C7   C6      0.00   0.0  0
 2OD  CONST_07  C16  C15  N2   C5      0.00   0.0  0
 2OD  CONST_08  O1   C2   C3   C4    180.00   0.0  0
 2OD  CONST_09  O2   C7   C6   C5    180.00   0.0  0
 2OD  CONST_10  O1   C2   C7   C6    180.00   0.0  0
 2OD  CONST_11  O2   C7   C2   C3    180.00   0.0  0
 2OD  CONST_12  C5   N2   C15  N3    180.00   0.0  0
 2OD  CONST_13  H4   C6   C5   C4    180.00   0.0  0
 2OD  CONST_14  H17  C3   C4   C5    180.00   0.0  0
 2OD  CONST_15  H2   N3   C15  C16   180.00   0.0  0
 2OD  CONST_16  H3   N3   C15  C16     0.00   0.0  0
 2OD  Var_01    C13  C12  C11  N1     19.58  30.0  1
 2OD  Var_02    C12  C13  C14  N1    -30.37  30.0  1
 2OD  Var_03    C18  C19  C16  C4    102.45  30.0  3
 2OD  Var_04    C18  C17  C16  C4   -102.48  30.0  3
 2OD  Var_05    C11  N1   C14  C13    44.20  30.0  1
 2OD  Var_06    C16  C19  C18  C17    16.32  30.0  1
 2OD  Var_07    C11  C12  C13  C14     6.48  30.0  1
 2OD  Var_08    C12  C11  N1   C14   -39.82  30.0  1
 2OD  Var_09    C2   C7   O2   C8   -178.53  30.0  2
 2OD  Var_10    C8   C9   C10  N1   -175.54  30.0  3
 2OD  Var_11    C9   C8   O2   C7    178.89  30.0  2
 2OD  Var_12    H18  C1   O1   C2   -178.83  30.0  3
 2OD  Var_13    O2   C8   C9   C10  -178.33  30.0  2

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
 2OD  plan-1  N3   0.020
 2OD  plan-1  C4   0.020
 2OD  plan-1  C5   0.020
 2OD  plan-1  C6   0.020
 2OD  plan-1  C7   0.020
 2OD  plan-1  C15  0.020
 2OD  plan-1  C17  0.020
 2OD  plan-1  C16  0.020
 2OD  plan-1  C19  0.020
 2OD  plan-1  C3   0.020
 2OD  plan-1  N2   0.020
 2OD  plan-1  C2   0.020
 2OD  plan-1  O1   0.020
 2OD  plan-1  O2   0.020
 2OD  plan-1  H2   0.020
 2OD  plan-1  H3   0.020
 2OD  plan-1  H4   0.020
 2OD  plan-1  H17  0.020

