# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:16:31 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (3S,5S,7S)-N-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methyl}tricyclo[3.3.1.1~3,7~]decan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C([NH2+]C12CC3CC(CC(C3)C1)C2)c4cc(on4)c5sccc5
#
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
 A2Y  A2Y  (3S,5S,7S)-N-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methyl}tricyclo[3.3.1.1~3,7~]decan-1-aminium  ligand  45  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A2Y
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
 A2Y  O     O  O     0  -0.337   2.8409  -1.8099   0.2437
 A2Y  S     S  S2    0   0.255   4.8439   1.5812  -0.2298
 A2Y  C1    C  CR15  0  -0.451   6.4606   1.2138  -0.6410
 A2Y  N1    N  N     0  -0.140   1.5381  -2.0216   0.5499
 A2Y  C2    C  CR15  0  -0.169   6.6751  -0.1301  -0.7174
 A2Y  N2    N  NT2   1  -0.696  -1.2082  -0.3884  -0.2663
 A2Y  C3    C  CR15  0  -0.194   5.5097  -0.8835  -0.4391
 A2Y  C4    C  CR15  0  -0.523   1.9391   0.1856   0.4228
 A2Y  C9    C  CR5   0   0.253   0.9992  -0.8415   0.6596
 A2Y  C10   C  CT    0   0.066  -2.6854  -0.0834  -0.1329
 A2Y  C11   C  CR5   0   0.513   3.0871  -0.4973   0.1639
 A2Y  C12   C  CR5   0  -0.311   4.4290  -0.0900  -0.1564
 A2Y  C61   C  CH2   0  -0.430  -3.1971   0.1583  -1.5535
 A2Y  C62   C  CH2   0  -0.436  -2.8884   1.1694   0.7149
 A2Y  C63   C  CH2   0  -0.435  -3.4112  -1.2706   0.4934
 A2Y  C71   C  CR16  0  -0.259  -4.6923   0.4782  -1.4984
 A2Y  C72   C  CR16  0  -0.256  -4.3898   1.4832   0.7642
 A2Y  C73   C  CR16  0  -0.256  -4.9107  -0.9516   0.5376
 A2Y  C81   C  C     0  -0.423  -4.9108   1.7322  -0.6509
 A2Y  C82   C  C     0  -0.425  -5.1326   0.3003   1.3889
 A2Y  C83   C  C     0  -0.424  -5.4340  -0.7067  -0.8782
 A2Y  H44   H  HCR5  0   0.303   1.7809   1.2511   0.4505
 A2Y  H1    H  HCR5  0   0.310   7.1688   2.0110  -0.8055
 A2Y  H2    H  HCR5  0   0.279   7.6306  -0.5678  -0.9656
 A2Y  H3    H  HCR5  0   0.279   5.4759  -1.9633  -0.4516
 A2Y  H15   H  HCH2  0   0.331  -0.6103   0.0930   1.6935
 A2Y  H25   H  HCH2  0   0.334  -0.8393  -1.6371   1.3815
 A2Y  H161  H  HCH2  0   0.258  -2.6469   0.9852  -2.0146
 A2Y  H261  H  HCH2  0   0.258  -3.0262  -0.7295  -2.1711
 A2Y  H362  H  HCH2  0   0.260  -2.5206   1.0195   1.7337
 A2Y  H462  H  HCH2  0   0.258  -2.3352   2.0139   0.2903
 A2Y  H563  H  HCH2  0   0.259  -3.2275  -2.1798  -0.0879
 A2Y  H663  H  HCH2  0   0.260  -3.0535  -1.4526   1.5111
 A2Y  H171  H  HCR6  0   0.248  -5.0482   0.6503  -2.5169
 A2Y  H272  H  HCR6  0   0.248  -4.5325   2.3756   1.3777
 A2Y  H373  H  HCR6  0   0.248  -5.4312  -1.8017   0.9845
 A2Y  H181  H  H     0   0.235  -4.3959   2.5871  -1.0989
 A2Y  H281  H  H     0   0.238  -5.9745   1.9836  -0.6192
 A2Y  H382  H  H     0   0.235  -4.7813   0.1313   2.4115
 A2Y  H482  H  H     0   0.239  -6.2014   0.5226   1.4542
 A2Y  H583  H  H     0   0.238  -6.5083  -0.5027  -0.8485
 A2Y  H683  H  H     0   0.235  -5.2997  -1.6004  -1.4950
 A2Y  H1N2  H  HNT2  0   0.466  -0.7675   0.4049  -0.7393
 A2Y  H2N2  H  HNT2  0   0.468  -1.1014  -1.1707  -0.9176
 A2Y  C5    C  CH2   0  -0.409  -0.4491  -0.7073   0.9764

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
 A2Y  O    N1    aromatic  1.355  0.020  1.355
 A2Y  O    C11   aromatic  1.338  0.020  1.338
 A2Y  S    C1    aromatic  1.708  0.020  1.708
 A2Y  S    C12   aromatic  1.724  0.020  1.724
 A2Y  C1   C2    aromatic  1.363  0.020  1.363
 A2Y  C1   H1    single    0.930  0.020  1.080
 A2Y  N1   C9    aromatic  1.302  0.020  1.302
 A2Y  C2   C3    aromatic  1.415  0.020  1.415
 A2Y  C2   H2    single    0.930  0.020  1.080
 A2Y  N2   C5    single    1.491  0.020  1.491
 A2Y  N2   C10   single    1.514  0.020  1.514
 A2Y  N2   H1N2  single    0.890  0.020  1.040
 A2Y  N2   H2N2  single    0.890  0.020  1.040
 A2Y  C3   C12   aromatic  1.370  0.020  1.370
 A2Y  C3   H3    single    0.930  0.020  1.080
 A2Y  C4   C9    aromatic  1.412  0.020  1.412
 A2Y  C4   C11   aromatic  1.361  0.020  1.361
 A2Y  C4   H44   single    0.930  0.020  1.080
 A2Y  C5   C9    single    1.489  0.020  1.489
 A2Y  C5   H15   single    0.970  0.020  1.090
 A2Y  C5   H25   single    0.970  0.020  1.090
 A2Y  C10  C61   single    1.529  0.020  1.529
 A2Y  C10  C62   single    1.526  0.020  1.526
 A2Y  C10  C63   single    1.526  0.020  1.526
 A2Y  C11  C12   single    1.438  0.020  1.438
 A2Y  C61  C71   single    1.530  0.020  1.530
 A2Y  C61  H161  single    0.970  0.020  1.090
 A2Y  C61  H261  single    0.970  0.020  1.090
 A2Y  C62  C72   single    1.535  0.020  1.535
 A2Y  C62  H362  single    0.970  0.020  1.090
 A2Y  C62  H462  single    0.970  0.020  1.090
 A2Y  C63  C73   single    1.534  0.020  1.534
 A2Y  C63  H563  single    0.970  0.020  1.090
 A2Y  C63  H663  single    0.970  0.020  1.090
 A2Y  C71  C81   single    1.529  0.020  1.529
 A2Y  C71  C83   single    1.529  0.020  1.529
 A2Y  C71  H171  single    0.970  0.020  1.090
 A2Y  C72  C81   single    1.528  0.020  1.528
 A2Y  C72  C82   single    1.530  0.020  1.530
 A2Y  C72  H272  single    0.970  0.020  1.090
 A2Y  C73  C82   single    1.530  0.020  1.530
 A2Y  C73  C83   single    1.529  0.020  1.529
 A2Y  C73  H373  single    0.970  0.020  1.090
 A2Y  C81  H181  single    0.970  0.020  1.090
 A2Y  C81  H281  single    0.970  0.020  1.090
 A2Y  C82  H382  single    0.970  0.020  1.090
 A2Y  C82  H482  single    0.970  0.020  1.090
 A2Y  C83  H583  single    0.970  0.020  1.090
 A2Y  C83  H683  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
 A2Y  C11   O    N1    110.10  3.000
 A2Y  C12   S    C1     91.69  3.000
 A2Y  H1    C1   C2    128.07  3.000
 A2Y  H1    C1   S     119.93  3.000
 A2Y  C2    C1   S     111.99  3.000
 A2Y  C9    N1   O     105.98  3.000
 A2Y  H2    C2   C3    123.92  3.000
 A2Y  H2    C2   C1    123.49  3.000
 A2Y  C3    C2   C1    112.60  3.000
 A2Y  H2N2  N2   H1N2  104.69  3.000
 A2Y  H2N2  N2   C10   108.17  3.000
 A2Y  H1N2  N2   C10   107.74  3.000
 A2Y  H2N2  N2   C5    108.29  3.000
 A2Y  H1N2  N2   C5    109.38  3.000
 A2Y  C10   N2   C5    117.80  3.000
 A2Y  H3    C3   C12   123.81  3.000
 A2Y  H3    C3   C2    123.75  3.000
 A2Y  C12   C3   C2    112.44  3.000
 A2Y  H44   C4   C11   128.69  3.000
 A2Y  H44   C4   C9    128.10  3.000
 A2Y  C11   C4   C9    103.20  3.000
 A2Y  C5    C9   C4    128.15  3.000
 A2Y  C5    C9   N1    120.15  3.000
 A2Y  C4    C9   N1    111.69  3.000
 A2Y  C63   C10  C62   110.33  3.000
 A2Y  C63   C10  C61   110.19  3.000
 A2Y  C62   C10  C61   109.99  3.000
 A2Y  C63   C10  N2    110.09  3.000
 A2Y  C62   C10  N2    110.12  3.000
 A2Y  C61   C10  N2    106.05  3.000
 A2Y  C12   C11  C4    133.42  3.000
 A2Y  C12   C11  O     117.57  3.000
 A2Y  C4    C11  O     109.02  3.000
 A2Y  C11   C12  C3    128.15  3.000
 A2Y  C11   C12  S     120.58  3.000
 A2Y  C3    C12  S     111.27  3.000
 A2Y  H261  C61  H161  107.24  3.000
 A2Y  H261  C61  C71   110.02  3.000
 A2Y  H161  C61  C71   110.38  3.000
 A2Y  H261  C61  C10   110.10  3.000
 A2Y  H161  C61  C10   110.02  3.000
 A2Y  C71   C61  C10   109.06  3.000
 A2Y  H462  C62  H362  107.29  3.000
 A2Y  H462  C62  C72   110.42  3.000
 A2Y  H362  C62  C72   109.09  3.000
 A2Y  H462  C62  C10   110.51  3.000
 A2Y  H362  C62  C10   111.12  3.000
 A2Y  C72   C62  C10   108.41  3.000
 A2Y  H663  C63  H563  107.51  3.000
 A2Y  H663  C63  C73   109.12  3.000
 A2Y  H563  C63  C73   110.62  3.000
 A2Y  H663  C63  C10   110.84  3.000
 A2Y  H563  C63  C10   110.39  3.000
 A2Y  C73   C63  C10   108.36  3.000
 A2Y  H171  C71  C83   110.01  3.000
 A2Y  H171  C71  C81   109.93  3.000
 A2Y  C83   C71  C81   109.96  3.000
 A2Y  H171  C71  C61   108.52  3.000
 A2Y  C83   C71  C61   109.06  3.000
 A2Y  C81   C71  C61   109.33  3.000
 A2Y  H272  C72  C82   109.81  3.000
 A2Y  H272  C72  C81   110.02  3.000
 A2Y  C82   C72  C81   109.78  3.000
 A2Y  H272  C72  C62   108.23  3.000
 A2Y  C82   C72  C62   109.27  3.000
 A2Y  C81   C72  C62   109.70  3.000
 A2Y  H373  C73  C83   109.90  3.000
 A2Y  H373  C73  C82   109.87  3.000
 A2Y  C83   C73  C82   109.54  3.000
 A2Y  H373  C73  C63   108.41  3.000
 A2Y  C83   C73  C63   109.95  3.000
 A2Y  C82   C73  C63   109.14  3.000
 A2Y  H281  C81  H181  106.86  3.000
 A2Y  H281  C81  C72   110.01  3.000
 A2Y  H181  C81  C72   110.25  3.000
 A2Y  H281  C81  C71   110.10  3.000
 A2Y  H181  C81  C71   110.28  3.000
 A2Y  C72   C81  C71   109.32  3.000
 A2Y  H482  C82  H382  106.82  3.000
 A2Y  H482  C82  C73   109.95  3.000
 A2Y  H382  C82  C73   110.30  3.000
 A2Y  H482  C82  C72   109.97  3.000
 A2Y  H382  C82  C72   110.19  3.000
 A2Y  C73   C82  C72   109.57  3.000
 A2Y  H683  C83  H583  106.75  3.000
 A2Y  H683  C83  C73   110.43  3.000
 A2Y  H583  C83  C73   109.93  3.000
 A2Y  H683  C83  C71   110.16  3.000
 A2Y  H583  C83  C71   110.05  3.000
 A2Y  C73   C83  C71   109.49  3.000
 A2Y  H25   C5   H15   109.33  3.000
 A2Y  H25   C5   C9    110.58  3.000
 A2Y  H15   C5   C9    110.56  3.000
 A2Y  H25   C5   N2    108.12  3.000
 A2Y  H15   C5   N2    108.49  3.000
 A2Y  C9    C5   N2    109.71  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
 A2Y  CONST_01  C4   C9   N1   O      0.00   0.0  0
 A2Y  CONST_02  C9   C4   C11  O      0.00   0.0  0
 A2Y  CONST_03  S    C12  C11  O    180.00   0.0  0
 A2Y  CONST_04  C3   C12  C11  O      0.00   0.0  0
 A2Y  CONST_05  C3   C2   C1   S      0.00   0.0  0
 A2Y  CONST_06  C2   C3   C12  S      0.00   0.0  0
 A2Y  CONST_07  C4   C11  C12  S      0.00   0.0  0
 A2Y  CONST_08  C3   C12  S    C1     0.00   0.0  0
 A2Y  CONST_09  C11  C12  S    C1   180.00   0.0  0
 A2Y  CONST_10  C12  C3   C2   C1     0.00   0.0  0
 A2Y  CONST_11  C4   C11  O    N1     0.00   0.0  0
 A2Y  CONST_12  C12  C11  O    N1   180.00   0.0  0
 A2Y  CONST_13  C11  C4   C9   N1     0.00   0.0  0
 A2Y  CONST_14  C12  S    C1   C2     0.00   0.0  0
 A2Y  CONST_15  C11  C12  C3   C2   180.00   0.0  0
 A2Y  CONST_16  C4   C11  C12  C3   180.00   0.0  0
 A2Y  CONST_17  C11  O    N1   C9     0.00   0.0  0
 A2Y  CONST_18  C12  C11  C4   C9   180.00   0.0  0
 A2Y  CONST_19  C5   C9   N1   O    180.00   0.0  0
 A2Y  CONST_20  C11  C4   C9   C5   180.00   0.0  0
 A2Y  CONST_21  H44  C4   C11  O    180.00   0.0  0
 A2Y  CONST_22  H2   C2   C1   S    180.00   0.0  0
 A2Y  CONST_23  H3   C3   C12  S    180.00   0.0  0
 A2Y  CONST_24  H1   C1   C2   C3   180.00   0.0  0
 A2Y  Var_01    N2   C5   C9   N1  -101.70  30.0  1
 A2Y  Var_02    C10  N2   C5   C9  -174.37  30.0  1

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
 A2Y  chir_01  C10  C61  C62  C63  negativ
 A2Y  chir_02  C71  C61  C81  C83  positiv
 A2Y  chir_03  C72  C62  C81  C82  negativ
 A2Y  chir_04  C73  C63  C82  C83  negativ

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
 A2Y  plan-1  O    0.020
 A2Y  plan-1  N1   0.020
 A2Y  plan-1  C4   0.020
 A2Y  plan-1  C9   0.020
 A2Y  plan-1  C11  0.020
 A2Y  plan-1  C12  0.020
 A2Y  plan-1  H44  0.020
 A2Y  plan-1  C5   0.020
 A2Y  plan-2  S    0.020
 A2Y  plan-2  C1   0.020
 A2Y  plan-2  C2   0.020
 A2Y  plan-2  C3   0.020
 A2Y  plan-2  C11  0.020
 A2Y  plan-2  C12  0.020
 A2Y  plan-2  H1   0.020
 A2Y  plan-2  H2   0.020
 A2Y  plan-2  H3   0.020

