# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:58:07 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[[(5~{Z})-8-azanyl-11,12-dihydrobenzo[c][1,2]benzodiazocin-3-yl]amino]ethanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2CCc3ccc(NCC=O)cc3N=Nc2c1
#
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
 XY5  XY5  2-[[(5~{Z})-8-azanyl-11,12-dihydrobenzo[c][1,2]benzodiazocin-3-yl]amino]ethanal  ligand  37  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XY5
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
 XY5  CA    C  CH2   0  -0.387  -4.0394   1.0534  -0.8744
 XY5  C     C  C1    0   0.173  -5.1815   1.9725  -0.5328
 XY5  O     O  O     0  -0.372  -5.8427   2.5548  -1.3522
 XY5  CB1   C  CR6   0   0.149  -0.1308  -0.8143   1.3449
 XY5  NB1   N  N     0  -0.218   0.8327  -0.6869   2.3902
 XY5  CB2   C  CR16  0  -0.372  -1.1134   0.1510   1.2410
 XY5  NB2   N  NH1   0  -0.711  -3.1068   0.9945   0.2166
 XY5  CB3   C  CR6   0   0.371  -2.1276   0.0240   0.2835
 XY5  CA1   C  CR6   0   0.129   2.4164  -0.1671   0.7839
 XY5  CA2   C  CR6   0   0.105   2.5515  -1.1559  -0.1915
 XY5  CA3   C  CR16  0  -0.325   3.0145  -0.7221  -1.4337
 XY5  CA4   C  CR16  0  -0.308   3.3320   0.5959  -1.7036
 XY5  CA5   C  CR6   0   0.294   3.2075   1.5699  -0.7072
 XY5  CA6   C  CR16  0  -0.340   2.7532   1.1586   0.5466
 XY5  CA7   C  CH2   0  -0.476   2.2819  -2.6219   0.0248
 XY5  CB4   C  CR16  0  -0.336  -2.1217  -1.1101  -0.5346
 XY5  CB5   C  CR16  0  -0.328  -1.1433  -2.0820  -0.3787
 XY5  CB6   C  CR6   0   0.126  -0.1241  -1.9650   0.5549
 XY5  CB7   C  CH2   0  -0.530   0.9543  -2.9915   0.7253
 XY5  NA1   N  N     0  -0.219   2.0076  -0.4366   2.1290
 XY5  NA2   N  NH2   0  -0.863   3.5770   2.8769  -0.9351
 XY5  HA2   H  HCH2  0   0.282  -4.4993   0.0679  -1.0151
 XY5  HA3   H  HCH2  0   0.260  -3.5999   1.3387  -1.8381
 XY5  H1    H  H     0   0.200  -5.3957   2.0511   0.5483
 XY5  HB22  H  HNH1  0   0.388  -2.8131   1.8949   0.5634
 XY5  HA31  H  HCR6  0   0.250   3.1233  -1.4524  -2.2272
 XY5  HA41  H  HCR6  0   0.257   3.6842   0.8741  -2.6895
 XY5  HA61  H  HCR6  0   0.258   2.6566   1.8797   1.3503
 XY5  HA72  H  HCH2  0   0.247   2.2969  -3.0979  -0.9565
 XY5  HA71  H  HCH2  0   0.252   3.1058  -3.0742   0.5845
 XY5  HB41  H  HCR6  0   0.266  -2.8756  -1.2510  -1.2970
 XY5  HB51  H  HCR6  0   0.250  -1.1707  -2.9555  -1.0199
 XY5  HB72  H  HCH2  0   0.264   0.6134  -3.9484   0.3287
 XY5  HB71  H  HCH2  0   0.244   1.1357  -3.1611   1.7885
 XY5  HA21  H  HNH2  0   0.380   3.5575   3.1773  -1.8964
 XY5  H2    H  HNH2  0   0.380   3.1733   3.5639  -0.3192
 XY5  HB21  H  HCR6  0   0.261  -1.1003   1.0075   1.9055

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
 XY5  CA7  CB7   single    1.546  0.020  1.546
 XY5  CA7  CA2   single    1.506  0.020  1.506
 XY5  CB7  CB6   single    1.499  0.020  1.499
 XY5  NA1  NB1   double    1.229  0.020  1.229
 XY5  NA1  CA1   single    1.431  0.020  1.431
 XY5  NB1  CB1   single    1.427  0.020  1.427
 XY5  CA2  CA1   aromatic  1.395  0.020  1.395
 XY5  CA2  CA3   aromatic  1.395  0.020  1.395
 XY5  CA1  CA6   aromatic  1.388  0.020  1.388
 XY5  CB6  CB1   aromatic  1.396  0.020  1.396
 XY5  CB6  CB5   aromatic  1.387  0.020  1.387
 XY5  CB1  CB2   aromatic  1.381  0.020  1.381
 XY5  CA3  CA4   aromatic  1.382  0.020  1.382
 XY5  CB5  CB4   aromatic  1.388  0.020  1.388
 XY5  CA6  CA5   aromatic  1.396  0.020  1.396
 XY5  CA4  CA5   aromatic  1.399  0.020  1.399
 XY5  CB2  CB3   aromatic  1.401  0.020  1.401
 XY5  CA5  NA2   single    1.377  0.020  1.377
 XY5  CB4  CB3   aromatic  1.398  0.020  1.398
 XY5  CB3  NB2   single    1.380  0.020  1.380
 XY5  O    C     double    1.203  0.020  1.203
 XY5  NB2  CA    single    1.437  0.020  1.437
 XY5  C    CA    single    1.505  0.020  1.505
 XY5  CA   HA2   single    0.970  0.020  1.090
 XY5  CA   HA3   single    0.970  0.020  1.090
 XY5  C    H1    single    0.930  0.020  1.080
 XY5  CB2  HB21  single    0.930  0.020  1.080
 XY5  NB2  HB22  single    0.890  0.020  1.040
 XY5  CA3  HA31  single    0.930  0.020  1.080
 XY5  CA4  HA41  single    0.930  0.020  1.080
 XY5  CA6  HA61  single    0.930  0.020  1.080
 XY5  CA7  HA72  single    0.970  0.020  1.090
 XY5  CA7  HA71  single    0.970  0.020  1.090
 XY5  CB4  HB41  single    0.930  0.020  1.080
 XY5  CB5  HB51  single    0.930  0.020  1.080
 XY5  CB7  HB72  single    0.970  0.020  1.090
 XY5  CB7  HB71  single    0.970  0.020  1.090
 XY5  NA2  HA21  single    0.890  0.020  1.040
 XY5  NA2  H2    single    0.890  0.020  1.040

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
 XY5  HA3   CA   HA2   106.80  3.000
 XY5  HA3   CA   NB2   114.70  3.000
 XY5  HA2   CA   NB2   109.44  3.000
 XY5  HA3   CA   C     110.16  3.000
 XY5  HA2   CA   C     105.05  3.000
 XY5  NB2   CA   C     110.19  3.000
 XY5  H1    C    O     121.70  3.000
 XY5  H1    C    CA    114.37  3.000
 XY5  O     C    CA    123.91  3.000
 XY5  CB6   CB1  CB2   122.48  3.000
 XY5  CB2   CB1  NB1   118.22  3.000
 XY5  CB6   CB1  NB1   119.00  3.000
 XY5  NA1   NB1  CB1   120.52  3.000
 XY5  HB21  CB2  CB3   119.96  3.000
 XY5  HB21  CB2  CB1   119.83  3.000
 XY5  CB3   CB2  CB1   120.21  3.000
 XY5  HB22  NB2  CB3   113.86  3.000
 XY5  HB22  NB2  CA    114.43  3.000
 XY5  CB3   NB2  CA    121.74  3.000
 XY5  CB4   CB3  NB2   123.02  3.000
 XY5  NB2   CB3  CB2   118.89  3.000
 XY5  CB4   CB3  CB2   118.06  3.000
 XY5  NA1   CA1  CA6   114.19  3.000
 XY5  CA6   CA1  CA2   122.25  3.000
 XY5  NA1   CA1  CA2   123.44  3.000
 XY5  CA7   CA2  CA3   119.34  3.000
 XY5  CA3   CA2  CA1   115.74  3.000
 XY5  CA7   CA2  CA1   124.89  3.000
 XY5  HA31  CA3  CA4   118.45  3.000
 XY5  HA31  CA3  CA2   118.41  3.000
 XY5  CA4   CA3  CA2   123.14  3.000
 XY5  HA41  CA4  CA5   119.89  3.000
 XY5  HA41  CA4  CA3   119.82  3.000
 XY5  CA5   CA4  CA3   120.29  3.000
 XY5  NA2   CA5  CA6   121.05  3.000
 XY5  NA2   CA5  CA4   121.27  3.000
 XY5  CA6   CA5  CA4   117.62  3.000
 XY5  HA61  CA6  CA5   119.93  3.000
 XY5  HA61  CA6  CA1   119.13  3.000
 XY5  CA5   CA6  CA1   120.93  3.000
 XY5  HA71  CA7  HA72  105.64  3.000
 XY5  HA71  CA7  CB7   108.42  3.000
 XY5  HA72  CA7  CB7   108.36  3.000
 XY5  HA71  CA7  CA2   109.95  3.000
 XY5  HA72  CA7  CA2   107.05  3.000
 XY5  CB7   CA7  CA2   116.84  3.000
 XY5  HB41  CB4  CB5   118.64  3.000
 XY5  HB41  CB4  CB3   121.01  3.000
 XY5  CB5   CB4  CB3   120.35  3.000
 XY5  HB51  CB5  CB6   118.99  3.000
 XY5  HB51  CB5  CB4   118.69  3.000
 XY5  CB6   CB5  CB4   122.31  3.000
 XY5  CB7   CB6  CB5   123.20  3.000
 XY5  CB5   CB6  CB1   116.54  3.000
 XY5  CB7   CB6  CB1   120.25  3.000
 XY5  HB71  CB7  HB72  105.65  3.000
 XY5  HB71  CB7  CB6   109.67  3.000
 XY5  HB72  CB7  CB6   109.56  3.000
 XY5  HB71  CB7  CA7   109.62  3.000
 XY5  HB72  CB7  CA7   108.27  3.000
 XY5  CB6   CB7  CA7   113.74  3.000
 XY5  CA1   NA1  NB1   120.72  3.000
 XY5  H2    NA2  HA21  111.86  3.000
 XY5  H2    NA2  CA5   116.01  3.000
 XY5  HA21  NA2  CA5   115.83  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
 XY5  CONST_01  CB4   CB3  CB2  CB1    0.00   0.0  0
 XY5  CONST_02  CB5   CB4  CB3  CB2    0.00   0.0  0
 XY5  CONST_03  CB6   CB5  CB4  CB3    0.00   0.0  0
 XY5  CONST_04  CA4   CA5  CA6  CA1    0.00   0.0  0
 XY5  CONST_05  CA5   CA4  CA3  CA2    0.00   0.0  0
 XY5  CONST_06  CA6   CA5  CA4  CA3    0.00   0.0  0
 XY5  CONST_07  NB2   CB3  CB2  CB1  180.00   0.0  0
 XY5  CONST_08  CB5   CB4  CB3  NB2  180.00   0.0  0
 XY5  CONST_09  NA2   CA5  CA6  CA1  180.00   0.0  0
 XY5  CONST_10  NA2   CA5  CA4  CA3  180.00   0.0  0
 XY5  CONST_11  HB41  CB4  CB3  CB2  180.00   0.0  0
 XY5  CONST_12  HB51  CB5  CB4  CB3  180.00   0.0  0
 XY5  CONST_13  HA41  CA4  CA3  CA2  180.00   0.0  0
 XY5  CONST_14  HA61  CA6  CA5  CA4  180.00   0.0  0
 XY5  CONST_15  HA31  CA3  CA4  CA5  180.00   0.0  0
 XY5  CONST_16  HB21  CB2  CB3  CB4  180.00   0.0  0
 XY5  CONST_17  CB2   CB3  NB2  CA   180.00   0.0  0
 XY5  CONST_18  CB4   CB3  NB2  CA     0.00   0.0  0
 XY5  Var_01    CB3   NB2  CA   C    166.16  30.0  1
 XY5  Var_02    NB2   CA   C    O    154.19  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
 XY5  plan-1  CA1   0.020
 XY5  plan-1  CA2   0.020
 XY5  plan-1  CA3   0.020
 XY5  plan-1  CA4   0.020
 XY5  plan-1  CA5   0.020
 XY5  plan-1  CA6   0.020
 XY5  plan-1  CA7   0.020
 XY5  plan-1  NA1   0.020
 XY5  plan-1  NA2   0.020
 XY5  plan-1  HA31  0.020
 XY5  plan-1  HA41  0.020
 XY5  plan-1  HA61  0.020
 XY5  plan-2  CB1   0.020
 XY5  plan-2  NB1   0.020
 XY5  plan-2  CB2   0.020
 XY5  plan-2  NB2   0.020
 XY5  plan-2  CB3   0.020
 XY5  plan-2  CB4   0.020
 XY5  plan-2  CB5   0.020
 XY5  plan-2  CB6   0.020
 XY5  plan-2  CB7   0.020
 XY5  plan-2  HB41  0.020
 XY5  plan-2  HB51  0.020
 XY5  plan-2  HB21  0.020
 XY5  plan-3  CA    0.020
 XY5  plan-3  NB2   0.020
 XY5  plan-3  CB3   0.020
 XY5  plan-3  HB22  0.020
 XY5  plan-4  CA5   0.020
 XY5  plan-4  NA2   0.020
 XY5  plan-4  HA21  0.020
 XY5  plan-4  H2    0.020
 XY5  plan-5  CA    0.020
 XY5  plan-5  C     0.020
 XY5  plan-5  O     0.020
 XY5  plan-5  H1    0.020

