# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:37:47 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 8-fluoranyl-5-methyl-1,2,3,6-tetrahydro-1,5-benzodiazocin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1Cc2cc(F)ccc2NCCC1=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
 LZY  LZY  8-fluoranyl-5-methyl-1,2,3,6-tetrahydro-1,5-benzodiazocin-4-one  ligand  28  15  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LZY
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
 LZY  N1   N  NH1   0  -0.689  -4.3373  -32.7271  -15.8328
 LZY  C4   C  CR6   0   0.512  -5.4223  -30.1424  -18.9179
 LZY  C5   C  CR16  0  -0.416  -4.1607  -30.0568  -18.3679
 LZY  C6   C  CR16  0  -0.328  -3.8307  -30.9173  -17.3338
 LZY  C7   C  CR6   0   0.310  -4.7314  -31.8723  -16.8521
 LZY  C8   C  CH2   0  -0.331  -5.2301  -33.0253  -14.7235
 LZY  C10  C  C     0   0.539  -5.8028  -35.0203  -16.2106
 LZY  N    N  NT    0  -0.419  -6.4176  -34.3716  -17.2241
 LZY  C    C  CH3   0  -0.521  -6.2105  -34.8469  -18.5781
 LZY  O    O  O     0  -0.504  -5.2022  -36.0705  -16.3997
 LZY  C1   C  CH2   0  -0.430  -6.9848  -33.0456  -17.0859
 LZY  C2   C  CR6   0   0.113  -6.0005  -31.9598  -17.4537
 LZY  C3   C  CR16  0  -0.479  -6.3325  -31.0812  -18.4793
 LZY  C9   C  CH2   0  -0.594  -5.8953  -34.4144  -14.8250
 LZY  F    F  F     0  -0.325  -5.7716  -29.3019  -19.9121
 LZY  H1   H  HNH1  0   0.382  -3.3927  -32.5515  -15.5300
 LZY  H2   H  HCR6  0   0.277  -3.4465  -29.3261  -18.7248
 LZY  H3   H  HCR6  0   0.267  -2.8476  -30.8435  -16.8845
 LZY  H4   H  HCH2  0   0.277  -4.6387  -32.9952  -13.8097
 LZY  H5   H  HCH2  0   0.244  -5.9812  -32.2400  -14.6155
 LZY  H6   H  HCH3  0   0.252  -6.3753  -35.9196  -18.6432
 LZY  H7   H  HCH3  0   0.242  -6.9229  -34.3548  -19.2371
 LZY  H8   H  HCH3  0   0.236  -5.2041  -34.6289  -18.9429
 LZY  H9   H  HCH2  0   0.284  -7.3911  -32.9167  -16.0845
 LZY  H10  H  HCH2  0   0.287  -7.8456  -32.9799  -17.7533
 LZY  H11  H  HCR6  0   0.272  -7.3068  -31.1477  -18.9494
 LZY  H12  H  HCH2  0   0.272  -6.9376  -34.3609  -14.5007
 LZY  H13  H  HCH2  0   0.271  -5.3977  -35.1133  -14.1546

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
 LZY  F    C4   single    1.348  0.020  1.348
 LZY  C4   C3   aromatic  1.379  0.020  1.379
 LZY  C4   C5   aromatic  1.379  0.020  1.379
 LZY  C    N    single    1.450  0.020  1.450
 LZY  C3   C2   aromatic  1.391  0.020  1.391
 LZY  C5   C6   aromatic  1.385  0.020  1.385
 LZY  C2   C1   single    1.511  0.020  1.511
 LZY  C2   C7   aromatic  1.407  0.020  1.407
 LZY  C6   C7   aromatic  1.398  0.020  1.398
 LZY  N    C1   single    1.449  0.020  1.449
 LZY  N    C10  single    1.351  0.020  1.351
 LZY  C7   N1   single    1.387  0.020  1.387
 LZY  O    C10  double    1.224  0.020  1.224
 LZY  C10  C9   single    1.515  0.020  1.515
 LZY  N1   C8   single    1.455  0.020  1.455
 LZY  C9   C8   single    1.544  0.020  1.544
 LZY  N1   H1   single    0.890  0.020  1.040
 LZY  C5   H2   single    0.930  0.020  1.080
 LZY  C6   H3   single    0.930  0.020  1.080
 LZY  C8   H4   single    0.970  0.020  1.090
 LZY  C8   H5   single    0.970  0.020  1.090
 LZY  C    H6   single    0.970  0.020  1.090
 LZY  C    H7   single    0.970  0.020  1.090
 LZY  C    H8   single    0.970  0.020  1.090
 LZY  C1   H9   single    0.970  0.020  1.090
 LZY  C1   H10  single    0.970  0.020  1.090
 LZY  C3   H11  single    0.930  0.020  1.080
 LZY  C9   H12  single    0.970  0.020  1.090
 LZY  C9   H13  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
 LZY  H1   N1   C8   112.46  3.000
 LZY  H1   N1   C7   112.32  3.000
 LZY  C8   N1   C7   120.81  3.000
 LZY  F    C4   C3   119.21  3.000
 LZY  C3   C4   C5   121.28  3.000
 LZY  F    C4   C5   119.51  3.000
 LZY  H2   C5   C6   120.56  3.000
 LZY  H2   C5   C4   120.94  3.000
 LZY  C6   C5   C4   118.50  3.000
 LZY  H3   C6   C7   119.21  3.000
 LZY  H3   C6   C5   118.91  3.000
 LZY  C7   C6   C5   121.87  3.000
 LZY  C2   C7   C6   118.43  3.000
 LZY  C6   C7   N1   119.40  3.000
 LZY  C2   C7   N1   122.14  3.000
 LZY  H5   C8   H4   105.71  3.000
 LZY  H5   C8   C9   110.93  3.000
 LZY  H4   C8   C9   108.31  3.000
 LZY  H5   C8   N1   110.49  3.000
 LZY  H4   C8   N1   107.52  3.000
 LZY  C9   C8   N1   113.50  3.000
 LZY  C9   C10  O    120.94  3.000
 LZY  C9   C10  N    117.79  3.000
 LZY  O    C10  N    121.27  3.000
 LZY  C1   N    C    116.42  3.000
 LZY  C1   N    C10  123.09  3.000
 LZY  C    N    C10  118.56  3.000
 LZY  H8   C    H7   108.10  3.000
 LZY  H8   C    H6   108.45  3.000
 LZY  H7   C    H6   108.11  3.000
 LZY  H8   C    N    112.21  3.000
 LZY  H7   C    N    108.89  3.000
 LZY  H6   C    N    110.95  3.000
 LZY  H10  C1   H9   105.14  3.000
 LZY  H10  C1   C2   108.77  3.000
 LZY  H9   C1   C2   112.46  3.000
 LZY  H10  C1   N    107.79  3.000
 LZY  H9   C1   N    110.01  3.000
 LZY  C2   C1   N    112.30  3.000
 LZY  C3   C2   C1   118.55  3.000
 LZY  C1   C2   C7   121.88  3.000
 LZY  C3   C2   C7   119.43  3.000
 LZY  H11  C3   C2   119.72  3.000
 LZY  H11  C3   C4   119.81  3.000
 LZY  C2   C3   C4   120.46  3.000
 LZY  H13  C9   H12  106.53  3.000
 LZY  H13  C9   C10  106.17  3.000
 LZY  H12  C9   C10  110.43  3.000
 LZY  H13  C9   C8   109.89  3.000
 LZY  H12  C9   C8   110.33  3.000
 LZY  C10  C9   C8   113.19  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
 LZY  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 LZY  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 LZY  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 LZY  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 LZY  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 LZY  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 LZY  CONST_07  C9   C10  N    C1     0.00   0.0  0
 LZY  CONST_08  F    C4   C5   C6   180.00   0.0  0
 LZY  CONST_09  F    C4   C3   C2   180.00   0.0  0
 LZY  CONST_10  C9   C10  N    C    180.00   0.0  0
 LZY  CONST_11  C1   N    C10  O    180.00   0.0  0
 LZY  CONST_12  H3   C6   C7   N1     0.00   0.0  0
 LZY  CONST_13  H11  C3   C4   C5   180.00   0.0  0
 LZY  CONST_14  H2   C5   C6   C7   180.00   0.0  0
 LZY  CONST_15  O    C10  N    C      0.00   0.0  0
 LZY  Var_01    C10  C9   C8   N1   -16.12  30.0  1
 LZY  Var_02    C8   N1   C7   C6   136.91  30.0  1
 LZY  Var_03    N    C1   C2   C7   -54.54  30.0  1
 LZY  Var_04    C9   C8   N1   C7   103.17  30.0  1
 LZY  Var_05    N    C10  C9   C8   -62.93  30.0  1
 LZY  Var_06    C2   C1   N    C10   91.77  30.0  1
 LZY  Var_07    H6   C    N    C10   49.67  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
 LZY  plan-1  C10  0.020
 LZY  plan-1  N    0.020
 LZY  plan-1  C    0.020
 LZY  plan-1  O    0.020
 LZY  plan-1  C1   0.020
 LZY  plan-1  C9   0.020
 LZY  plan-2  N1   0.020
 LZY  plan-2  C4   0.020
 LZY  plan-2  C5   0.020
 LZY  plan-2  C6   0.020
 LZY  plan-2  C7   0.020
 LZY  plan-2  C1   0.020
 LZY  plan-2  C2   0.020
 LZY  plan-2  C3   0.020
 LZY  plan-2  F    0.020
 LZY  plan-2  H2   0.020
 LZY  plan-2  H3   0.020
 LZY  plan-2  H11  0.020

