# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 17:48:57 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-[4-(2H-1,3-benzodioxole-5-carbonyl)-2,3,4,5-tetrahydro-1H-1,4-diazepin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC=C1)C(=O)c2ccc3OCOc3c2
#
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
 LFJ  LFJ  1-[4-(2H-1,3-benzodioxole-5-carbonyl)-2,3,4,5-tetrahydro-1H-1,4-diazepin-1-yl]ethan-1-one  ligand  37  21  .  2022-07-25  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_LFJ
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
 LFJ  N1   N  NT    0  -0.445  -0.9159  -0.8774   0.4525
 LFJ  C4   C  C1    0  -0.030  -2.7853   1.4941  -0.2874
 LFJ  C5   C  C     0   0.524  -4.9815   0.5294  -0.0027
 LFJ  C6   C  CH3   0  -0.807  -5.4410   1.9202   0.3544
 LFJ  C7   C  CH2   0  -0.307  -3.1230  -0.9214  -0.6566
 LFJ  C8   C  CH2   0  -0.325  -2.1890  -1.5623   0.3618
 LFJ  C10  C  CR16  0  -0.362   2.6295  -1.1363   0.4351
 LFJ  C13  C  CR56  0   0.304   3.7694   0.7922  -0.4634
 LFJ  C15  C  CR16  0  -0.267   1.4535   0.5545  -0.8510
 LFJ  C1   C  C     0   0.515   0.2085  -1.4606  -0.0216
 LFJ  C11  C  CR56  0   0.312   3.7664  -0.3924   0.2594
 LFJ  C12  C  CH2   0   0.070   5.8137   0.4736   0.3533
 LFJ  C14  C  CR16  0  -0.332   2.6286   1.2894  -1.0418
 LFJ  C2   C  CH2   0  -0.367  -0.9628   0.4246   1.0918
 LFJ  C3   C  C1    0  -0.276  -1.5741   1.5173   0.2595
 LFJ  C9   C  CR6   0  -0.086   1.4445  -0.6257  -0.1204
 LFJ  N2   N  NT    0  -0.495  -3.6476   0.3812  -0.2712
 LFJ  O1   O  O     0  -0.487   0.2496  -2.6320  -0.3755
 LFJ  O2   O  O     0  -0.480  -5.7554  -0.4121  -0.0360
 LFJ  O3   O  O     0  -0.485   5.0213  -0.6574   0.6915
 LFJ  O4   O  O     0  -0.481   5.0219   1.2964  -0.4963
 LFJ  H1   H  H     0   0.280  -3.1469   2.3685  -0.8153
 LFJ  H2   H  HCH3  0   0.270  -4.8652   2.3345   1.1820
 LFJ  H3   H  HCH3  0   0.272  -5.3319   2.6033  -0.4895
 LFJ  H4   H  HCH3  0   0.274  -6.4904   1.8901   0.6352
 LFJ  H5   H  HCH2  0   0.258  -2.6031  -0.8210  -1.6120
 LFJ  H6   H  HCH2  0   0.273  -3.9678  -1.5875  -0.8120
 LFJ  H7   H  HCH2  0   0.276  -2.0165  -2.5942   0.0666
 LFJ  H8   H  HCH2  0   0.255  -2.6629  -1.5774   1.3474
 LFJ  H10  H  HCR6  0   0.268   0.5391   0.9185  -1.3008
 LFJ  H11  H  HCH2  0   0.238   6.0815   1.0257   1.2593
 LFJ  H12  H  HCR6  0   0.279   2.6318   2.2014  -1.6225
 LFJ  H13  H  HCH2  0   0.278  -1.5465   0.3105   2.0120
 LFJ  H14  H  HCH2  0   0.287   0.0355   0.7163   1.4046
 LFJ  H15  H  H     0   0.275  -0.9948   2.4232   0.1294
 LFJ  H16  H  HCH2  0   0.247   6.7104   0.1520  -0.1771
 LFJ  H9   H  HCR6  0   0.278   2.6402  -2.0665   0.9877

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
 LFJ  O4   C12  single    1.423  0.020  1.423
 LFJ  O4   C13  single    1.351  0.020  1.351
 LFJ  C12  O3   single    1.422  0.020  1.422
 LFJ  C14  C13  aromatic  1.372  0.020  1.372
 LFJ  C14  C15  aromatic  1.399  0.020  1.399
 LFJ  C13  C11  aromatic  1.388  0.020  1.388
 LFJ  O3   C11  single    1.353  0.020  1.353
 LFJ  C15  C9   aromatic  1.388  0.020  1.388
 LFJ  C11  C10  aromatic  1.370  0.020  1.370
 LFJ  C9   C10  aromatic  1.405  0.020  1.405
 LFJ  C9   C1   single    1.495  0.020  1.495
 LFJ  C1   O1   double    1.224  0.020  1.224
 LFJ  C1   N1   single    1.352  0.020  1.352
 LFJ  N1   C8   single    1.448  0.020  1.448
 LFJ  N1   C2   single    1.451  0.020  1.451
 LFJ  C8   C7   single    1.523  0.020  1.523
 LFJ  C2   C3   single    1.503  0.020  1.503
 LFJ  C3   C4   double    1.329  0.020  1.329
 LFJ  C7   N2   single    1.456  0.020  1.456
 LFJ  C4   N2   single    1.408  0.020  1.408
 LFJ  N2   C5   single    1.369  0.020  1.369
 LFJ  O2   C5   double    1.219  0.020  1.219
 LFJ  C5   C6   single    1.508  0.020  1.508
 LFJ  C4   H1   single    0.930  0.020  1.080
 LFJ  C6   H2   single    0.970  0.020  1.090
 LFJ  C6   H3   single    0.970  0.020  1.090
 LFJ  C6   H4   single    0.970  0.020  1.090
 LFJ  C7   H5   single    0.970  0.020  1.090
 LFJ  C7   H6   single    0.970  0.020  1.090
 LFJ  C8   H7   single    0.970  0.020  1.090
 LFJ  C8   H8   single    0.970  0.020  1.090
 LFJ  C10  H9   single    0.930  0.020  1.080
 LFJ  C15  H10  single    0.930  0.020  1.080
 LFJ  C12  H11  single    0.970  0.020  1.090
 LFJ  C14  H12  single    0.930  0.020  1.080
 LFJ  C2   H13  single    0.970  0.020  1.090
 LFJ  C2   H14  single    0.970  0.020  1.090
 LFJ  C3   H15  single    0.930  0.020  1.080
 LFJ  C12  H16  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
 LFJ  C2   N1   C1   124.62  3.000
 LFJ  C2   N1   C8   115.05  3.000
 LFJ  C1   N1   C8   120.32  3.000
 LFJ  H1   C4   N2   116.05  3.000
 LFJ  H1   C4   C3   119.37  3.000
 LFJ  N2   C4   C3   124.55  3.000
 LFJ  O2   C5   N2   121.98  3.000
 LFJ  O2   C5   C6   121.69  3.000
 LFJ  N2   C5   C6   116.32  3.000
 LFJ  H4   C6   H3   108.29  3.000
 LFJ  H4   C6   H2   108.93  3.000
 LFJ  H3   C6   H2   107.24  3.000
 LFJ  H4   C6   C5   109.27  3.000
 LFJ  H3   C6   C5   111.34  3.000
 LFJ  H2   C6   C5   111.68  3.000
 LFJ  H6   C7   H5   107.53  3.000
 LFJ  H6   C7   N2   107.82  3.000
 LFJ  H5   C7   N2   108.71  3.000
 LFJ  H6   C7   C8   108.32  3.000
 LFJ  H5   C7   C8   109.37  3.000
 LFJ  N2   C7   C8   114.85  3.000
 LFJ  H8   C8   H7   107.48  3.000
 LFJ  H8   C8   C7   110.04  3.000
 LFJ  H7   C8   C7   108.37  3.000
 LFJ  H8   C8   N1   109.33  3.000
 LFJ  H7   C8   N1   109.05  3.000
 LFJ  C7   C8   N1   112.45  3.000
 LFJ  H9   C10  C9   121.51  3.000
 LFJ  H9   C10  C11  121.61  3.000
 LFJ  C9   C10  C11  116.87  3.000
 LFJ  O4   C13  C14  128.72  3.000
 LFJ  C14  C13  C11  121.80  3.000
 LFJ  O4   C13  C11  109.47  3.000
 LFJ  H10  C15  C9   119.96  3.000
 LFJ  H10  C15  C14  118.45  3.000
 LFJ  C9   C15  C14  121.59  3.000
 LFJ  O1   C1   C9   119.17  3.000
 LFJ  O1   C1   N1   122.81  3.000
 LFJ  C9   C1   N1   118.02  3.000
 LFJ  O3   C11  C13  109.35  3.000
 LFJ  O3   C11  C10  128.48  3.000
 LFJ  C13  C11  C10  122.15  3.000
 LFJ  H16  C12  H11  110.51  3.000
 LFJ  H16  C12  O4   109.74  3.000
 LFJ  H11  C12  O4   109.80  3.000
 LFJ  H16  C12  O3   109.84  3.000
 LFJ  H11  C12  O3   109.93  3.000
 LFJ  O4   C12  O3   106.96  3.000
 LFJ  H12  C14  C15  121.25  3.000
 LFJ  H12  C14  C13  121.97  3.000
 LFJ  C15  C14  C13  116.78  3.000
 LFJ  H14  C2   H13  106.00  3.000
 LFJ  H14  C2   C3   109.75  3.000
 LFJ  H13  C2   C3   108.91  3.000
 LFJ  H14  C2   N1   109.76  3.000
 LFJ  H13  C2   N1   107.08  3.000
 LFJ  C3   C2   N1   114.92  3.000
 LFJ  H15  C3   C2   117.19  3.000
 LFJ  H15  C3   C4   116.91  3.000
 LFJ  C2   C3   C4   125.84  3.000
 LFJ  C1   C9   C15  121.00  3.000
 LFJ  C1   C9   C10  117.93  3.000
 LFJ  C15  C9   C10  120.78  3.000
 LFJ  C7   N2   C5   119.99  3.000
 LFJ  C5   N2   C4   120.90  3.000
 LFJ  C7   N2   C4   118.91  3.000
 LFJ  C12  O3   C11  106.57  3.000
 LFJ  C12  O4   C13  106.60  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
 LFJ  CONST_01  C14  C13  C11  C10    0.00   0.0  0
 LFJ  CONST_02  C14  C15  C9   C10    0.00   0.0  0
 LFJ  CONST_03  C9   C15  C14  C13    0.00   0.0  0
 LFJ  CONST_04  C9   C10  C11  C13    0.00   0.0  0
 LFJ  CONST_05  C11  C13  C14  C15    0.00   0.0  0
 LFJ  CONST_06  C11  C10  C9   C15    0.00   0.0  0
 LFJ  CONST_07  C14  C15  C9   C1   180.00   0.0  0
 LFJ  CONST_08  C11  C10  C9   C1   180.00   0.0  0
 LFJ  CONST_09  H10  C15  C9   C10  180.00   0.0  0
 LFJ  CONST_10  H9   C10  C11  C13  180.00   0.0  0
 LFJ  CONST_11  H12  C14  C13  C11  180.00   0.0  0
 LFJ  Var_01    O3   C12  O4   C13    9.92  30.0  1
 LFJ  Var_02    O4   C12  O3   C11  -10.03  30.0  1
 LFJ  Var_03    C14  C13  O4   C12  174.98  30.0  1
 LFJ  Var_04    C15  C9   C1   N1   -56.41  30.0  2
 LFJ  Var_05    H2   C6   C5   N2   -54.09  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
 LFJ  plan-1  C4   0.020
 LFJ  plan-1  C5   0.020
 LFJ  plan-1  C6   0.020
 LFJ  plan-1  C7   0.020
 LFJ  plan-1  N2   0.020
 LFJ  plan-1  O2   0.020
 LFJ  plan-2  C10  0.020
 LFJ  plan-2  C13  0.020
 LFJ  plan-2  C15  0.020
 LFJ  plan-2  C1   0.020
 LFJ  plan-2  C11  0.020
 LFJ  plan-2  C14  0.020
 LFJ  plan-2  C9   0.020
 LFJ  plan-2  O3   0.020
 LFJ  plan-2  O4   0.020
 LFJ  plan-2  H10  0.020
 LFJ  plan-2  H12  0.020
 LFJ  plan-2  H9   0.020
 LFJ  plan-3  N1   0.020
 LFJ  plan-3  C8   0.020
 LFJ  plan-3  C1   0.020
 LFJ  plan-3  C2   0.020
 LFJ  plan-3  C9   0.020
 LFJ  plan-3  O1   0.020

