# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:15:38 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-{4-[(2-methylphenyl)methyl]-1,4-diazepan-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCCN(CC1)Cc2ccccc2C
#
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
 T4Y  T4Y  1-{4-[(2-methylphenyl)methyl]-1,4-diazepan-1-yl}ethan-1-one  ligand  40  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4Y
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
 T4Y  N1   N  NT    0  -0.440  -2.8456   0.1018  -0.5742
 T4Y  C4   C  CR16  0  -0.264   3.9257   1.9107   0.3608
 T4Y  C5   C  CR16  0  -0.298   2.7962   1.3623   0.9554
 T4Y  C6   C  CR6   0   0.080   2.3763   0.0699   0.6605
 T4Y  C7   C  CH2   0  -0.364   1.1454  -0.4916   1.3236
 T4Y  C8   C  CH2   0  -0.276  -0.9713  -1.5714   0.9386
 T4Y  C10  C  CH2   0  -0.285  -3.1397  -1.3155  -0.4293
 T4Y  C13  C  C     0   0.521  -3.7040   1.0770  -0.2009
 T4Y  N    N  NT    0  -0.400   0.0468  -0.6897   0.3911
 T4Y  O    O  O     0  -0.515  -3.4150   2.2659  -0.2892
 T4Y  C1   C  CR6   0   0.071   3.1128  -0.7017  -0.2516
 T4Y  C11  C  CH2   0  -0.338  -1.5577   0.4732  -1.1316
 T4Y  C12  C  CH2   0  -0.261  -0.4544   0.5815  -0.0888
 T4Y  C14  C  CH3   0  -0.805  -5.0531   0.6520   0.3315
 T4Y  C2   C  CR16  0  -0.301   4.2425  -0.1413  -0.8418
 T4Y  C3   C  CR16  0  -0.256   4.6510   1.1533  -0.5453
 T4Y  C9   C  CH2   0  -0.489  -1.9009  -2.1495  -0.1266
 T4Y  H5   H  HCR6  0   0.250   4.2306   2.9206   0.6026
 T4Y  H6   H  HCR6  0   0.245   2.2235   1.9533   1.6612
 T4Y  H8   H  HCH2  0   0.244   1.3929  -1.4615   1.7638
 T4Y  H7   H  HCH2  0   0.220   0.8559   0.1624   2.1637
 T4Y  H9   H  HCH2  0   0.237  -0.4487  -2.4044   1.4120
 T4Y  H10  H  HCH2  0   0.197  -1.5631  -1.0880   1.7360
 T4Y  H13  H  HCH2  0   0.255  -3.8426  -1.4478   0.3907
 T4Y  H14  H  HCH2  0   0.243  -3.6243  -1.7041  -1.3314
 T4Y  H1   H  HCH3  0   0.254   1.6950  -2.1474  -0.9701
 T4Y  H    H  HCH3  0   0.242   3.3851  -2.5509  -1.3144
 T4Y  H2   H  HCH3  0   0.238   2.7294  -2.7456   0.3081
 T4Y  H15  H  HCH2  0   0.253  -1.2806  -0.2465  -1.9041
 T4Y  H16  H  HCH2  0   0.263  -1.6580   1.4371  -1.6258
 T4Y  H18  H  HCH2  0   0.193  -0.8189   1.2150   0.7386
 T4Y  H17  H  HCH2  0   0.241   0.3767   1.1211  -0.5483
 T4Y  H22  H  HCH3  0   0.266  -4.9603   0.1836   1.3133
 T4Y  H19  H  HCH3  0   0.267  -5.6840   1.5308   0.4371
 T4Y  H20  H  HCH3  0   0.262  -5.5540  -0.0617  -0.3222
 T4Y  H3   H  HCR6  0   0.244   4.8166  -0.7331  -1.5455
 T4Y  H4   H  HCR6  0   0.250   5.5333   1.5634  -1.0200
 T4Y  H11  H  HCH2  0   0.241  -1.3193  -2.3388  -1.0309
 T4Y  H12  H  HCH2  0   0.256  -2.2608  -3.1248   0.2083
 T4Y  C    C  CH3   0  -0.742   2.7119  -2.1102  -0.5806

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
 T4Y  C1   C    single    1.501  0.020  1.501
 T4Y  C1   C2   aromatic  1.392  0.020  1.392
 T4Y  C3   C2   aromatic  1.390  0.020  1.390
 T4Y  C4   C3   aromatic  1.386  0.020  1.386
 T4Y  C5   C4   aromatic  1.389  0.020  1.389
 T4Y  C6   C5   aromatic  1.390  0.020  1.390
 T4Y  C6   C1   aromatic  1.403  0.020  1.403
 T4Y  C7   C6   single    1.507  0.020  1.507
 T4Y  N    C7   single    1.455  0.020  1.455
 T4Y  C8   N    single    1.454  0.020  1.454
 T4Y  C9   C8   single    1.527  0.020  1.527
 T4Y  C10  C9   single    1.524  0.020  1.524
 T4Y  N1   C10  single    1.455  0.020  1.455
 T4Y  N1   C11  single    1.452  0.020  1.452
 T4Y  C11  C12  single    1.522  0.020  1.522
 T4Y  C12  N    single    1.448  0.020  1.448
 T4Y  C13  N1   single    1.352  0.020  1.352
 T4Y  C13  O    double    1.227  0.020  1.227
 T4Y  C14  C13  single    1.511  0.020  1.511
 T4Y  C4   H5   single    0.930  0.020  1.080
 T4Y  C5   H6   single    0.930  0.020  1.080
 T4Y  C7   H8   single    0.970  0.020  1.090
 T4Y  C7   H7   single    0.970  0.020  1.090
 T4Y  C8   H9   single    0.970  0.020  1.090
 T4Y  C8   H10  single    0.970  0.020  1.090
 T4Y  C10  H13  single    0.970  0.020  1.090
 T4Y  C10  H14  single    0.970  0.020  1.090
 T4Y  C    H1   single    0.970  0.020  1.090
 T4Y  C    H    single    0.970  0.020  1.090
 T4Y  C    H2   single    0.970  0.020  1.090
 T4Y  C11  H15  single    0.970  0.020  1.090
 T4Y  C11  H16  single    0.970  0.020  1.090
 T4Y  C12  H18  single    0.970  0.020  1.090
 T4Y  C12  H17  single    0.970  0.020  1.090
 T4Y  C14  H22  single    0.970  0.020  1.090
 T4Y  C14  H19  single    0.970  0.020  1.090
 T4Y  C14  H20  single    0.970  0.020  1.090
 T4Y  C2   H3   single    0.930  0.020  1.080
 T4Y  C3   H4   single    0.930  0.020  1.080
 T4Y  C9   H11  single    0.970  0.020  1.090
 T4Y  C9   H12  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
 T4Y  C11  N1   C13  119.00  3.000
 T4Y  C13  N1   C10  123.16  3.000
 T4Y  C11  N1   C10  117.83  3.000
 T4Y  H5   C4   C3   120.57  3.000
 T4Y  H5   C4   C5   120.12  3.000
 T4Y  C3   C4   C5   119.31  3.000
 T4Y  H6   C5   C6   119.03  3.000
 T4Y  H6   C5   C4   119.53  3.000
 T4Y  C6   C5   C4   121.44  3.000
 T4Y  C1   C6   C7   120.65  3.000
 T4Y  C7   C6   C5   119.98  3.000
 T4Y  C1   C6   C5   119.36  3.000
 T4Y  H7   C7   H8   106.18  3.000
 T4Y  H7   C7   N    111.76  3.000
 T4Y  H8   C7   N    107.95  3.000
 T4Y  H7   C7   C6   109.18  3.000
 T4Y  H8   C7   C6   108.83  3.000
 T4Y  N    C7   C6   112.68  3.000
 T4Y  H10  C8   H9   106.11  3.000
 T4Y  H10  C8   C9   110.06  3.000
 T4Y  H9   C8   C9   107.76  3.000
 T4Y  H10  C8   N    112.44  3.000
 T4Y  H9   C8   N    106.91  3.000
 T4Y  C9   C8   N    113.15  3.000
 T4Y  H14  C10  H13  106.96  3.000
 T4Y  H14  C10  C9   109.22  3.000
 T4Y  H13  C10  C9   107.99  3.000
 T4Y  H14  C10  N1   110.67  3.000
 T4Y  H13  C10  N1   108.92  3.000
 T4Y  C9   C10  N1   112.87  3.000
 T4Y  C14  C13  O    120.54  3.000
 T4Y  C14  C13  N1   117.47  3.000
 T4Y  O    C13  N1   121.99  3.000
 T4Y  C12  N    C8   114.50  3.000
 T4Y  C12  N    C7   110.75  3.000
 T4Y  C8   N    C7   111.72  3.000
 T4Y  C2   C1   C    120.10  3.000
 T4Y  C2   C1   C6   118.69  3.000
 T4Y  C    C1   C6   121.21  3.000
 T4Y  H16  C11  H15  106.63  3.000
 T4Y  H16  C11  C12  108.36  3.000
 T4Y  H15  C11  C12  110.35  3.000
 T4Y  H16  C11  N1   108.62  3.000
 T4Y  H15  C11  N1   109.16  3.000
 T4Y  C12  C11  N1   113.47  3.000
 T4Y  H17  C12  H18  106.44  3.000
 T4Y  H17  C12  C11  107.37  3.000
 T4Y  H18  C12  C11  108.36  3.000
 T4Y  H17  C12  N    108.04  3.000
 T4Y  H18  C12  N    111.69  3.000
 T4Y  C11  C12  N    114.54  3.000
 T4Y  H20  C14  H19  108.72  3.000
 T4Y  H20  C14  H22  107.31  3.000
 T4Y  H19  C14  H22  107.99  3.000
 T4Y  H20  C14  C13  112.52  3.000
 T4Y  H19  C14  C13  108.96  3.000
 T4Y  H22  C14  C13  111.20  3.000
 T4Y  H3   C2   C3   119.43  3.000
 T4Y  H3   C2   C1   119.03  3.000
 T4Y  C3   C2   C1   121.53  3.000
 T4Y  H4   C3   C2   119.93  3.000
 T4Y  H4   C3   C4   120.41  3.000
 T4Y  C2   C3   C4   119.66  3.000
 T4Y  H12  C9   H11  105.94  3.000
 T4Y  H12  C9   C10  106.37  3.000
 T4Y  H11  C9   C10  111.31  3.000
 T4Y  H12  C9   C8   108.95  3.000
 T4Y  H11  C9   C8   108.61  3.000
 T4Y  C10  C9   C8   115.22  3.000
 T4Y  H2   C    H    107.62  3.000
 T4Y  H2   C    H1   106.61  3.000
 T4Y  H    C    H1   108.80  3.000
 T4Y  H2   C    C1   111.29  3.000
 T4Y  H    C    C1   111.25  3.000
 T4Y  H1   C    C1   111.08  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
 T4Y  CONST_01  C1   C2   C3   C4    0.00   0.0  0
 T4Y  CONST_02  C1   C6   C5   C4    0.00   0.0  0
 T4Y  CONST_03  C2   C3   C4   C5    0.00   0.0  0
 T4Y  CONST_04  C2   C1   C6   C5    0.00   0.0  0
 T4Y  CONST_05  C3   C4   C5   C6    0.00   0.0  0
 T4Y  CONST_06  C3   C2   C1   C6    0.00   0.0  0
 T4Y  CONST_07  C7   C6   C5   C4  180.00   0.0  0
 T4Y  CONST_08  C    C1   C6   C5  180.00   0.0  0
 T4Y  CONST_09  C2   C1   C6   C7  180.00   0.0  0
 T4Y  CONST_10  C3   C2   C1   C   180.00   0.0  0
 T4Y  CONST_11  H3   C2   C3   C4  180.00   0.0  0
 T4Y  CONST_12  H4   C3   C4   C5  180.00   0.0  0
 T4Y  CONST_13  H5   C4   C5   C6  180.00   0.0  0
 T4Y  CONST_14  H6   C5   C6   C1  180.00   0.0  0
 T4Y  Var_01    N    C7   C6   C5  111.89  30.0  3
 T4Y  Var_02    H1   C    C1   C6   57.81  30.0  2
 T4Y  Var_03    H22  C14  C13  N1   70.08  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
 T4Y  plan-1  C4   0.020
 T4Y  plan-1  C5   0.020
 T4Y  plan-1  C6   0.020
 T4Y  plan-1  C7   0.020
 T4Y  plan-1  C1   0.020
 T4Y  plan-1  C2   0.020
 T4Y  plan-1  C3   0.020
 T4Y  plan-1  H5   0.020
 T4Y  plan-1  H6   0.020
 T4Y  plan-1  H3   0.020
 T4Y  plan-1  H4   0.020
 T4Y  plan-1  C    0.020
 T4Y  plan-2  N1   0.020
 T4Y  plan-2  C10  0.020
 T4Y  plan-2  C13  0.020
 T4Y  plan-2  O    0.020
 T4Y  plan-2  C11  0.020
 T4Y  plan-2  C14  0.020

