# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:05:43 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (5R)-N-benzyl-5-ethyl-1-methyl-1,4-diazepane-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@]1(CCN(C)CCN1)C(=O)NCc2ccccc2
#
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
 RJJ  RJJ  (5R)-N-benzyl-5-ethyl-1-methyl-1,4-diazepane-5-carboxamide  ligand  45  20  .  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_RJJ
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
 RJJ  C10  C  CR16  0  -0.240   3.4973  -1.0784   1.6414
 RJJ  C13  C  CR16  0  -0.293   3.3900   0.7279  -0.4593
 RJJ  C15  C  CH2   0  -0.269  -1.2804  -1.3810  -1.8185
 RJJ  C17  C  CH3   0  -0.517   0.8840  -2.3949  -1.3886
 RJJ  C01  C  CH3   0  -0.661  -4.2624   2.0092   0.5894
 RJJ  C02  C  CH2   0  -0.425  -3.5635   1.4173  -0.6273
 RJJ  C03  C  CT    0   0.009  -2.2634   0.6122  -0.4085
 RJJ  C04  C  C     0   0.550  -1.1335   1.5441   0.0997
 RJJ  C07  C  CH2   0  -0.320   1.2775   1.7574   0.4519
 RJJ  C08  C  CR6   0   0.061   2.4177   0.7780   0.5331
 RJJ  C09  C  CR16  0  -0.281   2.4807  -0.1366   1.5824
 RJJ  C11  C  CR16  0  -0.266   4.4668  -1.1185   0.6460
 RJJ  C12  C  CR16  0  -0.241   4.4112  -0.2132  -0.4042
 RJJ  C14  C  CH2   0  -0.477  -1.8708   0.0259  -1.8001
 RJJ  C18  C  CH2   0  -0.282  -0.7185  -2.1622   0.3919
 RJJ  C19  C  CH2   0  -0.329  -1.5068  -1.1662   1.2432
 RJJ  N06  N  NH1   0  -0.649   0.1087   1.0756  -0.0632
 RJJ  N16  N  NT    0  -0.448  -0.2073  -1.6018  -0.8516
 RJJ  N20  N  NH1   0  -0.595  -2.5538  -0.3878   0.6157
 RJJ  O05  O  O     0  -0.498  -1.3538   2.6398   0.6029
 RJJ  H1   H  HCR6  0   0.255   3.5336  -1.7810   2.4640
 RJJ  H2   H  HCR6  0   0.251   3.3527   1.4306  -1.2835
 RJJ  H3   H  HCH2  0   0.212  -2.0767  -2.1239  -1.6777
 RJJ  H4   H  HCH2  0   0.243  -0.8922  -1.5536  -2.8240
 RJJ  H5   H  HCH3  0   0.205   0.5916  -3.4256  -1.6319
 RJJ  H6   H  HCH3  0   0.236   1.2674  -1.9287  -2.2959
 RJJ  H7   H  HCH3  0   0.239   1.7009  -2.4323  -0.6670
 RJJ  H8   H  HCH3  0   0.211  -5.2653   2.3377   0.3113
 RJJ  H9   H  HCH3  0   0.216  -4.3665   1.2663   1.3794
 RJJ  H10  H  HCH3  0   0.229  -3.7320   2.8645   0.9960
 RJJ  H11  H  HCH2  0   0.222  -4.2622   0.7249  -1.1087
 RJJ  H12  H  HCH2  0   0.226  -3.3715   2.1951  -1.3722
 RJJ  H13  H  HCH2  0   0.244   1.0626   2.1704   1.4409
 RJJ  H14  H  HCH2  0   0.244   1.5508   2.6013  -0.1885
 RJJ  H15  H  HCR6  0   0.249   1.7238  -0.1134   2.3583
 RJJ  H16  H  HCR6  0   0.255   5.2621  -1.8511   0.6912
 RJJ  H17  H  HCR6  0   0.255   5.1620  -0.2384  -1.1833
 RJJ  H18  H  HCH2  0   0.237  -1.1905   0.7127  -2.3098
 RJJ  H19  H  HCH2  0   0.243  -2.7647  -0.0113  -2.4284
 RJJ  H20  H  HCH2  0   0.234   0.1269  -2.5111   0.9915
 RJJ  H21  H  HCH2  0   0.204  -1.3413  -3.0471   0.1838
 RJJ  H22  H  HCH2  0   0.243  -1.9754  -1.7383   2.0481
 RJJ  H23  H  HCH2  0   0.229  -0.8119  -0.4878   1.7404
 RJJ  H24  H  HNH1  0   0.440   0.2209   0.1126  -0.4157
 RJJ  H26  H  HNH1  0   0.347  -3.3134  -0.9799   0.3053

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
 RJJ  C12  C13  aromatic  1.390  0.020  1.390
 RJJ  C12  C11  aromatic  1.388  0.020  1.388
 RJJ  C13  C08  aromatic  1.390  0.020  1.390
 RJJ  C11  C10  aromatic  1.390  0.020  1.390
 RJJ  N20  C19  single    1.448  0.020  1.448
 RJJ  N20  C03  single    1.461  0.020  1.461
 RJJ  C08  C09  aromatic  1.393  0.020  1.393
 RJJ  C08  C07  single    1.505  0.020  1.505
 RJJ  C10  C09  aromatic  1.387  0.020  1.387
 RJJ  C19  C18  single    1.529  0.020  1.529
 RJJ  C02  C03  single    1.545  0.020  1.545
 RJJ  C02  C01  single    1.523  0.020  1.523
 RJJ  N06  C07  single    1.448  0.020  1.448
 RJJ  N06  C04  single    1.338  0.020  1.338
 RJJ  C03  C04  single    1.550  0.020  1.550
 RJJ  C03  C14  single    1.560  0.020  1.560
 RJJ  C18  N16  single    1.457  0.020  1.457
 RJJ  C04  O05  double    1.226  0.020  1.226
 RJJ  C14  C15  single    1.526  0.020  1.526
 RJJ  N16  C15  single    1.461  0.020  1.461
 RJJ  N16  C17  single    1.452  0.020  1.452
 RJJ  C10  H1   single    0.930  0.020  1.080
 RJJ  C13  H2   single    0.930  0.020  1.080
 RJJ  C15  H3   single    0.970  0.020  1.090
 RJJ  C15  H4   single    0.970  0.020  1.090
 RJJ  C17  H5   single    0.970  0.020  1.090
 RJJ  C17  H6   single    0.970  0.020  1.090
 RJJ  C17  H7   single    0.970  0.020  1.090
 RJJ  C01  H8   single    0.970  0.020  1.090
 RJJ  C01  H9   single    0.970  0.020  1.090
 RJJ  C01  H10  single    0.970  0.020  1.090
 RJJ  C02  H11  single    0.970  0.020  1.090
 RJJ  C02  H12  single    0.970  0.020  1.090
 RJJ  C07  H13  single    0.970  0.020  1.090
 RJJ  C07  H14  single    0.970  0.020  1.090
 RJJ  C09  H15  single    0.930  0.020  1.080
 RJJ  C11  H16  single    0.930  0.020  1.080
 RJJ  C12  H17  single    0.930  0.020  1.080
 RJJ  C14  H18  single    0.970  0.020  1.090
 RJJ  C14  H19  single    0.970  0.020  1.090
 RJJ  C18  H20  single    0.970  0.020  1.090
 RJJ  C18  H21  single    0.970  0.020  1.090
 RJJ  C19  H22  single    0.970  0.020  1.090
 RJJ  C19  H23  single    0.970  0.020  1.090
 RJJ  N06  H24  single    0.860  0.020  1.020
 RJJ  N20  H26  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
 RJJ  H1   C10  C11  120.14  3.000
 RJJ  H1   C10  C09  119.85  3.000
 RJJ  C11  C10  C09  120.02  3.000
 RJJ  H2   C13  C12  119.64  3.000
 RJJ  H2   C13  C08  119.70  3.000
 RJJ  C12  C13  C08  120.66  3.000
 RJJ  H4   C15  H3   105.60  3.000
 RJJ  H4   C15  N16  108.93  3.000
 RJJ  H3   C15  N16  110.21  3.000
 RJJ  H4   C15  C14  107.13  3.000
 RJJ  H3   C15  C14  109.98  3.000
 RJJ  N16  C15  C14  114.56  3.000
 RJJ  H7   C17  H6   107.57  3.000
 RJJ  H7   C17  H5   108.28  3.000
 RJJ  H6   C17  H5   108.10  3.000
 RJJ  H7   C17  N16  109.69  3.000
 RJJ  H6   C17  N16  109.80  3.000
 RJJ  H5   C17  N16  113.23  3.000
 RJJ  H10  C01  H9   108.20  3.000
 RJJ  H10  C01  H8   107.90  3.000
 RJJ  H9   C01  H8   107.59  3.000
 RJJ  H10  C01  C02  112.42  3.000
 RJJ  H9   C01  C02  110.99  3.000
 RJJ  H8   C01  C02  109.58  3.000
 RJJ  H12  C02  H11  105.20  3.000
 RJJ  H12  C02  C03  108.62  3.000
 RJJ  H11  C02  C03  105.65  3.000
 RJJ  H12  C02  C01  110.37  3.000
 RJJ  H11  C02  C01  107.70  3.000
 RJJ  C03  C02  C01  118.40  3.000
 RJJ  N20  C03  C14  114.72  3.000
 RJJ  C14  C03  C04  109.56  3.000
 RJJ  N20  C03  C04  109.06  3.000
 RJJ  C14  C03  C02  106.34  3.000
 RJJ  C04  C03  C02  110.28  3.000
 RJJ  N20  C03  C02  106.79  3.000
 RJJ  O05  C04  N06  122.00  3.000
 RJJ  O05  C04  C03  122.75  3.000
 RJJ  N06  C04  C03  115.24  3.000
 RJJ  H14  C07  H13  106.70  3.000
 RJJ  H14  C07  N06  110.90  3.000
 RJJ  H13  C07  N06  109.94  3.000
 RJJ  H14  C07  C08  110.14  3.000
 RJJ  H13  C07  C08  110.24  3.000
 RJJ  N06  C07  C08  108.92  3.000
 RJJ  C09  C08  C07  120.13  3.000
 RJJ  C07  C08  C13  120.98  3.000
 RJJ  C09  C08  C13  118.83  3.000
 RJJ  H15  C09  C08  119.56  3.000
 RJJ  H15  C09  C10  119.72  3.000
 RJJ  C08  C09  C10  120.72  3.000
 RJJ  H16  C11  C12  120.18  3.000
 RJJ  H16  C11  C10  120.14  3.000
 RJJ  C12  C11  C10  119.68  3.000
 RJJ  H17  C12  C11  120.12  3.000
 RJJ  H17  C12  C13  119.80  3.000
 RJJ  C11  C12  C13  120.08  3.000
 RJJ  H19  C14  H18  105.21  3.000
 RJJ  H19  C14  C03  108.64  3.000
 RJJ  H18  C14  C03  109.66  3.000
 RJJ  H19  C14  C15  106.15  3.000
 RJJ  H18  C14  C15  109.45  3.000
 RJJ  C03  C14  C15  117.04  3.000
 RJJ  H21  C18  H20  106.51  3.000
 RJJ  H21  C18  N16  110.25  3.000
 RJJ  H20  C18  N16  108.63  3.000
 RJJ  H21  C18  C19  109.68  3.000
 RJJ  H20  C18  C19  107.52  3.000
 RJJ  N16  C18  C19  113.93  3.000
 RJJ  H23  C19  H22  105.24  3.000
 RJJ  H23  C19  N20  108.90  3.000
 RJJ  H22  C19  N20  106.89  3.000
 RJJ  H23  C19  C18  109.29  3.000
 RJJ  H22  C19  C18  106.86  3.000
 RJJ  N20  C19  C18  118.80  3.000
 RJJ  H24  N06  C07  118.25  3.000
 RJJ  H24  N06  C04  118.00  3.000
 RJJ  C07  N06  C04  122.79  3.000
 RJJ  C18  N16  C17  111.68  3.000
 RJJ  C17  N16  C15  112.94  3.000
 RJJ  C18  N16  C15  111.42  3.000
 RJJ  H26  N20  C19  111.17  3.000
 RJJ  H26  N20  C03  109.56  3.000
 RJJ  C19  N20  C03  121.89  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
 RJJ  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 RJJ  CONST_02  C13  C08  C09  C10     0.00   0.0  0
 RJJ  CONST_03  C11  C12  C13  C08     0.00   0.0  0
 RJJ  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 RJJ  CONST_05  C12  C13  C08  C09     0.00   0.0  0
 RJJ  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 RJJ  CONST_07  C07  C08  C09  C10   180.00   0.0  0
 RJJ  CONST_08  C12  C13  C08  C07   180.00   0.0  0
 RJJ  CONST_09  H17  C12  C11  C10   180.00   0.0  0
 RJJ  CONST_10  H16  C11  C12  C13   180.00   0.0  0
 RJJ  CONST_11  H15  C09  C08  C13   180.00   0.0  0
 RJJ  CONST_12  H1   C10  C09  C08   180.00   0.0  0
 RJJ  CONST_13  H2   C13  C08  C09   180.00   0.0  0
 RJJ  CONST_14  C07  N06  C04  C03   180.00   0.0  0
 RJJ  CONST_15  H24  N06  C04  C03     0.00   0.0  0
 RJJ  CONST_16  O05  C04  N06  C07     0.00   0.0  0
 RJJ  Var_01    N06  C07  C08  C13    98.99  30.0  2
 RJJ  Var_02    C08  C07  N06  C04   160.40  30.0  3
 RJJ  Var_03    H8   C01  C02  C03  -166.83  30.0  3

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
 RJJ  chir_01  C03  N20  C04  C14  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
 RJJ  plan-1  C10  0.020
 RJJ  plan-1  C13  0.020
 RJJ  plan-1  C07  0.020
 RJJ  plan-1  C08  0.020
 RJJ  plan-1  C09  0.020
 RJJ  plan-1  C11  0.020
 RJJ  plan-1  C12  0.020
 RJJ  plan-1  H1   0.020
 RJJ  plan-1  H2   0.020
 RJJ  plan-1  H15  0.020
 RJJ  plan-1  H16  0.020
 RJJ  plan-1  H17  0.020
 RJJ  plan-2  C03  0.020
 RJJ  plan-2  C04  0.020
 RJJ  plan-2  C07  0.020
 RJJ  plan-2  N06  0.020
 RJJ  plan-2  O05  0.020
 RJJ  plan-2  H24  0.020

