# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:22:55 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (7R)-N-benzyl-1,7-diethyl-2,3,6,7-tetrahydro-1H-1,4-diazepine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCN=CC[C@]1(CC)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
 RK1  RK1  (7R)-N-benzyl-1,7-diethyl-2,3,6,7-tetrahydro-1H-1,4-diazepine-7-carboxamide  ligand  46  21  .  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_RK1
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
 RK1  C10  C  CH2   0  -0.465  -1.9215  -0.2976  -2.0554
 RK1  C15  C  CH2   0  -0.320   1.6348  -1.4530   0.1652
 RK1  C17  C  CR16  0  -0.287   3.3233   0.1769   1.0645
 RK1  C20  C  CR16  0  -0.242   4.5834   0.3490  -1.3997
 RK1  C21  C  CR16  0  -0.286   3.4883  -0.4881  -1.2342
 RK1  C01  C  CH3   0  -0.681  -1.4145   3.5796  -0.5094
 RK1  C02  C  CH2   0  -0.291  -2.0518   2.2431  -0.8638
 RK1  C04  C  CH2   0  -0.308  -1.8467   1.4026   1.3452
 RK1  C05  C  CH2   0  -0.370  -1.6470   0.2913   2.3674
 RK1  C07  C  C1    0  -0.052  -3.3179  -1.1227   1.4654
 RK1  C08  C  CH2   0  -0.504  -3.2567  -0.6896   0.0281
 RK1  C09  C  CT    0  -0.013  -1.8979  -0.2164  -0.5059
 RK1  C11  C  CH3   0  -0.671  -1.9126  -1.6960  -2.6634
 RK1  C12  C  C     0   0.585  -0.7884  -1.1937  -0.0776
 RK1  C16  C  CR6   0   0.052   2.8499  -0.5841  -0.0008
 RK1  C18  C  CR16  0  -0.241   4.4173   1.0164   0.9025
 RK1  C19  C  CR16  0  -0.264   5.0499   1.1036  -0.3308
 RK1  N03  N  NT    0  -0.435  -1.5407   1.1367  -0.0588
 RK1  N06  N  N     0  -0.332  -2.6498  -0.7453   2.4661
 RK1  N14  N  NH1   0  -0.620   0.4458  -0.6820  -0.1364
 RK1  O13  O  O     0  -0.491  -1.0208  -2.3617   0.2012
 RK1  H1   H  HCH2  0   0.248  -2.8134   0.2261  -2.4066
 RK1  H2   H  HCH2  0   0.249  -1.0605   0.2482  -2.4479
 RK1  H3   H  HCH2  0   0.253   1.6924  -2.3158  -0.5027
 RK1  H4   H  HCH2  0   0.249   1.5855  -1.8435   1.1861
 RK1  H6   H  HCR6  0   0.257   5.0736   0.4113  -2.3627
 RK1  H7   H  HCR6  0   0.252   3.1289  -1.0768  -2.0702
 RK1  H8   H  HCH3  0   0.237  -1.7064   4.3249  -1.2496
 RK1  H9   H  HCH3  0   0.229  -1.7151   3.9605   0.4662
 RK1  H10  H  HCH3  0   0.225  -0.3264   3.4996  -0.5248
 RK1  H11  H  HCH2  0   0.196  -3.1477   2.3316  -0.7748
 RK1  H12  H  HCH2  0   0.252  -1.8362   2.0611  -1.9127
 RK1  H13  H  HCH2  0   0.206  -2.8841   1.7613   1.4576
 RK1  H14  H  HCH2  0   0.254  -1.2120   2.2267   1.6745
 RK1  H15  H  HCH2  0   0.245  -0.6573  -0.1674   2.2843
 RK1  H16  H  HCH2  0   0.255  -1.6285   0.7935   3.3381
 RK1  H17  H  H     0   0.235  -4.0673  -1.8913   1.6614
 RK1  H18  H  HCH2  0   0.263  -3.6218  -1.5293  -0.5640
 RK1  H19  H  HCH2  0   0.275  -3.9907   0.1096  -0.1347
 RK1  H20  H  HCH3  0   0.229  -0.9554  -2.1999  -2.5354
 RK1  H21  H  HCH3  0   0.228  -2.6881  -2.3423  -2.2528
 RK1  H22  H  HCH3  0   0.238  -2.0926  -1.6148  -3.7353
 RK1  H23  H  HCR6  0   0.258   4.7771   1.6009   1.7394
 RK1  H24  H  HCR6  0   0.258   5.9052   1.7547  -0.4567
 RK1  H26  H  HNH1  0   0.394   0.5131   0.3180  -0.2649
 RK1  H5   H  HCR6  0   0.252   2.8367   0.1087   2.0307

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
 RK1  C01  C02  single    1.523  0.020  1.523
 RK1  C02  N03  single    1.461  0.020  1.461
 RK1  C05  C04  single    1.523  0.020  1.523
 RK1  C05  N06  single    1.446  0.020  1.446
 RK1  C04  N03  single    1.461  0.020  1.461
 RK1  N03  C09  single    1.469  0.020  1.469
 RK1  N06  C07  double    1.261  0.020  1.261
 RK1  C11  C10  single    1.525  0.020  1.525
 RK1  C09  C08  single    1.535  0.020  1.535
 RK1  C09  C10  single    1.552  0.020  1.552
 RK1  C09  C12  single    1.539  0.020  1.539
 RK1  C08  C07  single    1.502  0.020  1.502
 RK1  N14  C12  single    1.337  0.020  1.337
 RK1  N14  C15  single    1.449  0.020  1.449
 RK1  C12  O13  double    1.223  0.020  1.223
 RK1  C18  C19  aromatic  1.389  0.020  1.389
 RK1  C18  C17  aromatic  1.388  0.020  1.388
 RK1  C19  C20  aromatic  1.389  0.020  1.389
 RK1  C17  C16  aromatic  1.392  0.020  1.392
 RK1  C20  C21  aromatic  1.388  0.020  1.388
 RK1  C16  C21  aromatic  1.392  0.020  1.392
 RK1  C16  C15  single    1.503  0.020  1.503
 RK1  C10  H1   single    0.970  0.020  1.090
 RK1  C10  H2   single    0.970  0.020  1.090
 RK1  C15  H3   single    0.970  0.020  1.090
 RK1  C15  H4   single    0.970  0.020  1.090
 RK1  C17  H5   single    0.930  0.020  1.080
 RK1  C20  H6   single    0.930  0.020  1.080
 RK1  C21  H7   single    0.930  0.020  1.080
 RK1  C01  H8   single    0.970  0.020  1.090
 RK1  C01  H9   single    0.970  0.020  1.090
 RK1  C01  H10  single    0.970  0.020  1.090
 RK1  C02  H11  single    0.970  0.020  1.090
 RK1  C02  H12  single    0.970  0.020  1.090
 RK1  C04  H13  single    0.970  0.020  1.090
 RK1  C04  H14  single    0.970  0.020  1.090
 RK1  C05  H15  single    0.970  0.020  1.090
 RK1  C05  H16  single    0.970  0.020  1.090
 RK1  C07  H17  single    0.930  0.020  1.080
 RK1  C08  H18  single    0.970  0.020  1.090
 RK1  C08  H19  single    0.970  0.020  1.090
 RK1  C11  H20  single    0.970  0.020  1.090
 RK1  C11  H21  single    0.970  0.020  1.090
 RK1  C11  H22  single    0.970  0.020  1.090
 RK1  C18  H23  single    0.930  0.020  1.080
 RK1  C19  H24  single    0.930  0.020  1.080
 RK1  N14  H26  single    0.860  0.020  1.020

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
 RK1  H2   C10  H1   106.76  3.000
 RK1  H2   C10  C11  108.08  3.000
 RK1  H1   C10  C11  108.43  3.000
 RK1  H2   C10  C09  108.70  3.000
 RK1  H1   C10  C09  107.96  3.000
 RK1  C11  C10  C09  116.49  3.000
 RK1  H4   C15  H3   106.92  3.000
 RK1  H4   C15  N14  110.32  3.000
 RK1  H3   C15  N14  109.65  3.000
 RK1  H4   C15  C16  110.23  3.000
 RK1  H3   C15  C16  110.27  3.000
 RK1  N14  C15  C16  109.44  3.000
 RK1  H5   C17  C18  119.72  3.000
 RK1  H5   C17  C16  119.67  3.000
 RK1  C18  C17  C16  120.61  3.000
 RK1  H6   C20  C19  120.08  3.000
 RK1  H6   C20  C21  119.87  3.000
 RK1  C19  C20  C21  120.05  3.000
 RK1  H7   C21  C16  119.59  3.000
 RK1  H7   C21  C20  119.82  3.000
 RK1  C16  C21  C20  120.59  3.000
 RK1  H10  C01  H9   108.27  3.000
 RK1  H10  C01  H8   107.91  3.000
 RK1  H9   C01  H8   107.16  3.000
 RK1  H10  C01  C02  110.48  3.000
 RK1  H9   C01  C02  113.56  3.000
 RK1  H8   C01  C02  109.27  3.000
 RK1  H12  C02  H11  106.78  3.000
 RK1  H12  C02  N03  109.62  3.000
 RK1  H11  C02  N03  111.35  3.000
 RK1  H12  C02  C01  106.78  3.000
 RK1  H11  C02  C01  109.07  3.000
 RK1  N03  C02  C01  112.97  3.000
 RK1  H14  C04  H13  105.70  3.000
 RK1  H14  C04  N03  107.80  3.000
 RK1  H13  C04  N03  110.73  3.000
 RK1  H14  C04  C05  105.80  3.000
 RK1  H13  C04  C05  106.98  3.000
 RK1  N03  C04  C05  118.98  3.000
 RK1  H16  C05  H15  104.17  3.000
 RK1  H16  C05  N06  106.30  3.000
 RK1  H15  C05  N06  109.39  3.000
 RK1  H16  C05  C04  105.25  3.000
 RK1  H15  C05  C04  111.93  3.000
 RK1  N06  C05  C04  118.56  3.000
 RK1  H17  C07  N06  115.60  3.000
 RK1  H17  C07  C08  113.76  3.000
 RK1  N06  C07  C08  130.64  3.000
 RK1  H19  C08  H18  104.85  3.000
 RK1  H19  C08  C09  108.42  3.000
 RK1  H18  C08  C09  110.18  3.000
 RK1  H19  C08  C07  108.95  3.000
 RK1  H18  C08  C07  106.49  3.000
 RK1  C09  C08  C07  117.25  3.000
 RK1  N03  C09  C12  108.96  3.000
 RK1  C12  C09  C08  110.21  3.000
 RK1  N03  C09  C08  113.16  3.000
 RK1  C12  C09  C10  104.80  3.000
 RK1  C08  C09  C10  108.53  3.000
 RK1  N03  C09  C10  110.84  3.000
 RK1  H22  C11  H21  107.29  3.000
 RK1  H22  C11  H20  107.16  3.000
 RK1  H21  C11  H20  107.86  3.000
 RK1  H22  C11  C10  108.83  3.000
 RK1  H21  C11  C10  112.92  3.000
 RK1  H20  C11  C10  112.49  3.000
 RK1  O13  C12  N14  123.42  3.000
 RK1  O13  C12  C09  122.19  3.000
 RK1  N14  C12  C09  114.20  3.000
 RK1  C21  C16  C17  118.97  3.000
 RK1  C21  C16  C15  120.56  3.000
 RK1  C17  C16  C15  120.43  3.000
 RK1  H23  C18  C19  120.09  3.000
 RK1  H23  C18  C17  119.88  3.000
 RK1  C19  C18  C17  120.03  3.000
 RK1  H24  C19  C18  120.07  3.000
 RK1  H24  C19  C20  120.18  3.000
 RK1  C18  C19  C20  119.75  3.000
 RK1  C09  N03  C04  114.15  3.000
 RK1  C09  N03  C02  116.42  3.000
 RK1  C04  N03  C02  108.56  3.000
 RK1  C07  N06  C05  121.86  3.000
 RK1  H26  N14  C12  116.47  3.000
 RK1  H26  N14  C15  119.90  3.000
 RK1  C12  N14  C15  122.99  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
 RK1  CONST_01  C20  C19  C18  C17    0.00   0.0  0
 RK1  CONST_02  C20  C21  C16  C17    0.00   0.0  0
 RK1  CONST_03  C18  C19  C20  C21    0.00   0.0  0
 RK1  CONST_04  C18  C17  C16  C21    0.00   0.0  0
 RK1  CONST_05  C19  C18  C17  C16    0.00   0.0  0
 RK1  CONST_06  C19  C20  C21  C16    0.00   0.0  0
 RK1  CONST_07  C18  C17  C16  C15  180.00   0.0  0
 RK1  CONST_08  C20  C21  C16  C15  180.00   0.0  0
 RK1  CONST_09  H24  C19  C18  C17  180.00   0.0  0
 RK1  CONST_10  H7   C21  C16  C17  180.00   0.0  0
 RK1  CONST_11  H23  C18  C19  C20  180.00   0.0  0
 RK1  CONST_12  H5   C17  C16  C21  180.00   0.0  0
 RK1  CONST_13  H6   C20  C21  C16  180.00   0.0  0
 RK1  CONST_14  C09  C12  N14  C15  180.00   0.0  0
 RK1  CONST_15  H26  N14  C12  C09    0.00   0.0  0
 RK1  CONST_16  O13  C12  N14  C15    0.00   0.0  0
 RK1  Var_01    N14  C15  C16  C17   88.51  30.0  2
 RK1  Var_02    C16  C15  N14  C12  179.82  30.0  3
 RK1  Var_03    H20  C11  C10  C09  -70.42  30.0  3
 RK1  Var_04    H8   C01  C02  N03  170.39  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
 RK1  chir_01  C09  C08  N03  C12  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
 RK1  plan-1  C15  0.020
 RK1  plan-1  C17  0.020
 RK1  plan-1  C20  0.020
 RK1  plan-1  C21  0.020
 RK1  plan-1  C16  0.020
 RK1  plan-1  C18  0.020
 RK1  plan-1  C19  0.020
 RK1  plan-1  H6   0.020
 RK1  plan-1  H7   0.020
 RK1  plan-1  H23  0.020
 RK1  plan-1  H24  0.020
 RK1  plan-1  H5   0.020
 RK1  plan-2  C15  0.020
 RK1  plan-2  C09  0.020
 RK1  plan-2  C12  0.020
 RK1  plan-2  N14  0.020
 RK1  plan-2  O13  0.020
 RK1  plan-2  H26  0.020

