# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:08:41 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N~2~-[(benzyloxy)carbonyl]-N-[(3R)-1-cyanopyrrolidin-3-yl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H]2CCN(C2)C#N
#
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
 NBL  NBL  N~2~-[(benzyloxy)carbonyl]-N-[(3R)-1-cyanopyrrolidin-3-yl]-L-leucinamide  ligand  52  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NBL
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
 NBL  C1    C  CH3   0  -0.659  -2.4092   3.4463   1.4688
 NBL  C2    C  CH1   0  -0.255  -1.9231   3.5605   0.0267
 NBL  C3    C  CH3   0  -0.649  -1.7158   5.0244  -0.3492
 NBL  C4    C  CH2   0  -0.407  -0.6223   2.7909  -0.2072
 NBL  C5    C  CH1   0  -0.203  -0.6857   1.2795   0.0429
 NBL  N6    N  NH1   0  -0.663   0.6009   0.6530  -0.1567
 NBL  C7    C  C     0   0.764   1.5063   0.5461   0.8337
 NBL  O8    O  O     0  -0.520   1.3111   0.8369   1.9965
 NBL  O9    O  O2    0  -0.480   2.6596   0.0545   0.3693
 NBL  C10   C  CH2   0  -0.240   3.7179  -0.1225   1.3191
 NBL  C11   C  CR6   0   0.076   4.8835  -0.6937   0.5713
 NBL  C12   C  CR16  0  -0.292   5.8559   0.1456   0.0362
 NBL  C13   C  CR16  0  -0.242   6.9235  -0.3784  -0.6803
 NBL  C14   C  CR16  0  -0.261   7.0252  -1.7504  -0.8696
 NBL  C15   C  CR16  0  -0.242   6.0588  -2.5953  -0.3385
 NBL  C16   C  CR16  0  -0.289   4.9935  -2.0679   0.3777
 NBL  C17   C  C     0   0.568  -1.6649   0.6288  -0.9265
 NBL  O18   O  O     0  -0.487  -1.3823   0.4892  -2.1075
 NBL  N19   N  NH1   0  -0.637  -2.8437   0.2624  -0.4060
 NBL  C20   C  CH1   0  -0.140  -3.9057  -0.3169  -1.2047
 NBL  C21   C  CH2   0  -0.518  -5.1962  -0.3810  -0.3912
 NBL  C22   C  CH2   0  -0.261  -5.0264  -1.6167   0.4885
 NBL  N23   N  NT    0  -0.479  -4.1516  -2.4610  -0.3288
 NBL  C24   C  CH2   0  -0.248  -3.6467  -1.7882  -1.5252
 NBL  C25   C  CSP   0   0.290  -3.8689  -3.6991  -0.0299
 NBL  N26   N  NS    0  -0.358  -3.6168  -4.8009   0.2368
 NBL  H11   H  HCH3  0   0.235  -3.3017   4.0532   1.6269
 NBL  H12A  H  HCH3  0   0.219  -2.6640   2.4234   1.7504
 NBL  H13A  H  HCH3  0   0.221  -1.6433   3.7965   2.1648
 NBL  H2    H  HCH1  0   0.226  -2.7006   3.1565  -0.6321
 NBL  H31   H  HCH3  0   0.216  -0.9500   5.4826   0.2812
 NBL  H32   H  HCH3  0   0.228  -1.3955   5.1277  -1.3873
 NBL  H33   H  HCH3  0   0.229  -2.6342   5.5997  -0.2247
 NBL  H41   H  HCH2  0   0.236  -0.2815   2.9538  -1.2341
 NBL  H42   H  HCH2  0   0.239   0.1546   3.2004   0.4465
 NBL  H5    H  HCH1  0   0.275  -0.9943   1.0877   1.0716
 NBL  HN6   H  HNH1  0   0.399   0.8969   0.4915  -1.1077
 NBL  H101  H  HCH2  0   0.248   3.9813   0.8364   1.7701
 NBL  H102  H  HCH2  0   0.248   3.3973  -0.7964   2.1161
 NBL  H12   H  HCR6  0   0.255   5.7814   1.2162   0.1864
 NBL  H13   H  HCR6  0   0.258   7.6764   0.2832  -1.0883
 NBL  H14   H  HCR6  0   0.259   7.8592  -2.1614  -1.4236
 NBL  H15   H  HCR6  0   0.259   6.1362  -3.6654  -0.4812
 NBL  H16   H  HCR6  0   0.255   4.2446  -2.7307   0.7955
 NBL  H19   H  HNH1  0   0.409  -2.9885   0.3713   0.5855
 NBL  H20   H  HCH1  0   0.292  -4.0294   0.2639  -2.1185
 NBL  H211  H  HCH2  0   0.279  -5.3815   0.5226   0.1890
 NBL  H212  H  HCH2  0   0.281  -6.0345  -0.5165  -1.0747
 NBL  H221  H  HCH2  0   0.257  -4.5491  -1.3824   1.4427
 NBL  H222  H  HCH2  0   0.272  -5.9748  -2.1111   0.6956
 NBL  H241  H  HCH2  0   0.261  -4.2090  -2.0897  -2.4123
 NBL  H242  H  HCH2  0   0.277  -2.5943  -2.0119  -1.6901

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
 NBL  C1   C2    single    1.526  0.020  1.526
 NBL  C1   H11   single    0.970  0.020  1.090
 NBL  C1   H12A  single    0.970  0.020  1.090
 NBL  C1   H13A  single    0.970  0.020  1.090
 NBL  C2   C3    single    1.526  0.020  1.526
 NBL  C2   C4    single    1.529  0.020  1.529
 NBL  C2   H2    single    0.970  0.020  1.090
 NBL  C3   H31   single    0.970  0.020  1.090
 NBL  C3   H32   single    0.970  0.020  1.090
 NBL  C3   H33   single    0.970  0.020  1.090
 NBL  C4   C5    single    1.533  0.020  1.533
 NBL  C4   H41   single    0.970  0.020  1.090
 NBL  C4   H42   single    0.970  0.020  1.090
 NBL  C5   N6    single    1.445  0.020  1.445
 NBL  C5   C17   single    1.524  0.020  1.524
 NBL  C5   H5    single    0.970  0.020  1.090
 NBL  N6   C7    single    1.346  0.020  1.346
 NBL  N6   HN6   single    0.860  0.020  1.020
 NBL  C7   O8    double    1.214  0.020  1.214
 NBL  C7   O9    single    1.337  0.020  1.337
 NBL  O9   C10   single    1.433  0.020  1.433
 NBL  C10  C11   single    1.498  0.020  1.498
 NBL  C10  H101  single    0.970  0.020  1.090
 NBL  C10  H102  single    0.970  0.020  1.090
 NBL  C11  C12   aromatic  1.391  0.020  1.391
 NBL  C11  C16   aromatic  1.392  0.020  1.392
 NBL  C12  C13   aromatic  1.388  0.020  1.388
 NBL  C12  H12   single    0.930  0.020  1.080
 NBL  C13  C14   aromatic  1.389  0.020  1.389
 NBL  C13  H13   single    0.930  0.020  1.080
 NBL  C14  C15   aromatic  1.389  0.020  1.389
 NBL  C14  H14   single    0.930  0.020  1.080
 NBL  C15  C16   aromatic  1.388  0.020  1.388
 NBL  C15  H15   single    0.930  0.020  1.080
 NBL  C16  H16   single    0.930  0.020  1.080
 NBL  C17  O18   double    1.222  0.020  1.222
 NBL  C17  N19   single    1.340  0.020  1.340
 NBL  N19  C20   single    1.450  0.020  1.450
 NBL  N19  H19   single    0.860  0.020  1.020
 NBL  C20  C21   single    1.527  0.020  1.527
 NBL  C20  C24   single    1.528  0.020  1.528
 NBL  C20  H20   single    0.970  0.020  1.090
 NBL  C21  C22   single    1.526  0.020  1.526
 NBL  C21  H211  single    0.970  0.020  1.090
 NBL  C21  H212  single    0.970  0.020  1.090
 NBL  C22  N23   single    1.465  0.020  1.465
 NBL  C22  H221  single    0.970  0.020  1.090
 NBL  C22  H222  single    0.970  0.020  1.090
 NBL  N23  C24   single    1.462  0.020  1.462
 NBL  N23  C25   single    1.305  0.020  1.305
 NBL  C24  H241  single    0.970  0.020  1.090
 NBL  C24  H242  single    0.970  0.020  1.090
 NBL  C25  N26   triple    1.161  0.020  1.161

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
 NBL  H13A  C1   H12A  107.44  3.000
 NBL  H13A  C1   H11   107.63  3.000
 NBL  H12A  C1   H11   107.05  3.000
 NBL  H13A  C1   C2    110.77  3.000
 NBL  H12A  C1   C2    112.86  3.000
 NBL  H11   C1   C2    110.85  3.000
 NBL  H2    C2   C4    109.02  3.000
 NBL  H2    C2   C3    107.57  3.000
 NBL  C4    C2   C3    109.24  3.000
 NBL  H2    C2   C1    108.32  3.000
 NBL  C4    C2   C1    112.19  3.000
 NBL  C3    C2   C1    110.37  3.000
 NBL  H33   C3   H32   107.81  3.000
 NBL  H33   C3   H31   107.64  3.000
 NBL  H32   C3   H31   107.67  3.000
 NBL  H33   C3   C2    111.31  3.000
 NBL  H32   C3   C2    111.42  3.000
 NBL  H31   C3   C2    110.82  3.000
 NBL  H42   C4   H41   106.48  3.000
 NBL  H42   C4   C5    107.50  3.000
 NBL  H41   C4   C5    108.22  3.000
 NBL  H42   C4   C2    108.91  3.000
 NBL  H41   C4   C2    109.48  3.000
 NBL  C5    C4   C2    115.84  3.000
 NBL  H5    C5   C17   110.06  3.000
 NBL  H5    C5   N6    107.81  3.000
 NBL  C17   C5   N6    107.41  3.000
 NBL  H5    C5   C4    109.80  3.000
 NBL  C17   C5   C4    110.10  3.000
 NBL  N6    C5   C4    111.59  3.000
 NBL  HN6   N6   C7    118.90  3.000
 NBL  HN6   N6   C5    117.44  3.000
 NBL  C7    N6   C5    122.13  3.000
 NBL  O9    C7   O8    124.01  3.000
 NBL  O9    C7   N6    110.73  3.000
 NBL  O8    C7   N6    125.26  3.000
 NBL  C10   O9   C7    116.89  3.000
 NBL  H102  C10  H101  108.14  3.000
 NBL  H102  C10  C11   110.95  3.000
 NBL  H101  C10  C11   110.69  3.000
 NBL  H102  C10  O9    110.07  3.000
 NBL  H101  C10  O9    110.09  3.000
 NBL  C11   C10  O9    106.91  3.000
 NBL  C16   C11  C12   119.12  3.000
 NBL  C16   C11  C10   120.48  3.000
 NBL  C12   C11  C10   120.38  3.000
 NBL  H12   C12  C13   119.81  3.000
 NBL  H12   C12  C11   119.64  3.000
 NBL  C13   C12  C11   120.54  3.000
 NBL  H13   C13  C14   120.11  3.000
 NBL  H13   C13  C12   119.93  3.000
 NBL  C14   C13  C12   119.97  3.000
 NBL  H14   C14  C15   120.05  3.000
 NBL  H14   C14  C13   120.09  3.000
 NBL  C15   C14  C13   119.86  3.000
 NBL  H15   C15  C16   119.91  3.000
 NBL  H15   C15  C14   120.08  3.000
 NBL  C16   C15  C14   120.01  3.000
 NBL  H16   C16  C15   119.80  3.000
 NBL  H16   C16  C11   119.70  3.000
 NBL  C15   C16  C11   120.51  3.000
 NBL  N19   C17  O18   123.20  3.000
 NBL  N19   C17  C5    115.79  3.000
 NBL  O18   C17  C5    120.99  3.000
 NBL  H19   N19  C20   118.68  3.000
 NBL  H19   N19  C17   118.62  3.000
 NBL  C20   N19  C17   122.68  3.000
 NBL  H20   C20  C24   110.89  3.000
 NBL  H20   C20  C21   111.92  3.000
 NBL  C24   C20  C21   102.39  3.000
 NBL  H20   C20  N19   109.40  3.000
 NBL  C24   C20  N19   112.09  3.000
 NBL  C21   C20  N19   110.03  3.000
 NBL  H212  C21  H211  107.83  3.000
 NBL  H212  C21  C22   110.27  3.000
 NBL  H211  C21  C22   112.55  3.000
 NBL  H212  C21  C20   108.73  3.000
 NBL  H211  C21  C20   113.11  3.000
 NBL  C22   C21  C20   104.30  3.000
 NBL  H222  C22  H221  108.16  3.000
 NBL  H222  C22  N23   111.37  3.000
 NBL  H221  C22  N23   110.50  3.000
 NBL  H222  C22  C21   112.34  3.000
 NBL  H221  C22  C21   112.24  3.000
 NBL  N23   C22  C21   102.21  3.000
 NBL  C25   N23  C24   123.31  3.000
 NBL  C25   N23  C22   123.26  3.000
 NBL  C24   N23  C22   113.42  3.000
 NBL  H242  C24  H241  108.53  3.000
 NBL  H242  C24  N23   111.29  3.000
 NBL  H241  C24  N23   111.07  3.000
 NBL  H242  C24  C20   113.18  3.000
 NBL  H241  C24  C20   110.41  3.000
 NBL  N23   C24  C20   102.29  3.000
 NBL  N26   C25  N23   180.00  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
 NBL  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 NBL  CONST_02  C14  C15  C16  C11    0.00   0.0  0
 NBL  CONST_03  C15  C16  C11  C12    0.00   0.0  0
 NBL  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 NBL  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 NBL  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 NBL  CONST_07  C13  C12  C11  C10  180.00   0.0  0
 NBL  CONST_08  C15  C16  C11  C10  180.00   0.0  0
 NBL  CONST_09  H13  C13  C12  C11  180.00   0.0  0
 NBL  CONST_10  H15  C15  C16  C11  180.00   0.0  0
 NBL  CONST_11  H16  C16  C11  C12  180.00   0.0  0
 NBL  CONST_12  H14  C14  C13  C12  180.00   0.0  0
 NBL  CONST_13  H12  C12  C13  C14  180.00   0.0  0
 NBL  CONST_14  C20  N19  C17  C5   180.00   0.0  0
 NBL  CONST_15  C20  N19  C17  O18    0.00   0.0  0
 NBL  CONST_16  H19  N19  C17  C5     0.00   0.0  0
 NBL  Var_01    N23  C22  C21  C20  -28.79  30.0  1
 NBL  Var_02    C22  N23  C24  C20   16.91  30.0  1
 NBL  Var_03    C24  N23  C22  C21    7.34  30.0  1
 NBL  Var_04    C12  C11  C10  O9    92.75  30.0  2
 NBL  Var_05    C11  C10  O9   C7   179.30  30.0  3
 NBL  Var_06    C5   C4   C2   C1    60.86  30.0  3
 NBL  Var_07    O8   C7   N6   C5     7.09  30.0  2
 NBL  Var_08    H31  C3   C2   C1    61.78  30.0  3
 NBL  Var_09    H11  C1   C2   C3    54.33  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
 NBL  chir_01  C5   C4   N6   C17  positiv
 NBL  chir_02  C20  N19  C21  C24  positiv

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
 NBL  plan-1  C10  0.020
 NBL  plan-1  C11  0.020
 NBL  plan-1  C12  0.020
 NBL  plan-1  C13  0.020
 NBL  plan-1  C14  0.020
 NBL  plan-1  C15  0.020
 NBL  plan-1  C16  0.020
 NBL  plan-1  H12  0.020
 NBL  plan-1  H13  0.020
 NBL  plan-1  H14  0.020
 NBL  plan-1  H15  0.020
 NBL  plan-1  H16  0.020
 NBL  plan-2  C5   0.020
 NBL  plan-2  C17  0.020
 NBL  plan-2  O18  0.020
 NBL  plan-2  N19  0.020
 NBL  plan-2  C20  0.020
 NBL  plan-2  H19  0.020
 NBL  plan-3  N6   0.020
 NBL  plan-3  C7   0.020
 NBL  plan-3  O8   0.020
 NBL  plan-3  O9   0.020

