# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:43:54 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: ethyl N-{[3-(3-aminopyridin-4-yl)benzyl]carbamoyl}glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CNC(=O)NCc1cccc(c1)c2ccncc2N
#
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
 4ZZ  4ZZ  'ethyl N-{[3-(3-aminopyridin-4-yl)benzyl]carbamoyl}glycinate'  ligand  44  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4ZZ
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
 4ZZ  C14  C  CR6   0   0.067  -3.3494  -0.0924   0.2932
 4ZZ  C15  C  CR16  0  -0.314  -2.9162  -0.8637   1.3706
 4ZZ  C16  C  CR16  0  -0.221  -1.5848  -1.2430   1.4632
 4ZZ  C17  C  CR16  0  -0.310  -0.6749  -0.8671   0.4862
 4ZZ  C22  C  CR16  0  -0.099  -6.3458   2.1473  -0.0998
 4ZZ  C20  C  CR16  0  -0.150  -7.1231   0.0267   0.1552
 4ZZ  C19  C  CR6   0   0.196  -5.8378  -0.5222   0.2705
 4ZZ  C18  C  CR6   0   0.101  -4.7514   0.3661   0.1917
 4ZZ  C2   C  CH2   0  -0.183   7.8371   0.3975   1.0362
 4ZZ  C13  C  CR16  0  -0.360  -2.4216   0.2844  -0.6781
 4ZZ  C1   C  CH3   0  -0.690   8.9575  -0.6116   1.0826
 4ZZ  C6   C  CH2   0  -0.359   4.5595  -0.3253  -0.4934
 4ZZ  C4   C  C     0   0.564   5.6139   0.4813   0.2243
 4ZZ  C12  C  CR6   0   0.134  -1.0877  -0.0963  -0.5969
 4ZZ  C11  C  CH2   0  -0.359  -0.1268   0.3077  -1.6923
 4ZZ  O3   O  O2    0  -0.452   6.7229  -0.2174   0.3626
 4ZZ  O5   O  O     0  -0.448   5.4603   1.6097   0.6201
 4ZZ  N7   N  NH1   0  -0.696   3.3628   0.4505  -0.6441
 4ZZ  O9   O  O     0  -0.548   2.2440  -1.2253  -1.6677
 4ZZ  N10  N  NH1   0  -0.674   1.1648   0.7286  -1.2191
 4ZZ  N21  N  N     0  -0.391  -7.3752   1.3115  -0.0192
 4ZZ  C23  C  CR16  0  -0.364  -5.0348   1.7141  -0.0029
 4ZZ  H1   H  HCR6  0   0.261  -3.6117  -1.1517   2.1484
 4ZZ  H2   H  HCR6  0   0.258  -1.2542  -1.8337   2.3077
 4ZZ  H3   H  HCR6  0   0.255   0.3574  -1.1813   0.5731
 4ZZ  H4   H  HCR6  0   0.254  -6.5705   3.1977  -0.2430
 4ZZ  H5   H  HCR6  0   0.258  -7.9819  -0.6373   0.2085
 4ZZ  H6   H  HCH2  0   0.240   7.5348   0.6937   2.0421
 4ZZ  H7   H  HCH2  0   0.241   8.1387   1.2955   0.4942
 4ZZ  H8   H  HCR6  0   0.252  -2.7500   0.8821  -1.5219
 4ZZ  H9   H  HCH3  0   0.238   8.6660  -1.5083   1.6294
 4ZZ  H10  H  HCH3  0   0.238   9.2810  -0.9003   0.0829
 4ZZ  H11  H  HCH3  0   0.242   9.8115  -0.1718   1.5964
 4ZZ  H12  H  HCH2  0   0.280   4.9658  -0.6356  -1.4608
 4ZZ  H13  H  HCH2  0   0.278   4.3855  -1.2443   0.0763
 4ZZ  H14  H  HCH2  0   0.267   0.0155  -0.5253  -2.3815
 4ZZ  H15  H  HCH2  0   0.263  -0.5705   1.1161  -2.2762
 4ZZ  H16  H  HNH1  0   0.397   3.3305   1.3536  -0.1981
 4ZZ  H17  H  HNH1  0   0.394   1.2114   1.6167  -0.7461
 4ZZ  H18  H  HCR6  0   0.265  -4.2268   2.4321  -0.0620
 4ZZ  H19  H  HNH2  0   0.385  -6.4730  -2.4398   0.2155
 4ZZ  H20  H  HNH2  0   0.385  -4.8144  -2.2768   0.1721
 4ZZ  N24  N  NH2   0  -0.853  -5.6840  -1.8723   0.4826
 4ZZ  C8   C  C     0   0.756   2.2507  -0.0900  -1.2011

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
 4ZZ  O9   C8   double    1.227  0.020  1.227
 4ZZ  C11  N10  single    1.439  0.020  1.439
 4ZZ  C11  C12  single    1.512  0.020  1.512
 4ZZ  C8   N10  single    1.360  0.020  1.360
 4ZZ  C8   N7   single    1.356  0.020  1.356
 4ZZ  C22  C23  aromatic  1.384  0.020  1.384
 4ZZ  C22  N21  aromatic  1.328  0.020  1.328
 4ZZ  C23  C18  aromatic  1.391  0.020  1.391
 4ZZ  C12  C13  aromatic  1.389  0.020  1.389
 4ZZ  C12  C17  aromatic  1.392  0.020  1.392
 4ZZ  C6   N7   single    1.434  0.020  1.434
 4ZZ  C6   C4   single    1.509  0.020  1.509
 4ZZ  C13  C14  aromatic  1.395  0.020  1.395
 4ZZ  N21  C20  aromatic  1.321  0.020  1.321
 4ZZ  O3   C4   single    1.318  0.020  1.318
 4ZZ  O3   C2   single    1.440  0.020  1.440
 4ZZ  C17  C16  aromatic  1.387  0.020  1.387
 4ZZ  C4   O5   double    1.206  0.020  1.206
 4ZZ  C14  C18  single    1.479  0.020  1.479
 4ZZ  C14  C15  aromatic  1.394  0.020  1.394
 4ZZ  C18  C19  aromatic  1.406  0.020  1.406
 4ZZ  C1   C2   single    1.509  0.020  1.509
 4ZZ  C16  C15  aromatic  1.388  0.020  1.388
 4ZZ  C20  C19  aromatic  1.402  0.020  1.402
 4ZZ  C19  N24  single    1.375  0.020  1.375
 4ZZ  C15  H1   single    0.930  0.020  1.080
 4ZZ  C16  H2   single    0.930  0.020  1.080
 4ZZ  C17  H3   single    0.930  0.020  1.080
 4ZZ  C22  H4   single    0.930  0.020  1.080
 4ZZ  C20  H5   single    0.930  0.020  1.080
 4ZZ  C2   H6   single    0.970  0.020  1.090
 4ZZ  C2   H7   single    0.970  0.020  1.090
 4ZZ  C13  H8   single    0.930  0.020  1.080
 4ZZ  C1   H9   single    0.970  0.020  1.090
 4ZZ  C1   H10  single    0.970  0.020  1.090
 4ZZ  C1   H11  single    0.970  0.020  1.090
 4ZZ  C6   H12  single    0.970  0.020  1.090
 4ZZ  C6   H13  single    0.970  0.020  1.090
 4ZZ  C11  H14  single    0.970  0.020  1.090
 4ZZ  C11  H15  single    0.970  0.020  1.090
 4ZZ  N7   H16  single    0.860  0.020  1.020
 4ZZ  N10  H17  single    0.860  0.020  1.020
 4ZZ  C23  H18  single    0.930  0.020  1.080
 4ZZ  N24  H19  single    0.890  0.020  1.040
 4ZZ  N24  H20  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
 4ZZ  C13  C14  C18  119.94  3.000
 4ZZ  C18  C14  C15  121.28  3.000
 4ZZ  C13  C14  C15  118.74  3.000
 4ZZ  H1   C15  C16  119.73  3.000
 4ZZ  H1   C15  C14  120.20  3.000
 4ZZ  C16  C15  C14  120.07  3.000
 4ZZ  H2   C16  C17  119.81  3.000
 4ZZ  H2   C16  C15  119.63  3.000
 4ZZ  C17  C16  C15  120.56  3.000
 4ZZ  H3   C17  C12  120.40  3.000
 4ZZ  H3   C17  C16  119.36  3.000
 4ZZ  C12  C17  C16  120.24  3.000
 4ZZ  H4   C22  C23  120.60  3.000
 4ZZ  H4   C22  N21  117.20  3.000
 4ZZ  C23  C22  N21  122.20  3.000
 4ZZ  H5   C20  N21  116.74  3.000
 4ZZ  H5   C20  C19  118.75  3.000
 4ZZ  N21  C20  C19  124.51  3.000
 4ZZ  N24  C19  C18  122.86  3.000
 4ZZ  N24  C19  C20  119.96  3.000
 4ZZ  C18  C19  C20  117.16  3.000
 4ZZ  C23  C18  C19  117.57  3.000
 4ZZ  C19  C18  C14  122.22  3.000
 4ZZ  C23  C18  C14  120.21  3.000
 4ZZ  H7   C2   H6   108.12  3.000
 4ZZ  H7   C2   O3   109.45  3.000
 4ZZ  H6   C2   O3   109.44  3.000
 4ZZ  H7   C2   C1   111.13  3.000
 4ZZ  H6   C2   C1   111.03  3.000
 4ZZ  O3   C2   C1   107.66  3.000
 4ZZ  H8   C13  C12  119.14  3.000
 4ZZ  H8   C13  C14  119.27  3.000
 4ZZ  C12  C13  C14  121.59  3.000
 4ZZ  H11  C1   H10  107.87  3.000
 4ZZ  H11  C1   H9   107.77  3.000
 4ZZ  H10  C1   H9   108.77  3.000
 4ZZ  H11  C1   C2   109.06  3.000
 4ZZ  H10  C1   C2   111.68  3.000
 4ZZ  H9   C1   C2   111.54  3.000
 4ZZ  H13  C6   H12  106.32  3.000
 4ZZ  H13  C6   N7   112.09  3.000
 4ZZ  H12  C6   N7   111.74  3.000
 4ZZ  H13  C6   C4   108.18  3.000
 4ZZ  H12  C6   C4   108.21  3.000
 4ZZ  N7   C6   C4   110.11  3.000
 4ZZ  O5   C4   O3   124.67  3.000
 4ZZ  O5   C4   C6   124.57  3.000
 4ZZ  O3   C4   C6   110.76  3.000
 4ZZ  C11  C12  C13  119.64  3.000
 4ZZ  C13  C12  C17  118.81  3.000
 4ZZ  C11  C12  C17  121.54  3.000
 4ZZ  H15  C11  H14  106.30  3.000
 4ZZ  H15  C11  N10  108.92  3.000
 4ZZ  H14  C11  N10  108.31  3.000
 4ZZ  H15  C11  C12  109.10  3.000
 4ZZ  H14  C11  C12  109.68  3.000
 4ZZ  N10  C11  C12  114.23  3.000
 4ZZ  C4   O3   C2   118.28  3.000
 4ZZ  H16  N7   C8   120.84  3.000
 4ZZ  H16  N7   C6   117.71  3.000
 4ZZ  C8   N7   C6   120.79  3.000
 4ZZ  H17  N10  C11  117.00  3.000
 4ZZ  H17  N10  C8   119.18  3.000
 4ZZ  C11  N10  C8   123.04  3.000
 4ZZ  C20  N21  C22  118.17  3.000
 4ZZ  H18  C23  C18  119.89  3.000
 4ZZ  H18  C23  C22  119.71  3.000
 4ZZ  C18  C23  C22  120.40  3.000
 4ZZ  H20  N24  H19  111.58  3.000
 4ZZ  H20  N24  C19  116.29  3.000
 4ZZ  H19  N24  C19  115.10  3.000
 4ZZ  N10  C8   O9   123.18  3.000
 4ZZ  N10  C8   N7   114.86  3.000
 4ZZ  O9   C8   N7   121.95  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
 4ZZ  CONST_01  C17  C12  C13  C14     0.00   0.0  0
 4ZZ  CONST_02  C22  C23  C18  C14   180.00   0.0  0
 4ZZ  CONST_03  C20  C19  C18  C14   180.00   0.0  0
 4ZZ  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 4ZZ  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 4ZZ  CONST_08  C12  C17  C16  C15     0.00   0.0  0
 4ZZ  CONST_09  C13  C12  C17  C16     0.00   0.0  0
 4ZZ  CONST_10  C13  C14  C15  C16     0.00   0.0  0
 4ZZ  CONST_11  C18  C14  C15  C16   180.00   0.0  0
 4ZZ  CONST_12  C19  C18  C23  C22     0.00   0.0  0
 4ZZ  CONST_13  C19  C20  N21  C22     0.00   0.0  0
 4ZZ  CONST_14  C23  C22  N21  C20     0.00   0.0  0
 4ZZ  CONST_15  C23  C18  C19  C20     0.00   0.0  0
 4ZZ  CONST_17  N21  C22  C23  C18     0.00   0.0  0
 4ZZ  CONST_18  C12  C13  C14  C18   180.00   0.0  0
 4ZZ  CONST_19  N21  C20  C19  C18     0.00   0.0  0
 4ZZ  CONST_21  C11  C12  C13  C14   180.00   0.0  0
 4ZZ  CONST_22  N24  C19  C18  C14     0.00   0.0  0
 4ZZ  CONST_23  C11  C12  C17  C16   180.00   0.0  0
 4ZZ  CONST_24  N24  C19  C20  N21   180.00   0.0  0
 4ZZ  CONST_25  N24  C19  C18  C23   180.00   0.0  0
 4ZZ  CONST_26  H18  C23  C18  C14     0.00   0.0  0
 4ZZ  CONST_27  H2   C16  C15  C14   180.00   0.0  0
 4ZZ  CONST_28  H8   C13  C14  C15   180.00   0.0  0
 4ZZ  CONST_29  H3   C17  C16  C15   180.00   0.0  0
 4ZZ  CONST_30  H1   C15  C16  C17   180.00   0.0  0
 4ZZ  CONST_31  H5   C20  N21  C22   180.00   0.0  0
 4ZZ  CONST_32  H4   C22  N21  C20   180.00   0.0  0
 4ZZ  CONST_35  O9   C8   N7   C6      0.00   0.0  0
 4ZZ  CONST_36  O9   C8   N10  C11     0.00   0.0  0
 4ZZ  CONST_37  N10  C8   N7   C6    180.00   0.0  0
 4ZZ  CONST_38  N7   C8   N10  C11   180.00   0.0  0
 4ZZ  CONST_39  H17  N10  C8   O9    180.00   0.0  0
 4ZZ  CONST_40  H16  N7   C8   O9    180.00   0.0  0
 4ZZ  Var_01    N10  C11  C12  C17   -42.29  30.0  2
 4ZZ  Var_02    C12  C11  N10  C8     98.52  30.0  1
 4ZZ  Var_03    C6   C4   O3   C2   -179.61  30.0  3
 4ZZ  Var_04    C8   N7   C6   C4   -176.63  30.0  3
 4ZZ  Var_05    N7   C6   C4   O3   -179.63  30.0  1
 4ZZ  Var_06    H6   C2   O3   C4     58.18  30.0  3
 4ZZ  Var_07    H9   C1   C2   O3    -60.61  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
 4ZZ  plan-1  C14  0.020
 4ZZ  plan-1  C22  0.020
 4ZZ  plan-1  C20  0.020
 4ZZ  plan-1  C19  0.020
 4ZZ  plan-1  C18  0.020
 4ZZ  plan-1  N21  0.020
 4ZZ  plan-1  C23  0.020
 4ZZ  plan-1  H4   0.020
 4ZZ  plan-1  H5   0.020
 4ZZ  plan-1  H18  0.020
 4ZZ  plan-1  N24  0.020
 4ZZ  plan-2  C14  0.020
 4ZZ  plan-2  C15  0.020
 4ZZ  plan-2  C16  0.020
 4ZZ  plan-2  C17  0.020
 4ZZ  plan-2  C18  0.020
 4ZZ  plan-2  C13  0.020
 4ZZ  plan-2  C12  0.020
 4ZZ  plan-2  C11  0.020
 4ZZ  plan-2  H1   0.020
 4ZZ  plan-2  H2   0.020
 4ZZ  plan-2  H3   0.020
 4ZZ  plan-2  H8   0.020
 4ZZ  plan-3  C6   0.020
 4ZZ  plan-3  C11  0.020
 4ZZ  plan-3  N7   0.020
 4ZZ  plan-3  O9   0.020
 4ZZ  plan-3  N10  0.020
 4ZZ  plan-3  H16  0.020
 4ZZ  plan-3  H17  0.020
 4ZZ  plan-3  C8   0.020
 4ZZ  plan-4  C19  0.020
 4ZZ  plan-4  H19  0.020
 4ZZ  plan-4  H20  0.020
 4ZZ  plan-4  N24  0.020
 4ZZ  plan-5  C6   0.020
 4ZZ  plan-5  C4   0.020
 4ZZ  plan-5  O3   0.020
 4ZZ  plan-5  O5   0.020

