# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:03:08 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: ethyl N-{[3-(pyridin-3-yl)benzyl]carbamoyl}glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CNC(=O)NCc1cccc(c1)c2cccnc2
#
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
 4ZP  4ZP  'ethyl N-{[3-(pyridin-3-yl)benzyl]carbamoyl}glycinate'  ligand  42  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4ZP
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
 4ZP  C1   C  CH2   0  -0.328   0.3474   3.4223   0.3294
 4ZP  C2   C  CR16  0  -0.303   2.6969   3.3735  -0.5383
 4ZP  C3   C  CR16  0  -0.227   3.8867   2.7232  -0.8254
 4ZP  C4   C  CR16  0  -0.326   4.0219   1.3654  -0.5727
 4ZP  C5   C  CR6   0   0.110   2.9622   0.6493  -0.0204
 4ZP  C6   C  CR16  0  -0.362   1.7728   1.3203   0.2723
 4ZP  C7   C  CR6   0   0.103   1.6252   2.6748   0.0133
 4ZP  C8   C  CR6   0  -0.008   3.0895  -0.7947   0.2461
 4ZP  C9   C  CR16  0  -0.098   2.0221  -1.6668   0.0257
 4ZP  C11  C  CR16  0  -0.071   3.2077  -3.4872   0.7006
 4ZP  N10  N  N     0  -0.398   2.0708  -2.9725   0.2463
 4ZP  C12  C  CR16  0  -0.316   4.3367  -2.7203   0.9463
 4ZP  C13  C  CR16  0  -0.196   4.2744  -1.3563   0.7173
 4ZP  N14  N  NH1   0  -0.684  -0.7578   2.6084   0.7518
 4ZP  C15  C  C     0   0.745  -1.4629   1.8557  -0.1376
 4ZP  N16  N  NH1   0  -0.692  -2.3646   1.0093   0.4173
 4ZP  C17  C  CH2   0  -0.360  -3.2296   0.2135  -0.4039
 4ZP  C18  C  C     0   0.564  -4.1047  -0.6620   0.4603
 4ZP  O19  O  O     0  -0.538  -1.3010   1.9402  -1.3499
 4ZP  O20  O  O     0  -0.448  -4.1051  -0.6513   1.6657
 4ZP  O21  O  O2    0  -0.452  -4.8722  -1.4344  -0.2828
 4ZP  C22  C  CH2   0  -0.184  -5.7825  -2.3300   0.3818
 4ZP  C23  C  CH3   0  -0.690  -6.5400  -3.0873  -0.6805
 4ZP  H1   H  HCH2  0   0.273   0.5421   4.1435   1.1251
 4ZP  H2   H  HCH2  0   0.259   0.0550   4.0093  -0.5426
 4ZP  H4   H  HCR6  0   0.258   4.7116   3.2729  -1.2598
 4ZP  H5   H  HCR6  0   0.255   4.9461   0.8616  -0.8274
 4ZP  H6   H  HCR6  0   0.240   0.9596   0.7736   0.7340
 4ZP  H7   H  HCR6  0   0.253   1.0857  -1.2850  -0.3691
 4ZP  H8   H  HCR6  0   0.266   3.2220  -4.5569   0.8761
 4ZP  H9   H  HCR6  0   0.274   5.2411  -3.1824   1.3170
 4ZP  H10  H  HCR6  0   0.271   5.1352  -0.7309   0.9190
 4ZP  H11  H  HNH1  0   0.397  -0.8313   2.4021   1.7345
 4ZP  H12  H  HNH1  0   0.398  -2.5459   1.0298   1.4087
 4ZP  H13  H  HCH2  0   0.279  -3.8829   0.8236  -1.0375
 4ZP  H14  H  HCH2  0   0.281  -2.6588  -0.4313  -1.0781
 4ZP  H15  H  HCH2  0   0.241  -5.2198  -3.0112   1.0223
 4ZP  H16  H  HCH2  0   0.241  -6.4626  -1.7553   1.0128
 4ZP  H17  H  HCH3  0   0.239  -7.1181  -2.4173  -1.3163
 4ZP  H18  H  HCH3  0   0.239  -5.8714  -3.6756  -1.3085
 4ZP  H19  H  HCH3  0   0.242  -7.2356  -3.7735  -0.1981
 4ZP  H3   H  HCR6  0   0.252   2.5995   4.4331  -0.7458

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
 4ZP  O19  C15  double    1.226  0.020  1.226
 4ZP  C1   N14  single    1.436  0.020  1.436
 4ZP  C1   C7   single    1.514  0.020  1.514
 4ZP  C15  N14  single    1.362  0.020  1.362
 4ZP  C15  N16  single    1.356  0.020  1.356
 4ZP  C7   C6   aromatic  1.387  0.020  1.387
 4ZP  C7   C2   aromatic  1.393  0.020  1.393
 4ZP  C9   N10  aromatic  1.325  0.020  1.325
 4ZP  C9   C8   aromatic  1.396  0.020  1.396
 4ZP  C6   C5   aromatic  1.397  0.020  1.397
 4ZP  N10  C11  aromatic  1.328  0.020  1.328
 4ZP  N16  C17  single    1.434  0.020  1.434
 4ZP  C17  C18  single    1.510  0.020  1.510
 4ZP  C2   C3   aromatic  1.386  0.020  1.386
 4ZP  O21  C18  single    1.318  0.020  1.318
 4ZP  O21  C22  single    1.440  0.020  1.440
 4ZP  C5   C8   single    1.474  0.020  1.474
 4ZP  C5   C4   aromatic  1.393  0.020  1.393
 4ZP  C18  O20  double    1.206  0.020  1.206
 4ZP  C8   C13  aromatic  1.393  0.020  1.393
 4ZP  C23  C22  single    1.509  0.020  1.509
 4ZP  C11  C12  aromatic  1.387  0.020  1.387
 4ZP  C3   C4   aromatic  1.388  0.020  1.388
 4ZP  C13  C12  aromatic  1.385  0.020  1.385
 4ZP  C1   H1   single    0.970  0.020  1.090
 4ZP  C1   H2   single    0.970  0.020  1.090
 4ZP  C2   H3   single    0.930  0.020  1.080
 4ZP  C3   H4   single    0.930  0.020  1.080
 4ZP  C4   H5   single    0.930  0.020  1.080
 4ZP  C6   H6   single    0.930  0.020  1.080
 4ZP  C9   H7   single    0.930  0.020  1.080
 4ZP  C11  H8   single    0.930  0.020  1.080
 4ZP  C12  H9   single    0.930  0.020  1.080
 4ZP  C13  H10  single    0.930  0.020  1.080
 4ZP  N14  H11  single    0.860  0.020  1.020
 4ZP  N16  H12  single    0.860  0.020  1.020
 4ZP  C17  H13  single    0.970  0.020  1.090
 4ZP  C17  H14  single    0.970  0.020  1.090
 4ZP  C22  H15  single    0.970  0.020  1.090
 4ZP  C22  H16  single    0.970  0.020  1.090
 4ZP  C23  H17  single    0.970  0.020  1.090
 4ZP  C23  H18  single    0.970  0.020  1.090
 4ZP  C23  H19  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
 4ZP  H2   C1   H1   105.96  3.000
 4ZP  H2   C1   N14  109.49  3.000
 4ZP  H1   C1   N14  107.30  3.000
 4ZP  H2   C1   C7   108.96  3.000
 4ZP  H1   C1   C7   109.15  3.000
 4ZP  N14  C1   C7   115.54  3.000
 4ZP  H3   C2   C7   119.79  3.000
 4ZP  H3   C2   C3   119.74  3.000
 4ZP  C7   C2   C3   120.47  3.000
 4ZP  H4   C3   C4   119.72  3.000
 4ZP  H4   C3   C2   119.94  3.000
 4ZP  C4   C3   C2   120.33  3.000
 4ZP  H5   C4   C5   120.21  3.000
 4ZP  H5   C4   C3   119.71  3.000
 4ZP  C5   C4   C3   120.07  3.000
 4ZP  C8   C5   C6   120.42  3.000
 4ZP  C8   C5   C4   120.64  3.000
 4ZP  C6   C5   C4   118.95  3.000
 4ZP  H6   C6   C7   119.51  3.000
 4ZP  H6   C6   C5   119.10  3.000
 4ZP  C7   C6   C5   121.38  3.000
 4ZP  C6   C7   C2   118.80  3.000
 4ZP  C2   C7   C1   118.97  3.000
 4ZP  C6   C7   C1   122.22  3.000
 4ZP  C13  C8   C9   116.86  3.000
 4ZP  C13  C8   C5   121.97  3.000
 4ZP  C9   C8   C5   121.17  3.000
 4ZP  H7   C9   N10  116.02  3.000
 4ZP  H7   C9   C8   119.82  3.000
 4ZP  N10  C9   C8   124.14  3.000
 4ZP  H8   C11  C12  120.41  3.000
 4ZP  H8   C11  N10  116.68  3.000
 4ZP  C12  C11  N10  122.90  3.000
 4ZP  C11  N10  C9   118.05  3.000
 4ZP  H9   C12  C13  121.03  3.000
 4ZP  H9   C12  C11  120.36  3.000
 4ZP  C13  C12  C11  118.61  3.000
 4ZP  H10  C13  C12  120.16  3.000
 4ZP  H10  C13  C8   120.41  3.000
 4ZP  C12  C13  C8   119.43  3.000
 4ZP  H11  N14  C15  119.10  3.000
 4ZP  H11  N14  C1   117.35  3.000
 4ZP  C15  N14  C1   121.31  3.000
 4ZP  O19  C15  N16  122.39  3.000
 4ZP  N16  C15  N14  114.97  3.000
 4ZP  O19  C15  N14  122.64  3.000
 4ZP  H12  N16  C17  117.78  3.000
 4ZP  H12  N16  C15  120.63  3.000
 4ZP  C17  N16  C15  120.89  3.000
 4ZP  H14  C17  H13  106.44  3.000
 4ZP  H14  C17  C18  108.27  3.000
 4ZP  H13  C17  C18  107.96  3.000
 4ZP  H14  C17  N16  111.43  3.000
 4ZP  H13  C17  N16  112.45  3.000
 4ZP  C18  C17  N16  110.10  3.000
 4ZP  O21  C18  O20  124.65  3.000
 4ZP  O20  C18  C17  124.57  3.000
 4ZP  O21  C18  C17  110.77  3.000
 4ZP  C22  O21  C18  118.20  3.000
 4ZP  H16  C22  H15  108.11  3.000
 4ZP  H16  C22  C23  111.01  3.000
 4ZP  H15  C22  C23  111.03  3.000
 4ZP  H16  C22  O21  109.47  3.000
 4ZP  H15  C22  O21  109.46  3.000
 4ZP  C23  C22  O21  107.74  3.000
 4ZP  H19  C23  H18  107.87  3.000
 4ZP  H19  C23  H17  107.87  3.000
 4ZP  H18  C23  H17  108.74  3.000
 4ZP  H19  C23  C22  108.95  3.000
 4ZP  H18  C23  C22  111.64  3.000
 4ZP  H17  C23  C22  111.62  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
 4ZP  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 4ZP  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 4ZP  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 4ZP  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 4ZP  CONST_05  C8   C5   C4   C3    180.00   0.0  0
 4ZP  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 4ZP  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 4ZP  CONST_10  N10  C9   C8   C5    180.00   0.0  0
 4ZP  CONST_11  C12  C13  C8   C5    180.00   0.0  0
 4ZP  CONST_14  C8   C5   C6   C7    180.00   0.0  0
 4ZP  CONST_15  C11  N10  C9   C8      0.00   0.0  0
 4ZP  CONST_16  C11  C12  C13  C8      0.00   0.0  0
 4ZP  CONST_17  C12  C11  N10  C9      0.00   0.0  0
 4ZP  CONST_18  C12  C13  C8   C9      0.00   0.0  0
 4ZP  CONST_19  C13  C8   C9   N10     0.00   0.0  0
 4ZP  CONST_20  C13  C12  C11  N10     0.00   0.0  0
 4ZP  CONST_21  C5   C6   C7   C1    180.00   0.0  0
 4ZP  CONST_22  C3   C2   C7   C1    180.00   0.0  0
 4ZP  CONST_23  H6   C6   C7   C2    180.00   0.0  0
 4ZP  CONST_24  H5   C4   C3   C2    180.00   0.0  0
 4ZP  CONST_25  H3   C2   C3   C4    180.00   0.0  0
 4ZP  CONST_26  H7   C9   C8   C5      0.00   0.0  0
 4ZP  CONST_27  H10  C13  C8   C5      0.00   0.0  0
 4ZP  CONST_28  H4   C3   C4   C5    180.00   0.0  0
 4ZP  CONST_29  H9   C12  C13  C8    180.00   0.0  0
 4ZP  CONST_30  H8   C11  N10  C9    180.00   0.0  0
 4ZP  CONST_31  O19  C15  N14  C1      0.00   0.0  0
 4ZP  CONST_32  O19  C15  N16  C17     0.00   0.0  0
 4ZP  CONST_33  N16  C15  N14  C1    180.00   0.0  0
 4ZP  CONST_34  C17  N16  C15  N14   180.00   0.0  0
 4ZP  CONST_35  H11  N14  C15  O19   180.00   0.0  0
 4ZP  CONST_36  H12  N16  C15  O19   180.00   0.0  0
 4ZP  Var_01    N14  C1   C7   C2    173.22  30.0  2
 4ZP  Var_02    C15  N14  C1   C7    -75.25  30.0  3
 4ZP  Var_03    C18  C17  N16  C15   178.52  30.0  3
 4ZP  Var_04    O21  C18  C17  N16  -177.76  30.0  3
 4ZP  Var_05    C23  C22  O21  C18   179.74  30.0  3
 4ZP  Var_06    H17  C23  C22  O21   -61.04  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
 4ZP  plan-1  C1   0.020
 4ZP  plan-1  C2   0.020
 4ZP  plan-1  C3   0.020
 4ZP  plan-1  C4   0.020
 4ZP  plan-1  C5   0.020
 4ZP  plan-1  C6   0.020
 4ZP  plan-1  C7   0.020
 4ZP  plan-1  C8   0.020
 4ZP  plan-1  H4   0.020
 4ZP  plan-1  H5   0.020
 4ZP  plan-1  H6   0.020
 4ZP  plan-1  H3   0.020
 4ZP  plan-2  C5   0.020
 4ZP  plan-2  C8   0.020
 4ZP  plan-2  C9   0.020
 4ZP  plan-2  C11  0.020
 4ZP  plan-2  N10  0.020
 4ZP  plan-2  C12  0.020
 4ZP  plan-2  C13  0.020
 4ZP  plan-2  H7   0.020
 4ZP  plan-2  H8   0.020
 4ZP  plan-2  H9   0.020
 4ZP  plan-2  H10  0.020
 4ZP  plan-3  C1   0.020
 4ZP  plan-3  N14  0.020
 4ZP  plan-3  C15  0.020
 4ZP  plan-3  N16  0.020
 4ZP  plan-3  C17  0.020
 4ZP  plan-3  O19  0.020
 4ZP  plan-3  H11  0.020
 4ZP  plan-3  H12  0.020
 4ZP  plan-4  C17  0.020
 4ZP  plan-4  C18  0.020
 4ZP  plan-4  O20  0.020
 4ZP  plan-4  O21  0.020

