# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:11:11 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: ethyl N-{[3-(pyridin-4-yl)benzyl]carbamoyl}glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CNC(=O)NCc1cccc(c1)c2ccncc2
#
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
 4ZM  4ZM  'ethyl N-{[3-(pyridin-4-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_4ZM
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
 4ZM  N    N  NH1   0  -0.664   2.0473   0.6831   1.4608
 4ZM  C    C  CH3   0  -0.689   7.0939   1.3035  -1.6787
 4ZM  O    O  O2    0  -0.456   5.1046   1.1039  -0.3841
 4ZM  N1   N  NH1   0  -0.682   0.7577  -1.1737   1.8742
 4ZM  C1   C  CH2   0  -0.179   6.3843   0.4936  -0.6216
 4ZM  O1   O  O     0  -0.448   4.6090  -0.3904   1.2038
 4ZM  N2   N  N     0  -0.408  -4.9513   3.1051  -0.2200
 4ZM  C2   C  C     0   0.582   4.3239   0.5739   0.5425
 4ZM  O2   O  O     0  -0.531   1.6981  -0.8580  -0.1631
 4ZM  C3   C  CH2   0  -0.423   3.0356   1.3639   0.6836
 4ZM  C4   C  C     0   0.742   1.5150  -0.4801   0.9871
 4ZM  C5   C  CH2   0  -0.330   0.0403  -2.3525   1.4735
 4ZM  C6   C  CR6   0   0.114  -1.1588  -2.1044   0.5855
 4ZM  C7   C  CR16  0  -0.356  -1.8197  -0.8843   0.5742
 4ZM  C8   C  CR6   0   0.115  -2.9533  -0.6823  -0.2139
 4ZM  C11  C  CR16  0  -0.308  -1.6420  -3.1375  -0.2127
 4ZM  C10  C  CR16  0  -0.227  -2.7682  -2.9514  -1.0003
 4ZM  C9   C  CR16  0  -0.322  -3.4260  -1.7309  -1.0016
 4ZM  C12  C  CR6   0   0.171  -3.6402   0.6228  -0.2148
 4ZM  C16  C  CR16  0  -0.379  -5.0270   0.7153  -0.3207
 4ZM  C15  C  CR16  0  -0.060  -5.6254   1.9647  -0.3174
 4ZM  C14  C  CR16  0  -0.060  -3.6296   3.0195  -0.1216
 4ZM  C13  C  CR16  0  -0.375  -2.9351   1.8207  -0.1135
 4ZM  H1   H  HNH1  0   0.398   2.0539   0.8476   2.4542
 4ZM  H2   H  HCH3  0   0.237   6.5253   1.3409  -2.6079
 4ZM  H3   H  HCH3  0   0.237   7.2823   2.3233  -1.3434
 4ZM  H4   H  HCH3  0   0.240   8.0561   0.8405  -1.8953
 4ZM  H5   H  HNH1  0   0.400   0.5485  -0.7736   2.7737
 4ZM  H6   H  HCH2  0   0.237   6.2386  -0.5374  -0.9495
 4ZM  H7   H  HCH2  0   0.236   6.9614   0.4737   0.3047
 4ZM  H8   H  HCH2  0   0.280   2.6536   1.6191  -0.3056
 4ZM  H9   H  HCH2  0   0.304   3.2705   2.3095   1.1765
 4ZM  H10  H  HCH2  0   0.256   0.7166  -3.0480   0.9732
 4ZM  H11  H  HCH2  0   0.276  -0.2899  -2.8533   2.3854
 4ZM  H12  H  HCR6  0   0.245  -1.4574  -0.0784   1.2016
 4ZM  H13  H  HCR6  0   0.253  -1.1319  -4.0940  -0.2208
 4ZM  H14  H  HCR6  0   0.259  -3.1291  -3.7570  -1.6262
 4ZM  H15  H  HCR6  0   0.257  -4.2918  -1.5898  -1.6361
 4ZM  H16  H  HCR6  0   0.269  -5.6451  -0.1703  -0.3866
 4ZM  H17  H  HCR6  0   0.265  -6.7044   2.0437  -0.3922
 4ZM  H18  H  HCR6  0   0.265  -3.0863   3.9553  -0.0486
 4ZM  H19  H  HCR6  0   0.263  -1.8550   1.8329  -0.0494

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
 4ZM  O2   C4   double    1.224  0.020  1.224
 4ZM  C5   N1   single    1.437  0.020  1.437
 4ZM  C5   C6   single    1.513  0.020  1.513
 4ZM  C4   N1   single    1.357  0.020  1.357
 4ZM  C4   N    single    1.364  0.020  1.364
 4ZM  C3   N    single    1.430  0.020  1.430
 4ZM  C3   C2   single    1.518  0.020  1.518
 4ZM  C6   C7   aromatic  1.388  0.020  1.388
 4ZM  C6   C11  aromatic  1.392  0.020  1.392
 4ZM  O    C2   single    1.323  0.020  1.323
 4ZM  O    C1   single    1.437  0.020  1.437
 4ZM  C7   C8   aromatic  1.395  0.020  1.395
 4ZM  C11  C10  aromatic  1.387  0.020  1.387
 4ZM  C2   O1   double    1.203  0.020  1.203
 4ZM  C    C1   single    1.509  0.020  1.509
 4ZM  C8   C9   aromatic  1.394  0.020  1.394
 4ZM  C8   C12  single    1.475  0.020  1.475
 4ZM  C10  C9   aromatic  1.386  0.020  1.386
 4ZM  C12  C16  aromatic  1.394  0.020  1.394
 4ZM  C12  C13  aromatic  1.394  0.020  1.394
 4ZM  C16  C15  aromatic  1.385  0.020  1.385
 4ZM  C13  C14  aromatic  1.385  0.020  1.385
 4ZM  C15  N2   aromatic  1.328  0.020  1.328
 4ZM  C14  N2   aromatic  1.328  0.020  1.328
 4ZM  N    H1   single    0.890  0.020  1.040
 4ZM  C    H2   single    0.970  0.020  1.090
 4ZM  C    H3   single    0.970  0.020  1.090
 4ZM  C    H4   single    0.970  0.020  1.090
 4ZM  N1   H5   single    0.860  0.020  1.020
 4ZM  C1   H6   single    0.970  0.020  1.090
 4ZM  C1   H7   single    0.970  0.020  1.090
 4ZM  C3   H8   single    0.970  0.020  1.090
 4ZM  C3   H9   single    0.970  0.020  1.090
 4ZM  C5   H10  single    0.970  0.020  1.090
 4ZM  C5   H11  single    0.970  0.020  1.090
 4ZM  C7   H12  single    0.930  0.020  1.080
 4ZM  C11  H13  single    0.930  0.020  1.080
 4ZM  C10  H14  single    0.930  0.020  1.080
 4ZM  C9   H15  single    0.930  0.020  1.080
 4ZM  C16  H16  single    0.930  0.020  1.080
 4ZM  C15  H17  single    0.930  0.020  1.080
 4ZM  C14  H18  single    0.930  0.020  1.080
 4ZM  C13  H19  single    0.930  0.020  1.080

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
 4ZM  H1   N    C4   118.97  3.000
 4ZM  H1   N    C3   117.00  3.000
 4ZM  C4   N    C3   119.14  3.000
 4ZM  H4   C    H3   107.83  3.000
 4ZM  H4   C    H2   107.81  3.000
 4ZM  H3   C    H2   108.68  3.000
 4ZM  H4   C    C1   109.06  3.000
 4ZM  H3   C    C1   111.59  3.000
 4ZM  H2   C    C1   111.73  3.000
 4ZM  C2   O    C1   118.10  3.000
 4ZM  H5   N1   C5   118.13  3.000
 4ZM  H5   N1   C4   119.80  3.000
 4ZM  C5   N1   C4   121.04  3.000
 4ZM  H7   C1   H6   107.95  3.000
 4ZM  H7   C1   O    109.77  3.000
 4ZM  H6   C1   O    109.38  3.000
 4ZM  H7   C1   C    110.83  3.000
 4ZM  H6   C1   C    111.05  3.000
 4ZM  O    C1   C    107.85  3.000
 4ZM  C14  N2   C15  117.07  3.000
 4ZM  C3   C2   O1   124.54  3.000
 4ZM  O1   C2   O    124.49  3.000
 4ZM  C3   C2   O    110.95  3.000
 4ZM  H9   C3   H8   106.38  3.000
 4ZM  H9   C3   C2   108.06  3.000
 4ZM  H8   C3   C2   109.56  3.000
 4ZM  H9   C3   N    108.40  3.000
 4ZM  H8   C3   N    111.25  3.000
 4ZM  C2   C3   N    112.92  3.000
 4ZM  O2   C4   N1   122.67  3.000
 4ZM  N1   C4   N    115.26  3.000
 4ZM  O2   C4   N    122.07  3.000
 4ZM  H11  C5   H10  106.14  3.000
 4ZM  H11  C5   C6   109.02  3.000
 4ZM  H10  C5   C6   109.06  3.000
 4ZM  H11  C5   N1   107.12  3.000
 4ZM  H10  C5   N1   109.95  3.000
 4ZM  C6   C5   N1   115.15  3.000
 4ZM  C11  C6   C7   118.85  3.000
 4ZM  C11  C6   C5   119.34  3.000
 4ZM  C7   C6   C5   121.77  3.000
 4ZM  H12  C7   C8   119.40  3.000
 4ZM  H12  C7   C6   119.34  3.000
 4ZM  C8   C7   C6   121.25  3.000
 4ZM  C12  C8   C9   120.49  3.000
 4ZM  C12  C8   C7   120.46  3.000
 4ZM  C9   C8   C7   119.06  3.000
 4ZM  H13  C11  C10  119.75  3.000
 4ZM  H13  C11  C6   119.72  3.000
 4ZM  C10  C11  C6   120.52  3.000
 4ZM  H14  C10  C9   119.77  3.000
 4ZM  H14  C10  C11  119.96  3.000
 4ZM  C9   C10  C11  120.26  3.000
 4ZM  H15  C9   C10  119.65  3.000
 4ZM  H15  C9   C8   120.28  3.000
 4ZM  C10  C9   C8   120.05  3.000
 4ZM  C13  C12  C16  116.86  3.000
 4ZM  C13  C12  C8   121.66  3.000
 4ZM  C16  C12  C8   121.48  3.000
 4ZM  H16  C16  C15  119.44  3.000
 4ZM  H16  C16  C12  121.24  3.000
 4ZM  C15  C16  C12  119.30  3.000
 4ZM  H17  C15  C16  119.69  3.000
 4ZM  H17  C15  N2   116.58  3.000
 4ZM  C16  C15  N2   123.73  3.000
 4ZM  H18  C14  C13  119.68  3.000
 4ZM  H18  C14  N2   116.60  3.000
 4ZM  C13  C14  N2   123.72  3.000
 4ZM  H19  C13  C14  119.41  3.000
 4ZM  H19  C13  C12  121.26  3.000
 4ZM  C14  C13  C12  119.32  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
 4ZM  CONST_01  C12  C16  C15  N2     0.00   0.0  0
 4ZM  CONST_02  C12  C13  C14  N2     0.00   0.0  0
 4ZM  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 4ZM  CONST_04  C12  C8   C7   C6   180.00   0.0  0
 4ZM  CONST_05  C9   C10  C11  C6     0.00   0.0  0
 4ZM  CONST_06  C10  C11  C6   C7     0.00   0.0  0
 4ZM  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 4ZM  CONST_10  C11  C6   C7   C8     0.00   0.0  0
 4ZM  CONST_11  C11  C10  C9   C8     0.00   0.0  0
 4ZM  CONST_12  C15  C16  C12  C8   180.00   0.0  0
 4ZM  CONST_13  C14  C13  C12  C8   180.00   0.0  0
 4ZM  CONST_14  C12  C8   C9   C10  180.00   0.0  0
 4ZM  CONST_17  C14  C13  C12  C16    0.00   0.0  0
 4ZM  CONST_18  C14  N2   C15  C16    0.00   0.0  0
 4ZM  CONST_19  C13  C12  C16  C15    0.00   0.0  0
 4ZM  CONST_20  C13  C14  N2   C15    0.00   0.0  0
 4ZM  CONST_21  C8   C7   C6   C5   180.00   0.0  0
 4ZM  CONST_22  C10  C11  C6   C5   180.00   0.0  0
 4ZM  CONST_23  H16  C16  C15  N2   180.00   0.0  0
 4ZM  CONST_24  H19  C13  C14  N2   180.00   0.0  0
 4ZM  CONST_25  H14  C10  C11  C6   180.00   0.0  0
 4ZM  CONST_26  H13  C11  C6   C7   180.00   0.0  0
 4ZM  CONST_27  H15  C9   C8   C7   180.00   0.0  0
 4ZM  CONST_28  H12  C7   C6   C11  180.00   0.0  0
 4ZM  CONST_29  H17  C15  C16  C12  180.00   0.0  0
 4ZM  CONST_30  H18  C14  C13  C12  180.00   0.0  0
 4ZM  CONST_31  C5   N1   C4   O2     0.00   0.0  0
 4ZM  CONST_32  C3   N    C4   O2     0.00   0.0  0
 4ZM  CONST_33  C5   N1   C4   N    180.00   0.0  0
 4ZM  CONST_34  C3   N    C4   N1   180.00   0.0  0
 4ZM  CONST_35  H5   N1   C4   O2   180.00   0.0  0
 4ZM  CONST_36  H1   N    C4   O2   180.00   0.0  0
 4ZM  Var_01    C7   C6   C5   N1   -23.64  30.0  2
 4ZM  Var_02    C6   C5   N1   C4   -71.63  30.0  2
 4ZM  Var_03    O    C2   C3   N    167.72  30.0  3
 4ZM  Var_04    C3   C2   O    C1   178.50  30.0  3
 4ZM  Var_05    C4   N    C3   C2   -65.43  30.0  3
 4ZM  Var_06    H2   C    C1   O    -59.28  30.0  3
 4ZM  Var_07    H6   C1   O    C2    61.02  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
 4ZM  plan-1  C5   0.020
 4ZM  plan-1  C6   0.020
 4ZM  plan-1  C7   0.020
 4ZM  plan-1  C8   0.020
 4ZM  plan-1  C11  0.020
 4ZM  plan-1  C10  0.020
 4ZM  plan-1  C9   0.020
 4ZM  plan-1  C12  0.020
 4ZM  plan-1  H12  0.020
 4ZM  plan-1  H13  0.020
 4ZM  plan-1  H14  0.020
 4ZM  plan-1  H15  0.020
 4ZM  plan-2  N2   0.020
 4ZM  plan-2  C8   0.020
 4ZM  plan-2  C12  0.020
 4ZM  plan-2  C16  0.020
 4ZM  plan-2  C15  0.020
 4ZM  plan-2  C14  0.020
 4ZM  plan-2  C13  0.020
 4ZM  plan-2  H16  0.020
 4ZM  plan-2  H17  0.020
 4ZM  plan-2  H18  0.020
 4ZM  plan-2  H19  0.020
 4ZM  plan-3  N    0.020
 4ZM  plan-3  N1   0.020
 4ZM  plan-3  O2   0.020
 4ZM  plan-3  C3   0.020
 4ZM  plan-3  C4   0.020
 4ZM  plan-3  C5   0.020
 4ZM  plan-3  H1   0.020
 4ZM  plan-3  H5   0.020
 4ZM  plan-4  O    0.020
 4ZM  plan-4  O1   0.020
 4ZM  plan-4  C2   0.020
 4ZM  plan-4  C3   0.020

