# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:10:45 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: ethyl N-{[(2-aminopyridin-4-yl)methyl]carbamoyl}glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CNC(=O)NCc1ccnc(N)c1
#
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
 502  502  'ethyl N-{[(2-aminopyridin-4-yl)methyl]carbamoyl}glycinate'  ligand  34  18  .  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_502
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
 502  C1   C  CH2   0  -0.304   1.5767  -0.8205   1.7060
 502  C2   C  CR6   0   0.148   2.6387  -0.7427   0.6366
 502  C6   C  CR16  0  -0.079   4.3254  -1.7848  -0.6835
 502  C7   C  CR16  0  -0.363   3.3377  -1.8976   0.2726
 502  C3   C  CR16  0  -0.415   2.9766   0.4463   0.0273
 502  C4   C  CR6   0   0.452   4.0037   0.4570  -0.9332
 502  C9   C  C     0   0.722  -0.3336   0.3188   0.7273
 502  N5   N  N     0  -0.415   4.6619  -0.6459  -1.2830
 502  N8   N  NH1   0  -0.723   0.6153   0.2459   1.6954
 502  N10  N  NH1   0  -0.722  -1.0959   1.4497   0.7440
 502  O11  O  O     0  -0.465  -0.4842  -0.5570  -0.1145
 502  C12  C  CH2   0  -0.447  -2.2661   1.5143  -0.0747
 502  C13  C  C     0   0.594  -3.3496   0.5474   0.3663
 502  O14  O  O2    0  -0.462  -4.3155   0.4767  -0.5341
 502  O15  O  O     0  -0.363  -3.3422  -0.0571   1.4069
 502  C16  C  CH2   0  -0.205  -5.4420  -0.3713  -0.2520
 502  C17  C  CH3   0  -0.632  -6.3979  -0.2780  -1.4158
 502  N18  N  NH2   0  -0.826   4.3967   1.6257  -1.5186
 502  H1   H  HCH2  0   0.257   1.0694  -1.7845   1.6393
 502  H2   H  HCH2  0   0.275   2.0674  -0.8060   2.6809
 502  H3   H  HCR6  0   0.225   4.8811  -2.6642  -0.9927
 502  H4   H  HCR6  0   0.251   3.1079  -2.8584   0.7150
 502  H5   H  HCR6  0   0.269   2.4607   1.3663   0.2732
 502  H6   H  HNH1  0   0.391   0.7794   1.0357   2.2967
 502  H7   H  HNH1  0   0.394  -1.0787   2.0357   1.5631
 502  H8   H  HCH2  0   0.260  -2.6700   2.5275  -0.0233
 502  H9   H  HCH2  0   0.275  -2.0234   1.3341  -1.1229
 502  H10  H  HCH2  0   0.266  -5.0977  -1.3975  -0.1111
 502  H11  H  HCH2  0   0.176  -5.9212  -0.0470   0.6736
 502  H12  H  HCH3  0   0.211  -6.7596   0.7401  -1.5593
 502  H13  H  HCH3  0   0.215  -5.9386  -0.6199  -2.3430
 502  H14  H  HCH3  0   0.298  -7.2608  -0.9128  -1.2164
 502  H15  H  HNH2  0   0.373   3.7512   2.3973  -1.5023
 502  H16  H  HNH2  0   0.372   4.9130   1.5394  -2.3787

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
 502  O11  C9   double    1.224  0.020  1.224
 502  C1   N8   single    1.436  0.020  1.436
 502  C1   C2   single    1.509  0.020  1.509
 502  C9   N8   single    1.358  0.020  1.358
 502  C9   N10  single    1.364  0.020  1.364
 502  C3   C2   aromatic  1.378  0.020  1.378
 502  C3   C4   aromatic  1.406  0.020  1.406
 502  C2   C7   aromatic  1.398  0.020  1.398
 502  C12  N10  single    1.430  0.020  1.430
 502  C12  C13  single    1.518  0.020  1.518
 502  N18  C4   single    1.365  0.020  1.365
 502  C4   N5   aromatic  1.331  0.020  1.331
 502  O14  C13  single    1.322  0.020  1.322
 502  O14  C16  single    1.438  0.020  1.438
 502  C7   C6   aromatic  1.379  0.020  1.379
 502  C13  O15  double    1.203  0.020  1.203
 502  C17  C16  single    1.509  0.020  1.509
 502  N5   C6   aromatic  1.330  0.020  1.330
 502  C1   H1   single    0.970  0.020  1.090
 502  C1   H2   single    0.970  0.020  1.090
 502  C6   H3   single    0.930  0.020  1.080
 502  C7   H4   single    0.930  0.020  1.080
 502  C3   H5   single    0.930  0.020  1.080
 502  N8   H6   single    0.860  0.020  1.020
 502  N10  H7   single    0.890  0.020  1.040
 502  C12  H8   single    0.970  0.020  1.090
 502  C12  H9   single    0.970  0.020  1.090
 502  C16  H10  single    0.970  0.020  1.090
 502  C16  H11  single    0.970  0.020  1.090
 502  C17  H12  single    0.970  0.020  1.090
 502  C17  H13  single    0.970  0.020  1.090
 502  C17  H14  single    0.970  0.020  1.090
 502  N18  H15  single    0.890  0.020  1.040
 502  N18  H16  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
 502  H2   C1   H1   105.98  3.000
 502  H2   C1   N8   107.32  3.000
 502  H1   C1   N8   110.15  3.000
 502  H2   C1   C2   108.41  3.000
 502  H1   C1   C2   109.23  3.000
 502  N8   C1   C2   115.32  3.000
 502  C3   C2   C7   118.36  3.000
 502  C7   C2   C1   119.58  3.000
 502  C3   C2   C1   122.03  3.000
 502  H3   C6   N5   115.83  3.000
 502  H3   C6   C7   119.86  3.000
 502  N5   C6   C7   124.31  3.000
 502  H4   C7   C6   120.53  3.000
 502  H4   C7   C2   121.38  3.000
 502  C6   C7   C2   118.09  3.000
 502  H5   C3   C4   119.77  3.000
 502  H5   C3   C2   121.04  3.000
 502  C4   C3   C2   119.18  3.000
 502  N18  C4   N5   117.02  3.000
 502  N5   C4   C3   122.30  3.000
 502  N18  C4   C3   120.65  3.000
 502  O11  C9   N10  122.20  3.000
 502  N10  C9   N8   115.24  3.000
 502  O11  C9   N8   122.55  3.000
 502  C4   N5   C6   117.76  3.000
 502  H6   N8   C9   119.87  3.000
 502  H6   N8   C1   118.00  3.000
 502  C9   N8   C1   120.87  3.000
 502  H7   N10  C12  116.96  3.000
 502  H7   N10  C9   118.87  3.000
 502  C12  N10  C9   119.20  3.000
 502  H9   C12  H8   106.30  3.000
 502  H9   C12  C13  109.44  3.000
 502  H8   C12  C13  108.26  3.000
 502  H9   C12  N10  111.14  3.000
 502  H8   C12  N10  108.53  3.000
 502  C13  C12  N10  112.90  3.000
 502  O15  C13  O14  124.50  3.000
 502  O15  C13  C12  124.53  3.000
 502  O14  C13  C12  110.95  3.000
 502  C16  O14  C13  118.04  3.000
 502  H11  C16  H10  107.96  3.000
 502  H11  C16  C17  110.95  3.000
 502  H10  C16  C17  110.95  3.000
 502  H11  C16  O14  109.57  3.000
 502  H10  C16  O14  109.43  3.000
 502  C17  C16  O14  107.97  3.000
 502  H14  C17  H13  107.86  3.000
 502  H14  C17  H12  107.79  3.000
 502  H13  C17  H12  108.71  3.000
 502  H14  C17  C16  108.93  3.000
 502  H13  C17  C16  111.71  3.000
 502  H12  C17  C16  111.69  3.000
 502  H16  N18  H15  114.12  3.000
 502  H16  N18  C4   116.15  3.000
 502  H15  N18  C4   117.71  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
 502  CONST_01  N5   C4   C3   C2      0.00   0.0  0
 502  CONST_02  N5   C6   C7   C2      0.00   0.0  0
 502  CONST_03  C3   C2   C7   C6      0.00   0.0  0
 502  CONST_04  C3   C4   N5   C6      0.00   0.0  0
 502  CONST_05  C4   C3   C2   C7      0.00   0.0  0
 502  CONST_06  C4   N5   C6   C7      0.00   0.0  0
 502  CONST_07  C4   C3   C2   C1    180.00   0.0  0
 502  CONST_08  C6   C7   C2   C1    180.00   0.0  0
 502  CONST_09  N18  C4   C3   C2    180.00   0.0  0
 502  CONST_10  N18  C4   N5   C6    180.00   0.0  0
 502  CONST_11  H3   C6   C7   C2    180.00   0.0  0
 502  CONST_12  H5   C3   C2   C7    180.00   0.0  0
 502  CONST_13  H4   C7   C2   C3    180.00   0.0  0
 502  CONST_16  O11  C9   N8   C1      0.00   0.0  0
 502  CONST_17  C12  N10  C9   O11     0.00   0.0  0
 502  CONST_18  N10  C9   N8   C1    180.00   0.0  0
 502  CONST_19  C12  N10  C9   N8    180.00   0.0  0
 502  CONST_20  H6   N8   C9   O11   180.00   0.0  0
 502  CONST_21  H7   N10  C9   O11   180.00   0.0  0
 502  Var_01    N8   C1   C2   C7   -159.27  30.0  2
 502  Var_02    C9   N8   C1   C2     72.32  30.0  3
 502  Var_03    C13  C12  N10  C9     66.90  30.0  1
 502  Var_04    O14  C13  C12  N10  -169.64  30.0  3
 502  Var_05    C17  C16  O14  C13   179.80  30.0  3
 502  Var_06    H12  C17  C16  O14   -60.83  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
 502  plan-1  C1   0.020
 502  plan-1  C2   0.020
 502  plan-1  C6   0.020
 502  plan-1  C7   0.020
 502  plan-1  C3   0.020
 502  plan-1  C4   0.020
 502  plan-1  N5   0.020
 502  plan-1  N18  0.020
 502  plan-1  H3   0.020
 502  plan-1  H4   0.020
 502  plan-1  H5   0.020
 502  plan-2  C1   0.020
 502  plan-2  C9   0.020
 502  plan-2  N8   0.020
 502  plan-2  N10  0.020
 502  plan-2  O11  0.020
 502  plan-2  C12  0.020
 502  plan-2  H6   0.020
 502  plan-2  H7   0.020
 502  plan-3  C4   0.020
 502  plan-3  N18  0.020
 502  plan-3  H15  0.020
 502  plan-3  H16  0.020
 502  plan-4  C12  0.020
 502  plan-4  C13  0.020
 502  plan-4  O14  0.020
 502  plan-4  O15  0.020

