# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 03:38:34 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: methyl N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCNC(=O)C1=CC(=O)NC(=O)N1
#
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
 N18  N18  'methyl N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alaninate'  ligand  28  17  .  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_N18
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
 N18  N    N  NH1   0  -0.659  -0.6558  -0.1165  -0.0839
 N18  C    C  CH3   0  -0.425  -6.6824   0.6160   0.0095
 N18  O    O  O2    0  -0.453  -5.2939   0.9488  -0.0317
 N18  C1   C  C     0   0.610  -4.4231  -0.0482  -0.0086
 N18  C2   C  CH2   0  -0.632  -3.0076   0.4608  -0.0494
 N18  C3   C  CH2   0  -0.241  -1.9961  -0.6697  -0.0523
 N18  C4   C  C     0   0.550   0.4180  -0.8730   0.1272
 N18  C5   C  CR6   0   0.364   1.7539  -0.1776   0.0702
 N18  C6   C  CR16  0  -0.522   1.9499   1.1520   0.1293
 N18  C7   C  CR6   0   0.597   3.2995   1.6781   0.0844
 N18  C8   C  CR6   0   0.676   4.1105  -0.6508  -0.0575
 N18  N1   N  NR16  0  -0.719   4.2841   0.7100  -0.0122
 N18  N2   N  NR16  0  -0.722   2.7998  -1.0417  -0.0195
 N18  O1   O  O     0  -0.449  -4.7364  -1.2110   0.0411
 N18  O2   O  O     0  -0.474   0.3834  -2.0714   0.3598
 N18  O3   O  O     0  -0.454   3.5875   2.8584   0.1271
 N18  O4   O  O     0  -0.468   5.0324  -1.4342  -0.1277
 N18  H1   H  HNH1  0   0.422  -0.5432   0.8385  -0.3840
 N18  H2   H  HCH3  0   0.240  -6.9397   0.0976   0.9328
 N18  H3   H  HCH3  0   0.253  -7.2156   1.5611  -0.0327
 N18  H4   H  HCH3  0   0.240  -6.9708   0.0004  -0.8421
 N18  H5   H  HCH2  0   0.294  -2.8914   1.0898  -0.9373
 N18  H6   H  HCH2  0   0.297  -2.8486   1.1165   0.8117
 N18  H7   H  HCH2  0   0.258  -2.1507  -1.3230  -0.9143
 N18  H8   H  HCH2  0   0.260  -2.1061  -1.2823   0.8427
 N18  H9   H  HCR6  0   0.292   1.1400   1.8582   0.2298
 N18  H10  H  HNR6  0   0.431   5.2439   1.0330  -0.0401
 N18  H11  H  HNR6  0   0.433   2.6055  -2.0355  -0.0244

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
 N18  O3  C7   double  1.216  0.020  1.216
 N18  C7  C6   single  1.449  0.020  1.449
 N18  C7  N1   single  1.384  0.020  1.384
 N18  C6  C5   double  1.345  0.020  1.345
 N18  N1  C8   single  1.373  0.020  1.373
 N18  O2  C4   double  1.221  0.020  1.221
 N18  C5  N2   single  1.360  0.020  1.360
 N18  C5  C4   single  1.507  0.020  1.507
 N18  C8  N2   single  1.368  0.020  1.368
 N18  C8  O4   double  1.212  0.020  1.212
 N18  C4  N    single  1.330  0.020  1.330
 N18  O   C    single  1.428  0.020  1.428
 N18  O   C1   single  1.324  0.020  1.324
 N18  C2  C1   single  1.505  0.020  1.505
 N18  C2  C3   single  1.517  0.020  1.517
 N18  N   C3   single  1.450  0.020  1.450
 N18  C1  O1   double  1.205  0.020  1.205
 N18  N   H1   single  0.860  0.020  1.020
 N18  C   H2   single  0.970  0.020  1.090
 N18  C   H3   single  0.970  0.020  1.090
 N18  C   H4   single  0.970  0.020  1.090
 N18  C2  H5   single  0.970  0.020  1.090
 N18  C2  H6   single  0.970  0.020  1.090
 N18  C3  H7   single  0.970  0.020  1.090
 N18  C3  H8   single  0.970  0.020  1.090
 N18  C6  H9   single  0.930  0.020  1.080
 N18  N1  H10  single  0.860  0.020  1.020
 N18  N2  H11  single  0.860  0.020  1.020

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
 N18  H1   N   C4  119.74  3.000
 N18  H1   N   C3  118.13  3.000
 N18  C4   N   C3  121.70  3.000
 N18  H4   C   H3  109.35  3.000
 N18  H4   C   H2  109.33  3.000
 N18  H3   C   H2  109.33  3.000
 N18  H4   C   O   111.49  3.000
 N18  H3   C   O   105.87  3.000
 N18  H2   C   O   111.40  3.000
 N18  C1   O   C   117.61  3.000
 N18  O1   C1  C2  124.88  3.000
 N18  O1   C1  O   123.80  3.000
 N18  C2   C1  O   111.32  3.000
 N18  H6   C2  H5  106.18  3.000
 N18  H6   C2  C3  110.57  3.000
 N18  H5   C2  C3  110.85  3.000
 N18  H6   C2  C1  108.55  3.000
 N18  H5   C2  C1  108.44  3.000
 N18  C3   C2  C1  112.04  3.000
 N18  H8   C3  H7  107.31  3.000
 N18  H8   C3  C2  110.48  3.000
 N18  H7   C3  C2  110.66  3.000
 N18  H8   C3  N   108.99  3.000
 N18  H7   C3  N   109.97  3.000
 N18  C2   C3  N   109.39  3.000
 N18  O2   C4  C5  119.02  3.000
 N18  C5   C4  N   116.56  3.000
 N18  O2   C4  N   124.42  3.000
 N18  N2   C5  C6  121.26  3.000
 N18  N2   C5  C4  113.03  3.000
 N18  C6   C5  C4  125.69  3.000
 N18  H9   C6  C7  117.66  3.000
 N18  H9   C6  C5  122.79  3.000
 N18  C7   C6  C5  119.55  3.000
 N18  O3   C7  N1  120.86  3.000
 N18  N1   C7  C6  114.25  3.000
 N18  O3   C7  C6  124.89  3.000
 N18  O4   C8  N2  123.07  3.000
 N18  O4   C8  N1  123.13  3.000
 N18  N2   C8  N1  113.80  3.000
 N18  H10  N1  C8  115.79  3.000
 N18  H10  N1  C7  116.93  3.000
 N18  C8   N1  C7  127.28  3.000
 N18  H11  N2  C8  117.65  3.000
 N18  H11  N2  C5  118.45  3.000
 N18  C8   N2  C5  123.86  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
 N18  CONST_01  N1   C8  N2  C5     0.00   0.0  0
 N18  CONST_02  C8   N1  C7  C6     0.00   0.0  0
 N18  CONST_03  N2   C8  N1  C7     0.00   0.0  0
 N18  CONST_04  O4   C8  N2  C5   180.00   0.0  0
 N18  CONST_05  O4   C8  N1  C7   180.00   0.0  0
 N18  CONST_06  O3   C7  N1  C8   180.00   0.0  0
 N18  CONST_07  H10  N1  C7  C6   180.00   0.0  0
 N18  CONST_08  H11  N2  C8  N1   180.00   0.0  0
 N18  CONST_09  C5   C4  N   C3   180.00   0.0  0
 N18  CONST_10  H1   N   C4  C5     0.00   0.0  0
 N18  CONST_11  O2   C4  N   C3     0.00   0.0  0
 N18  Var_01    C6   C5  C4  N     16.00  30.0  2
 N18  Var_02    C1   C2  C3  N   -179.66  30.0  2
 N18  Var_03    C2   C1  O   C   -179.67  30.0  3
 N18  Var_04    C3   C2  C1  O   -178.83  30.0  1
 N18  Var_05    C4   N   C3  C2   168.78  30.0  2
 N18  Var_06    H2   C   O   C1    62.05  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
 N18  plan-1  C4   0.020
 N18  plan-1  C5   0.020
 N18  plan-1  C6   0.020
 N18  plan-1  C7   0.020
 N18  plan-1  C8   0.020
 N18  plan-1  N1   0.020
 N18  plan-1  N2   0.020
 N18  plan-1  O3   0.020
 N18  plan-1  O4   0.020
 N18  plan-1  H9   0.020
 N18  plan-1  H10  0.020
 N18  plan-1  H11  0.020
 N18  plan-2  O    0.020
 N18  plan-2  C1   0.020
 N18  plan-2  C2   0.020
 N18  plan-2  O1   0.020
 N18  plan-3  N    0.020
 N18  plan-3  C3   0.020
 N18  plan-3  C4   0.020
 N18  plan-3  C5   0.020
 N18  plan-3  O2   0.020
 N18  plan-3  H1   0.020

