# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:21:56 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (5~{R})-6-azanyl-5-(methylamino)-1-(phenylmethyl)-1,3-diazinane-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](N)N(Cc2ccccc2)C(=O)NC1=O
#
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
 I2Z  I2Z  "6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione"
  ligand  34  18  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I2Z
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
 I2Z  N1   N  NH2   0  -0.778  6.6793  31.4442  32.1531
 I2Z  N3   N  NH1   0  -0.716  4.6488  31.3661  28.5768
 I2Z  C4   C  CR6   0   0.111  4.9581  34.2507  31.8579
 I2Z  C5   C  CR16  0  -0.307  3.7155  34.6645  31.3783
 I2Z  C6   C  CR16  0  -0.239  2.7116  35.0514  32.2544
 I2Z  C7   C  CR16  0  -0.265  2.9358  35.0356  33.6257
 I2Z  C8   C  CR16  0  -0.241  4.1704  34.6301  34.1126
 I2Z  C10  C  C     0   0.734  5.1418  32.5749  29.0560
 I2Z  O1   O  O     0  -0.495  4.9900  33.5775  28.3805
 I2Z  C11  C  C     0   0.545  4.8610  30.1203  29.0917
 I2Z  O    O  O     0  -0.426  4.3726  29.1327  28.5901
 I2Z  C1   C  CH1   0  -0.282  5.8145  30.0938  30.2720
 I2Z  N    N  NH1   0  -0.579  5.7506  28.9008  31.0709
 I2Z  C    C  CH3   0  -0.540  4.5054  28.6552  31.7775
 I2Z  N2   N  NT    0  -0.505  5.7582  32.5419  30.2616
 I2Z  C2   C  CH1   0   0.107  5.6778  31.3590  31.1316
 I2Z  C3   C  CH2   0  -0.378  6.0488  33.8188  30.9069
 I2Z  C9   C  CR16  0  -0.288  5.1713  34.2368  33.2326
 I2Z  H1   H  HNH2  0   0.369  6.4180  30.8647  32.9379
 I2Z  H2   H  HNH2  0   0.355  7.5733  31.1073  31.8157
 I2Z  H4   H  HNH1  0   0.414  4.1293  31.4318  27.7102
 I2Z  H5   H  HCR6  0   0.250  3.5310  34.6960  30.3119
 I2Z  H6   H  HCR6  0   0.252  1.7536  35.3726  31.8654
 I2Z  H7   H  HCR6  0   0.253  2.1531  35.3398  34.3086
 I2Z  H8   H  HCR6  0   0.251  4.3550  34.6153  35.1793
 I2Z  H9   H  HCH1  0   0.302  6.8174  30.1358  29.8215
 I2Z  H10  H  HNH1  0   0.362  5.9866  28.1032  30.4980
 I2Z  H12  H  HCH3  0   0.243  4.5490  27.6591  32.2153
 I2Z  H13  H  HCH3  0   0.229  4.3835  29.3558  32.6043
 I2Z  H14  H  HCH3  0   0.208  3.6013  28.7063  31.1606
 I2Z  H15  H  HCH1  0   0.259  4.7034  31.3649  31.6344
 I2Z  H16  H  HCH2  0   0.271  6.9905  33.7290  31.4408
 I2Z  H17  H  HCH2  0   0.277  6.1864  34.5624  30.1256
 I2Z  H18  H  HCR6  0   0.246  6.1290  33.9091  33.6170

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
 I2Z  O1   C10  double    1.218  0.020  1.218
 I2Z  N3   C10  single    1.391  0.020  1.391
 I2Z  N3   C11  single    1.365  0.020  1.365
 I2Z  C10  N2   single    1.354  0.020  1.354
 I2Z  O    C11  double    1.211  0.020  1.211
 I2Z  C11  C1   single    1.518  0.020  1.518
 I2Z  N2   C3   single    1.460  0.020  1.460
 I2Z  N2   C2   single    1.471  0.020  1.471
 I2Z  C1   C2   single    1.536  0.020  1.536
 I2Z  C1   N    single    1.437  0.020  1.437
 I2Z  C3   C4   single    1.510  0.020  1.510
 I2Z  C2   N1   single    1.433  0.020  1.433
 I2Z  N    C    single    1.453  0.020  1.453
 I2Z  C5   C4   aromatic  1.395  0.020  1.395
 I2Z  C5   C6   aromatic  1.387  0.020  1.387
 I2Z  C4   C9   aromatic  1.391  0.020  1.391
 I2Z  C6   C7   aromatic  1.390  0.020  1.390
 I2Z  C9   C8   aromatic  1.390  0.020  1.390
 I2Z  C8   C7   aromatic  1.388  0.020  1.388
 I2Z  N1   H1   single    0.890  0.020  1.040
 I2Z  N1   H2   single    0.890  0.020  1.040
 I2Z  N3   H4   single    0.860  0.020  1.020
 I2Z  C5   H5   single    0.930  0.020  1.080
 I2Z  C6   H6   single    0.930  0.020  1.080
 I2Z  C7   H7   single    0.930  0.020  1.080
 I2Z  C8   H8   single    0.930  0.020  1.080
 I2Z  C1   H9   single    0.970  0.020  1.090
 I2Z  N    H10  single    0.890  0.020  1.040
 I2Z  C    H12  single    0.970  0.020  1.090
 I2Z  C    H13  single    0.970  0.020  1.090
 I2Z  C    H14  single    0.970  0.020  1.090
 I2Z  C2   H15  single    0.970  0.020  1.090
 I2Z  C3   H16  single    0.970  0.020  1.090
 I2Z  C3   H17  single    0.970  0.020  1.090
 I2Z  C9   H18  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
 I2Z  H2   N1   H1   107.24  3.000
 I2Z  H2   N1   C2   111.07  3.000
 I2Z  H1   N1   C2   109.81  3.000
 I2Z  H4   N3   C11  117.52  3.000
 I2Z  H4   N3   C10  114.86  3.000
 I2Z  C11  N3   C10  127.48  3.000
 I2Z  C9   C4   C3   120.58  3.000
 I2Z  C9   C4   C5   118.64  3.000
 I2Z  C3   C4   C5   120.78  3.000
 I2Z  H5   C5   C6   119.37  3.000
 I2Z  H5   C5   C4   119.94  3.000
 I2Z  C6   C5   C4   120.68  3.000
 I2Z  H6   C6   C7   120.05  3.000
 I2Z  H6   C6   C5   119.74  3.000
 I2Z  C7   C6   C5   120.21  3.000
 I2Z  H7   C7   C8   120.27  3.000
 I2Z  H7   C7   C6   120.18  3.000
 I2Z  C8   C7   C6   119.55  3.000
 I2Z  H8   C8   C9   119.82  3.000
 I2Z  H8   C8   C7   120.10  3.000
 I2Z  C9   C8   C7   120.08  3.000
 I2Z  N2   C10  O1   124.77  3.000
 I2Z  N2   C10  N3   116.54  3.000
 I2Z  O1   C10  N3   118.69  3.000
 I2Z  C1   C11  O    124.16  3.000
 I2Z  C1   C11  N3   114.02  3.000
 I2Z  O    C11  N3   121.71  3.000
 I2Z  H9   C1   C2   106.20  3.000
 I2Z  H9   C1   N    107.45  3.000
 I2Z  C2   C1   N    111.64  3.000
 I2Z  H9   C1   C11  104.69  3.000
 I2Z  N    C1   C11  114.76  3.000
 I2Z  C2   C1   C11  111.41  3.000
 I2Z  H10  N    C    110.04  3.000
 I2Z  H10  N    C1   109.26  3.000
 I2Z  C    N    C1   116.67  3.000
 I2Z  H14  C    H13  107.74  3.000
 I2Z  H14  C    H12  107.58  3.000
 I2Z  H13  C    H12  106.69  3.000
 I2Z  H14  C    N    115.19  3.000
 I2Z  H13  C    N    110.86  3.000
 I2Z  H12  C    N    108.42  3.000
 I2Z  C3   N2   C2   116.93  3.000
 I2Z  C2   N2   C10  121.42  3.000
 I2Z  C3   N2   C10  117.57  3.000
 I2Z  H15  C2   N2   108.39  3.000
 I2Z  H15  C2   C1   109.89  3.000
 I2Z  N2   C2   C1   109.07  3.000
 I2Z  H15  C2   N1   107.09  3.000
 I2Z  C1   C2   N1   112.69  3.000
 I2Z  N2   C2   N1   109.62  3.000
 I2Z  H17  C3   H16  107.45  3.000
 I2Z  H17  C3   N2   107.80  3.000
 I2Z  H16  C3   N2   108.51  3.000
 I2Z  H17  C3   C4   110.39  3.000
 I2Z  H16  C3   C4   109.90  3.000
 I2Z  N2   C3   C4   112.63  3.000
 I2Z  H18  C9   C8   119.86  3.000
 I2Z  H18  C9   C4   119.30  3.000
 I2Z  C8   C9   C4   120.83  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
 I2Z  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 I2Z  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 I2Z  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 I2Z  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 I2Z  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 I2Z  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 I2Z  CONST_07  C2   N2   C10  N3      0.00   0.0  0
 I2Z  CONST_08  N2   C10  N3   C11     0.00   0.0  0
 I2Z  CONST_09  C3   C4   C5   C6    180.00   0.0  0
 I2Z  CONST_10  C3   C4   C9   C8    180.00   0.0  0
 I2Z  CONST_11  C3   N2   C10  N3    180.00   0.0  0
 I2Z  CONST_12  C11  N3   C10  O1    180.00   0.0  0
 I2Z  CONST_13  C2   N2   C10  O1    180.00   0.0  0
 I2Z  CONST_14  H6   C6   C5   C4    180.00   0.0  0
 I2Z  CONST_15  H8   C8   C9   C4    180.00   0.0  0
 I2Z  CONST_16  H18  C9   C4   C5    180.00   0.0  0
 I2Z  CONST_17  H7   C7   C6   C5    180.00   0.0  0
 I2Z  CONST_18  H8   C8   C7   C6    180.00   0.0  0
 I2Z  CONST_19  H5   C5   C6   C7    180.00   0.0  0
 I2Z  CONST_20  H18  C9   C8   C7    180.00   0.0  0
 I2Z  CONST_21  H6   C6   C7   C8    180.00   0.0  0
 I2Z  CONST_22  H5   C5   C4   C9    180.00   0.0  0
 I2Z  CONST_23  H7   C7   C8   C9    180.00   0.0  0
 I2Z  CONST_24  H4   N3   C10  N2    180.00   0.0  0
 I2Z  CONST_25  C3   N2   C10  O1      0.00   0.0  0
 I2Z  CONST_26  H4   N3   C10  O1      0.00   0.0  0
 I2Z  Var_01    C1   C11  N3   C10    -3.81  30.0  1
 I2Z  Var_02    C10  N2   C3   C4     93.28  30.0  1
 I2Z  Var_03    C2   N2   C3   C4    -64.35  30.0  1
 I2Z  Var_04    N2   C3   C4   C5    -70.34  30.0  2
 I2Z  Var_05    O    C11  N3   C10   179.69  30.0  1
 I2Z  Var_06    C9   C4   C3   N2    109.32  30.0  2
 I2Z  Var_07    H4   N3   C11  C1    171.47  30.0  1
 I2Z  Var_08    H16  C3   C4   C5    168.55  30.0  2
 I2Z  Var_09    H17  C3   C4   C5     50.20  30.0  2
 I2Z  Var_10    H16  C3   N2   C10  -144.82  30.0  3
 I2Z  Var_11    H17  C3   N2   C10   -28.74  30.0  3
 I2Z  Var_12    H4   N3   C11  O      -5.03  30.0  1
 I2Z  Var_13    H16  C3   N2   C2     57.55  30.0  3
 I2Z  Var_14    H17  C3   N2   C2    173.63  30.0  3
 I2Z  Var_15    H16  C3   C4   C9    -11.79  30.0  2
 I2Z  Var_16    H17  C3   C4   C9   -130.14  30.0  2
 I2Z  Var_17    H12  C    N    C1    171.83  30.0  3
 I2Z  Var_18    H13  C    N    C1    -71.38  30.0  3
 I2Z  Var_19    H14  C    N    C1     51.27  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 I2Z  chir_01  C1  C11  C2  N   negativ
 I2Z  chir_02  C2  N2   N1  C1  positiv

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
 I2Z  plan-1  C4   0.020
 I2Z  plan-1  C5   0.020
 I2Z  plan-1  C6   0.020
 I2Z  plan-1  C7   0.020
 I2Z  plan-1  C8   0.020
 I2Z  plan-1  C3   0.020
 I2Z  plan-1  C9   0.020
 I2Z  plan-1  H5   0.020
 I2Z  plan-1  H6   0.020
 I2Z  plan-1  H7   0.020
 I2Z  plan-1  H8   0.020
 I2Z  plan-1  H18  0.020
 I2Z  plan-2  N3   0.020
 I2Z  plan-2  C10  0.020
 I2Z  plan-2  O1   0.020
 I2Z  plan-2  C11  0.020
 I2Z  plan-2  N2   0.020
 I2Z  plan-2  C2   0.020
 I2Z  plan-2  C3   0.020
 I2Z  plan-2  H4   0.020
 I2Z  plan-3  N3   0.020
 I2Z  plan-3  C11  0.020
 I2Z  plan-3  O    0.020
 I2Z  plan-3  C1   0.020

