# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 12:56:52 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 6-[[methyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC1=NC(=O)NC(=O)C1)Cc2ccccc2
#
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
 M3Z  M3Z  6-[[methyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione  ligand  33  18  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M3Z
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
 M3Z  CAC  C  CH3   0  -0.532   0.6953   0.1102   1.6869
 M3Z  CAF  C  CR16  0  -0.241   5.4197  -0.2102   0.4275
 M3Z  CAG  C  CR16  0  -0.313   4.2605  -0.9470   0.6425
 M3Z  CAH  C  CR16  0  -0.271   5.3942   0.8963  -0.4093
 M3Z  CAI  C  CR16  0  -0.280   3.0501   0.5201  -0.8149
 M3Z  CAJ  C  CH2   0  -0.673  -3.0757  -1.2841   0.0700
 M3Z  CAK  C  CH2   0  -0.324   1.8216  -1.4190   0.2194
 M3Z  CAL  C  CH2   0  -0.321  -0.5690  -1.3495   0.2752
 M3Z  CAQ  C  CR6   0   0.081   3.0674  -0.5942   0.0219
 M3Z  CAR  C  C     0   0.268  -1.7892  -0.5335  -0.0229
 M3Z  CAS  C  CR16  0  -0.242   4.2035   1.2603  -1.0286
 M3Z  CAT  C  C     0   0.581  -4.2717  -0.5470  -0.4480
 M3Z  CAU  C  C     0   0.605  -2.8276   1.4261  -0.6568
 M3Z  NAO  N  N     0  -0.430  -1.6872   0.6961  -0.3362
 M3Z  NAP  N  NH1   0  -0.694  -4.0436   0.7694  -0.7349
 M3Z  NAX  N  NT    0  -0.401   0.6442  -0.5963   0.4229
 M3Z  OAD  O  O     0  -0.430  -5.3613  -1.0537  -0.5803
 M3Z  OAE  O  O     0  -0.427  -2.7608   2.6092  -0.8859
 M3Z  H1   H  HCH3  0   0.200   0.6997  -0.5691   2.5529
 M3Z  H2   H  HCH3  0   0.243   1.5967   0.7203   1.7365
 M3Z  H3   H  HCH3  0   0.244  -0.1562   0.7816   1.7836
 M3Z  H5   H  HCR6  0   0.248   4.2845  -1.8033   1.3067
 M3Z  H6   H  HCR6  0   0.253   6.2938   1.4753  -0.5747
 M3Z  H7   H  HCR6  0   0.246   2.1204   0.8124  -1.2875
 M3Z  H8   H  HCH2  0   0.330  -2.9913  -2.2493  -0.4352
 M3Z  H9   H  HCH2  0   0.344  -3.2588  -1.5244   1.1238
 M3Z  H10  H  HCH2  0   0.256   1.6616  -2.0256  -0.6775
 M3Z  H11  H  HCH2  0   0.217   1.9821  -2.1326   1.0445
 M3Z  H12  H  HCH2  0   0.242  -0.7933  -1.9973   1.1413
 M3Z  H13  H  HCH2  0   0.292  -0.4705  -2.0403  -0.5713
 M3Z  H14  H  HCR6  0   0.252   4.1748   2.1249  -1.6796
 M3Z  H15  H  HNH1  0   0.425  -4.8366   1.3246  -1.0344
 M3Z  H4   H  HCR6  0   0.253   6.3392  -0.4967   0.9219

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
 M3Z  OAD  CAT  double    1.209  0.020  1.209
 M3Z  CAT  NAP  single    1.366  0.020  1.366
 M3Z  CAT  CAJ  single    1.497  0.020  1.497
 M3Z  NAP  CAU  single    1.384  0.020  1.384
 M3Z  CAJ  CAR  single    1.492  0.020  1.492
 M3Z  CAU  OAE  double    1.207  0.020  1.207
 M3Z  CAU  NAO  single    1.391  0.020  1.391
 M3Z  CAR  NAO  double    1.273  0.020  1.273
 M3Z  CAR  CAL  single    1.498  0.020  1.498
 M3Z  CAF  CAG  aromatic  1.390  0.020  1.390
 M3Z  CAF  CAH  aromatic  1.387  0.020  1.387
 M3Z  CAG  CAQ  aromatic  1.390  0.020  1.390
 M3Z  CAL  NAX  single    1.436  0.020  1.436
 M3Z  NAX  CAC  single    1.449  0.020  1.449
 M3Z  NAX  CAK  single    1.451  0.020  1.451
 M3Z  CAH  CAS  aromatic  1.391  0.020  1.391
 M3Z  CAQ  CAK  single    1.507  0.020  1.507
 M3Z  CAQ  CAI  aromatic  1.394  0.020  1.394
 M3Z  CAS  CAI  aromatic  1.387  0.020  1.387
 M3Z  CAC  H1   single    0.970  0.020  1.090
 M3Z  CAC  H2   single    0.970  0.020  1.090
 M3Z  CAC  H3   single    0.970  0.020  1.090
 M3Z  CAF  H4   single    0.930  0.020  1.080
 M3Z  CAG  H5   single    0.930  0.020  1.080
 M3Z  CAH  H6   single    0.930  0.020  1.080
 M3Z  CAI  H7   single    0.930  0.020  1.080
 M3Z  CAJ  H8   single    0.970  0.020  1.090
 M3Z  CAJ  H9   single    0.970  0.020  1.090
 M3Z  CAK  H10  single    0.970  0.020  1.090
 M3Z  CAK  H11  single    0.970  0.020  1.090
 M3Z  CAL  H12  single    0.970  0.020  1.090
 M3Z  CAL  H13  single    0.970  0.020  1.090
 M3Z  CAS  H14  single    0.930  0.020  1.080
 M3Z  NAP  H15  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
 M3Z  H3   CAC  H2   107.32  3.000
 M3Z  H3   CAC  H1   108.29  3.000
 M3Z  H2   CAC  H1   107.84  3.000
 M3Z  H3   CAC  NAX  110.53  3.000
 M3Z  H2   CAC  NAX  109.99  3.000
 M3Z  H1   CAC  NAX  112.68  3.000
 M3Z  H4   CAF  CAH  120.14  3.000
 M3Z  H4   CAF  CAG  119.82  3.000
 M3Z  CAH  CAF  CAG  120.04  3.000
 M3Z  H5   CAG  CAQ  119.54  3.000
 M3Z  H5   CAG  CAF  119.67  3.000
 M3Z  CAQ  CAG  CAF  120.79  3.000
 M3Z  H6   CAH  CAS  120.23  3.000
 M3Z  H6   CAH  CAF  120.23  3.000
 M3Z  CAS  CAH  CAF  119.54  3.000
 M3Z  H7   CAI  CAS  120.17  3.000
 M3Z  H7   CAI  CAQ  119.24  3.000
 M3Z  CAS  CAI  CAQ  120.59  3.000
 M3Z  H9   CAJ  H8   105.29  3.000
 M3Z  H9   CAJ  CAT  107.88  3.000
 M3Z  H8   CAJ  CAT  109.67  3.000
 M3Z  H9   CAJ  CAR  108.31  3.000
 M3Z  H8   CAJ  CAR  110.42  3.000
 M3Z  CAT  CAJ  CAR  114.80  3.000
 M3Z  H11  CAK  H10  106.00  3.000
 M3Z  H11  CAK  NAX  112.35  3.000
 M3Z  H10  CAK  NAX  108.09  3.000
 M3Z  H11  CAK  CAQ  109.39  3.000
 M3Z  H10  CAK  CAQ  108.47  3.000
 M3Z  NAX  CAK  CAQ  112.27  3.000
 M3Z  H13  CAL  H12  104.72  3.000
 M3Z  H13  CAL  NAX  109.50  3.000
 M3Z  H12  CAL  NAX  113.49  3.000
 M3Z  H13  CAL  CAR  105.23  3.000
 M3Z  H12  CAL  CAR  108.07  3.000
 M3Z  NAX  CAL  CAR  115.03  3.000
 M3Z  CAK  CAQ  CAI  120.40  3.000
 M3Z  CAI  CAQ  CAG  118.79  3.000
 M3Z  CAK  CAQ  CAG  120.79  3.000
 M3Z  NAO  CAR  CAL  120.66  3.000
 M3Z  CAL  CAR  CAJ  114.57  3.000
 M3Z  NAO  CAR  CAJ  124.76  3.000
 M3Z  H14  CAS  CAI  119.79  3.000
 M3Z  H14  CAS  CAH  119.96  3.000
 M3Z  CAI  CAS  CAH  120.25  3.000
 M3Z  OAD  CAT  NAP  122.09  3.000
 M3Z  NAP  CAT  CAJ  114.43  3.000
 M3Z  OAD  CAT  CAJ  123.46  3.000
 M3Z  OAE  CAU  NAP  120.20  3.000
 M3Z  OAE  CAU  NAO  120.84  3.000
 M3Z  NAP  CAU  NAO  118.95  3.000
 M3Z  CAU  NAO  CAR  119.86  3.000
 M3Z  H15  NAP  CAU  116.37  3.000
 M3Z  H15  NAP  CAT  117.34  3.000
 M3Z  CAU  NAP  CAT  126.29  3.000
 M3Z  CAL  NAX  CAK  111.96  3.000
 M3Z  CAK  NAX  CAC  111.73  3.000
 M3Z  CAL  NAX  CAC  112.05  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
 M3Z  CONST_01  CAI  CAQ  CAG  CAF     0.00   0.0  0
 M3Z  CONST_02  CAI  CAS  CAH  CAF     0.00   0.0  0
 M3Z  CONST_03  CAS  CAH  CAF  CAG     0.00   0.0  0
 M3Z  CONST_04  CAS  CAI  CAQ  CAG     0.00   0.0  0
 M3Z  CONST_05  CAQ  CAG  CAF  CAH     0.00   0.0  0
 M3Z  CONST_06  CAQ  CAI  CAS  CAH     0.00   0.0  0
 M3Z  CONST_07  CAU  NAP  CAT  CAJ     0.00   0.0  0
 M3Z  CONST_08  NAP  CAU  NAO  CAR     0.00   0.0  0
 M3Z  CONST_09  NAO  CAU  NAP  CAT     0.00   0.0  0
 M3Z  CONST_10  CAK  CAQ  CAG  CAF   180.00   0.0  0
 M3Z  CONST_11  CAS  CAI  CAQ  CAK   180.00   0.0  0
 M3Z  CONST_12  OAE  CAU  NAO  CAR   180.00   0.0  0
 M3Z  CONST_13  OAE  CAU  NAP  CAT   180.00   0.0  0
 M3Z  CONST_14  OAD  CAT  NAP  CAU   180.00   0.0  0
 M3Z  CONST_15  H14  CAS  CAH  CAF   180.00   0.0  0
 M3Z  CONST_16  H6   CAH  CAF  CAG   180.00   0.0  0
 M3Z  CONST_17  H7   CAI  CAQ  CAG   180.00   0.0  0
 M3Z  CONST_18  H5   CAG  CAF  CAH   180.00   0.0  0
 M3Z  CONST_19  H4   CAF  CAG  CAQ   180.00   0.0  0
 M3Z  CONST_20  H15  NAP  CAT  CAJ   180.00   0.0  0
 M3Z  Var_01    CAT  CAJ  CAR  CAL  -170.10  30.0  1
 M3Z  Var_02    NAX  CAK  CAQ  CAG   137.25  30.0  2
 M3Z  Var_03    NAX  CAL  CAR  CAJ  -169.43  30.0  3
 M3Z  Var_04    CAR  CAL  NAX  CAC    74.67  30.0  2
 M3Z  Var_05    CAQ  CAK  NAX  CAC   -68.00  30.0  3
 M3Z  Var_06    H1   CAC  NAX  CAK   -63.26  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
 M3Z  plan-1  CAF  0.020
 M3Z  plan-1  CAG  0.020
 M3Z  plan-1  CAH  0.020
 M3Z  plan-1  CAI  0.020
 M3Z  plan-1  CAK  0.020
 M3Z  plan-1  CAQ  0.020
 M3Z  plan-1  CAS  0.020
 M3Z  plan-1  H5   0.020
 M3Z  plan-1  H6   0.020
 M3Z  plan-1  H7   0.020
 M3Z  plan-1  H14  0.020
 M3Z  plan-1  H4   0.020
 M3Z  plan-2  CAJ  0.020
 M3Z  plan-2  CAR  0.020
 M3Z  plan-2  CAT  0.020
 M3Z  plan-2  CAU  0.020
 M3Z  plan-2  NAO  0.020
 M3Z  plan-2  NAP  0.020
 M3Z  plan-2  OAD  0.020
 M3Z  plan-2  OAE  0.020
 M3Z  plan-2  H15  0.020

