# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:10:23 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 6-[[(2-chloranyl-6-fluoranyl-phenyl)methyl-methyl-amino]methyl]-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC1=CC(=O)NC(=O)N1)Cc2c(F)cccc2Cl
#
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
 P0B  P0B  6-[[(2-chloranyl-6-fluoranyl-phenyl)methyl-methyl-amino]methyl]-1~{H}-pyrimidine-2,4-dione  ligand  33  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P0B
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
 P0B  CAA  C   CH3   0  -0.527   0.6973  -4.7254  4.6887
 P0B  CAF  C   CR16  0  -0.253  -0.8140   1.3091  6.3265
 P0B  CAG  C   CR16  0  -0.393  -0.0163   0.6428  7.2408
 P0B  CAH  C   CR16  0  -0.218  -1.4618   0.6116  5.3175
 P0B  CAI  C   CR16  0  -0.535   2.6977  -0.2688  4.8420
 P0B  CAJ  C   CH2   0  -0.348   1.9404  -2.6704  4.9832
 P0B  CAK  C   CH2   0  -0.331  -0.2551  -2.9564  5.9838
 P0B  CAN  C   CR6   0   0.541   0.1273  -0.7239  7.1118
 P0B  CAO  C   CR6   0  -0.073  -1.2943  -0.7603  5.2338
 P0B  CAP  C   CR6   0   0.433   1.9474  -1.2908  4.3845
 P0B  CAQ  C   CR6   0  -0.065  -0.4830  -1.4755  6.1162
 P0B  CAR  C   CR6   0   0.579   2.6529   1.0064  4.1742
 P0B  CAS  C   CR6   0   0.661   1.0234   0.0273  2.5934
 P0B  NAL  N   NR16  0  -0.700   1.1672  -1.1461  3.2801
 P0B  NAM  N   NR16  0  -0.718   1.7989   1.0476  3.0792
 P0B  NAT  N   NT    0  -0.426   0.6350  -3.2890  4.8781
 P0B  OAB  O   O     0  -0.475   3.2797   2.0010  4.4977
 P0B  OAC  O   O     0  -0.475   0.2834   0.1522  1.6394
 P0B  CL1  CL  CL    0  -0.105  -2.1244  -1.6039  3.9688
 P0B  H1   H   HCH3  0   0.243  -0.3039  -5.1091  4.4913
 P0B  H2   H   HCH3  0   0.246   1.3202  -4.9600  3.8263
 P0B  H3   H   HCH3  0   0.209   1.0991  -5.2641  5.5577
 P0B  H4   H   HCR6  0   0.280  -0.9381   2.3806  6.4005
 P0B  H5   H   HCR6  0   0.285   0.4956   1.1712  8.0336
 P0B  H6   H   HCR6  0   0.286  -2.0915   1.1297  4.6079
 P0B  H7   H   HCR6  0   0.279   3.3157  -0.3812  5.7203
 P0B  H9   H   HCH2  0   0.297   2.6535  -3.2644  4.4046
 P0B  H10  H   HCH2  0   0.258   2.3354  -2.6264  6.0051
 P0B  H11  H   HCH2  0   0.265  -1.2131  -3.4442  5.7938
 P0B  H12  H   HCH2  0   0.245   0.1162  -3.3661  6.9315
 P0B  H13  H   HNR6  0   0.423   1.7221   1.9313  2.5913
 P0B  H8   H   HNR6  0   0.419   0.5512  -1.9182  3.0492
 P0B  FAD  F   F     0  -0.308   0.9272  -1.3524  7.9872

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
 P0B  OAC  CAS  double    1.214  0.020  1.214
 P0B  CAS  NAM  single    1.371  0.020  1.371
 P0B  CAS  NAL  single    1.367  0.020  1.367
 P0B  NAM  CAR  single    1.389  0.020  1.389
 P0B  NAL  CAP  single    1.360  0.020  1.360
 P0B  CL1  CAO  single    1.732  0.020  1.732
 P0B  CAR  OAB  double    1.219  0.020  1.219
 P0B  CAR  CAI  single    1.440  0.020  1.440
 P0B  CAP  CAI  double    1.348  0.020  1.348
 P0B  CAP  CAJ  single    1.504  0.020  1.504
 P0B  CAA  NAT  single    1.450  0.020  1.450
 P0B  NAT  CAJ  single    1.448  0.020  1.448
 P0B  NAT  CAK  single    1.458  0.020  1.458
 P0B  CAO  CAH  aromatic  1.385  0.020  1.385
 P0B  CAO  CAQ  aromatic  1.396  0.020  1.396
 P0B  CAH  CAF  aromatic  1.387  0.020  1.387
 P0B  CAK  CAQ  single    1.504  0.020  1.504
 P0B  CAQ  CAN  aromatic  1.389  0.020  1.389
 P0B  CAF  CAG  aromatic  1.384  0.020  1.384
 P0B  CAN  CAG  aromatic  1.380  0.020  1.380
 P0B  CAN  FAD  single    1.342  0.020  1.342
 P0B  CAA  H1   single    0.970  0.020  1.090
 P0B  CAA  H2   single    0.970  0.020  1.090
 P0B  CAA  H3   single    0.970  0.020  1.090
 P0B  CAF  H4   single    0.930  0.020  1.080
 P0B  CAG  H5   single    0.930  0.020  1.080
 P0B  CAH  H6   single    0.930  0.020  1.080
 P0B  CAI  H7   single    0.930  0.020  1.080
 P0B  CAJ  H9   single    0.970  0.020  1.090
 P0B  CAJ  H10  single    0.970  0.020  1.090
 P0B  CAK  H11  single    0.970  0.020  1.090
 P0B  CAK  H12  single    0.970  0.020  1.090
 P0B  NAM  H13  single    0.860  0.020  1.020
 P0B  NAL  H8   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
 P0B  H3   CAA  H2   108.15  3.000
 P0B  H3   CAA  H1   107.85  3.000
 P0B  H2   CAA  H1   107.82  3.000
 P0B  H3   CAA  NAT  113.46  3.000
 P0B  H2   CAA  NAT  109.95  3.000
 P0B  H1   CAA  NAT  109.44  3.000
 P0B  H4   CAF  CAH  119.63  3.000
 P0B  H4   CAF  CAG  119.87  3.000
 P0B  CAH  CAF  CAG  120.50  3.000
 P0B  H5   CAG  CAN  120.20  3.000
 P0B  H5   CAG  CAF  121.45  3.000
 P0B  CAN  CAG  CAF  118.35  3.000
 P0B  H6   CAH  CAO  120.38  3.000
 P0B  H6   CAH  CAF  120.57  3.000
 P0B  CAO  CAH  CAF  119.05  3.000
 P0B  H7   CAI  CAR  119.15  3.000
 P0B  H7   CAI  CAP  121.05  3.000
 P0B  CAR  CAI  CAP  119.78  3.000
 P0B  H10  CAJ  H9   106.26  3.000
 P0B  H10  CAJ  NAT  114.17  3.000
 P0B  H9   CAJ  NAT  108.50  3.000
 P0B  H10  CAJ  CAP  109.42  3.000
 P0B  H9   CAJ  CAP  106.53  3.000
 P0B  NAT  CAJ  CAP  111.53  3.000
 P0B  H12  CAK  H11  106.29  3.000
 P0B  H12  CAK  NAT  111.30  3.000
 P0B  H11  CAK  NAT  107.57  3.000
 P0B  H12  CAK  CAQ  110.06  3.000
 P0B  H11  CAK  CAQ  108.80  3.000
 P0B  NAT  CAK  CAQ  112.58  3.000
 P0B  FAD  CAN  CAQ  118.43  3.000
 P0B  FAD  CAN  CAG  117.69  3.000
 P0B  CAQ  CAN  CAG  123.86  3.000
 P0B  CL1  CAO  CAQ  119.38  3.000
 P0B  CAQ  CAO  CAH  122.67  3.000
 P0B  CL1  CAO  CAH  117.95  3.000
 P0B  NAL  CAP  CAJ  114.73  3.000
 P0B  CAJ  CAP  CAI  124.26  3.000
 P0B  NAL  CAP  CAI  120.95  3.000
 P0B  CAO  CAQ  CAN  115.55  3.000
 P0B  CAN  CAQ  CAK  121.96  3.000
 P0B  CAO  CAQ  CAK  122.47  3.000
 P0B  OAB  CAR  NAM  120.06  3.000
 P0B  OAB  CAR  CAI  125.68  3.000
 P0B  NAM  CAR  CAI  114.26  3.000
 P0B  OAC  CAS  NAM  123.15  3.000
 P0B  NAM  CAS  NAL  113.67  3.000
 P0B  OAC  CAS  NAL  123.18  3.000
 P0B  H8   NAL  CAS  118.37  3.000
 P0B  H8   NAL  CAP  116.89  3.000
 P0B  CAS  NAL  CAP  124.03  3.000
 P0B  H13  NAM  CAS  115.86  3.000
 P0B  H13  NAM  CAR  116.90  3.000
 P0B  CAS  NAM  CAR  127.23  3.000
 P0B  CAK  NAT  CAJ  113.44  3.000
 P0B  CAK  NAT  CAA  110.56  3.000
 P0B  CAJ  NAT  CAA  113.19  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
 P0B  CONST_01  CAQ  CAO  CAH  CAF     0.00   0.0  0
 P0B  CONST_02  CAQ  CAN  CAG  CAF     0.00   0.0  0
 P0B  CONST_03  CAO  CAH  CAF  CAG     0.00   0.0  0
 P0B  CONST_04  CAO  CAQ  CAN  CAG     0.00   0.0  0
 P0B  CONST_05  CAN  CAQ  CAO  CAH     0.00   0.0  0
 P0B  CONST_06  CAN  CAG  CAF  CAH     0.00   0.0  0
 P0B  CONST_07  CAS  NAM  CAR  CAI     0.00   0.0  0
 P0B  CONST_08  NAM  CAS  NAL  CAP     0.00   0.0  0
 P0B  CONST_09  NAL  CAS  NAM  CAR     0.00   0.0  0
 P0B  CONST_10  CL1  CAO  CAH  CAF   180.00   0.0  0
 P0B  CONST_11  FAD  CAN  CAG  CAF   180.00   0.0  0
 P0B  CONST_12  CAK  CAQ  CAN  CAG   180.00   0.0  0
 P0B  CONST_13  CAK  CAQ  CAO  CAH   180.00   0.0  0
 P0B  CONST_14  CL1  CAO  CAQ  CAN   180.00   0.0  0
 P0B  CONST_15  FAD  CAN  CAQ  CAO   180.00   0.0  0
 P0B  CONST_16  OAC  CAS  NAL  CAP   180.00   0.0  0
 P0B  CONST_17  OAC  CAS  NAM  CAR   180.00   0.0  0
 P0B  CONST_18  OAB  CAR  NAM  CAS   180.00   0.0  0
 P0B  CONST_19  H6   CAH  CAF  CAG   180.00   0.0  0
 P0B  CONST_20  H5   CAG  CAF  CAH   180.00   0.0  0
 P0B  CONST_21  H4   CAF  CAG  CAN   180.00   0.0  0
 P0B  CONST_22  H13  NAM  CAR  CAI   180.00   0.0  0
 P0B  CONST_23  H8   NAL  CAS  NAM   180.00   0.0  0
 P0B  Var_01    NAT  CAJ  CAP  CAI   146.83  30.0  3
 P0B  Var_02    NAT  CAK  CAQ  CAN  -104.46  30.0  2
 P0B  Var_03    CAP  CAJ  NAT  CAA   146.36  30.0  3
 P0B  Var_04    CAQ  CAK  NAT  CAA  -173.13  30.0  3
 P0B  Var_05    H1   CAA  NAT  CAJ  -172.86  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
 P0B  plan-1  CAF  0.020
 P0B  plan-1  CAG  0.020
 P0B  plan-1  CAH  0.020
 P0B  plan-1  CAK  0.020
 P0B  plan-1  CAN  0.020
 P0B  plan-1  CAO  0.020
 P0B  plan-1  CAQ  0.020
 P0B  plan-1  CL1  0.020
 P0B  plan-1  H4   0.020
 P0B  plan-1  H5   0.020
 P0B  plan-1  H6   0.020
 P0B  plan-1  FAD  0.020
 P0B  plan-2  CAI  0.020
 P0B  plan-2  CAJ  0.020
 P0B  plan-2  CAP  0.020
 P0B  plan-2  CAR  0.020
 P0B  plan-2  CAS  0.020
 P0B  plan-2  NAL  0.020
 P0B  plan-2  NAM  0.020
 P0B  plan-2  OAB  0.020
 P0B  plan-2  OAC  0.020
 P0B  plan-2  H7   0.020
 P0B  plan-2  H13  0.020
 P0B  plan-2  H8   0.020

