Phosphate group - warning O.co2 with non C.2 or S.o2 neighbor.

[missuse]

Hi,

EDIT: issue is resolved, I should have used sdf (mol) format instead of mol2. Sorry to waste your time.

Initial problem:

I am trying to convert NADP from mol2 to pdbqt,

mk_prepare_ligand.py -i NADP.mol2 -o NADP.pdbqt

however I get the warning:

[16:15:43] NADP: warning - O.co2 with non C.2 or S.o2 neighbor.

I guess this is related to the phosphate groups:

https://github.com/rdkit/rdkit/issues/3246 https://github.com/rdkit/rdkit/issues/1806

I would be grateful for any suggestion on how to proceed?

All the best,

Milan

NADP.mol2:

@<TRIPOS>MOLECULE
NADP
 73 77 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 P           0.0400    5.3860   -0.1340 P.3     1  NADP    0.2182
      2 O           1.2730    6.0120    0.3750 O.co2   1  NADP   -0.4371
      3 O           0.1690    4.7430   -1.4530 O.2     1  NADP   -0.5170
      4 O          -1.2060    6.3690   -0.1190 O.3     1  NADP   -0.3246
      5 C          -1.5090    7.1140    1.0330 C.3     1  NADP    0.0836
      6 C          -2.7900    7.8730    0.7340 C.3     1  NADP    0.1133
      7 O          -3.3120    8.4770    1.9020 O.3     1  NADP   -0.3456
      8 C          -2.5710    9.0030   -0.2830 C.3     1  NADP    0.1141
      9 O          -3.7390    9.1680   -1.0600 O.3     1  NADP   -0.3864
     10 C          -2.4030   10.2360    0.5640 C.3     1  NADP    0.1351
     11 O          -2.7420   11.4140   -0.1630 O.3     1  NADP   -0.3569
     12 C          -3.3620    9.8900    1.7120 C.3     1  NADP    0.1672
     13 N          -3.0200   10.5350    2.9890 N.ar    1  NADP   -0.2855
     14 C          -1.8160   10.5150    3.6750 C.ar    1  NADP    0.1004
     15 N          -1.9900   11.2070    4.8310 N.ar    1  NADP   -0.2306
     16 C          -3.2750   11.6530    4.8680 C.ar    1  NADP    0.1473
     17 C          -3.9810   12.4160    5.7900 C.ar    1  NADP    0.1472
     18 N          -3.3700   12.8560    6.8790 N.pl3   1  NADP   -0.3413
     19 N          -5.3080   12.7170    5.5540 N.ar    1  NADP   -0.2188
     20 C          -5.9440   12.2720    4.4020 C.ar    1  NADP    0.1205
     21 N          -5.2290   11.5080    3.4860 N.ar    1  NADP   -0.2159
     22 C          -3.9300   11.2200    3.7240 C.ar    1  NADP    0.1674
     23 O          -0.3830    4.2530    1.0070 O.3     1  NADP   -0.2703
     24 P          -0.3840    2.6060    0.9830 P.3     1  NADP    0.2182
     25 O          -1.4650    2.1370    0.0490 O.2     1  NADP   -0.5170
     26 O           1.0140    2.1800    0.8190 O.co2   1  NADP   -0.4371
     27 O          -1.1360    2.2570    2.3560 O.3     1  NADP   -0.3246
     28 C          -0.5580    2.3320    3.5900 C.3     1  NADP    0.0836
     29 C          -0.6770    0.9790    4.2760 C.3     1  NADP    0.1133
     30 O          -0.3830   -0.1230    3.4040 O.3     1  NADP   -0.3457
     31 C           0.4050    1.0580    5.3350 C.3     1  NADP    0.1135
     32 O          -0.0020    0.4350    6.5150 O.3     1  NADP   -0.3864
     33 C           1.5440    0.3870    4.6150 C.3     1  NADP    0.1285
     34 O           2.5410    0.0130    5.5290 O.3     1  NADP   -0.3847
     35 C           0.7980   -0.7360    3.8850 C.3     1  NADP    0.1640
     36 N           1.6470   -1.4190    2.8760 N.ar    1  NADP   -0.3248
     37 C           2.1810   -0.7490    1.7980 C.ar    1  NADP    0.0192
     38 C           3.0200   -1.4270    0.9020 C.ar    1  NADP    0.0527
     39 C           3.4390   -0.7740   -0.3900 C.2     1  NADP    0.2429
     40 O           4.3480   -1.4520   -1.2280 O.2     1  NADP   -0.2704
     41 N           2.9240    0.4280   -0.6980 N.am    1  NADP   -0.3253
     42 C           3.3020   -2.7750    1.1090 C.ar    1  NADP   -0.0469
     43 C           2.7610   -3.4290    2.2120 C.ar    1  NADP   -0.0447
     44 C           1.9460   -2.7390    3.0900 C.ar    1  NADP    0.0071
     45 P          -2.2410   12.8770    0.3360 P.3     1  NADP   -0.0144
     46 O          -0.7700   12.8060    0.6190 O.co2   1  NADP   -0.5770
     47 O          -3.0440   13.2720    1.5500 O.co2   1  NADP   -0.5770
     48 O          -2.5540   13.8830   -0.7480 O.2     1  NADP   -0.6377
     49 H          -0.7158    7.7989    1.2490 H       1  NADP    0.0591
     50 H          -1.6275    6.4770    1.8845 H       1  NADP    0.0591
     51 H          -3.4674    7.1453    0.3384 H       1  NADP    0.0647
     52 H          -1.7438    8.8099   -0.9336 H       1  NADP    0.0648
     53 H          -4.4936    9.3435   -0.4763 H       1  NADP    0.2100
     54 H          -1.4101   10.4581    0.8953 H       1  NADP    0.0671
     55 H          -4.3328   10.2454    1.4360 H       1  NADP    0.0867
     56 H          -0.9449   10.0573    3.3640 H       1  NADP    0.1030
     57 H          -2.4236   12.6346    7.0359 H       1  NADP    0.1438
     58 H          -3.8620   13.4046    7.5319 H       1  NADP    0.1438
     59 H          -6.9341   12.5053    4.2282 H       1  NADP    0.1048
     60 H          -1.0569    3.0760    4.1752 H       1  NADP    0.0591
     61 H           0.4738    2.5972    3.4903 H       1  NADP    0.0591
     62 H          -1.6702    0.8059    4.6344 H       1  NADP    0.0647
     63 H           0.6631    2.0380    5.6784 H       1  NADP    0.0647
     64 H          -0.2652   -0.4789    6.3240 H       1  NADP    0.2100
     65 H           2.1093    0.9740    3.9216 H       1  NADP    0.0665
     66 H           2.1506   -0.5366    6.2264 H       1  NADP    0.2101
     67 H           0.5375   -1.5584    4.5180 H       1  NADP    0.0865
     68 H           1.9644    0.2491    1.6499 H       1  NADP    0.0817
     69 H           3.1828    0.8742   -1.5366 H       1  NADP    0.1453
     70 H           2.2878    0.8626   -0.0851 H       1  NADP    0.1453
     71 H           3.9085   -3.2859    0.4485 H       1  NADP    0.0626
     72 H           2.9678   -4.4270    2.3741 H       1  NADP    0.0632
     73 H           1.5588   -3.2231    3.9151 H       1  NADP    0.0810
@<TRIPOS>BOND
     1     3     1    2
     2    40    39    2
     3     9     8    1
     4    48    45    2
     5    41    39   am
     6    39    38    1
     7     8    10    1
     8     8     6    1
     9    11    45    1
    10    11    10    1
    11     1     4    1
    12     1     2    1
    13     1    23    1
    14     4     5    1
    15    25    24    2
    16    45    46    1
    17    45    47    1
    18    10    12    1
    19     6     5    1
    20     6     7    1
    21    26    24    1
    22    38    42   ar
    23    38    37   ar
    24    24    23    1
    25    24    27    1
    26    42    43   ar
    27    12     7    1
    28    12    13    1
    29    37    36   ar
    30    43    44   ar
    31    27    28    1
    32    36    44   ar
    33    36    35    1
    34    13    14   ar
    35    13    22   ar
    36    30    35    1
    37    30    29    1
    38    21    22   ar
    39    21    20   ar
    40    28    29    1
    41    14    15   ar
    42    22    16   ar
    43    35    33    1
    44    29    31    1
    45    20    19   ar
    46    33    31    1
    47    33    34    1
    48    15    16   ar
    49    16    17   ar
    50    31    32    1
    51    19    17   ar
    52    17    18    1
    53     5    49    1
    54     5    50    1
    55     6    51    1
    56     8    52    1
    57     9    53    1
    58    10    54    1
    59    12    55    1
    60    14    56    1
    61    18    57    1
    62    18    58    1
    63    20    59    1
    64    28    60    1
    65    28    61    1
    66    29    62    1
    67    31    63    1
    68    32    64    1
    69    33    65    1
    70    34    66    1
    71    35    67    1
    72    37    68    1
    73    41    69    1
    74    41    70    1
    75    42    71    1
    76    43    72    1
    77    44    73    1

[diogomart]

Hi, yes, SDF or MOL is better than MOL2 for RDKit.