Problems with F button with fragments bound to multiple chains

[rsanchezgarc]

I have uploaded to nsp13 target a few compounds. All inspirational fragments belong to chain B, but Fragalysis is selecting two of them from chain A and one from chain B.

I am pasting the sdf file.
################################

ver_1.2
RDKit 2D

1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END

<submitter_name> (1)
Ruben Sanchez Garcia

<submitter_email> (1)
[email protected]

<submitter_institution> (1)
University of Oxford

<generation_date> (1)
2021-02-11

(1)
Fragmenstein

<ref_url> (1)
https://github.com/matteoferla/Fragmenstein

(1)
The name of the compound

(1)
The SMILES of the compound

<ref_pdb> (1)
A pdb inlcuded in fragalysis or uploaded. E.g. x0830_0

<ref_mols> (1)
The inspirational fragments usded to propose the compound

<fragmensteinOld_score> (1)
Score

<LE_score> (1)
Score

<comRMSD_score> (1)
Score

<fragmensteinNew_score> (1)
Score

$$$$
x0020_0B_0-x0020_0B_1-x0020_0B_3-x0020_0B_4-x0029_
RDKit 3D

17 18 0 0 0 0 0 0 0 0999 V2000
-27.3110 40.2800 -57.4680 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.7820 41.5570 -57.5990 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.3330 42.4350 -58.7040 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.3510 39.8000 -58.5920 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.5560 40.1980 -56.1850 N 0 0 0 0 0 0 0 0 0 0 0 0
-28.4250 39.3630 -57.0970 N 0 0 0 0 0 0 0 0 0 0 0 0
-26.5110 40.5040 -59.9400 C 0 0 1 0 0 0 0 0 0 0 0 0
-26.8300 38.9820 -55.5650 C 0 0 0 0 0 0 0 0 0 0 0 0
-28.0170 38.4690 -56.1440 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.3370 41.9790 -59.7430 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.5790 39.9900 -60.9260 O 0 0 0 0 0 0 0 0 0 0 0 0
-24.7210 39.0260 -60.5150 C 0 0 0 0 0 0 0 0 0 0 0 0
-24.5570 38.8100 -59.2520 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.1160 38.4060 -61.5660 N 0 0 0 0 0 0 0 0 0 0 0 0
-23.6700 37.8220 -58.8990 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.1570 37.0090 -58.0360 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.4860 35.9480 -57.5380 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
1 4 1 0
1 5 1 0
1 6 1 0
4 7 1 0
5 8 1 0
6 9 1 0
8 9 2 0
3 10 1 0
7 10 1 0
7 11 1 6
11 12 1 0
12 13 2 3
12 14 1 0
13 15 1 0
15 16 2 3
16 17 1 0
M END

(2)
NC(=NN=CO)OC1CC=CC2(C1)NC=CN2

(2)

(2)
full

<∆∆G> (2)
-5.134296315835306

<∆G_bound> (2)
-4.412044765972153

<∆G_unbound> (2)
0.7222515498631529

(2)
0.9106801328390915

<N_constrained_atoms> (2)
16

<N_unconstrained_atoms> (2)
1

(2)
47.41563105583191

(2)
[]

(2)
[]

<fragmensteinOld_score> (2)
-1.516179

<LE_score> (2)
-0.302017

<comRMSD_score> (2)
0.91068

<fragmensteinNew_score> (2)
0.225068

<ref_mols> (2)
x0020_0B,x0029_0B,x0257_0B

<ref_pdb> (2)
x0020

(2)
NC(=NN=CO)O[C@@h]1CC=CC2(C1)NC=CN2

$$$$
x0020_0B_0-x0020_0B_3-x0020_0B_4-x0029_0B_3-x0257_
RDKit 3D

15 16 0 0 0 0 0 0 0 0999 V2000
-27.4400 40.4070 -57.4060 N 0 0 0 0 0 0 0 0 0 0 0 0
-27.9190 41.6780 -57.7450 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.5770 42.3430 -58.8590 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.5430 39.7210 -58.3910 C 0 0 1 0 0 0 0 0 0 0 0 0
-28.0850 39.5520 -56.5060 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.1390 40.5440 -59.6200 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.5260 38.3980 -56.0760 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.7010 38.6680 -57.6630 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.6690 41.7730 -59.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.2170 38.0520 -56.5680 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.2500 39.9890 -60.5880 O 0 0 0 0 0 0 0 0 0 0 0 0
-25.5350 37.0960 -55.8920 F 0 0 0 0 0 0 0 0 0 0 0 0
-24.2270 39.1350 -60.2650 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.6330 39.0260 -59.2070 O 0 0 0 0 0 0 0 0 0 0 0 0
-23.9080 38.3630 -61.3300 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
1 4 1 0
1 5 1 0
4 6 1 0
5 7 2 0
4 8 1 1
3 9 1 0
6 9 2 0
7 10 1 0
8 10 2 0
6 11 1 0
10 12 1 0
11 13 1 0
13 14 2 0
13 15 1 0
M END

(3)
NC(=O)OC1=CC=CN2C=CC(F)=CC12

(3)

(3)
full

<∆∆G> (3)
-3.2125426166164672

<∆G_bound> (3)
-2.8300333773251842

<∆G_unbound> (3)
0.3825092392912831

(3)
0.7860765441948585

<N_constrained_atoms> (3)
14

<N_unconstrained_atoms> (3)
1

(3)
40.579734325408936

(3)
[]

(3)
[]

<fragmensteinOld_score> (3)
-1.056432

<LE_score> (3)
-0.21417

<comRMSD_score> (3)
0.786077

<fragmensteinNew_score> (3)
0.458834

<ref_mols> (3)
x0020_0B,x0029_0B,x0257_0B

<ref_pdb> (3)
x0020

(3)
NC(=O)OC1=CC=CN2C=CC(F)=C[C@H]12

$$$$
x0020_0B_0-x0020_0B_1-x0020_0B_2-x0020_0B_3-x0029_
RDKit 3D

17 18 0 0 0 0 0 0 0 0999 V2000
-27.2700 40.4190 -57.1050 C 0 0 2 0 0 0 0 0 0 0 0 0
-26.5910 40.0480 -56.0010 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.0620 38.8240 -55.4190 C 0 0 0 0 0 0 0 0 0 0 0 0
-28.2500 39.3150 -57.2190 N 0 0 0 0 0 0 0 0 0 0 0 0
-25.9390 40.6350 -58.3040 S 0 0 2 0 0 0 0 0 0 0 0 0
-28.0180 41.7820 -57.1890 C 0 0 0 0 0 0 0 0 0 0 0 0
-28.1080 38.3320 -56.1100 O 0 0 0 0 0 0 0 0 0 0 0 0
-27.5710 42.5230 -58.4370 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.5280 42.0340 -59.0640 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.1670 39.4870 -59.5480 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.2460 39.5500 -60.6150 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.2790 38.6120 -60.6320 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.6950 38.1170 -59.5800 N 0 0 0 0 0 0 0 0 0 0 0 0
-23.9470 38.2160 -61.8680 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.1470 38.6520 -58.3780 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.1940 37.7880 -57.4310 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.8220 36.5210 -57.6540 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 1
2 3 2 0
1 4 1 0
1 5 1 0
1 6 1 0
3 7 1 0
4 7 1 0
6 8 1 0
5 9 1 0
8 9 2 0
5 10 1 6
10 11 1 0
11 12 1 0
12 13 2 3
12 14 1 0
13 15 1 0
15 16 2 3
16 17 1 0
M END

(4)
NC(=NN=CO)NC[SH]1C=CCC12C=CON2

(4)

(4)
full

<∆∆G> (4)
-1.4751787574132826

<∆G_bound> (4)
0.3709133769006228

<∆G_unbound> (4)
1.8460921343139054

(4)
0.998671641541427

<N_constrained_atoms> (4)
16

<N_unconstrained_atoms> (4)
1

(4)
40.927430391311646

(4)
[]

(4)
[]

<fragmensteinOld_score> (4)
-0.696364

<LE_score> (4)
-0.086775

<comRMSD_score> (4)
0.998672

<fragmensteinNew_score> (4)
0.616293

<ref_mols> (4)
x0020_0B,x0029_0B,x0257_0B

<ref_pdb> (4)
x0020

(4)
NC(=NN=CO)NC[S@H]1C=CC[C@]12C=CON2

$$$$
x0020_0B_0-x0020_0B_1-x0020_0B_4-x0029_0B_0-x0029_
RDKit 3D

11 12 0 0 0 0 0 0 0 0999 V2000
-27.3860 40.3310 -57.5180 N 0 0 0 0 0 0 0 0 0 0 0 0
-27.9220 41.5010 -58.0580 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.3310 42.2230 -59.0390 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.4010 39.6210 -58.4010 C 0 0 1 0 0 0 0 0 0 0 0 0
-28.1020 39.5340 -56.6130 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.5930 40.5630 -59.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
-27.6280 38.3730 -56.1240 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.7070 38.5150 -57.6090 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.0600 41.7930 -59.5830 C 0 0 0 0 0 0 0 0 0 0 0 0
-26.3190 37.9390 -56.5450 C 0 0 0 0 0 0 0 0 0 0 0 0
-25.7270 36.9440 -55.8500 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
1 4 1 0
1 5 1 0
4 6 1 1
5 7 2 0
4 8 1 0
3 9 1 0
6 9 2 0
7 10 1 0
8 10 2 0
10 11 1 0
M END

(5)
FC1=CC2C=CC=CN2C=C1

(5)

(5)
full

<∆∆G> (5)
-3.2838353846670283

<∆G_bound> (5)
-3.263028341871855

<∆G_unbound> (5)
0.020807042795173373

(5)
0.8433382363870275

<N_constrained_atoms> (5)
11

<N_unconstrained_atoms> (5)
0

(5)
31.971383333206177

(5)
[]

(5)
[]

<fragmensteinOld_score> (5)
-0.913429

<LE_score> (5)
-0.29853

<comRMSD_score> (5)
0.843338

<fragmensteinNew_score> (5)
0.681693

<ref_mols> (5)
x0020_0B,x0029_0B,x0257_0B

<ref_pdb> (5)
x0020

(5)
FC1=C[C@@h]2C=CC=CN2C=C1

$$$$