FMO DATABASE

FMODB ID: 7N65K

Calculation Name: 3JV6-B-Xray547

Preferred Name: Nuclear factor NF-kappa-B p100 subunit

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JV6

Chain ID: B

ChEMBL ID: CHEMBL3879845

UniProt ID: Q9WTK5

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-859437.486957
FMO2-HF: Nuclear repulsion	815985.809213
FMO2-HF: Total energy	-43451.677743
FMO2-MP2: Total energy	-43578.845876

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:225:ALA)

Summations of interaction energy for fragment #1(A:225:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
4.571	6.088	-0.003	-0.569	-0.944	-0.001

Interaction energy analysis for fragmet #1(A:225:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.926

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	227	ASN	0	0.043	0.023	3.845	-4.837	-3.806	-0.003	-0.389	-0.639	0.000
87	A	311	ARG	1	0.782	0.904	3.791	55.455	55.823	0.001	-0.137	-0.231	-0.001
92	A	316	ASP	-1	-0.850	-0.937	4.129	-59.332	-59.214	-0.001	-0.043	-0.074	0.000
4	A	228	LEU	0	0.009	0.018	5.864	2.477	2.477	0.000	0.000	0.000	0.000
5	A	229	LYS	1	0.936	0.951	8.519	24.423	24.423	0.000	0.000	0.000	0.000
6	A	230	ILE	0	0.053	0.035	12.070	0.432	0.432	0.000	0.000	0.000	0.000
7	A	231	SER	0	-0.040	-0.039	15.448	0.264	0.264	0.000	0.000	0.000	0.000
8	A	232	ARG	1	0.910	0.941	17.704	13.911	13.911	0.000	0.000	0.000	0.000
9	A	233	MET	0	-0.002	0.000	19.766	-0.607	-0.607	0.000	0.000	0.000	0.000
10	A	234	ASP	-1	-0.912	-0.947	22.667	-11.103	-11.103	0.000	0.000	0.000	0.000
11	A	235	LYS	1	0.890	0.950	25.902	11.200	11.200	0.000	0.000	0.000	0.000
12	A	236	THR	0	-0.007	-0.009	24.448	-0.332	-0.332	0.000	0.000	0.000	0.000
13	A	237	ALA	0	0.021	0.010	26.845	0.097	0.097	0.000	0.000	0.000	0.000
14	A	238	GLY	0	0.017	0.007	29.790	-0.070	-0.070	0.000	0.000	0.000	0.000
15	A	239	SER	0	0.019	0.025	31.172	0.153	0.153	0.000	0.000	0.000	0.000
16	A	240	VAL	0	0.007	0.002	31.954	-0.335	-0.335	0.000	0.000	0.000	0.000
17	A	241	ARG	1	0.976	0.971	32.580	8.280	8.280	0.000	0.000	0.000	0.000
18	A	242	GLY	0	-0.009	0.015	30.053	-0.078	-0.078	0.000	0.000	0.000	0.000
19	A	243	GLY	0	-0.001	-0.005	29.219	0.351	0.351	0.000	0.000	0.000	0.000
20	A	244	ASP	-1	-0.880	-0.937	29.313	-9.989	-9.989	0.000	0.000	0.000	0.000
21	A	245	GLU	-1	-0.904	-0.958	27.223	-11.324	-11.324	0.000	0.000	0.000	0.000
22	A	246	VAL	0	0.011	0.013	23.148	0.259	0.259	0.000	0.000	0.000	0.000
23	A	247	TYR	0	0.056	0.031	23.050	-0.552	-0.552	0.000	0.000	0.000	0.000
24	A	248	LEU	0	-0.008	0.002	16.131	0.042	0.042	0.000	0.000	0.000	0.000
25	A	249	LEU	0	-0.005	-0.005	18.098	-0.296	-0.296	0.000	0.000	0.000	0.000
26	A	250	CYS	0	-0.051	-0.034	12.917	0.296	0.296	0.000	0.000	0.000	0.000
27	A	251	ASP	-1	-0.823	-0.903	9.901	-25.796	-25.796	0.000	0.000	0.000	0.000
28	A	252	LYS	1	0.880	0.950	7.220	29.591	29.591	0.000	0.000	0.000	0.000
29	A	253	VAL	0	0.016	0.017	7.725	-4.608	-4.608	0.000	0.000	0.000	0.000
30	A	254	GLN	0	-0.002	-0.024	8.186	1.953	1.953	0.000	0.000	0.000	0.000
31	A	255	LYS	1	0.910	0.955	10.138	16.759	16.759	0.000	0.000	0.000	0.000
32	A	256	ASP	-1	-0.807	-0.906	13.155	-17.393	-17.393	0.000	0.000	0.000	0.000
33	A	257	ASP	-1	-0.874	-0.953	7.962	-34.080	-34.080	0.000	0.000	0.000	0.000
34	A	258	ILE	0	-0.059	-0.014	10.301	-0.772	-0.772	0.000	0.000	0.000	0.000
35	A	259	GLU	-1	-0.880	-0.949	12.261	-18.237	-18.237	0.000	0.000	0.000	0.000
36	A	260	VAL	0	0.006	-0.001	14.110	-1.340	-1.340	0.000	0.000	0.000	0.000
37	A	261	ARG	1	0.869	0.937	16.323	17.999	17.999	0.000	0.000	0.000	0.000
38	A	262	PHE	0	0.035	-0.006	17.935	-0.380	-0.380	0.000	0.000	0.000	0.000
39	A	263	TYR	0	0.003	-0.015	18.013	-0.407	-0.407	0.000	0.000	0.000	0.000
40	A	264	GLU	-1	-0.737	-0.828	22.373	-11.041	-11.041	0.000	0.000	0.000	0.000
41	A	265	ASP	-1	-0.963	-0.984	20.727	-15.292	-15.292	0.000	0.000	0.000	0.000
42	A	266	ASP	-1	-0.883	-0.934	23.669	-11.052	-11.052	0.000	0.000	0.000	0.000
43	A	267	GLU	-1	-0.917	-0.972	26.609	-10.964	-10.964	0.000	0.000	0.000	0.000
44	A	268	ASN	0	-0.128	-0.051	29.033	0.002	0.002	0.000	0.000	0.000	0.000
45	A	269	GLY	0	0.055	0.034	24.856	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	270	TRP	0	-0.022	-0.013	24.477	-0.373	-0.373	0.000	0.000	0.000	0.000
47	A	271	GLN	0	0.036	0.004	20.072	-1.197	-1.197	0.000	0.000	0.000	0.000
48	A	272	ALA	0	-0.046	-0.012	22.474	0.574	0.574	0.000	0.000	0.000	0.000
49	A	273	PHE	0	0.007	-0.011	17.058	-0.631	-0.631	0.000	0.000	0.000	0.000
50	A	274	GLY	0	-0.025	-0.006	20.250	0.690	0.690	0.000	0.000	0.000	0.000
51	A	275	ASP	-1	-0.944	-0.965	20.987	-12.861	-12.861	0.000	0.000	0.000	0.000
52	A	276	PHE	0	0.014	-0.018	16.213	-0.114	-0.114	0.000	0.000	0.000	0.000
53	A	277	SER	0	0.021	0.023	21.464	-0.152	-0.152	0.000	0.000	0.000	0.000
54	A	278	PRO	0	-0.007	-0.018	17.477	-0.298	-0.298	0.000	0.000	0.000	0.000
55	A	279	THR	0	-0.058	-0.035	18.602	-0.556	-0.556	0.000	0.000	0.000	0.000
56	A	280	ASP	-1	-0.802	-0.888	21.028	-13.255	-13.255	0.000	0.000	0.000	0.000
57	A	281	VAL	0	-0.038	-0.008	14.165	-0.415	-0.415	0.000	0.000	0.000	0.000
58	A	282	HIS	0	0.038	0.018	17.035	-0.472	-0.472	0.000	0.000	0.000	0.000
59	A	283	LYS	1	0.937	0.942	16.534	13.949	13.949	0.000	0.000	0.000	0.000
60	A	284	GLN	0	-0.013	-0.004	10.726	-2.102	-2.102	0.000	0.000	0.000	0.000
61	A	285	TYR	0	-0.011	0.005	11.375	-2.684	-2.684	0.000	0.000	0.000	0.000
62	A	286	ALA	0	0.008	0.003	14.645	0.590	0.590	0.000	0.000	0.000	0.000
63	A	287	ILE	0	-0.029	-0.008	14.429	-0.621	-0.621	0.000	0.000	0.000	0.000
64	A	288	VAL	0	-0.004	0.011	18.603	0.284	0.284	0.000	0.000	0.000	0.000
65	A	289	PHE	0	-0.014	-0.006	20.413	-0.325	-0.325	0.000	0.000	0.000	0.000
66	A	290	ARG	1	0.892	0.953	23.130	11.212	11.212	0.000	0.000	0.000	0.000
67	A	291	THR	0	0.006	0.006	24.890	-0.363	-0.363	0.000	0.000	0.000	0.000
68	A	292	PRO	0	0.042	0.041	23.623	0.430	0.430	0.000	0.000	0.000	0.000
69	A	293	PRO	0	0.013	0.012	26.580	0.083	0.083	0.000	0.000	0.000	0.000
70	A	294	TYR	0	-0.054	-0.060	28.625	-0.087	-0.087	0.000	0.000	0.000	0.000
71	A	295	HIS	1	0.806	0.893	29.109	10.751	10.751	0.000	0.000	0.000	0.000
72	A	296	LYS	1	0.888	0.947	31.665	8.673	8.673	0.000	0.000	0.000	0.000
73	A	297	MET	0	0.056	0.025	33.679	-0.031	-0.031	0.000	0.000	0.000	0.000
74	A	298	LYS	1	0.983	0.995	36.957	7.361	7.361	0.000	0.000	0.000	0.000
75	A	299	ILE	0	-0.052	-0.017	34.228	0.049	0.049	0.000	0.000	0.000	0.000
76	A	300	GLU	-1	-0.836	-0.921	38.183	-7.420	-7.420	0.000	0.000	0.000	0.000
77	A	301	ARG	1	0.874	0.933	37.202	8.102	8.102	0.000	0.000	0.000	0.000
78	A	302	PRO	0	0.020	-0.007	34.427	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	303	VAL	0	-0.005	0.017	30.135	0.020	0.020	0.000	0.000	0.000	0.000
80	A	304	THR	0	-0.048	-0.026	27.014	-0.088	-0.088	0.000	0.000	0.000	0.000
81	A	305	VAL	0	0.009	0.026	24.617	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	306	PHE	0	-0.023	-0.019	20.566	-0.110	-0.110	0.000	0.000	0.000	0.000
83	A	307	LEU	0	-0.011	-0.003	18.995	0.058	0.058	0.000	0.000	0.000	0.000
84	A	308	GLN	0	0.005	0.005	14.061	0.076	0.076	0.000	0.000	0.000	0.000
85	A	309	LEU	0	-0.012	0.003	11.546	0.430	0.430	0.000	0.000	0.000	0.000
86	A	310	LYS	1	0.944	0.964	10.638	20.990	20.990	0.000	0.000	0.000	0.000
88	A	312	LYS	1	0.912	0.965	9.406	20.619	20.619	0.000	0.000	0.000	0.000
89	A	313	ARG	1	0.891	0.950	7.772	32.816	32.816	0.000	0.000	0.000	0.000
90	A	314	GLY	0	-0.016	-0.013	7.010	0.634	0.634	0.000	0.000	0.000	0.000
91	A	315	GLY	0	0.022	0.021	8.076	1.173	1.173	0.000	0.000	0.000	0.000
93	A	317	VAL	0	0.005	-0.005	7.786	2.145	2.145	0.000	0.000	0.000	0.000
94	A	318	SER	0	-0.054	-0.028	9.217	-2.533	-2.533	0.000	0.000	0.000	0.000
95	A	319	ASP	-1	-0.897	-0.942	11.491	-21.802	-21.802	0.000	0.000	0.000	0.000
96	A	320	SER	0	-0.042	-0.015	14.169	0.029	0.029	0.000	0.000	0.000	0.000
97	A	321	LYS	1	0.861	0.941	17.159	17.770	17.770	0.000	0.000	0.000	0.000
98	A	322	GLN	0	0.030	0.008	20.132	0.428	0.428	0.000	0.000	0.000	0.000
99	A	323	PHE	0	-0.007	-0.008	23.680	-0.078	-0.078	0.000	0.000	0.000	0.000
100	A	324	THR	0	-0.013	-0.003	25.751	0.122	0.122	0.000	0.000	0.000	0.000
101	A	325	TYR	0	-0.020	-0.019	26.919	0.009	0.009	0.000	0.000	0.000	0.000
102	A	326	TYR	0	0.015	0.001	31.432	0.247	0.247	0.000	0.000	0.000	0.000
103	A	327	PRO	0	0.006	-0.019	35.010	-0.091	-0.091	0.000	0.000	0.000	0.000
104	A	328	VAL	0	-0.068	-0.031	37.914	-0.036	-0.036	0.000	0.000	0.000	0.000
105	A	329	VAL	0	-0.039	-0.012	39.298	0.105	0.105	0.000	0.000	0.000	0.000
106	A	330	GLU	-1	-0.943	-0.979	42.213	-7.073	-7.073	0.000	0.000	0.000	0.000
107	A	331	ASP	-2	-1.936	-1.952	45.483	-13.595	-13.595	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:225:ALA)