FMO DATABASE

FMODB ID: ZV5QN

Calculation Name: 3BFO-A-Xray372

Preferred Name: Mucosa-associated lymphoid tissue lymphoma translocation protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BFO

Chain ID: A

ChEMBL ID: CHEMBL3632452

UniProt ID: Q9UDY8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-597631.866736
FMO2-HF: Nuclear repulsion	562506.31218
FMO2-HF: Total energy	-35125.554556
FMO2-MP2: Total energy	-35226.074724

3D Structure

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:SER)

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

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.
-10.067	-7.42	11.616	-6.869	-7.392	-0.057

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.010

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

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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	LEU	0	-0.002	0.018	3.881	0.081	1.919	-0.009	-0.914	-0.915	0.005
4	A	228	GLN	0	-0.040	-0.035	6.352	0.636	0.636	0.000	0.000	0.000	0.000
5	A	229	ILE	0	0.035	0.031	8.296	-0.110	-0.110	0.000	0.000	0.000	0.000
6	A	230	CYS	0	-0.091	-0.048	8.970	0.135	0.135	0.000	0.000	0.000	0.000
7	A	231	VAL	0	-0.018	-0.001	11.725	0.042	0.042	0.000	0.000	0.000	0.000
8	A	232	GLU	-1	-0.770	-0.889	15.135	-0.229	-0.229	0.000	0.000	0.000	0.000
9	A	233	PRO	0	-0.002	0.013	17.599	0.009	0.009	0.000	0.000	0.000	0.000
10	A	234	THR	0	-0.054	-0.038	21.044	0.017	0.017	0.000	0.000	0.000	0.000
11	A	235	SER	0	0.038	0.017	24.350	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	236	GLN	0	-0.019	-0.003	26.951	0.012	0.012	0.000	0.000	0.000	0.000
13	A	237	LYS	1	0.789	0.876	30.734	0.061	0.061	0.000	0.000	0.000	0.000
14	A	238	LEU	0	-0.005	0.005	31.937	0.001	0.001	0.000	0.000	0.000	0.000
15	A	239	MET	0	0.028	0.021	36.024	0.004	0.004	0.000	0.000	0.000	0.000
16	A	240	PRO	0	0.042	0.018	38.514	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	241	GLY	0	-0.007	0.002	39.275	0.004	0.004	0.000	0.000	0.000	0.000
18	A	242	SER	0	-0.046	-0.039	35.429	0.001	0.001	0.000	0.000	0.000	0.000
19	A	243	THR	0	-0.038	-0.026	30.649	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	244	LEU	0	-0.015	0.011	28.562	0.004	0.004	0.000	0.000	0.000	0.000
21	A	245	VAL	0	-0.008	-0.024	24.619	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	246	LEU	0	-0.008	0.015	23.024	0.007	0.007	0.000	0.000	0.000	0.000
23	A	247	GLN	0	0.008	-0.009	18.051	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	248	CYS	0	-0.026	-0.001	15.815	0.000	0.000	0.000	0.000	0.000	0.000
25	A	249	VAL	0	-0.007	-0.011	11.645	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	250	ALA	0	0.049	0.025	8.956	0.085	0.085	0.000	0.000	0.000	0.000
27	A	251	VAL	0	-0.045	-0.011	4.774	-0.229	-0.141	-0.001	-0.003	-0.083	0.000
28	A	252	GLY	0	0.058	0.010	2.746	0.133	0.580	0.277	-0.325	-0.398	-0.001
29	A	253	SER	0	-0.081	-0.039	2.105	-0.099	0.993	4.062	-1.944	-3.210	-0.009
30	A	254	PRO	0	0.100	0.042	1.973	-9.502	-10.416	7.289	-3.668	-2.707	-0.052
31	A	255	ILE	0	-0.030	-0.006	5.340	-0.497	-0.527	-0.001	-0.002	0.033	0.000
32	A	256	PRO	0	-0.057	-0.016	6.058	0.170	0.170	0.000	0.000	0.000	0.000
33	A	257	HIS	0	-0.004	0.013	9.093	0.288	0.288	0.000	0.000	0.000	0.000
34	A	258	TYR	0	0.045	0.005	10.723	0.011	0.011	0.000	0.000	0.000	0.000
35	A	259	GLN	0	-0.049	-0.043	15.747	0.008	0.008	0.000	0.000	0.000	0.000
36	A	260	TRP	0	-0.013	-0.004	19.315	0.010	0.010	0.000	0.000	0.000	0.000
37	A	261	PHE	0	0.011	0.013	20.628	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	262	LYS	1	0.882	0.934	24.749	0.136	0.136	0.000	0.000	0.000	0.000
39	A	263	ASN	0	-0.012	-0.014	28.250	0.002	0.002	0.000	0.000	0.000	0.000
40	A	264	GLU	-1	-0.854	-0.917	26.768	-0.171	-0.171	0.000	0.000	0.000	0.000
41	A	265	LEU	0	-0.003	0.020	27.864	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	266	PRO	0	-0.018	-0.002	24.365	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	267	LEU	0	0.000	-0.007	25.128	0.015	0.015	0.000	0.000	0.000	0.000
44	A	268	THR	0	0.029	-0.003	25.043	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	269	HIS	0	-0.005	-0.005	24.325	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	270	GLU	-1	-0.865	-0.912	23.252	-0.228	-0.228	0.000	0.000	0.000	0.000
47	A	271	THR	0	-0.032	-0.028	18.903	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	272	LYS	1	0.909	0.953	17.796	0.256	0.256	0.000	0.000	0.000	0.000
49	A	273	LYS	1	0.969	0.990	11.297	0.617	0.617	0.000	0.000	0.000	0.000
50	A	274	LEU	0	-0.019	-0.009	17.023	0.022	0.022	0.000	0.000	0.000	0.000
51	A	275	TYR	0	0.023	0.028	20.782	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	276	MET	0	-0.021	-0.027	23.855	0.009	0.009	0.000	0.000	0.000	0.000
53	A	277	VAL	0	0.034	0.031	27.229	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	278	PRO	0	-0.020	-0.001	30.978	0.005	0.005	0.000	0.000	0.000	0.000
55	A	279	TYR	0	0.013	-0.001	33.400	0.005	0.005	0.000	0.000	0.000	0.000
56	A	280	VAL	0	-0.038	-0.003	33.508	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	281	ASP	-1	-0.816	-0.912	36.165	-0.068	-0.068	0.000	0.000	0.000	0.000
58	A	282	LEU	0	-0.007	-0.026	37.212	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	283	GLU	-1	-0.890	-0.936	34.985	-0.119	-0.119	0.000	0.000	0.000	0.000
60	A	284	HIS	0	0.002	0.012	32.730	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	285	GLN	0	0.040	0.044	32.722	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	286	GLY	0	-0.007	-0.007	32.488	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	287	THR	0	-0.003	0.006	27.575	0.000	0.000	0.000	0.000	0.000	0.000
64	A	288	TYR	0	-0.060	-0.062	25.332	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	289	TRP	0	-0.053	-0.055	20.358	0.000	0.000	0.000	0.000	0.000	0.000
66	A	290	CYS	0	-0.015	0.007	17.698	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	291	HIS	0	-0.013	-0.001	16.016	-0.054	-0.054	0.000	0.000	0.000	0.000
68	A	292	VAL	0	-0.017	-0.026	11.050	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	293	TYR	0	0.015	-0.011	11.162	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	294	ASN	0	0.011	-0.013	5.062	0.484	0.484	0.000	0.000	0.000	0.000
71	A	295	ASP	-1	-0.883	-0.939	7.959	-1.633	-1.633	0.000	0.000	0.000	0.000
72	A	296	ARG	1	0.793	0.868	4.475	2.301	2.427	-0.001	-0.013	-0.112	0.000
73	A	297	ASP	-1	-0.773	-0.850	6.273	-2.359	-2.359	0.000	0.000	0.000	0.000
74	A	298	SER	0	-0.005	-0.017	9.154	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	299	GLN	0	-0.034	-0.025	10.896	0.092	0.092	0.000	0.000	0.000	0.000
76	A	300	ASP	-1	-0.783	-0.868	13.979	-0.339	-0.339	0.000	0.000	0.000	0.000
77	A	301	SER	0	-0.017	-0.023	16.807	0.018	0.018	0.000	0.000	0.000	0.000
78	A	302	LYS	1	0.829	0.901	16.785	0.120	0.120	0.000	0.000	0.000	0.000
79	A	303	LYS	1	0.874	0.953	20.714	0.205	0.205	0.000	0.000	0.000	0.000
80	A	304	VAL	0	-0.041	-0.010	23.395	0.015	0.015	0.000	0.000	0.000	0.000
81	A	305	GLU	-1	-0.889	-0.953	26.046	-0.097	-0.097	0.000	0.000	0.000	0.000
82	A	306	ILE	0	-0.022	-0.005	27.922	0.004	0.004	0.000	0.000	0.000	0.000
83	A	307	ILE	0	0.008	-0.001	31.518	0.001	0.001	0.000	0.000	0.000	0.000
84	A	308	ILE	0	-0.034	-0.019	34.618	0.000	0.000	0.000	0.000	0.000	0.000
85	A	309	ASP	-1	-0.783	-0.865	37.705	-0.059	-0.059	0.000	0.000	0.000	0.000

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