FMO DATABASE

FMODB ID: 6YVQZ

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	OptHSide
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	-599134.971745
FMO2-HF: Nuclear repulsion	564009.588791
FMO2-HF: Total energy	-35125.382954
FMO2-MP2: Total energy	-35225.937394

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.
-10.347	-5.455	7.721	-6.185	-6.426	-0.051

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 : -0.018 / q_NPA : -0.004

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	0.030	3.818	-0.626	1.383	-0.011	-0.988	-1.010	0.006
4	A	228	GLN	0	-0.031	-0.033	6.268	0.747	0.747	0.000	0.000	0.000	0.000
5	A	229	ILE	0	0.031	0.024	8.217	-0.127	-0.127	0.000	0.000	0.000	0.000
6	A	230	CYS	0	-0.090	-0.042	9.061	0.148	0.148	0.000	0.000	0.000	0.000
7	A	231	VAL	0	-0.013	0.001	11.759	0.051	0.051	0.000	0.000	0.000	0.000
8	A	232	GLU	-1	-0.766	-0.898	15.164	-0.240	-0.240	0.000	0.000	0.000	0.000
9	A	233	PRO	0	-0.015	0.009	17.721	0.011	0.011	0.000	0.000	0.000	0.000
10	A	234	THR	0	-0.042	-0.030	21.034	0.015	0.015	0.000	0.000	0.000	0.000
11	A	235	SER	0	0.040	0.022	24.253	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	236	GLN	0	-0.004	0.000	26.760	0.013	0.013	0.000	0.000	0.000	0.000
13	A	237	LYS	1	0.800	0.882	30.489	0.065	0.065	0.000	0.000	0.000	0.000
14	A	238	LEU	0	-0.004	0.000	31.388	0.002	0.002	0.000	0.000	0.000	0.000
15	A	239	MET	0	0.041	0.028	35.608	0.004	0.004	0.000	0.000	0.000	0.000
16	A	240	PRO	0	0.038	0.020	38.015	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	241	GLY	0	-0.024	-0.007	38.812	0.004	0.004	0.000	0.000	0.000	0.000
18	A	242	SER	0	-0.042	-0.036	35.238	0.001	0.001	0.000	0.000	0.000	0.000
19	A	243	THR	0	-0.024	-0.018	30.244	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	244	LEU	0	-0.028	0.001	28.134	0.003	0.003	0.000	0.000	0.000	0.000
21	A	245	VAL	0	0.008	-0.009	24.469	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	246	LEU	0	-0.008	0.017	22.901	0.005	0.005	0.000	0.000	0.000	0.000
23	A	247	GLN	0	0.004	-0.015	17.992	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	248	CYS	0	-0.033	0.000	15.609	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	249	VAL	0	-0.015	-0.012	11.674	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	250	ALA	0	0.055	0.025	9.092	0.088	0.088	0.000	0.000	0.000	0.000
27	A	251	VAL	0	-0.053	-0.017	4.848	-0.100	-0.100	0.000	0.000	0.000	0.000
28	A	252	GLY	0	0.060	0.014	2.762	0.104	0.450	0.215	-0.256	-0.305	-0.002
29	A	253	SER	0	-0.084	-0.027	2.216	0.435	2.272	2.196	-1.555	-2.478	-0.006
30	A	254	PRO	0	0.101	0.025	2.055	-9.936	-9.337	5.322	-3.380	-2.540	-0.049
31	A	255	ILE	0	-0.030	-0.002	5.450	-0.515	-0.515	0.000	0.000	0.000	0.000
32	A	256	PRO	0	-0.054	-0.015	6.439	0.183	0.183	0.000	0.000	0.000	0.000
33	A	257	HIS	0	-0.025	0.001	9.395	0.289	0.289	0.000	0.000	0.000	0.000
34	A	258	TYR	0	0.050	0.010	10.637	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	259	GLN	0	-0.044	-0.031	15.783	0.016	0.016	0.000	0.000	0.000	0.000
36	A	260	TRP	0	-0.005	0.000	19.296	0.008	0.008	0.000	0.000	0.000	0.000
37	A	261	PHE	0	0.007	0.008	20.382	0.001	0.001	0.000	0.000	0.000	0.000
38	A	262	LYS	1	0.931	0.967	24.626	0.145	0.145	0.000	0.000	0.000	0.000
39	A	263	ASN	0	0.004	-0.002	27.925	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	264	GLU	-1	-0.869	-0.936	27.232	-0.179	-0.179	0.000	0.000	0.000	0.000
41	A	265	LEU	0	-0.018	0.003	28.026	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	266	PRO	0	-0.021	0.003	24.279	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	267	LEU	0	-0.003	-0.006	25.248	0.019	0.019	0.000	0.000	0.000	0.000
44	A	268	THR	0	0.026	-0.014	25.245	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	269	HIS	0	-0.032	-0.019	24.324	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	270	GLU	-1	-0.860	-0.911	23.250	-0.235	-0.235	0.000	0.000	0.000	0.000
47	A	271	THR	0	-0.017	-0.015	18.754	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	272	LYS	1	0.918	0.960	17.827	0.264	0.264	0.000	0.000	0.000	0.000
49	A	273	LYS	1	0.985	0.996	11.478	0.645	0.645	0.000	0.000	0.000	0.000
50	A	274	LEU	0	-0.026	-0.011	17.183	0.022	0.022	0.000	0.000	0.000	0.000
51	A	275	TYR	0	0.024	0.030	20.875	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	276	MET	0	-0.034	-0.037	23.807	0.009	0.009	0.000	0.000	0.000	0.000
53	A	277	VAL	0	0.034	0.030	27.097	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	278	PRO	0	-0.019	-0.002	30.721	0.006	0.006	0.000	0.000	0.000	0.000
55	A	279	TYR	0	0.032	0.018	33.174	0.005	0.005	0.000	0.000	0.000	0.000
56	A	280	VAL	0	-0.065	-0.029	33.141	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	281	ASP	-1	-0.786	-0.899	35.894	-0.072	-0.072	0.000	0.000	0.000	0.000
58	A	282	LEU	0	-0.009	-0.024	37.006	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	283	GLU	-1	-0.925	-0.950	35.203	-0.124	-0.124	0.000	0.000	0.000	0.000
60	A	284	HIS	0	-0.001	0.005	32.491	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	285	GLN	0	0.028	0.045	32.415	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	286	GLY	0	0.001	-0.006	31.938	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	287	THR	0	-0.002	0.006	27.452	0.002	0.002	0.000	0.000	0.000	0.000
64	A	288	TYR	0	-0.058	-0.065	24.858	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	289	TRP	0	-0.063	-0.048	20.255	0.000	0.000	0.000	0.000	0.000	0.000
66	A	290	CYS	0	-0.015	0.004	17.625	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	291	HIS	0	-0.018	-0.008	16.056	-0.059	-0.059	0.000	0.000	0.000	0.000
68	A	292	VAL	0	-0.011	-0.026	10.939	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	293	TYR	0	0.027	-0.002	11.057	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	294	ASN	0	0.019	-0.016	5.084	0.516	0.516	0.000	0.000	0.000	0.000
71	A	295	ASP	-1	-0.905	-0.948	8.110	-1.534	-1.534	0.000	0.000	0.000	0.000
72	A	296	ARG	1	0.781	0.858	4.748	2.159	2.260	-0.001	-0.006	-0.093	0.000
73	A	297	ASP	-1	-0.784	-0.850	6.569	-2.207	-2.207	0.000	0.000	0.000	0.000
74	A	298	SER	0	0.015	-0.016	9.479	-0.051	-0.051	0.000	0.000	0.000	0.000
75	A	299	GLN	0	-0.048	-0.028	10.488	0.108	0.108	0.000	0.000	0.000	0.000
76	A	300	ASP	-1	-0.799	-0.874	13.919	-0.379	-0.379	0.000	0.000	0.000	0.000
77	A	301	SER	0	-0.048	-0.041	17.051	0.028	0.028	0.000	0.000	0.000	0.000
78	A	302	LYS	1	0.870	0.915	17.039	0.127	0.127	0.000	0.000	0.000	0.000
79	A	303	LYS	1	0.880	0.973	20.733	0.220	0.220	0.000	0.000	0.000	0.000
80	A	304	VAL	0	-0.029	-0.004	23.402	0.017	0.017	0.000	0.000	0.000	0.000
81	A	305	GLU	-1	-0.920	-0.960	26.056	-0.100	-0.100	0.000	0.000	0.000	0.000
82	A	306	ILE	0	-0.033	-0.015	27.705	0.004	0.004	0.000	0.000	0.000	0.000
83	A	307	ILE	0	-0.016	-0.018	31.233	0.002	0.002	0.000	0.000	0.000	0.000
84	A	308	ILE	0	-0.017	-0.008	34.120	0.000	0.000	0.000	0.000	0.000	0.000
85	A	309	ASP	-1	-0.798	-0.877	37.354	-0.064	-0.064	0.000	0.000	0.000	0.000

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