FMO DATABASE

FMODB ID: 2N31R

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	OptH
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	-598419.527611
FMO2-HF: Nuclear repulsion	563294.536175
FMO2-HF: Total energy	-35124.991437
FMO2-MP2: Total energy	-35225.545915

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.
-11.051	-5.752	7.768	-6.434	-6.634	-0.041

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 : -0.021 / q_NPA : -0.008

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	0.009	0.031	3.818	0.631	2.833	-0.001	-1.080	-1.121	0.007
4	A	228	GLN	0	-0.058	-0.046	6.356	0.372	0.372	0.000	0.000	0.000	0.000
5	A	229	ILE	0	0.037	0.023	7.940	-0.053	-0.053	0.000	0.000	0.000	0.000
6	A	230	CYS	0	-0.085	-0.042	8.810	0.123	0.123	0.000	0.000	0.000	0.000
7	A	231	VAL	0	-0.015	0.000	11.577	0.003	0.003	0.000	0.000	0.000	0.000
8	A	232	GLU	-1	-0.803	-0.919	14.927	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	233	PRO	0	-0.025	0.004	17.504	0.003	0.003	0.000	0.000	0.000	0.000
10	A	234	THR	0	-0.040	-0.031	20.777	0.014	0.014	0.000	0.000	0.000	0.000
11	A	235	SER	0	0.036	0.020	24.022	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	236	GLN	0	-0.001	-0.004	26.597	0.008	0.008	0.000	0.000	0.000	0.000
13	A	237	LYS	1	0.825	0.916	30.236	0.021	0.021	0.000	0.000	0.000	0.000
14	A	238	LEU	0	-0.002	0.000	31.185	0.001	0.001	0.000	0.000	0.000	0.000
15	A	239	MET	0	0.034	0.025	35.318	0.001	0.001	0.000	0.000	0.000	0.000
16	A	240	PRO	0	0.034	0.002	37.819	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	241	GLY	0	-0.023	-0.010	38.787	0.003	0.003	0.000	0.000	0.000	0.000
18	A	242	SER	0	-0.038	-0.014	34.770	0.001	0.001	0.000	0.000	0.000	0.000
19	A	243	THR	0	-0.010	-0.014	30.064	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	244	LEU	0	-0.035	-0.004	28.065	0.004	0.004	0.000	0.000	0.000	0.000
21	A	245	VAL	0	0.011	-0.008	24.266	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	246	LEU	0	-0.022	0.011	22.925	0.007	0.007	0.000	0.000	0.000	0.000
23	A	247	GLN	0	-0.002	-0.020	17.617	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	248	CYS	0	-0.024	0.007	15.636	0.005	0.005	0.000	0.000	0.000	0.000
25	A	249	VAL	0	-0.012	-0.011	11.241	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	250	ALA	0	0.055	0.029	9.143	0.077	0.077	0.000	0.000	0.000	0.000
27	A	251	VAL	0	-0.064	-0.021	4.709	-0.290	-0.193	-0.001	-0.005	-0.091	0.000
28	A	252	GLY	0	0.064	0.015	3.304	-0.273	0.438	0.054	-0.398	-0.367	0.002
29	A	253	SER	0	-0.095	-0.029	2.250	-0.223	1.353	2.263	-1.467	-2.373	-0.001
30	A	254	PRO	0	0.113	0.026	2.034	-10.653	-10.051	5.454	-3.476	-2.580	-0.049
31	A	255	ILE	0	-0.035	-0.008	5.465	-0.333	-0.333	0.000	0.000	0.000	0.000
32	A	256	PRO	0	-0.049	-0.012	6.748	0.072	0.072	0.000	0.000	0.000	0.000
33	A	257	HIS	0	-0.029	0.002	9.449	0.222	0.222	0.000	0.000	0.000	0.000
34	A	258	TYR	0	0.045	0.009	11.386	0.014	0.014	0.000	0.000	0.000	0.000
35	A	259	GLN	0	-0.029	-0.023	15.925	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	260	TRP	0	-0.024	-0.004	19.279	0.011	0.011	0.000	0.000	0.000	0.000
37	A	261	PHE	0	0.010	0.006	20.268	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	262	LYS	1	0.956	0.977	24.734	0.094	0.094	0.000	0.000	0.000	0.000
39	A	263	ASN	0	-0.012	-0.004	28.180	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	264	GLU	-1	-0.946	-0.979	27.476	-0.112	-0.112	0.000	0.000	0.000	0.000
41	A	265	LEU	0	-0.025	-0.001	27.982	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	266	PRO	0	-0.010	0.005	24.271	0.000	0.000	0.000	0.000	0.000	0.000
43	A	267	LEU	0	-0.011	-0.009	25.226	0.012	0.012	0.000	0.000	0.000	0.000
44	A	268	THR	0	0.023	-0.016	25.241	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	269	HIS	0	-0.017	-0.010	24.363	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	270	GLU	-1	-0.874	-0.916	23.522	-0.137	-0.137	0.000	0.000	0.000	0.000
47	A	271	THR	0	-0.006	-0.007	18.737	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	272	LYS	1	0.921	0.961	18.144	0.162	0.162	0.000	0.000	0.000	0.000
49	A	273	LYS	1	0.993	1.000	11.917	0.303	0.303	0.000	0.000	0.000	0.000
50	A	274	LEU	0	-0.024	-0.009	17.459	0.020	0.020	0.000	0.000	0.000	0.000
51	A	275	TYR	0	0.019	0.023	21.021	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	276	MET	0	-0.032	-0.035	24.075	0.010	0.010	0.000	0.000	0.000	0.000
53	A	277	VAL	0	0.025	0.026	27.246	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	278	PRO	0	-0.011	0.000	30.916	0.005	0.005	0.000	0.000	0.000	0.000
55	A	279	TYR	0	0.041	0.031	33.255	0.004	0.004	0.000	0.000	0.000	0.000
56	A	280	VAL	0	-0.087	-0.042	33.159	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	281	ASP	-1	-0.768	-0.898	35.968	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	282	LEU	0	-0.014	-0.022	37.146	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	283	GLU	-1	-0.967	-0.968	36.471	-0.066	-0.066	0.000	0.000	0.000	0.000
60	A	284	HIS	0	0.013	0.003	32.754	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	285	GLN	0	0.021	0.048	32.578	0.000	0.000	0.000	0.000	0.000	0.000
62	A	286	GLY	0	-0.001	-0.009	32.082	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	287	THR	0	0.023	0.022	27.307	0.003	0.003	0.000	0.000	0.000	0.000
64	A	288	TYR	0	-0.071	-0.079	24.980	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	289	TRP	0	-0.011	-0.018	19.968	0.012	0.012	0.000	0.000	0.000	0.000
66	A	290	CYS	0	-0.012	0.004	17.964	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	291	HIS	0	-0.017	-0.015	15.869	-0.044	-0.044	0.000	0.000	0.000	0.000
68	A	292	VAL	0	-0.002	-0.019	11.172	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	293	TYR	0	0.016	-0.005	10.990	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	294	ASN	0	0.022	-0.012	5.100	0.447	0.447	0.000	0.000	0.000	0.000
71	A	295	ASP	-1	-0.926	-0.956	8.258	-1.383	-1.383	0.000	0.000	0.000	0.000
72	A	296	ARG	1	0.805	0.885	4.692	2.229	2.340	-0.001	-0.008	-0.102	0.000
73	A	297	ASP	-1	-0.789	-0.869	6.528	-1.976	-1.976	0.000	0.000	0.000	0.000
74	A	298	SER	0	0.003	-0.024	9.401	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	299	GLN	0	-0.038	-0.020	10.442	0.113	0.113	0.000	0.000	0.000	0.000
76	A	300	ASP	-1	-0.817	-0.875	13.870	-0.259	-0.259	0.000	0.000	0.000	0.000
77	A	301	SER	0	-0.035	-0.036	16.798	0.030	0.030	0.000	0.000	0.000	0.000
78	A	302	LYS	1	0.923	0.945	17.627	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	303	LYS	1	0.914	0.991	20.442	0.116	0.116	0.000	0.000	0.000	0.000
80	A	304	VAL	0	-0.021	-0.002	23.150	0.012	0.012	0.000	0.000	0.000	0.000
81	A	305	GLU	-1	-0.940	-0.970	25.802	-0.048	-0.048	0.000	0.000	0.000	0.000
82	A	306	ILE	0	-0.037	-0.015	27.573	0.005	0.005	0.000	0.000	0.000	0.000
83	A	307	ILE	0	-0.007	-0.005	31.088	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	308	ILE	0	-0.022	-0.017	34.066	0.001	0.001	0.000	0.000	0.000	0.000
85	A	309	ASP	-1	-0.823	-0.909	37.205	-0.025	-0.025	0.000	0.000	0.000	0.000

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