FMO DATABASE

FMODB ID: JLY19

Calculation Name: 3MVN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MVN

Chain ID: A

ChEMBL ID:

UniProt ID: Q7VN73

Base Structure: X-ray

Registration Date: 2023-06-22

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1094899.439131
FMO2-HF: Nuclear repulsion	1046600.67494
FMO2-HF: Total energy	-48298.76419
FMO2-MP2: Total energy	-48442.004126

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:317:ARG)

Summations of interaction energy for fragment #1(A:317:ARG)

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.
-89.939	-85.878	3.21	-3.43	-3.841	-0.023

Interaction energy analysis for fragmet #1(A:317:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.938 / q_NPA : 0.959

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	319	GLU	-1	-0.865	-0.911	3.556	-25.186	-23.394	-0.003	-0.792	-0.997	0.003
4	A	320	VAL	0	0.012	-0.008	4.942	2.833	2.932	-0.001	-0.006	-0.092	0.000
5	A	321	LYS	1	0.781	0.886	7.443	25.028	25.028	0.000	0.000	0.000	0.000
6	A	322	GLY	0	0.008	0.002	10.528	1.332	1.332	0.000	0.000	0.000	0.000
7	A	323	VAL	0	-0.031	-0.016	13.838	-0.606	-0.606	0.000	0.000	0.000	0.000
8	A	324	VAL	0	0.001	0.012	16.666	0.599	0.599	0.000	0.000	0.000	0.000
9	A	325	ASN	0	0.010	0.003	19.803	0.051	0.051	0.000	0.000	0.000	0.000
10	A	326	ASN	0	-0.013	-0.031	20.314	0.102	0.102	0.000	0.000	0.000	0.000
11	A	327	ILE	0	-0.022	0.024	16.765	-0.279	-0.279	0.000	0.000	0.000	0.000
12	A	328	THR	0	-0.009	-0.001	12.004	0.087	0.087	0.000	0.000	0.000	0.000
13	A	329	VAL	0	-0.020	-0.005	11.657	-0.056	-0.056	0.000	0.000	0.000	0.000
14	A	330	TYR	0	-0.035	-0.041	6.973	-1.021	-1.021	0.000	0.000	0.000	0.000
15	A	331	ASP	-1	-0.766	-0.856	5.995	-21.630	-21.630	0.000	0.000	0.000	0.000
16	A	332	ASP	-1	-0.793	-0.904	2.326	-57.981	-56.442	3.201	-2.481	-2.259	-0.026
17	A	333	PHE	0	0.018	0.007	3.674	2.514	3.145	0.013	-0.151	-0.493	0.000
18	A	334	ALA	0	-0.024	0.007	5.391	2.570	2.570	0.000	0.000	0.000	0.000
19	A	335	HIS	1	0.873	0.915	7.355	26.997	26.997	0.000	0.000	0.000	0.000
20	A	336	HIS	0	0.032	0.015	10.696	1.626	1.626	0.000	0.000	0.000	0.000
21	A	337	PRO	0	0.086	0.038	11.290	-1.938	-1.938	0.000	0.000	0.000	0.000
22	A	338	THR	0	0.035	0.022	11.049	-0.206	-0.206	0.000	0.000	0.000	0.000
23	A	339	ALA	0	-0.027	-0.006	6.961	-1.550	-1.550	0.000	0.000	0.000	0.000
24	A	340	ILE	0	0.002	0.003	7.755	-2.221	-2.221	0.000	0.000	0.000	0.000
25	A	341	THR	0	0.031	-0.001	9.940	0.330	0.330	0.000	0.000	0.000	0.000
26	A	342	ALA	0	-0.034	-0.007	6.535	0.146	0.146	0.000	0.000	0.000	0.000
27	A	343	THR	0	-0.038	-0.037	4.896	-2.304	-2.304	0.000	0.000	0.000	0.000
28	A	344	ILE	0	0.017	0.008	6.244	0.402	0.402	0.000	0.000	0.000	0.000
29	A	345	ASP	-1	-0.923	-0.949	9.610	-23.632	-23.632	0.000	0.000	0.000	0.000
30	A	346	ALA	0	-0.036	-0.022	5.699	0.646	0.646	0.000	0.000	0.000	0.000
31	A	347	LEU	0	-0.010	-0.003	7.606	0.418	0.418	0.000	0.000	0.000	0.000
32	A	348	ARG	1	0.822	0.881	8.862	18.869	18.869	0.000	0.000	0.000	0.000
33	A	349	ALA	0	-0.039	-0.028	10.604	1.405	1.405	0.000	0.000	0.000	0.000
34	A	350	LYS	1	0.848	0.918	8.448	28.523	28.523	0.000	0.000	0.000	0.000
35	A	351	VAL	0	-0.011	0.010	11.862	0.952	0.952	0.000	0.000	0.000	0.000
36	A	352	GLY	0	0.002	0.015	14.429	1.221	1.221	0.000	0.000	0.000	0.000
37	A	353	GLN	0	-0.001	-0.012	16.905	-0.703	-0.703	0.000	0.000	0.000	0.000
38	A	354	GLN	0	-0.032	0.002	16.868	0.340	0.340	0.000	0.000	0.000	0.000
39	A	355	ARG	1	0.780	0.855	16.796	12.390	12.390	0.000	0.000	0.000	0.000
40	A	356	ILE	0	0.015	0.007	11.724	-0.487	-0.487	0.000	0.000	0.000	0.000
41	A	357	LEU	0	-0.030	-0.015	14.581	0.729	0.729	0.000	0.000	0.000	0.000
42	A	358	ALA	0	0.025	0.015	12.566	-0.903	-0.903	0.000	0.000	0.000	0.000
43	A	359	VAL	0	-0.009	-0.011	12.318	1.215	1.215	0.000	0.000	0.000	0.000
44	A	360	LEU	0	0.017	0.008	12.154	-1.278	-1.278	0.000	0.000	0.000	0.000
45	A	361	GLU	-1	-0.776	-0.854	12.724	-15.940	-15.940	0.000	0.000	0.000	0.000
46	A	362	PRO	0	-0.021	-0.002	13.933	-0.977	-0.977	0.000	0.000	0.000	0.000
47	A	363	ARG	1	0.780	0.874	13.587	18.301	18.301	0.000	0.000	0.000	0.000
48	A	373	LYS	1	0.855	0.890	21.224	11.395	11.395	0.000	0.000	0.000	0.000
49	A	374	HIS	0	0.107	0.048	21.444	-0.413	-0.413	0.000	0.000	0.000	0.000
50	A	375	GLU	-1	-0.925	-0.952	18.464	-15.926	-15.926	0.000	0.000	0.000	0.000
51	A	376	LEU	0	-0.032	-0.012	15.333	-0.835	-0.835	0.000	0.000	0.000	0.000
52	A	377	ALA	0	0.057	0.038	17.330	-0.643	-0.643	0.000	0.000	0.000	0.000
53	A	378	THR	0	-0.007	-0.020	18.501	-0.078	-0.078	0.000	0.000	0.000	0.000
54	A	379	SER	0	-0.107	-0.066	13.624	-0.641	-0.641	0.000	0.000	0.000	0.000
55	A	380	LEU	0	0.002	-0.013	13.864	-1.080	-1.080	0.000	0.000	0.000	0.000
56	A	381	GLN	0	-0.006	0.006	16.048	0.834	0.834	0.000	0.000	0.000	0.000
57	A	382	ASP	-1	-0.836	-0.899	14.842	-17.552	-17.552	0.000	0.000	0.000	0.000
58	A	383	ALA	0	-0.008	0.007	14.841	0.163	0.163	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.785	-0.880	16.452	-14.481	-14.481	0.000	0.000	0.000	0.000
60	A	385	SER	0	-0.059	-0.040	18.109	0.772	0.772	0.000	0.000	0.000	0.000
61	A	386	VAL	0	0.003	0.008	16.985	-0.999	-0.999	0.000	0.000	0.000	0.000
62	A	387	PHE	0	0.017	0.007	16.877	0.903	0.903	0.000	0.000	0.000	0.000
63	A	388	ILE	0	-0.039	-0.019	16.385	-1.041	-1.041	0.000	0.000	0.000	0.000
64	A	389	TYR	0	-0.015	-0.017	17.252	0.490	0.490	0.000	0.000	0.000	0.000
65	A	390	GLN	0	-0.038	-0.039	19.049	-0.568	-0.568	0.000	0.000	0.000	0.000
66	A	391	PRO	0	-0.010	0.001	19.049	0.436	0.436	0.000	0.000	0.000	0.000
67	A	392	PRO	0	0.045	0.032	22.231	0.351	0.351	0.000	0.000	0.000	0.000
68	A	393	THR	0	-0.034	-0.002	21.299	0.440	0.440	0.000	0.000	0.000	0.000
69	A	394	ILE	0	0.042	0.010	24.368	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	395	GLU	-1	-0.976	-0.997	25.687	-10.462	-10.462	0.000	0.000	0.000	0.000
71	A	396	TRP	0	-0.057	-0.029	19.276	0.042	0.042	0.000	0.000	0.000	0.000
72	A	397	GLN	0	-0.029	-0.027	24.764	-0.108	-0.108	0.000	0.000	0.000	0.000
73	A	398	VAL	0	0.043	0.015	21.191	-0.265	-0.265	0.000	0.000	0.000	0.000
74	A	399	SER	0	0.028	0.016	23.470	-0.271	-0.271	0.000	0.000	0.000	0.000
75	A	400	GLU	-1	-0.770	-0.860	26.269	-10.729	-10.729	0.000	0.000	0.000	0.000
76	A	401	VAL	0	-0.054	-0.015	19.726	-0.116	-0.116	0.000	0.000	0.000	0.000
77	A	402	LEU	0	0.038	0.006	20.666	-0.166	-0.166	0.000	0.000	0.000	0.000
78	A	403	ALA	0	-0.023	-0.006	23.638	0.098	0.098	0.000	0.000	0.000	0.000
79	A	404	ASN	0	-0.110	-0.050	24.030	0.544	0.544	0.000	0.000	0.000	0.000
80	A	405	LEU	0	-0.052	-0.011	20.014	-0.292	-0.292	0.000	0.000	0.000	0.000
81	A	406	ALA	0	0.003	-0.001	24.244	0.447	0.447	0.000	0.000	0.000	0.000
82	A	407	GLN	0	-0.049	-0.017	19.808	0.944	0.944	0.000	0.000	0.000	0.000
83	A	408	PRO	0	-0.043	-0.031	22.900	0.168	0.168	0.000	0.000	0.000	0.000
84	A	409	ALA	0	0.033	0.024	21.593	-0.675	-0.675	0.000	0.000	0.000	0.000
85	A	410	ILE	0	-0.058	-0.022	21.528	0.584	0.584	0.000	0.000	0.000	0.000
86	A	411	SER	0	-0.007	-0.022	21.152	-0.575	-0.575	0.000	0.000	0.000	0.000
87	A	412	ALA	0	0.006	0.000	22.209	0.440	0.440	0.000	0.000	0.000	0.000
88	A	413	ASP	-1	-0.797	-0.895	22.374	-11.084	-11.084	0.000	0.000	0.000	0.000
89	A	414	ASP	-1	-0.830	-0.908	24.080	-11.201	-11.201	0.000	0.000	0.000	0.000
90	A	415	VAL	0	-0.029	-0.015	18.553	-0.297	-0.297	0.000	0.000	0.000	0.000
91	A	416	ASP	-1	-0.793	-0.878	21.000	-11.889	-11.889	0.000	0.000	0.000	0.000
92	A	417	GLU	-1	-0.812	-0.900	23.418	-9.965	-9.965	0.000	0.000	0.000	0.000
93	A	418	LEU	0	-0.036	-0.014	17.626	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	419	VAL	0	-0.002	-0.005	18.899	-0.255	-0.255	0.000	0.000	0.000	0.000
95	A	420	MET	0	-0.029	-0.006	20.926	0.170	0.170	0.000	0.000	0.000	0.000
96	A	421	ARG	1	0.787	0.875	22.383	10.666	10.666	0.000	0.000	0.000	0.000
97	A	422	ILE	0	0.014	0.013	16.958	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	423	VAL	0	0.031	-0.001	20.822	0.061	0.061	0.000	0.000	0.000	0.000
99	A	424	GLN	0	-0.040	-0.013	23.086	0.144	0.144	0.000	0.000	0.000	0.000
100	A	425	GLN	0	-0.041	-0.009	22.360	0.162	0.162	0.000	0.000	0.000	0.000
101	A	426	ALA	0	0.002	0.019	20.410	-0.086	-0.086	0.000	0.000	0.000	0.000
102	A	427	LYS	1	0.896	0.943	21.411	11.363	11.363	0.000	0.000	0.000	0.000
103	A	428	PRO	0	0.014	0.007	21.302	-0.530	-0.530	0.000	0.000	0.000	0.000
104	A	429	ASN	0	-0.038	-0.026	19.505	0.146	0.146	0.000	0.000	0.000	0.000
105	A	430	ASP	-1	-0.757	-0.825	17.695	-13.905	-13.905	0.000	0.000	0.000	0.000
106	A	431	HIS	0	0.031	0.008	12.552	-1.358	-1.358	0.000	0.000	0.000	0.000
107	A	432	ILE	0	0.004	0.007	13.253	-0.302	-0.302	0.000	0.000	0.000	0.000
108	A	433	LEU	0	0.003	0.000	6.685	-1.251	-1.251	0.000	0.000	0.000	0.000
109	A	434	ILE	0	0.006	0.010	9.472	0.995	0.995	0.000	0.000	0.000	0.000
110	A	435	MET	0	-0.045	-0.016	7.512	-2.998	-2.998	0.000	0.000	0.000	0.000
111	A	436	SER	0	0.053	-0.018	8.199	1.970	1.970	0.000	0.000	0.000	0.000
112	A	437	ASN	0	-0.041	-0.004	8.471	-1.419	-1.419	0.000	0.000	0.000	0.000
113	A	438	GLY	0	0.012	-0.004	10.119	0.685	0.685	0.000	0.000	0.000	0.000
114	A	439	ALA	0	0.020	0.002	11.758	-0.480	-0.480	0.000	0.000	0.000	0.000
115	A	440	PHE	0	0.061	0.041	12.321	0.490	0.490	0.000	0.000	0.000	0.000
116	A	441	GLY	0	0.020	0.007	15.012	0.318	0.318	0.000	0.000	0.000	0.000
117	A	442	GLY	0	-0.001	-0.004	15.123	0.610	0.610	0.000	0.000	0.000	0.000
118	A	443	ILE	0	0.013	0.005	13.531	0.208	0.208	0.000	0.000	0.000	0.000
119	A	444	HIS	0	0.007	-0.018	10.337	1.383	1.383	0.000	0.000	0.000	0.000
120	A	445	GLN	0	0.008	0.013	13.782	0.520	0.520	0.000	0.000	0.000	0.000
121	A	446	LYS	1	0.790	0.887	16.616	12.772	12.772	0.000	0.000	0.000	0.000
122	A	447	LEU	0	0.020	0.008	15.010	0.543	0.543	0.000	0.000	0.000	0.000
123	A	448	LEU	0	-0.015	-0.018	13.932	0.498	0.498	0.000	0.000	0.000	0.000
124	A	449	THR	0	-0.046	-0.018	18.183	0.604	0.604	0.000	0.000	0.000	0.000
125	A	450	ALA	0	-0.020	-0.019	21.397	0.422	0.422	0.000	0.000	0.000	0.000
126	A	451	LEU	0	-0.036	-0.011	18.547	0.314	0.314	0.000	0.000	0.000	0.000
127	A	452	ALA	0	-0.054	-0.016	22.505	0.293	0.293	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:317:ARG)