FMO DATABASE

FMODB ID: 857LY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1090135.39116
FMO2-HF: Nuclear repulsion	1041837.405362
FMO2-HF: Total energy	-48297.985798
FMO2-MP2: Total energy	-48441.278128

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.
-84.997	-81.575	2.737	-2.835	-3.323	-0.025

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 : 0.915 / q_NPA : 0.933

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	-0.905	-0.938	3.649	-23.768	-22.499	0.000	-0.399	-0.870	0.001
4	A	320	VAL	0	-0.001	-0.009	4.692	2.271	2.366	-0.001	-0.007	-0.087	0.000
5	A	321	LYS	1	0.861	0.937	8.356	21.667	21.667	0.000	0.000	0.000	0.000
6	A	322	GLY	0	0.013	-0.003	10.647	1.137	1.137	0.000	0.000	0.000	0.000
7	A	323	VAL	0	-0.025	-0.010	13.750	-0.652	-0.652	0.000	0.000	0.000	0.000
8	A	324	VAL	0	0.006	0.018	16.408	0.568	0.568	0.000	0.000	0.000	0.000
9	A	325	ASN	0	0.019	0.006	19.814	0.003	0.003	0.000	0.000	0.000	0.000
10	A	326	ASN	0	-0.008	-0.033	19.869	0.016	0.016	0.000	0.000	0.000	0.000
11	A	327	ILE	0	-0.017	0.025	16.797	-0.302	-0.302	0.000	0.000	0.000	0.000
12	A	328	THR	0	-0.013	0.001	11.617	0.161	0.161	0.000	0.000	0.000	0.000
13	A	329	VAL	0	0.001	0.009	11.929	-0.196	-0.196	0.000	0.000	0.000	0.000
14	A	330	TYR	0	-0.049	-0.067	6.990	-0.899	-0.899	0.000	0.000	0.000	0.000
15	A	331	ASP	-1	-0.837	-0.918	6.973	-19.665	-19.665	0.000	0.000	0.000	0.000
16	A	332	ASP	-1	-0.823	-0.939	2.354	-55.117	-53.278	2.739	-2.414	-2.164	-0.026
17	A	333	PHE	0	0.031	0.013	4.170	2.220	2.439	-0.001	-0.015	-0.202	0.000
18	A	334	ALA	0	-0.029	0.019	5.755	2.253	2.253	0.000	0.000	0.000	0.000
19	A	335	HIS	1	0.883	0.904	7.563	26.163	26.163	0.000	0.000	0.000	0.000
20	A	336	HIS	0	0.003	0.003	10.816	1.941	1.941	0.000	0.000	0.000	0.000
21	A	337	PRO	0	0.097	0.040	11.609	-1.879	-1.879	0.000	0.000	0.000	0.000
22	A	338	THR	0	0.048	0.020	10.368	-0.131	-0.131	0.000	0.000	0.000	0.000
23	A	339	ALA	0	-0.022	-0.010	7.071	-1.478	-1.478	0.000	0.000	0.000	0.000
24	A	340	ILE	0	-0.001	0.005	7.972	-2.185	-2.185	0.000	0.000	0.000	0.000
25	A	341	THR	0	0.026	0.010	10.221	0.248	0.248	0.000	0.000	0.000	0.000
26	A	342	ALA	0	-0.035	-0.013	6.824	0.072	0.072	0.000	0.000	0.000	0.000
27	A	343	THR	0	-0.024	-0.018	5.111	-2.202	-2.202	0.000	0.000	0.000	0.000
28	A	344	ILE	0	0.009	0.005	6.733	0.106	0.106	0.000	0.000	0.000	0.000
29	A	345	ASP	-1	-0.896	-0.939	9.878	-23.547	-23.547	0.000	0.000	0.000	0.000
30	A	346	ALA	0	-0.046	-0.023	5.730	0.374	0.374	0.000	0.000	0.000	0.000
31	A	347	LEU	0	-0.027	-0.018	7.741	0.755	0.755	0.000	0.000	0.000	0.000
32	A	348	ARG	1	0.824	0.882	8.766	18.979	18.979	0.000	0.000	0.000	0.000
33	A	349	ALA	0	-0.036	-0.014	10.369	1.368	1.368	0.000	0.000	0.000	0.000
34	A	350	LYS	1	0.870	0.931	8.503	29.150	29.150	0.000	0.000	0.000	0.000
35	A	351	VAL	0	-0.009	0.008	11.736	1.146	1.146	0.000	0.000	0.000	0.000
36	A	352	GLY	0	-0.002	0.020	14.179	1.289	1.289	0.000	0.000	0.000	0.000
37	A	353	GLN	0	0.003	-0.018	16.767	-0.681	-0.681	0.000	0.000	0.000	0.000
38	A	354	GLN	0	-0.038	0.008	16.825	0.147	0.147	0.000	0.000	0.000	0.000
39	A	355	ARG	1	0.796	0.878	16.968	12.341	12.341	0.000	0.000	0.000	0.000
40	A	356	ILE	0	0.020	0.002	11.835	-0.523	-0.523	0.000	0.000	0.000	0.000
41	A	357	LEU	0	-0.037	-0.021	14.854	0.740	0.740	0.000	0.000	0.000	0.000
42	A	358	ALA	0	0.002	0.006	12.820	-0.901	-0.901	0.000	0.000	0.000	0.000
43	A	359	VAL	0	0.006	-0.006	12.581	1.173	1.173	0.000	0.000	0.000	0.000
44	A	360	LEU	0	0.002	0.003	12.098	-1.242	-1.242	0.000	0.000	0.000	0.000
45	A	361	GLU	-1	-0.840	-0.911	13.186	-14.803	-14.803	0.000	0.000	0.000	0.000
46	A	362	PRO	0	-0.028	-0.012	14.072	-1.125	-1.125	0.000	0.000	0.000	0.000
47	A	363	ARG	1	0.855	0.932	14.058	17.752	17.752	0.000	0.000	0.000	0.000
48	A	373	LYS	1	0.985	0.983	21.557	11.484	11.484	0.000	0.000	0.000	0.000
49	A	374	HIS	0	0.114	0.048	22.225	-0.257	-0.257	0.000	0.000	0.000	0.000
50	A	375	GLU	-1	-0.921	-0.962	18.780	-15.924	-15.924	0.000	0.000	0.000	0.000
51	A	376	LEU	0	-0.038	-0.014	15.948	-0.769	-0.769	0.000	0.000	0.000	0.000
52	A	377	ALA	0	0.048	0.043	17.773	-0.646	-0.646	0.000	0.000	0.000	0.000
53	A	378	THR	0	0.013	0.006	18.463	-0.110	-0.110	0.000	0.000	0.000	0.000
54	A	379	SER	0	-0.131	-0.080	13.958	-0.641	-0.641	0.000	0.000	0.000	0.000
55	A	380	LEU	0	0.001	-0.024	14.092	-1.104	-1.104	0.000	0.000	0.000	0.000
56	A	381	GLN	0	0.016	0.011	16.320	0.875	0.875	0.000	0.000	0.000	0.000
57	A	382	ASP	-1	-0.856	-0.907	14.933	-17.502	-17.502	0.000	0.000	0.000	0.000
58	A	383	ALA	0	-0.048	-0.004	14.857	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	384	ASP	-1	-0.766	-0.877	16.496	-14.433	-14.433	0.000	0.000	0.000	0.000
60	A	385	SER	0	-0.067	-0.046	18.238	0.809	0.809	0.000	0.000	0.000	0.000
61	A	386	VAL	0	0.019	0.012	17.032	-0.991	-0.991	0.000	0.000	0.000	0.000
62	A	387	PHE	0	-0.007	-0.008	17.153	0.947	0.947	0.000	0.000	0.000	0.000
63	A	388	ILE	0	-0.040	-0.022	16.802	-0.921	-0.921	0.000	0.000	0.000	0.000
64	A	389	TYR	0	0.006	0.012	17.761	0.722	0.722	0.000	0.000	0.000	0.000
65	A	390	GLN	0	-0.018	-0.025	19.390	-0.475	-0.475	0.000	0.000	0.000	0.000
66	A	391	PRO	0	-0.011	0.008	19.650	0.414	0.414	0.000	0.000	0.000	0.000
67	A	392	PRO	0	0.025	0.004	22.340	0.229	0.229	0.000	0.000	0.000	0.000
68	A	393	THR	0	-0.031	-0.006	21.733	0.359	0.359	0.000	0.000	0.000	0.000
69	A	394	ILE	0	0.068	0.020	24.761	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	395	GLU	-1	-0.969	-0.991	25.927	-10.289	-10.289	0.000	0.000	0.000	0.000
71	A	396	TRP	0	-0.089	-0.045	19.615	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	397	GLN	0	0.064	0.030	25.436	-0.151	-0.151	0.000	0.000	0.000	0.000
73	A	398	VAL	0	0.018	0.001	21.792	-0.246	-0.246	0.000	0.000	0.000	0.000
74	A	399	SER	0	0.046	0.017	24.083	-0.190	-0.190	0.000	0.000	0.000	0.000
75	A	400	GLU	-1	-0.990	-0.987	26.848	-10.283	-10.283	0.000	0.000	0.000	0.000
76	A	401	VAL	0	-0.055	-0.026	20.229	-0.147	-0.147	0.000	0.000	0.000	0.000
77	A	402	LEU	0	0.007	-0.021	20.879	-0.217	-0.217	0.000	0.000	0.000	0.000
78	A	403	ALA	0	-0.003	0.019	24.043	0.096	0.096	0.000	0.000	0.000	0.000
79	A	404	ASN	0	-0.074	-0.035	24.400	0.520	0.520	0.000	0.000	0.000	0.000
80	A	405	LEU	0	-0.068	-0.014	20.210	-0.181	-0.181	0.000	0.000	0.000	0.000
81	A	406	ALA	0	0.026	0.016	24.239	0.333	0.333	0.000	0.000	0.000	0.000
82	A	407	GLN	0	-0.067	-0.030	19.815	0.970	0.970	0.000	0.000	0.000	0.000
83	A	408	PRO	0	-0.045	-0.032	23.206	0.134	0.134	0.000	0.000	0.000	0.000
84	A	409	ALA	0	0.046	0.028	21.888	-0.670	-0.670	0.000	0.000	0.000	0.000
85	A	410	ILE	0	-0.064	-0.024	21.845	0.601	0.601	0.000	0.000	0.000	0.000
86	A	411	SER	0	0.030	0.005	21.523	-0.551	-0.551	0.000	0.000	0.000	0.000
87	A	412	ALA	0	-0.039	-0.022	22.325	0.436	0.436	0.000	0.000	0.000	0.000
88	A	413	ASP	-1	-0.903	-0.948	22.683	-10.721	-10.721	0.000	0.000	0.000	0.000
89	A	414	ASP	-1	-0.783	-0.887	24.300	-10.565	-10.565	0.000	0.000	0.000	0.000
90	A	415	VAL	0	-0.009	-0.022	19.135	-0.229	-0.229	0.000	0.000	0.000	0.000
91	A	416	ASP	-1	-0.816	-0.891	21.460	-11.242	-11.242	0.000	0.000	0.000	0.000
92	A	417	GLU	-1	-0.954	-0.978	23.815	-9.796	-9.796	0.000	0.000	0.000	0.000
93	A	418	LEU	0	-0.013	-0.013	17.912	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	419	VAL	0	-0.002	-0.004	19.347	-0.250	-0.250	0.000	0.000	0.000	0.000
95	A	420	MET	0	-0.036	-0.013	21.248	0.179	0.179	0.000	0.000	0.000	0.000
96	A	421	ARG	1	0.870	0.935	22.510	10.448	10.448	0.000	0.000	0.000	0.000
97	A	422	ILE	0	0.010	0.001	17.003	0.001	0.001	0.000	0.000	0.000	0.000
98	A	423	VAL	0	0.010	0.000	20.916	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	424	GLN	0	-0.038	-0.009	23.043	0.141	0.141	0.000	0.000	0.000	0.000
100	A	425	GLN	0	0.009	0.020	22.388	0.019	0.019	0.000	0.000	0.000	0.000
101	A	426	ALA	0	-0.018	0.006	20.018	-0.076	-0.076	0.000	0.000	0.000	0.000
102	A	427	LYS	1	0.901	0.944	21.399	11.466	11.466	0.000	0.000	0.000	0.000
103	A	428	PRO	0	0.020	0.007	21.172	-0.521	-0.521	0.000	0.000	0.000	0.000
104	A	429	ASN	0	-0.028	-0.019	19.525	0.202	0.202	0.000	0.000	0.000	0.000
105	A	430	ASP	-1	-0.747	-0.826	17.737	-13.887	-13.887	0.000	0.000	0.000	0.000
106	A	431	HIS	0	0.026	0.023	12.521	-1.298	-1.298	0.000	0.000	0.000	0.000
107	A	432	ILE	0	0.002	0.004	13.464	-0.052	-0.052	0.000	0.000	0.000	0.000
108	A	433	LEU	0	0.011	0.001	6.743	-1.063	-1.063	0.000	0.000	0.000	0.000
109	A	434	ILE	0	-0.019	-0.002	9.378	1.043	1.043	0.000	0.000	0.000	0.000
110	A	435	MET	0	-0.016	-0.002	7.653	-2.322	-2.322	0.000	0.000	0.000	0.000
111	A	436	SER	0	0.057	0.006	8.616	1.609	1.609	0.000	0.000	0.000	0.000
112	A	437	ASN	0	-0.035	-0.008	9.026	-0.478	-0.478	0.000	0.000	0.000	0.000
113	A	438	GLY	0	0.003	-0.009	10.491	0.512	0.512	0.000	0.000	0.000	0.000
114	A	439	ALA	0	0.029	0.007	12.287	-0.466	-0.466	0.000	0.000	0.000	0.000
115	A	440	PHE	0	0.059	0.038	12.796	0.316	0.316	0.000	0.000	0.000	0.000
116	A	441	GLY	0	0.031	0.004	15.708	0.268	0.268	0.000	0.000	0.000	0.000
117	A	442	GLY	0	-0.015	-0.007	16.092	0.541	0.541	0.000	0.000	0.000	0.000
118	A	443	ILE	0	0.029	0.017	14.214	0.291	0.291	0.000	0.000	0.000	0.000
119	A	444	HIS	0	0.050	0.019	12.285	0.792	0.792	0.000	0.000	0.000	0.000
120	A	445	GLN	0	-0.007	0.000	14.442	0.694	0.694	0.000	0.000	0.000	0.000
121	A	446	LYS	1	0.827	0.900	17.340	12.133	12.133	0.000	0.000	0.000	0.000
122	A	447	LEU	0	0.028	0.013	15.379	0.514	0.514	0.000	0.000	0.000	0.000
123	A	448	LEU	0	-0.024	-0.004	14.534	0.406	0.406	0.000	0.000	0.000	0.000
124	A	449	THR	0	-0.036	-0.010	18.762	0.562	0.562	0.000	0.000	0.000	0.000
125	A	450	ALA	0	-0.025	-0.019	21.869	0.378	0.378	0.000	0.000	0.000	0.000
126	A	451	LEU	0	-0.055	-0.028	18.336	0.306	0.306	0.000	0.000	0.000	0.000
127	A	452	ALA	0	-0.048	-0.009	22.544	0.261	0.261	0.000	0.000	0.000	0.000

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