FMO DATABASE

FMODB ID: K3483

Calculation Name: 3RNV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RNV

Chain ID: A

ChEMBL ID:

UniProt ID: P89509

Base Structure: X-ray

Registration Date: 2023-06-20

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1076809.357148
FMO2-HF: Nuclear repulsion	1027277.704796
FMO2-HF: Total energy	-49531.652352
FMO2-MP2: Total energy	-49674.990659

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:336:MET)

Summations of interaction energy for fragment #1(A:336:MET)

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.
-1.051	1.603	-0.024	-1.395	-1.236	0.008

Interaction energy analysis for fragmet #1(A:336:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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	338	ILE	0	-0.023	-0.022	3.826	-0.110	2.544	-0.024	-1.395	-1.236	0.008
4	A	339	ALA	0	0.022	0.007	6.625	-0.107	-0.107	0.000	0.000	0.000	0.000
5	A	340	LYS	1	0.954	0.975	9.508	0.107	0.107	0.000	0.000	0.000	0.000
6	A	341	GLU	-1	-0.841	-0.935	12.497	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	342	GLY	0	0.020	0.005	16.172	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	343	TYR	0	0.007	-0.022	12.809	0.000	0.000	0.000	0.000	0.000	0.000
9	A	344	CYS	0	-0.017	0.004	11.232	-0.080	-0.080	0.000	0.000	0.000	0.000
10	A	345	TYR	0	0.026	-0.006	11.574	-0.167	-0.167	0.000	0.000	0.000	0.000
11	A	346	ILE	0	-0.001	0.006	8.750	-0.073	-0.073	0.000	0.000	0.000	0.000
12	A	347	ASN	0	0.008	-0.004	7.160	-0.685	-0.685	0.000	0.000	0.000	0.000
13	A	348	ILE	0	0.014	0.014	8.723	-0.203	-0.203	0.000	0.000	0.000	0.000
14	A	349	PHE	0	0.044	-0.012	11.029	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	350	LEU	0	-0.037	-0.018	5.044	0.178	0.178	0.000	0.000	0.000	0.000
16	A	351	ALA	0	0.022	0.020	6.612	-0.307	-0.307	0.000	0.000	0.000	0.000
17	A	352	MET	0	-0.045	-0.004	8.007	0.267	0.267	0.000	0.000	0.000	0.000
18	A	353	LEU	0	-0.030	-0.011	6.002	0.217	0.217	0.000	0.000	0.000	0.000
19	A	354	VAL	0	-0.008	0.005	7.253	0.140	0.140	0.000	0.000	0.000	0.000
20	A	355	ASN	0	-0.043	-0.026	9.638	0.124	0.124	0.000	0.000	0.000	0.000
21	A	356	VAL	0	-0.054	-0.013	11.489	0.088	0.088	0.000	0.000	0.000	0.000
22	A	357	LYS	1	0.923	0.973	12.974	0.321	0.321	0.000	0.000	0.000	0.000
23	A	358	GLU	-1	-0.819	-0.922	12.408	-0.330	-0.330	0.000	0.000	0.000	0.000
24	A	359	SER	0	-0.083	-0.040	14.162	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	360	GLN	0	0.022	-0.005	15.354	0.017	0.017	0.000	0.000	0.000	0.000
26	A	361	ALA	0	0.065	0.047	10.048	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	362	LYS	1	0.950	0.962	11.258	0.260	0.260	0.000	0.000	0.000	0.000
28	A	363	GLU	-1	-0.900	-0.933	12.620	-0.331	-0.331	0.000	0.000	0.000	0.000
29	A	364	PHE	0	0.098	0.051	11.044	0.012	0.012	0.000	0.000	0.000	0.000
30	A	365	THR	0	-0.012	-0.024	8.444	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	366	LYS	1	0.904	0.961	10.965	0.335	0.335	0.000	0.000	0.000	0.000
32	A	367	VAL	0	0.030	0.042	14.155	0.044	0.044	0.000	0.000	0.000	0.000
33	A	368	VAL	0	0.013	0.003	10.899	0.037	0.037	0.000	0.000	0.000	0.000
34	A	369	ARG	1	0.782	0.882	10.701	0.432	0.432	0.000	0.000	0.000	0.000
35	A	370	ASP	-1	-0.814	-0.916	13.277	-0.225	-0.225	0.000	0.000	0.000	0.000
36	A	371	LYS	1	0.779	0.889	16.870	0.286	0.286	0.000	0.000	0.000	0.000
37	A	372	LEU	0	0.004	0.001	15.669	0.018	0.018	0.000	0.000	0.000	0.000
38	A	373	VAL	0	-0.008	-0.006	12.874	0.025	0.025	0.000	0.000	0.000	0.000
39	A	374	GLY	0	-0.021	-0.008	16.276	0.038	0.038	0.000	0.000	0.000	0.000
40	A	375	GLU	-1	-0.827	-0.889	19.453	-0.216	-0.216	0.000	0.000	0.000	0.000
41	A	376	LEU	0	-0.043	-0.015	17.238	0.009	0.009	0.000	0.000	0.000	0.000
42	A	377	GLY	0	0.035	0.030	19.285	0.027	0.027	0.000	0.000	0.000	0.000
43	A	378	LYS	1	0.864	0.943	18.292	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	379	TRP	0	-0.025	-0.017	18.722	0.010	0.010	0.000	0.000	0.000	0.000
45	A	380	PRO	0	0.043	0.051	18.436	0.020	0.020	0.000	0.000	0.000	0.000
46	A	381	THR	0	-0.010	-0.045	21.233	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	382	LEU	0	0.006	-0.010	19.842	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	383	LEU	0	0.012	0.006	21.758	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	384	ASP	-1	-0.806	-0.860	22.588	-0.204	-0.204	0.000	0.000	0.000	0.000
50	A	385	VAL	0	0.009	0.001	16.687	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	386	ALA	0	0.010	-0.001	18.895	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	387	THR	0	-0.018	-0.021	20.587	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	388	ALA	0	0.002	0.004	18.471	0.002	0.002	0.000	0.000	0.000	0.000
54	A	389	CYS	0	-0.073	-0.040	16.928	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	390	TYR	0	-0.026	-0.013	18.270	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	391	PHE	0	0.010	0.003	19.719	0.015	0.015	0.000	0.000	0.000	0.000
57	A	392	LEU	0	0.023	0.008	14.671	0.008	0.008	0.000	0.000	0.000	0.000
58	A	393	LYS	1	0.889	0.944	18.662	0.281	0.281	0.000	0.000	0.000	0.000
59	A	394	VAL	0	-0.028	-0.010	20.027	0.015	0.015	0.000	0.000	0.000	0.000
60	A	395	PHE	0	-0.030	-0.007	20.271	0.026	0.026	0.000	0.000	0.000	0.000
61	A	396	TYR	0	-0.096	-0.077	16.752	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	397	PRO	0	0.049	0.021	18.112	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	398	ASP	-1	-0.864	-0.938	17.222	-0.325	-0.325	0.000	0.000	0.000	0.000
64	A	399	VAL	0	0.019	0.006	13.852	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	400	ALA	0	-0.052	-0.029	15.768	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	401	ASN	0	-0.029	-0.029	17.690	0.011	0.011	0.000	0.000	0.000	0.000
67	A	402	ALA	0	0.021	0.040	12.056	0.020	0.020	0.000	0.000	0.000	0.000
68	A	403	GLU	-1	-0.926	-0.956	12.042	-0.351	-0.351	0.000	0.000	0.000	0.000
69	A	404	LEU	0	-0.049	-0.026	11.319	-0.160	-0.160	0.000	0.000	0.000	0.000
70	A	405	PRO	0	0.025	0.013	8.490	0.099	0.099	0.000	0.000	0.000	0.000
71	A	406	ARG	1	0.804	0.887	10.922	0.185	0.185	0.000	0.000	0.000	0.000
72	A	407	MET	0	-0.012	-0.003	13.826	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	408	LEU	0	-0.002	-0.002	16.447	0.036	0.036	0.000	0.000	0.000	0.000
74	A	409	VAL	0	-0.007	-0.007	18.859	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	410	ASP	-1	-0.774	-0.855	22.203	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	411	HIS	0	0.007	-0.012	24.602	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	412	LYS	1	0.938	0.980	27.946	0.013	0.013	0.000	0.000	0.000	0.000
78	A	413	THR	0	-0.058	-0.068	25.136	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	414	LYS	1	0.866	0.946	26.628	0.060	0.060	0.000	0.000	0.000	0.000
80	A	415	ILE	0	0.001	0.014	20.483	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	416	ILE	0	-0.017	-0.010	18.047	0.010	0.010	0.000	0.000	0.000	0.000
82	A	417	HIS	0	0.034	0.003	16.334	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	418	VAL	0	-0.014	-0.002	11.029	0.006	0.006	0.000	0.000	0.000	0.000
84	A	419	VAL	0	-0.035	-0.028	11.204	0.024	0.024	0.000	0.000	0.000	0.000
85	A	420	ASP	-1	-0.842	-0.902	6.879	-0.976	-0.976	0.000	0.000	0.000	0.000
86	A	421	SER	0	0.016	0.001	8.369	0.202	0.202	0.000	0.000	0.000	0.000
87	A	422	TYR	0	0.068	0.041	11.111	-0.064	-0.064	0.000	0.000	0.000	0.000
88	A	423	GLY	0	0.019	0.014	14.157	-0.047	-0.047	0.000	0.000	0.000	0.000
89	A	424	SER	0	0.003	-0.008	17.433	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	425	LEU	0	0.024	0.024	19.162	0.003	0.003	0.000	0.000	0.000	0.000
91	A	426	SER	0	0.019	0.031	19.052	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	427	THR	0	-0.019	-0.026	20.372	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	428	GLY	0	0.055	0.024	23.382	0.010	0.010	0.000	0.000	0.000	0.000
94	A	429	TYR	0	0.027	0.003	25.212	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	430	HIS	0	-0.001	-0.001	23.202	0.002	0.002	0.000	0.000	0.000	0.000
96	A	431	VAL	0	-0.022	0.011	18.826	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	432	LEU	0	0.017	0.016	19.790	0.012	0.012	0.000	0.000	0.000	0.000
98	A	433	LYS	1	0.927	0.961	19.474	0.096	0.096	0.000	0.000	0.000	0.000
99	A	434	THR	0	-0.032	-0.010	18.303	0.016	0.016	0.000	0.000	0.000	0.000
100	A	435	ASN	0	0.058	0.018	16.706	-0.039	-0.039	0.000	0.000	0.000	0.000
101	A	436	THR	0	0.012	0.004	15.500	-0.031	-0.031	0.000	0.000	0.000	0.000
102	A	437	VAL	0	0.066	0.038	14.675	0.041	0.041	0.000	0.000	0.000	0.000
103	A	438	GLU	-1	-0.761	-0.865	17.286	-0.210	-0.210	0.000	0.000	0.000	0.000
104	A	439	GLN	0	-0.052	-0.024	20.135	0.025	0.025	0.000	0.000	0.000	0.000
105	A	440	LEU	0	0.050	0.029	17.509	0.033	0.033	0.000	0.000	0.000	0.000
106	A	441	ILE	0	0.021	0.008	20.047	0.032	0.032	0.000	0.000	0.000	0.000
107	A	442	LYS	1	0.772	0.856	22.834	0.253	0.253	0.000	0.000	0.000	0.000
108	A	443	PHE	0	-0.040	-0.015	23.712	0.020	0.020	0.000	0.000	0.000	0.000
109	A	444	THR	0	0.022	0.006	23.791	0.025	0.025	0.000	0.000	0.000	0.000
110	A	445	ARG	1	0.942	0.975	25.921	0.187	0.187	0.000	0.000	0.000	0.000
111	A	446	CYS	0	-0.055	-0.001	28.333	0.016	0.016	0.000	0.000	0.000	0.000
112	A	447	ASN	0	0.046	0.005	31.049	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	448	LEU	0	-0.004	0.006	33.368	0.006	0.006	0.000	0.000	0.000	0.000
114	A	449	GLU	-1	-0.786	-0.888	32.367	-0.131	-0.131	0.000	0.000	0.000	0.000
115	A	450	SER	0	-0.027	-0.008	29.337	0.005	0.005	0.000	0.000	0.000	0.000
116	A	451	SER	0	0.053	0.010	30.319	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	452	LEU	0	-0.001	-0.013	25.093	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	453	LYS	1	0.843	0.932	25.331	0.129	0.129	0.000	0.000	0.000	0.000
119	A	454	HIS	0	0.022	0.003	25.814	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	455	TYR	0	-0.086	-0.051	24.004	0.015	0.015	0.000	0.000	0.000	0.000
121	A	456	ARG	1	0.905	0.965	22.317	0.088	0.088	0.000	0.000	0.000	0.000
122	A	457	VAL	0	0.019	0.016	16.542	0.001	0.001	0.000	0.000	0.000	0.000
123	A	458	GLY	0	-0.012	0.002	15.602	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:336:MET)