FMO DATABASE

FMODB ID: 4316N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1081463.485961
FMO2-HF: Nuclear repulsion	1031931.643571
FMO2-HF: Total energy	-49531.84239
FMO2-MP2: Total energy	-49675.168679

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.
-1.007	1.84	-0.02	-1.475	-1.351	0.007

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 : 0.020 / q_NPA : 0.013

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

Sort

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	-0.020	-0.017	3.867	0.063	2.745	-0.019	-1.443	-1.220	0.007
4	A	339	ALA	0	0.029	0.018	6.887	-0.200	-0.200	0.000	0.000	0.000	0.000
5	A	340	LYS	1	0.932	0.965	9.946	0.133	0.133	0.000	0.000	0.000	0.000
6	A	341	GLU	-1	-0.832	-0.927	12.758	-0.091	-0.091	0.000	0.000	0.000	0.000
7	A	342	GLY	0	0.050	0.019	16.438	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	343	TYR	0	0.011	-0.023	12.739	0.009	0.009	0.000	0.000	0.000	0.000
9	A	344	CYS	0	-0.011	0.013	11.184	-0.058	-0.058	0.000	0.000	0.000	0.000
10	A	345	TYR	0	0.010	-0.013	11.469	-0.191	-0.191	0.000	0.000	0.000	0.000
11	A	346	ILE	0	0.007	0.009	8.462	-0.078	-0.078	0.000	0.000	0.000	0.000
12	A	347	ASN	0	0.001	-0.005	7.185	-0.688	-0.688	0.000	0.000	0.000	0.000
13	A	348	ILE	0	0.017	0.008	8.399	-0.261	-0.261	0.000	0.000	0.000	0.000
14	A	349	PHE	0	0.041	-0.013	10.521	0.024	0.024	0.000	0.000	0.000	0.000
15	A	350	LEU	0	-0.044	-0.021	4.715	0.062	0.227	-0.001	-0.032	-0.131	0.000
16	A	351	ALA	0	0.032	0.023	5.974	-0.353	-0.353	0.000	0.000	0.000	0.000
17	A	352	MET	0	-0.049	-0.009	7.283	0.315	0.315	0.000	0.000	0.000	0.000
18	A	353	LEU	0	-0.017	-0.002	5.364	0.292	0.292	0.000	0.000	0.000	0.000
19	A	354	VAL	0	-0.011	0.003	6.881	0.206	0.206	0.000	0.000	0.000	0.000
20	A	355	ASN	0	-0.041	-0.020	9.136	0.129	0.129	0.000	0.000	0.000	0.000
21	A	356	VAL	0	-0.039	-0.012	10.747	0.084	0.084	0.000	0.000	0.000	0.000
22	A	357	LYS	1	0.896	0.958	12.362	0.327	0.327	0.000	0.000	0.000	0.000
23	A	358	GLU	-1	-0.849	-0.932	12.115	-0.253	-0.253	0.000	0.000	0.000	0.000
24	A	359	SER	0	-0.064	-0.038	13.755	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	360	GLN	0	0.043	0.016	15.357	0.012	0.012	0.000	0.000	0.000	0.000
26	A	361	ALA	0	0.044	0.039	9.766	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	362	LYS	1	0.965	0.971	10.934	0.181	0.181	0.000	0.000	0.000	0.000
28	A	363	GLU	-1	-0.902	-0.923	12.531	-0.285	-0.285	0.000	0.000	0.000	0.000
29	A	364	PHE	0	0.085	0.033	10.821	0.013	0.013	0.000	0.000	0.000	0.000
30	A	365	THR	0	-0.012	-0.028	8.411	-0.093	-0.093	0.000	0.000	0.000	0.000
31	A	366	LYS	1	0.892	0.961	10.787	0.295	0.295	0.000	0.000	0.000	0.000
32	A	367	VAL	0	0.015	0.024	14.094	0.032	0.032	0.000	0.000	0.000	0.000
33	A	368	VAL	0	0.023	0.007	10.648	0.030	0.030	0.000	0.000	0.000	0.000
34	A	369	ARG	1	0.792	0.888	10.398	0.392	0.392	0.000	0.000	0.000	0.000
35	A	370	ASP	-1	-0.808	-0.911	13.102	-0.197	-0.197	0.000	0.000	0.000	0.000
36	A	371	LYS	1	0.794	0.891	16.669	0.288	0.288	0.000	0.000	0.000	0.000
37	A	372	LEU	0	0.008	0.015	15.674	0.017	0.017	0.000	0.000	0.000	0.000
38	A	373	VAL	0	-0.022	-0.020	12.504	0.015	0.015	0.000	0.000	0.000	0.000
39	A	374	GLY	0	-0.037	-0.011	15.941	0.042	0.042	0.000	0.000	0.000	0.000
40	A	375	GLU	-1	-0.830	-0.904	19.200	-0.222	-0.222	0.000	0.000	0.000	0.000
41	A	376	LEU	0	-0.027	-0.010	16.939	0.010	0.010	0.000	0.000	0.000	0.000
42	A	377	GLY	0	0.036	0.034	19.483	0.019	0.019	0.000	0.000	0.000	0.000
43	A	378	LYS	1	0.822	0.908	17.793	0.009	0.009	0.000	0.000	0.000	0.000
44	A	379	TRP	0	-0.037	-0.013	18.824	0.011	0.011	0.000	0.000	0.000	0.000
45	A	380	PRO	0	0.055	0.057	18.279	0.018	0.018	0.000	0.000	0.000	0.000
46	A	381	THR	0	-0.026	-0.054	21.169	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	382	LEU	0	-0.004	-0.011	19.646	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	383	LEU	0	0.018	0.011	21.452	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	384	ASP	-1	-0.794	-0.845	22.014	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	385	VAL	0	0.019	0.005	16.141	-0.027	-0.027	0.000	0.000	0.000	0.000
51	A	386	ALA	0	0.025	0.011	18.210	-0.047	-0.047	0.000	0.000	0.000	0.000
52	A	387	THR	0	-0.028	-0.025	20.103	0.001	0.001	0.000	0.000	0.000	0.000
53	A	388	ALA	0	0.005	0.003	17.722	0.002	0.002	0.000	0.000	0.000	0.000
54	A	389	CYS	0	-0.063	-0.036	16.365	-0.054	-0.054	0.000	0.000	0.000	0.000
55	A	390	TYR	0	-0.030	-0.012	17.655	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	391	PHE	0	0.003	-0.007	19.308	0.015	0.015	0.000	0.000	0.000	0.000
57	A	392	LEU	0	0.019	0.005	13.904	0.007	0.007	0.000	0.000	0.000	0.000
58	A	393	LYS	1	0.886	0.936	17.884	0.293	0.293	0.000	0.000	0.000	0.000
59	A	394	VAL	0	-0.047	-0.020	19.424	0.018	0.018	0.000	0.000	0.000	0.000
60	A	395	PHE	0	-0.018	-0.001	19.925	0.029	0.029	0.000	0.000	0.000	0.000
61	A	396	TYR	0	-0.090	-0.070	16.323	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	397	PRO	0	0.044	0.021	17.666	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	398	ASP	-1	-0.841	-0.920	16.720	-0.323	-0.323	0.000	0.000	0.000	0.000
64	A	399	VAL	0	0.016	-0.001	13.331	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	400	ALA	0	-0.050	-0.023	15.439	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	401	ASN	0	-0.037	-0.032	17.285	0.008	0.008	0.000	0.000	0.000	0.000
67	A	402	ALA	0	0.037	0.047	11.645	0.012	0.012	0.000	0.000	0.000	0.000
68	A	403	GLU	-1	-0.929	-0.954	11.862	-0.368	-0.368	0.000	0.000	0.000	0.000
69	A	404	LEU	0	-0.049	-0.026	11.004	-0.171	-0.171	0.000	0.000	0.000	0.000
70	A	405	PRO	0	0.022	0.012	8.009	0.137	0.137	0.000	0.000	0.000	0.000
71	A	406	ARG	1	0.793	0.878	10.630	0.222	0.222	0.000	0.000	0.000	0.000
72	A	407	MET	0	0.011	0.017	13.895	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	408	LEU	0	0.013	0.013	16.159	0.044	0.044	0.000	0.000	0.000	0.000
74	A	409	VAL	0	-0.013	-0.010	18.372	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	410	ASP	-1	-0.760	-0.848	21.761	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	411	HIS	0	0.023	0.010	24.368	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	412	LYS	1	0.919	0.963	27.730	0.022	0.022	0.000	0.000	0.000	0.000
78	A	413	THR	0	-0.059	-0.068	25.132	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	414	LYS	1	0.867	0.945	26.465	0.069	0.069	0.000	0.000	0.000	0.000
80	A	415	ILE	0	-0.003	0.008	20.535	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	416	ILE	0	-0.005	-0.007	17.619	0.009	0.009	0.000	0.000	0.000	0.000
82	A	417	HIS	0	0.041	0.013	16.118	-0.038	-0.038	0.000	0.000	0.000	0.000
83	A	418	VAL	0	-0.007	0.000	10.843	0.016	0.016	0.000	0.000	0.000	0.000
84	A	419	VAL	0	-0.031	-0.025	11.069	-0.025	-0.025	0.000	0.000	0.000	0.000
85	A	420	ASP	-1	-0.843	-0.900	6.788	-1.068	-1.068	0.000	0.000	0.000	0.000
86	A	421	SER	0	0.009	-0.002	8.447	0.227	0.227	0.000	0.000	0.000	0.000
87	A	422	TYR	0	0.060	0.040	11.133	-0.071	-0.071	0.000	0.000	0.000	0.000
88	A	423	GLY	0	0.021	0.015	14.211	-0.040	-0.040	0.000	0.000	0.000	0.000
89	A	424	SER	0	0.015	-0.001	17.184	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	425	LEU	0	0.015	0.023	18.745	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	426	SER	0	0.010	0.025	19.224	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	427	THR	0	-0.016	-0.028	20.215	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	428	GLY	0	0.073	0.026	22.891	0.016	0.016	0.000	0.000	0.000	0.000
94	A	429	TYR	0	0.014	0.003	24.757	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	430	HIS	0	-0.014	-0.003	22.952	0.002	0.002	0.000	0.000	0.000	0.000
96	A	431	VAL	0	-0.009	0.000	18.642	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	432	LEU	0	0.020	0.018	19.516	0.014	0.014	0.000	0.000	0.000	0.000
98	A	433	LYS	1	0.940	0.975	18.993	0.103	0.103	0.000	0.000	0.000	0.000
99	A	434	THR	0	-0.036	-0.016	18.012	0.022	0.022	0.000	0.000	0.000	0.000
100	A	435	ASN	0	0.037	0.005	16.175	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	436	THR	0	0.022	0.003	15.062	-0.034	-0.034	0.000	0.000	0.000	0.000
102	A	437	VAL	0	0.079	0.040	14.118	0.056	0.056	0.000	0.000	0.000	0.000
103	A	438	GLU	-1	-0.766	-0.866	16.821	-0.215	-0.215	0.000	0.000	0.000	0.000
104	A	439	GLN	0	-0.063	-0.027	19.711	0.025	0.025	0.000	0.000	0.000	0.000
105	A	440	LEU	0	0.033	0.015	16.867	0.035	0.035	0.000	0.000	0.000	0.000
106	A	441	ILE	0	0.012	0.006	19.438	0.035	0.035	0.000	0.000	0.000	0.000
107	A	442	LYS	1	0.766	0.853	22.212	0.260	0.260	0.000	0.000	0.000	0.000
108	A	443	PHE	0	-0.019	-0.002	23.311	0.021	0.021	0.000	0.000	0.000	0.000
109	A	444	THR	0	0.039	0.013	23.367	0.027	0.027	0.000	0.000	0.000	0.000
110	A	445	ARG	1	0.941	0.975	25.475	0.198	0.198	0.000	0.000	0.000	0.000
111	A	446	CYS	0	-0.026	0.015	27.977	0.017	0.017	0.000	0.000	0.000	0.000
112	A	447	ASN	0	0.023	0.001	30.597	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	448	LEU	0	0.011	0.007	32.826	0.007	0.007	0.000	0.000	0.000	0.000
114	A	449	GLU	-1	-0.764	-0.871	31.763	-0.143	-0.143	0.000	0.000	0.000	0.000
115	A	450	SER	0	-0.027	-0.013	29.013	0.005	0.005	0.000	0.000	0.000	0.000
116	A	451	SER	0	0.041	0.005	29.575	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	452	LEU	0	0.009	-0.001	24.710	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	453	LYS	1	0.808	0.903	24.913	0.137	0.137	0.000	0.000	0.000	0.000
119	A	454	HIS	0	0.016	-0.003	25.475	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	455	TYR	0	-0.075	-0.051	23.749	0.018	0.018	0.000	0.000	0.000	0.000
121	A	456	ARG	1	0.873	0.951	22.127	0.099	0.099	0.000	0.000	0.000	0.000
122	A	457	VAL	0	0.019	0.010	16.172	0.001	0.001	0.000	0.000	0.000	0.000
123	A	458	GLY	0	-0.033	-0.008	15.528	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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