FMO DATABASE

FMODB ID: K37K3

Calculation Name: 3RNV-A-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	124
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1080411.127754
FMO2-HF: Nuclear repulsion	1030728.688748
FMO2-HF: Total energy	-49682.439006
FMO2-MP2: Total energy	-49826.16705

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:335:ACE )

Summations of interaction energy for fragment #1(A:335:ACE )

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.
2.032	2.99	-0.004	-0.423	-0.532	-0.001

Interaction energy analysis for fragmet #1(A:335:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.005

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	337	TYR	0	-0.004	0.021	3.873	0.792	1.750	-0.004	-0.423	-0.532	-0.001
4	A	338	ILE	0	-0.023	-0.018	6.556	-0.070	-0.070	0.000	0.000	0.000	0.000
5	A	339	ALA	0	0.029	0.012	10.306	0.087	0.087	0.000	0.000	0.000	0.000
6	A	340	LYS	1	0.948	0.968	12.942	0.212	0.212	0.000	0.000	0.000	0.000
7	A	341	GLU	-1	-0.887	-0.950	16.302	-0.109	-0.109	0.000	0.000	0.000	0.000
8	A	342	GLY	0	0.043	0.018	19.398	0.003	0.003	0.000	0.000	0.000	0.000
9	A	343	TYR	0	-0.018	-0.035	16.503	0.017	0.017	0.000	0.000	0.000	0.000
10	A	344	CYS	0	0.014	0.022	13.649	-0.035	-0.035	0.000	0.000	0.000	0.000
11	A	345	TYR	0	-0.001	-0.017	13.296	0.008	0.008	0.000	0.000	0.000	0.000
12	A	346	ILE	0	0.004	0.004	11.533	0.029	0.029	0.000	0.000	0.000	0.000
13	A	347	ASN	0	0.012	-0.005	9.228	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	348	ILE	0	0.012	0.017	9.577	0.092	0.092	0.000	0.000	0.000	0.000
15	A	349	PHE	0	0.038	-0.009	11.805	0.057	0.057	0.000	0.000	0.000	0.000
16	A	350	LEU	0	-0.045	-0.022	7.066	0.056	0.056	0.000	0.000	0.000	0.000
17	A	351	ALA	0	0.026	0.024	7.301	0.174	0.174	0.000	0.000	0.000	0.000
18	A	352	MET	0	-0.049	-0.018	8.347	0.093	0.093	0.000	0.000	0.000	0.000
19	A	353	LEU	0	-0.027	-0.014	7.028	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	354	VAL	0	-0.021	0.005	6.262	0.036	0.036	0.000	0.000	0.000	0.000
21	A	355	ASN	0	-0.031	-0.013	8.757	0.005	0.005	0.000	0.000	0.000	0.000
22	A	356	VAL	0	-0.041	-0.004	11.258	-0.085	-0.085	0.000	0.000	0.000	0.000
23	A	357	LYS	1	0.989	0.992	12.254	-0.101	-0.101	0.000	0.000	0.000	0.000
24	A	358	GLU	-1	-0.819	-0.924	11.500	0.232	0.232	0.000	0.000	0.000	0.000
25	A	359	SER	0	-0.096	-0.042	13.406	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	360	GLN	0	0.003	-0.014	15.203	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	361	ALA	0	0.064	0.050	10.604	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	362	LYS	1	0.953	0.956	12.587	0.006	0.006	0.000	0.000	0.000	0.000
29	A	363	GLU	-1	-0.931	-0.962	14.352	0.015	0.015	0.000	0.000	0.000	0.000
30	A	364	PHE	0	0.097	0.053	11.849	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	365	THR	0	0.001	-0.012	11.106	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	366	LYS	1	0.899	0.946	13.259	0.004	0.004	0.000	0.000	0.000	0.000
33	A	367	VAL	0	0.037	0.043	16.859	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	368	VAL	0	0.010	0.003	13.237	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	369	ARG	1	0.841	0.910	14.399	0.142	0.142	0.000	0.000	0.000	0.000
36	A	370	ASP	-1	-0.870	-0.937	16.697	-0.099	-0.099	0.000	0.000	0.000	0.000
37	A	371	LYS	1	0.805	0.910	19.799	0.018	0.018	0.000	0.000	0.000	0.000
38	A	372	LEU	0	0.000	-0.007	17.581	0.000	0.000	0.000	0.000	0.000	0.000
39	A	373	VAL	0	0.008	0.006	16.575	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	374	GLY	0	-0.027	-0.010	19.631	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	375	GLU	-1	-0.876	-0.923	23.109	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	376	LEU	0	-0.045	-0.017	19.613	0.004	0.004	0.000	0.000	0.000	0.000
43	A	377	GLY	0	0.039	0.035	22.707	0.001	0.001	0.000	0.000	0.000	0.000
44	A	378	LYS	1	0.869	0.939	21.568	0.102	0.102	0.000	0.000	0.000	0.000
45	A	379	TRP	0	-0.021	-0.010	21.168	0.007	0.007	0.000	0.000	0.000	0.000
46	A	380	PRO	0	0.052	0.056	20.522	0.009	0.009	0.000	0.000	0.000	0.000
47	A	381	THR	0	0.038	0.002	22.963	0.003	0.003	0.000	0.000	0.000	0.000
48	A	382	LEU	0	0.012	-0.004	20.585	0.002	0.002	0.000	0.000	0.000	0.000
49	A	383	LEU	0	-0.004	-0.003	22.646	0.008	0.008	0.000	0.000	0.000	0.000
50	A	384	ASP	-1	-0.847	-0.916	24.467	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	385	VAL	0	-0.001	0.001	17.802	0.003	0.003	0.000	0.000	0.000	0.000
52	A	386	ALA	0	-0.010	-0.019	20.057	0.012	0.012	0.000	0.000	0.000	0.000
53	A	387	THR	0	-0.018	-0.018	21.453	0.011	0.011	0.000	0.000	0.000	0.000
54	A	388	ALA	0	0.014	0.011	19.962	0.004	0.004	0.000	0.000	0.000	0.000
55	A	389	CYS	0	-0.054	-0.025	17.583	0.012	0.012	0.000	0.000	0.000	0.000
56	A	390	TYR	0	-0.037	-0.016	19.311	0.016	0.016	0.000	0.000	0.000	0.000
57	A	391	PHE	0	0.015	0.005	21.018	0.002	0.002	0.000	0.000	0.000	0.000
58	A	392	LEU	0	0.016	0.004	15.696	0.003	0.003	0.000	0.000	0.000	0.000
59	A	393	LYS	1	0.875	0.929	19.498	-0.091	-0.091	0.000	0.000	0.000	0.000
60	A	394	VAL	0	-0.035	-0.010	20.493	0.006	0.006	0.000	0.000	0.000	0.000
61	A	395	PHE	0	-0.032	-0.010	20.900	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	396	TYR	0	-0.083	-0.048	16.845	0.001	0.001	0.000	0.000	0.000	0.000
63	A	397	PRO	0	0.040	0.020	18.200	0.017	0.017	0.000	0.000	0.000	0.000
64	A	398	ASP	-1	-0.887	-0.944	16.976	0.186	0.186	0.000	0.000	0.000	0.000
65	A	399	VAL	0	-0.004	-0.010	13.864	0.031	0.031	0.000	0.000	0.000	0.000
66	A	400	ALA	0	-0.033	-0.022	15.807	0.007	0.007	0.000	0.000	0.000	0.000
67	A	401	ASN	0	-0.042	-0.034	16.964	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	402	ALA	0	0.027	0.040	11.778	0.022	0.022	0.000	0.000	0.000	0.000
69	A	403	GLU	-1	-0.923	-0.958	11.134	0.375	0.375	0.000	0.000	0.000	0.000
70	A	404	LEU	0	-0.060	-0.031	10.829	0.034	0.034	0.000	0.000	0.000	0.000
71	A	405	PRO	0	0.037	0.022	9.019	0.005	0.005	0.000	0.000	0.000	0.000
72	A	406	ARG	1	0.885	0.957	11.087	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	407	MET	0	0.007	0.002	14.197	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	408	LEU	0	-0.006	-0.007	17.010	0.009	0.009	0.000	0.000	0.000	0.000
75	A	409	VAL	0	-0.017	-0.013	19.556	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	410	ASP	-1	-0.813	-0.909	23.007	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	411	HIS	0	0.019	0.003	25.605	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	412	LYS	1	0.924	0.978	28.900	0.028	0.028	0.000	0.000	0.000	0.000
79	A	413	THR	0	-0.037	-0.027	26.548	0.001	0.001	0.000	0.000	0.000	0.000
80	A	414	LYS	1	0.869	0.947	27.830	0.010	0.010	0.000	0.000	0.000	0.000
81	A	415	ILE	0	0.014	0.022	22.099	0.000	0.000	0.000	0.000	0.000	0.000
82	A	416	ILE	0	-0.045	-0.026	18.904	0.006	0.006	0.000	0.000	0.000	0.000
83	A	417	HIS	0	0.065	0.029	17.700	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	418	VAL	0	-0.021	-0.003	12.051	0.023	0.023	0.000	0.000	0.000	0.000
85	A	419	VAL	0	-0.043	-0.029	12.283	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	420	ASP	-1	-0.878	-0.942	7.478	0.358	0.358	0.000	0.000	0.000	0.000
87	A	421	SER	0	0.000	-0.009	8.795	-0.061	-0.061	0.000	0.000	0.000	0.000
88	A	422	TYR	0	0.028	0.017	11.453	0.047	0.047	0.000	0.000	0.000	0.000
89	A	423	GLY	0	0.002	-0.002	14.132	0.018	0.018	0.000	0.000	0.000	0.000
90	A	424	SER	0	-0.029	-0.023	17.650	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	425	LEU	0	0.034	0.023	19.460	0.010	0.010	0.000	0.000	0.000	0.000
92	A	426	SER	0	0.019	0.018	19.081	0.007	0.007	0.000	0.000	0.000	0.000
93	A	427	THR	0	-0.007	-0.019	20.131	0.007	0.007	0.000	0.000	0.000	0.000
94	A	428	GLY	0	0.032	0.013	23.180	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	429	TYR	0	0.019	-0.002	25.328	0.001	0.001	0.000	0.000	0.000	0.000
96	A	430	HIS	0	0.011	0.009	23.797	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	431	VAL	0	-0.010	0.019	18.990	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	432	LEU	0	0.014	0.015	20.173	0.004	0.004	0.000	0.000	0.000	0.000
99	A	433	LYS	1	0.922	0.961	19.584	-0.064	-0.064	0.000	0.000	0.000	0.000
100	A	434	THR	0	-0.038	-0.015	18.414	0.002	0.002	0.000	0.000	0.000	0.000
101	A	435	ASN	0	0.055	0.017	16.355	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	436	THR	0	0.011	0.005	14.989	0.023	0.023	0.000	0.000	0.000	0.000
103	A	437	VAL	0	0.069	0.038	14.765	-0.039	-0.039	0.000	0.000	0.000	0.000
104	A	438	GLU	-1	-0.812	-0.895	17.278	0.076	0.076	0.000	0.000	0.000	0.000
105	A	439	GLN	0	-0.096	-0.051	19.825	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	440	LEU	0	0.060	0.036	17.969	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	441	ILE	0	0.028	0.014	20.756	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	442	LYS	1	0.854	0.920	23.104	-0.112	-0.112	0.000	0.000	0.000	0.000
109	A	443	PHE	0	-0.034	-0.009	24.082	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	444	THR	0	0.014	-0.005	24.115	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	445	ARG	1	0.958	0.986	26.321	-0.066	-0.066	0.000	0.000	0.000	0.000
112	A	446	CYS	0	-0.068	-0.009	28.751	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	447	ASN	0	0.070	0.008	31.267	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	448	LEU	0	-0.020	0.001	33.748	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	449	GLU	-1	-0.859	-0.941	32.928	0.013	0.013	0.000	0.000	0.000	0.000
116	A	450	SER	0	-0.026	-0.010	29.910	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	451	SER	0	0.053	0.011	31.076	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	452	LEU	0	0.010	-0.009	25.589	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	453	LYS	1	0.874	0.971	26.195	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	454	HIS	0	0.037	0.019	26.798	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	455	TYR	0	-0.092	-0.057	25.099	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	456	ARG	1	0.887	0.945	24.198	0.028	0.028	0.000	0.000	0.000	0.000
123	A	457	VAL	0	0.007	0.007	17.903	0.003	0.003	0.000	0.000	0.000	0.000
124	A	458	GLY	-1	-0.853	-0.935	17.764	-0.122	-0.122	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:335:ACE )