FMO DATABASE

FMODB ID: Q12MY

Calculation Name: 3RNV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1075764.466172
FMO2-HF: Nuclear repulsion	1026233.35731
FMO2-HF: Total energy	-49531.108863
FMO2-MP2: Total energy	-49674.412892

3D Structure Molmil

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.
0.796	2.475	-0.02	-0.791	-0.869	0.003

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 : -0.018 / q_NPA : -0.024

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	-0.021	-0.018	3.826	-0.041	1.638	-0.020	-0.791	-0.869	0.003
4	A	339	ALA	0	0.030	0.010	6.566	0.074	0.074	0.000	0.000	0.000	0.000
5	A	340	LYS	1	0.966	0.978	9.489	-0.140	-0.140	0.000	0.000	0.000	0.000
6	A	341	GLU	-1	-0.884	-0.948	12.439	0.219	0.219	0.000	0.000	0.000	0.000
7	A	342	GLY	0	0.030	0.008	16.113	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	343	TYR	0	-0.005	-0.026	12.740	-0.036	-0.036	0.000	0.000	0.000	0.000
9	A	344	CYS	0	0.000	0.010	11.225	-0.043	-0.043	0.000	0.000	0.000	0.000
10	A	345	TYR	0	-0.004	-0.017	11.574	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	346	ILE	0	0.013	0.010	8.552	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	347	ASN	0	0.010	-0.006	7.382	-0.578	-0.578	0.000	0.000	0.000	0.000
13	A	348	ILE	0	0.012	0.018	8.562	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	349	PHE	0	0.039	-0.007	10.874	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	350	LEU	0	-0.039	-0.021	4.890	0.078	0.078	0.000	0.000	0.000	0.000
16	A	351	ALA	0	0.024	0.022	6.512	-0.264	-0.264	0.000	0.000	0.000	0.000
17	A	352	MET	0	-0.043	-0.015	7.851	0.089	0.089	0.000	0.000	0.000	0.000
18	A	353	LEU	0	-0.028	-0.015	6.051	0.074	0.074	0.000	0.000	0.000	0.000
19	A	354	VAL	0	-0.018	0.006	7.119	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	355	ASN	0	-0.027	-0.012	9.602	0.090	0.090	0.000	0.000	0.000	0.000
21	A	356	VAL	0	-0.040	-0.003	11.406	0.060	0.060	0.000	0.000	0.000	0.000
22	A	357	LYS	1	0.987	0.992	13.006	0.256	0.256	0.000	0.000	0.000	0.000
23	A	358	GLU	-1	-0.820	-0.924	12.499	-0.717	-0.717	0.000	0.000	0.000	0.000
24	A	359	SER	0	-0.094	-0.042	14.207	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	360	GLN	0	0.003	-0.014	15.409	0.027	0.027	0.000	0.000	0.000	0.000
26	A	361	ALA	0	0.068	0.051	10.056	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	362	LYS	1	0.949	0.955	11.297	0.674	0.674	0.000	0.000	0.000	0.000
28	A	363	GLU	-1	-0.931	-0.963	12.648	-0.358	-0.358	0.000	0.000	0.000	0.000
29	A	364	PHE	0	0.100	0.054	10.760	0.027	0.027	0.000	0.000	0.000	0.000
30	A	365	THR	0	-0.002	-0.014	8.512	-0.060	-0.060	0.000	0.000	0.000	0.000
31	A	366	LYS	1	0.900	0.947	10.996	0.505	0.505	0.000	0.000	0.000	0.000
32	A	367	VAL	0	0.040	0.045	14.177	0.060	0.060	0.000	0.000	0.000	0.000
33	A	368	VAL	0	0.019	0.005	10.905	0.056	0.056	0.000	0.000	0.000	0.000
34	A	369	ARG	1	0.827	0.904	10.637	0.596	0.596	0.000	0.000	0.000	0.000
35	A	370	ASP	-1	-0.868	-0.936	13.256	-0.287	-0.287	0.000	0.000	0.000	0.000
36	A	371	LYS	1	0.811	0.914	16.853	0.212	0.212	0.000	0.000	0.000	0.000
37	A	372	LEU	0	0.003	-0.005	15.785	0.029	0.029	0.000	0.000	0.000	0.000
38	A	373	VAL	0	0.001	0.001	12.866	0.038	0.038	0.000	0.000	0.000	0.000
39	A	374	GLY	0	-0.028	-0.011	16.239	0.040	0.040	0.000	0.000	0.000	0.000
40	A	375	GLU	-1	-0.868	-0.918	19.418	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	376	LEU	0	-0.043	-0.016	17.196	0.017	0.017	0.000	0.000	0.000	0.000
42	A	377	GLY	0	0.042	0.037	19.231	0.026	0.026	0.000	0.000	0.000	0.000
43	A	378	LYS	1	0.874	0.940	18.181	-0.128	-0.128	0.000	0.000	0.000	0.000
44	A	379	TRP	0	-0.029	-0.016	18.784	0.003	0.003	0.000	0.000	0.000	0.000
45	A	380	PRO	0	0.060	0.060	18.285	0.002	0.002	0.000	0.000	0.000	0.000
46	A	381	THR	0	0.040	0.003	21.233	0.017	0.017	0.000	0.000	0.000	0.000
47	A	382	LEU	0	0.007	-0.007	19.787	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	383	LEU	0	0.002	0.001	21.600	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	384	ASP	-1	-0.844	-0.915	22.873	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	385	VAL	0	-0.009	-0.004	16.614	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	386	ALA	0	-0.010	-0.019	18.753	-0.031	-0.031	0.000	0.000	0.000	0.000
52	A	387	THR	0	-0.014	-0.016	20.431	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	388	ALA	0	0.012	0.009	18.352	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	389	CYS	0	-0.057	-0.026	16.551	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	390	TYR	0	-0.030	-0.014	18.147	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	391	PHE	0	0.015	0.006	19.766	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	392	LEU	0	0.018	0.005	14.581	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	393	LYS	1	0.871	0.926	18.591	0.097	0.097	0.000	0.000	0.000	0.000
59	A	394	VAL	0	-0.031	-0.009	19.942	0.004	0.004	0.000	0.000	0.000	0.000
60	A	395	PHE	0	-0.028	-0.008	20.247	0.009	0.009	0.000	0.000	0.000	0.000
61	A	396	TYR	0	-0.085	-0.048	16.712	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	397	PRO	0	0.040	0.020	18.053	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	398	ASP	-1	-0.882	-0.942	17.448	-0.210	-0.210	0.000	0.000	0.000	0.000
64	A	399	VAL	0	-0.001	-0.010	13.709	0.011	0.011	0.000	0.000	0.000	0.000
65	A	400	ALA	0	-0.038	-0.024	15.652	0.024	0.024	0.000	0.000	0.000	0.000
66	A	401	ASN	0	-0.040	-0.034	17.516	0.011	0.011	0.000	0.000	0.000	0.000
67	A	402	ALA	0	0.026	0.041	11.920	0.032	0.032	0.000	0.000	0.000	0.000
68	A	403	GLU	-1	-0.923	-0.958	12.276	0.220	0.220	0.000	0.000	0.000	0.000
69	A	404	LEU	0	-0.058	-0.031	11.288	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	405	PRO	0	0.038	0.022	8.982	0.059	0.059	0.000	0.000	0.000	0.000
71	A	406	ARG	1	0.888	0.958	11.486	-0.631	-0.631	0.000	0.000	0.000	0.000
72	A	407	MET	0	0.002	-0.002	14.557	0.000	0.000	0.000	0.000	0.000	0.000
73	A	408	LEU	0	-0.002	-0.004	17.089	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	409	VAL	0	-0.019	-0.015	19.375	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	410	ASP	-1	-0.815	-0.910	22.620	0.177	0.177	0.000	0.000	0.000	0.000
76	A	411	HIS	0	0.025	0.004	24.710	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	412	LYS	1	0.930	0.982	27.956	-0.136	-0.136	0.000	0.000	0.000	0.000
78	A	413	THR	0	-0.034	-0.026	24.954	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	414	LYS	1	0.877	0.952	26.763	-0.091	-0.091	0.000	0.000	0.000	0.000
80	A	415	ILE	0	0.011	0.019	20.580	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	416	ILE	0	-0.021	-0.012	18.308	0.014	0.014	0.000	0.000	0.000	0.000
82	A	417	HIS	0	0.029	-0.002	16.291	0.005	0.005	0.000	0.000	0.000	0.000
83	A	418	VAL	0	-0.007	0.003	11.404	0.013	0.013	0.000	0.000	0.000	0.000
84	A	419	VAL	0	-0.049	-0.032	11.367	0.059	0.059	0.000	0.000	0.000	0.000
85	A	420	ASP	-1	-0.869	-0.936	7.726	1.279	1.279	0.000	0.000	0.000	0.000
86	A	421	SER	0	0.000	-0.009	8.988	0.336	0.336	0.000	0.000	0.000	0.000
87	A	422	TYR	0	0.035	0.022	11.607	-0.130	-0.130	0.000	0.000	0.000	0.000
88	A	423	GLY	0	0.005	0.000	14.744	-0.088	-0.088	0.000	0.000	0.000	0.000
89	A	424	SER	0	-0.034	-0.027	17.747	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	425	LEU	0	0.038	0.025	19.603	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	426	SER	0	0.018	0.018	19.985	0.019	0.019	0.000	0.000	0.000	0.000
92	A	427	THR	0	-0.003	-0.018	21.371	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	428	GLY	0	0.036	0.016	24.320	0.005	0.005	0.000	0.000	0.000	0.000
94	A	429	TYR	0	0.021	0.000	26.025	0.004	0.004	0.000	0.000	0.000	0.000
95	A	430	HIS	0	0.014	0.010	23.722	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	431	VAL	0	-0.015	0.015	19.664	0.023	0.023	0.000	0.000	0.000	0.000
97	A	432	LEU	0	0.015	0.015	20.272	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	433	LYS	1	0.922	0.961	20.020	-0.133	-0.133	0.000	0.000	0.000	0.000
99	A	434	THR	0	-0.035	-0.014	18.506	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	435	ASN	0	0.057	0.017	17.064	0.023	0.023	0.000	0.000	0.000	0.000
101	A	436	THR	0	0.014	0.007	15.701	0.006	0.006	0.000	0.000	0.000	0.000
102	A	437	VAL	0	0.068	0.038	14.627	0.013	0.013	0.000	0.000	0.000	0.000
103	A	438	GLU	-1	-0.814	-0.896	17.125	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	439	GLN	0	-0.090	-0.049	20.049	0.022	0.022	0.000	0.000	0.000	0.000
105	A	440	LEU	0	0.058	0.036	17.437	0.010	0.010	0.000	0.000	0.000	0.000
106	A	441	ILE	0	0.030	0.013	20.062	0.005	0.005	0.000	0.000	0.000	0.000
107	A	442	LYS	1	0.852	0.920	22.671	0.014	0.014	0.000	0.000	0.000	0.000
108	A	443	PHE	0	-0.034	-0.009	23.923	0.004	0.004	0.000	0.000	0.000	0.000
109	A	444	THR	0	0.013	-0.006	23.424	0.007	0.007	0.000	0.000	0.000	0.000
110	A	445	ARG	1	0.958	0.987	25.788	0.031	0.031	0.000	0.000	0.000	0.000
111	A	446	CYS	0	-0.066	-0.009	28.169	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	447	ASN	0	0.072	0.009	30.898	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	448	LEU	0	-0.017	0.003	33.484	0.002	0.002	0.000	0.000	0.000	0.000
114	A	449	GLU	-1	-0.858	-0.941	32.432	0.008	0.008	0.000	0.000	0.000	0.000
115	A	450	SER	0	-0.023	-0.008	29.479	0.007	0.007	0.000	0.000	0.000	0.000
116	A	451	SER	0	0.064	0.016	30.438	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	452	LEU	0	-0.007	-0.018	25.290	0.001	0.001	0.000	0.000	0.000	0.000
118	A	453	LYS	1	0.879	0.973	25.530	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	454	HIS	0	0.039	0.021	25.810	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	455	TYR	0	-0.093	-0.057	24.099	0.000	0.000	0.000	0.000	0.000	0.000
121	A	456	ARG	1	0.895	0.951	22.303	-0.079	-0.079	0.000	0.000	0.000	0.000
122	A	457	VAL	0	0.024	0.020	16.567	0.023	0.023	0.000	0.000	0.000	0.000
123	A	458	GLY	0	-0.005	0.004	15.583	-0.012	-0.012	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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