FMO DATABASE

FMODB ID: VRNG1

Calculation Name: 2E6X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2E6X

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIT3

Base Structure: X-ray

Registration Date: 2023-03-13

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-413587.294563
FMO2-HF: Nuclear repulsion	384942.269529
FMO2-HF: Total energy	-28645.025034
FMO2-MP2: Total energy	-28728.01557

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-1.177	3.939	2.917	-2.401	-5.631	-0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.020

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	3	LYS	1	0.848	0.903	2.244	-0.873	1.807	1.608	-1.432	-2.855	-0.004
4	A	4	ASP	-1	-0.833	-0.900	2.295	-4.381	-2.412	1.305	-0.869	-2.404	-0.005
5	A	5	LEU	0	0.013	0.005	3.880	1.166	1.633	0.004	-0.100	-0.372	0.000
6	A	6	LEU	0	0.006	-0.002	6.042	0.780	0.780	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.794	-0.876	6.680	-1.522	-1.522	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.753	0.871	6.408	3.000	3.000	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.039	-0.010	10.099	0.245	0.245	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.021	-0.006	11.957	0.159	0.159	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.053	-0.019	11.493	0.076	0.076	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.010	-0.009	9.907	-0.211	-0.211	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.009	0.006	8.129	0.116	0.116	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.059	-0.015	10.737	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.052	0.010	8.351	0.090	0.090	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.783	0.859	13.068	0.182	0.182	0.000	0.000	0.000	0.000
17	A	17	MET	0	-0.003	-0.004	14.339	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.042	0.027	17.376	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.868	0.943	20.662	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.045	0.039	23.461	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.921	-0.989	25.666	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.975	-0.976	29.061	0.026	0.026	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.922	-0.960	26.501	0.057	0.057	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.852	-0.900	27.204	0.091	0.091	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.005	-0.005	22.621	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.035	-0.009	16.675	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.010	0.001	19.786	0.006	0.006	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.012	-0.014	13.013	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.824	0.901	16.396	0.036	0.036	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.001	-0.022	11.467	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.086	0.052	13.991	0.039	0.039	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.044	0.033	13.449	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.034	0.006	14.239	0.054	0.054	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.002	0.010	15.761	0.034	0.034	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.050	0.029	18.225	0.030	0.030	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.046	-0.046	17.994	0.024	0.024	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.035	-0.027	19.711	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.925	0.959	22.265	0.132	0.132	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.006	-0.006	16.050	0.021	0.021	0.000	0.000	0.000	0.000
40	A	40	ARG	0	0.036	0.047	19.204	0.009	0.009	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.872	-0.920	24.810	-0.086	-0.086	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.012	0.011	22.251	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.018	0.003	26.175	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.871	0.941	25.715	0.042	0.042	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.007	0.023	20.739	0.005	0.005	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.007	0.004	24.498	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.028	-0.014	22.612	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.001	0.010	20.244	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	PRO	0	-0.003	-0.004	21.814	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.860	-0.945	17.530	0.209	0.209	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.039	0.017	19.537	0.014	0.014	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.913	-0.964	22.056	0.090	0.090	0.000	0.000	0.000	0.000
53	A	53	MET	0	0.027	0.010	15.865	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.941	0.982	17.950	-0.224	-0.224	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.760	0.851	18.965	-0.097	-0.097	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.006	0.010	20.717	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.001	-0.006	15.058	0.004	0.004	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.067	-0.038	18.379	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.856	-0.907	20.209	0.130	0.130	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.002	0.000	20.305	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.822	0.915	21.365	-0.123	-0.123	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.002	-0.010	16.449	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.881	0.944	19.755	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.004	-0.006	14.211	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.809	-0.898	17.282	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	TRP	0	-0.008	-0.003	13.448	-0.034	-0.034	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.058	-0.030	17.925	0.017	0.017	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.872	-0.929	19.080	-0.146	-0.146	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.988	-1.001	19.664	-0.184	-0.184	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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