FMO DATABASE

FMODB ID: R95K8

Calculation Name: 3GNA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNA

Chain ID: A

ChEMBL ID:

UniProt ID: P15919

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptH
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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-367517.990814
FMO2-HF: Nuclear repulsion	340000.291369
FMO2-HF: Total energy	-27517.699446
FMO2-MP2: Total energy	-27598.270351

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:389:GLY)

Summations of interaction energy for fragment #1(A:389:GLY)

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.
0.441	1.531	-0.016	-0.612	-0.463	0.003

Interaction energy analysis for fragmet #1(A:389:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.010

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	391	ARG	1	0.920	0.962	3.808	-0.405	0.685	-0.016	-0.612	-0.463	0.003
4	A	392	PRO	0	0.063	0.030	6.604	-0.313	-0.313	0.000	0.000	0.000	0.000
5	A	393	ARG	1	0.926	0.961	8.415	0.797	0.797	0.000	0.000	0.000	0.000
6	A	394	GLN	0	0.066	0.043	11.692	0.064	0.064	0.000	0.000	0.000	0.000
7	A	395	HIS	0	0.148	0.071	14.874	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	396	LEU	0	0.034	0.012	17.971	0.015	0.015	0.000	0.000	0.000	0.000
9	A	397	LEU	0	0.022	0.002	19.819	0.013	0.013	0.000	0.000	0.000	0.000
10	A	398	SER	0	-0.016	-0.002	19.115	0.014	0.014	0.000	0.000	0.000	0.000
11	A	399	LEU	0	-0.078	-0.021	16.162	0.008	0.008	0.000	0.000	0.000	0.000
12	A	400	THR	0	0.105	0.048	20.277	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	401	ARG	1	1.066	1.020	22.174	0.025	0.025	0.000	0.000	0.000	0.000
14	A	402	ARG	1	0.941	0.982	19.650	0.047	0.047	0.000	0.000	0.000	0.000
15	A	403	ALA	0	0.022	0.002	17.816	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	404	GLN	0	-0.026	-0.030	18.938	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	405	LYS	1	0.963	0.977	21.123	0.054	0.054	0.000	0.000	0.000	0.000
18	A	406	HIS	0	-0.041	-0.020	14.827	0.018	0.018	0.000	0.000	0.000	0.000
19	A	407	ARG	1	0.885	0.923	14.607	0.267	0.267	0.000	0.000	0.000	0.000
20	A	408	LEU	0	0.027	0.024	18.076	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	409	ARG	1	0.921	0.977	20.111	0.173	0.173	0.000	0.000	0.000	0.000
22	A	410	GLU	-1	-0.849	-0.939	19.187	-0.206	-0.206	0.000	0.000	0.000	0.000
23	A	411	LEU	0	0.038	0.031	22.111	0.009	0.009	0.000	0.000	0.000	0.000
24	A	412	LYS	1	0.904	0.939	24.010	0.111	0.111	0.000	0.000	0.000	0.000
25	A	413	ILE	0	-0.010	0.004	24.134	0.014	0.014	0.000	0.000	0.000	0.000
26	A	414	GLN	0	0.063	0.035	24.881	0.005	0.005	0.000	0.000	0.000	0.000
27	A	415	VAL	0	-0.016	-0.003	27.902	0.008	0.008	0.000	0.000	0.000	0.000
28	A	416	LYS	1	0.771	0.886	29.890	0.083	0.083	0.000	0.000	0.000	0.000
29	A	417	GLU	-1	-0.899	-0.974	29.041	-0.116	-0.116	0.000	0.000	0.000	0.000
30	A	418	PHE	0	-0.008	0.009	32.088	0.003	0.003	0.000	0.000	0.000	0.000
31	A	419	ALA	0	0.048	0.014	33.881	0.005	0.005	0.000	0.000	0.000	0.000
32	A	420	ASP	-1	-0.871	-0.921	35.301	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	421	LYS	1	0.868	0.929	33.110	0.100	0.100	0.000	0.000	0.000	0.000
34	A	422	GLU	-1	-0.923	-0.957	37.397	-0.072	-0.072	0.000	0.000	0.000	0.000
35	A	423	GLU	-1	-0.939	-0.959	38.248	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	424	GLY	0	-0.014	-0.001	40.376	0.003	0.003	0.000	0.000	0.000	0.000
37	A	425	GLY	0	-0.011	-0.022	37.741	0.002	0.002	0.000	0.000	0.000	0.000
38	A	426	ASP	-1	-0.888	-0.934	38.214	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	427	VAL	0	-0.020	-0.031	32.449	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	428	LYS	1	0.928	0.974	35.028	0.044	0.044	0.000	0.000	0.000	0.000
41	A	429	ALA	0	0.074	0.050	36.637	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	430	VAL	0	0.068	0.051	33.557	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	431	CYS	0	-0.090	-0.065	31.682	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	432	LEU	0	-0.011	0.002	33.430	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	433	THR	0	0.045	0.010	36.163	0.001	0.001	0.000	0.000	0.000	0.000
46	A	434	LEU	0	-0.029	-0.010	30.463	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	435	PHE	0	-0.044	-0.014	31.074	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	436	LEU	0	0.049	0.019	33.217	0.000	0.000	0.000	0.000	0.000	0.000
49	A	437	LEU	0	0.015	-0.004	35.896	0.002	0.002	0.000	0.000	0.000	0.000
50	A	438	ALA	0	-0.047	-0.019	31.027	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	439	LEU	0	-0.030	-0.011	33.110	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	440	ARG	1	0.859	0.925	34.845	0.053	0.053	0.000	0.000	0.000	0.000
53	A	441	ALA	0	-0.028	0.007	34.075	0.002	0.002	0.000	0.000	0.000	0.000
54	A	442	ARG	1	0.844	0.931	28.006	0.094	0.094	0.000	0.000	0.000	0.000
55	A	443	ASN	0	-0.029	-0.021	34.762	0.005	0.005	0.000	0.000	0.000	0.000
56	A	444	GLU	-1	-0.901	-0.955	33.169	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	445	HIS	0	0.017	-0.004	37.689	0.001	0.001	0.000	0.000	0.000	0.000
58	A	446	ARG	1	0.995	1.000	41.066	0.036	0.036	0.000	0.000	0.000	0.000
59	A	447	GLN	0	0.034	0.018	34.605	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	448	ALA	0	-0.004	-0.001	38.559	0.000	0.000	0.000	0.000	0.000	0.000
61	A	449	ASP	-1	-0.837	-0.928	39.528	-0.043	-0.043	0.000	0.000	0.000	0.000
62	A	450	GLU	-1	-0.963	-0.979	40.765	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	451	LEU	0	-0.063	-0.033	36.274	0.001	0.001	0.000	0.000	0.000	0.000
64	A	452	GLU	-1	-0.895	-0.967	40.147	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	453	ALA	0	-0.014	0.011	42.984	0.002	0.002	0.000	0.000	0.000	0.000
66	A	454	ILE	0	-0.087	-0.043	39.585	0.002	0.002	0.000	0.000	0.000	0.000
67	A	455	MET	0	-0.121	-0.058	39.188	0.001	0.001	0.000	0.000	0.000	0.000
68	A	456	GLN	0	0.019	0.026	43.120	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:389:GLY)