FMO DATABASE

FMODB ID: 43M9N

Calculation Name: 1GK6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GK6

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

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	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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-229862.151562
FMO2-HF: Nuclear repulsion	207383.063256
FMO2-HF: Total energy	-22479.088306
FMO2-MP2: Total energy	-22544.363094

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:355:MET)

Summations of interaction energy for fragment #1(A:355: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.
-18.117	-11.61	6.546	-4.422	-8.631	0.023

Interaction energy analysis for fragmet #1(A:355:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.018

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	357	GLN	0	0.015	0.003	2.397	-4.753	-0.495	2.543	-2.254	-4.548	0.007
4	A	358	LEU	0	0.005	-0.006	2.115	-9.046	-7.212	3.996	-2.077	-3.752	0.016
5	A	359	GLU	-1	-0.876	-0.934	3.845	-2.953	-2.538	0.007	-0.091	-0.331	0.000
6	A	360	ASP	-1	-0.786	-0.877	6.267	0.586	0.586	0.000	0.000	0.000	0.000
7	A	361	LYS	1	0.795	0.879	6.998	-1.509	-1.509	0.000	0.000	0.000	0.000
8	A	362	VAL	0	0.027	0.002	7.782	-0.368	-0.368	0.000	0.000	0.000	0.000
9	A	363	GLU	-1	-0.915	-0.947	9.721	0.134	0.134	0.000	0.000	0.000	0.000
10	A	364	GLU	-1	-0.800	-0.859	11.477	0.606	0.606	0.000	0.000	0.000	0.000
11	A	365	LEU	0	-0.021	-0.025	11.423	-0.108	-0.108	0.000	0.000	0.000	0.000
12	A	366	LEU	0	0.009	0.017	13.430	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	367	SER	0	-0.018	-0.017	15.627	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	368	LYS	1	0.830	0.889	15.562	-0.475	-0.475	0.000	0.000	0.000	0.000
15	A	369	ASN	0	0.009	-0.005	17.390	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	370	TYR	0	0.052	0.057	19.811	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	371	HIS	0	-0.036	-0.033	21.233	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	372	LEU	0	0.033	0.023	21.258	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	373	GLU	-1	-0.941	-0.970	23.247	0.150	0.150	0.000	0.000	0.000	0.000
20	A	374	ASN	0	-0.044	-0.027	25.563	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	375	GLU	-1	-0.945	-0.964	27.534	0.123	0.123	0.000	0.000	0.000	0.000
22	A	376	VAL	0	0.006	-0.012	27.733	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	377	ALA	0	-0.024	-0.011	30.069	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	378	ARG	1	0.952	0.976	31.965	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	379	LEU	0	0.018	0.005	31.567	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	380	LYS	1	0.974	0.992	31.351	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	381	LYS	1	0.820	0.904	36.077	-0.058	-0.058	0.000	0.000	0.000	0.000
28	A	382	LEU	0	0.002	0.006	37.147	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	383	VAL	0	0.016	0.004	37.992	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	384	GLY	0	0.015	0.012	40.251	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	385	ASP	-1	-0.842	-0.926	42.115	0.049	0.049	0.000	0.000	0.000	0.000
32	A	386	LEU	0	-0.001	-0.003	42.066	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	387	LEU	0	-0.025	-0.011	42.739	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	388	ASN	0	-0.021	-0.011	45.831	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	389	VAL	0	-0.018	-0.001	48.107	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	390	LYS	1	0.812	0.883	48.505	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	391	MET	0	0.019	0.026	50.043	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	392	ALA	0	-0.011	-0.010	52.307	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	393	LEU	0	0.024	0.004	52.463	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	394	ASP	-1	-0.814	-0.887	52.855	0.040	0.040	0.000	0.000	0.000	0.000
41	A	395	ILE	0	-0.011	-0.010	55.992	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	396	GLU	-1	-0.877	-0.889	58.522	0.027	0.027	0.000	0.000	0.000	0.000
43	A	397	ILE	0	0.005	-0.011	57.124	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	398	ALA	0	-0.008	-0.006	59.790	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	399	THR	0	-0.031	-0.024	61.630	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	400	TYR	0	-0.083	-0.066	63.022	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	401	ARG	1	0.870	0.938	60.250	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	402	LYS	1	0.820	0.893	65.876	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	403	LEU	0	-0.102	-0.062	67.689	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	404	LEU	0	-0.072	-0.037	68.421	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	405	GLU	-1	-0.925	-0.968	66.990	0.026	0.026	0.000	0.000	0.000	0.000
52	A	406	GLY	0	-0.029	0.008	70.525	0.000	0.000	0.000	0.000	0.000	0.000
53	A	407	GLU	-1	-0.910	-0.940	63.326	0.030	0.030	0.000	0.000	0.000	0.000
54	A	408	GLU	-1	-0.776	-0.856	65.829	0.025	0.025	0.000	0.000	0.000	0.000
55	A	409	SER	0	-0.070	-0.047	60.344	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:355:MET)