FMO DATABASE

FMODB ID: K3193

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

Total energy (hartree)

FMO2-HF: Electronic energy	-229769.970698
FMO2-HF: Nuclear repulsion	207291.329599
FMO2-HF: Total energy	-22478.641099
FMO2-MP2: Total energy	-22543.914259

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.
-17.499	-11.176	7.062	-4.465	-8.921	0.026

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 : 0.008 / q_NPA : -0.009

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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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	0.004	-0.005	2.157	-4.583	-0.740	3.346	-2.326	-4.863	0.010
4	A	358	LEU	0	0.013	-0.002	2.017	-8.848	-6.816	3.709	-2.061	-3.681	0.016
5	A	359	GLU	-1	-0.911	-0.944	3.808	-2.770	-2.322	0.007	-0.078	-0.377	0.000
6	A	360	ASP	-1	-0.810	-0.907	6.213	0.609	0.609	0.000	0.000	0.000	0.000
7	A	361	LYS	1	0.774	0.880	6.957	-1.537	-1.537	0.000	0.000	0.000	0.000
8	A	362	VAL	0	0.018	-0.003	7.685	-0.365	-0.365	0.000	0.000	0.000	0.000
9	A	363	GLU	-1	-0.923	-0.949	9.680	0.200	0.200	0.000	0.000	0.000	0.000
10	A	364	GLU	-1	-0.798	-0.885	11.438	0.587	0.587	0.000	0.000	0.000	0.000
11	A	365	LEU	0	-0.032	-0.034	11.388	-0.110	-0.110	0.000	0.000	0.000	0.000
12	A	366	LEU	0	0.008	0.018	13.384	-0.083	-0.083	0.000	0.000	0.000	0.000
13	A	367	SER	0	0.000	0.002	15.582	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	368	LYS	1	0.842	0.903	15.659	-0.449	-0.449	0.000	0.000	0.000	0.000
15	A	369	ASN	0	0.011	-0.005	17.286	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	370	TYR	0	0.043	0.051	19.770	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	371	HIS	0	-0.027	-0.027	21.191	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	372	LEU	0	0.028	0.018	21.139	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	373	GLU	-1	-0.937	-0.965	23.173	0.146	0.146	0.000	0.000	0.000	0.000
20	A	374	ASN	0	-0.038	-0.025	25.686	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	375	GLU	-1	-0.958	-0.971	27.496	0.117	0.117	0.000	0.000	0.000	0.000
22	A	376	VAL	0	0.005	-0.006	27.662	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	377	ALA	0	-0.027	-0.014	30.031	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	378	ARG	1	0.947	0.971	31.925	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	379	LEU	0	0.028	0.009	31.595	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	380	LYS	1	0.979	0.991	31.722	-0.101	-0.101	0.000	0.000	0.000	0.000
27	A	381	LYS	1	0.894	0.958	36.044	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	382	LEU	0	-0.017	-0.007	37.426	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	383	VAL	0	0.015	0.008	37.912	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	384	GLY	0	0.001	0.005	40.220	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	385	ASP	-1	-0.880	-0.957	42.085	0.049	0.049	0.000	0.000	0.000	0.000
32	A	386	LEU	0	-0.016	-0.012	42.080	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	387	LEU	0	-0.032	-0.012	42.735	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	388	ASN	0	-0.007	-0.007	45.959	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	389	VAL	0	-0.020	-0.002	48.074	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	390	LYS	1	0.862	0.908	48.606	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	391	MET	0	0.001	0.014	49.725	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	392	ALA	0	-0.001	-0.005	52.277	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	393	LEU	0	0.017	0.000	52.507	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	394	ASP	-1	-0.831	-0.895	53.013	0.038	0.038	0.000	0.000	0.000	0.000
41	A	395	ILE	0	-0.029	-0.019	56.018	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	396	GLU	-1	-0.878	-0.891	58.491	0.026	0.026	0.000	0.000	0.000	0.000
43	A	397	ILE	0	0.002	-0.008	57.069	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	398	ALA	0	-0.015	-0.015	59.834	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	399	THR	0	-0.035	-0.027	61.603	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	400	TYR	0	-0.082	-0.060	63.013	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	401	ARG	1	0.961	0.991	59.251	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	402	LYS	1	0.937	0.985	65.635	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	403	LEU	0	-0.101	-0.064	67.663	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	404	LEU	0	-0.085	-0.041	68.442	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	405	GLU	-1	-0.941	-0.974	66.764	0.025	0.025	0.000	0.000	0.000	0.000
52	A	406	GLY	0	-0.033	0.004	70.501	0.000	0.000	0.000	0.000	0.000	0.000
53	A	407	GLU	-1	-0.944	-0.978	64.296	0.028	0.028	0.000	0.000	0.000	0.000
54	A	408	GLU	-1	-0.945	-0.977	65.779	0.023	0.023	0.000	0.000	0.000	0.000
55	A	409	SER	0	-0.037	-0.016	60.301	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)