FMO DATABASE

FMODB ID: 53L2Z

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	OptAll
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	-230029.958196
FMO2-HF: Nuclear repulsion	207550.666514
FMO2-HF: Total energy	-22479.291682
FMO2-MP2: Total energy	-22544.482142

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.
-14.926	-9.286	4.589	-3.387	-6.844	0.006

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 : -0.031 / q_NPA : -0.022

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	0.040	0.019	2.649	-5.625	-2.400	2.580	-1.888	-3.918	-0.007
4	A	358	LEU	0	-0.015	-0.014	2.355	-6.288	-3.992	2.009	-1.456	-2.849	0.013
5	A	359	GLU	-1	-0.863	-0.934	4.724	-1.007	-0.888	0.000	-0.043	-0.077	0.000
6	A	360	ASP	-1	-0.796	-0.883	6.884	0.785	0.785	0.000	0.000	0.000	0.000
7	A	361	LYS	1	0.822	0.892	7.644	-2.113	-2.113	0.000	0.000	0.000	0.000
8	A	362	VAL	0	0.021	0.004	8.721	-0.545	-0.545	0.000	0.000	0.000	0.000
9	A	363	GLU	-1	-0.899	-0.943	10.656	0.520	0.520	0.000	0.000	0.000	0.000
10	A	364	GLU	-1	-0.816	-0.861	12.259	0.805	0.805	0.000	0.000	0.000	0.000
11	A	365	LEU	0	-0.023	-0.026	12.189	-0.203	-0.203	0.000	0.000	0.000	0.000
12	A	366	LEU	0	0.012	0.011	14.154	-0.159	-0.159	0.000	0.000	0.000	0.000
13	A	367	SER	0	-0.019	-0.016	16.471	-0.158	-0.158	0.000	0.000	0.000	0.000
14	A	368	LYS	1	0.813	0.884	15.596	-0.804	-0.804	0.000	0.000	0.000	0.000
15	A	369	ASN	0	0.003	0.002	18.193	-0.085	-0.085	0.000	0.000	0.000	0.000
16	A	370	TYR	0	0.064	0.050	20.655	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	371	HIS	0	-0.021	-0.019	21.998	-0.069	-0.069	0.000	0.000	0.000	0.000
18	A	372	LEU	0	0.028	0.020	22.063	-0.037	-0.037	0.000	0.000	0.000	0.000
19	A	373	GLU	-1	-0.947	-0.973	23.396	0.428	0.428	0.000	0.000	0.000	0.000
20	A	374	ASN	0	-0.035	-0.024	26.328	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	375	GLU	-1	-0.949	-0.968	28.166	0.251	0.251	0.000	0.000	0.000	0.000
22	A	376	VAL	0	0.016	-0.009	28.627	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	377	ALA	0	-0.023	-0.006	30.765	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	378	ARG	1	0.936	0.969	32.685	-0.186	-0.186	0.000	0.000	0.000	0.000
25	A	379	LEU	0	0.010	-0.005	32.081	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	380	LYS	1	0.958	0.979	31.868	-0.264	-0.264	0.000	0.000	0.000	0.000
27	A	381	LYS	1	0.823	0.907	36.715	-0.149	-0.149	0.000	0.000	0.000	0.000
28	A	382	LEU	0	-0.009	0.000	37.597	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	383	VAL	0	0.023	0.011	38.679	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	384	GLY	0	0.034	0.018	40.984	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	385	ASP	-1	-0.831	-0.902	42.908	0.127	0.127	0.000	0.000	0.000	0.000
32	A	386	LEU	0	0.000	-0.008	42.716	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	387	LEU	0	-0.002	0.002	43.615	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	388	ASN	0	-0.044	-0.026	46.380	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	389	VAL	0	-0.012	-0.003	48.891	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	390	LYS	1	0.804	0.883	49.251	-0.100	-0.100	0.000	0.000	0.000	0.000
37	A	391	MET	0	0.019	0.013	50.918	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	392	ALA	0	-0.013	-0.007	52.895	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	393	LEU	0	0.035	0.014	53.356	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	394	ASP	-1	-0.818	-0.890	53.296	0.089	0.089	0.000	0.000	0.000	0.000
41	A	395	ILE	0	-0.006	-0.003	56.443	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	396	GLU	-1	-0.882	-0.901	59.105	0.064	0.064	0.000	0.000	0.000	0.000
43	A	397	ILE	0	0.003	-0.007	57.783	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	398	ALA	0	0.010	0.004	60.601	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	399	THR	0	-0.049	-0.028	62.403	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	400	TYR	0	-0.086	-0.075	63.401	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	401	ARG	1	0.845	0.906	62.266	-0.064	-0.064	0.000	0.000	0.000	0.000
48	A	402	LYS	1	0.818	0.885	66.470	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	403	LEU	0	-0.074	-0.041	68.384	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	404	LEU	0	-0.062	-0.025	68.945	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	405	GLU	-1	-0.911	-0.956	67.288	0.055	0.055	0.000	0.000	0.000	0.000
52	A	406	GLY	0	-0.021	0.007	70.912	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	407	GLU	-1	-0.914	-0.938	63.774	0.064	0.064	0.000	0.000	0.000	0.000
54	A	408	GLU	-1	-0.784	-0.863	66.748	0.059	0.059	0.000	0.000	0.000	0.000
55	A	409	SER	0	-0.082	-0.043	61.271	0.002	0.002	0.000	0.000	0.000	0.000

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