FMO DATABASE

FMODB ID: GNZK1

Calculation Name: 2I3S-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3S

Chain ID: B

ChEMBL ID:

UniProt ID: P41695

Base Structure: X-ray

Registration Date: 2023-06-19

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-145430.406065
FMO2-HF: Nuclear repulsion	130305.939136
FMO2-HF: Total energy	-15124.466929
FMO2-MP2: Total energy	-15168.777643

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(B:315:LYS)

Summations of interaction energy for fragment #1(B:315:LYS)

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.
-71.12	-66.6	1.239	-2.716	-3.043	-0.022

Interaction energy analysis for fragmet #1(B:315:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 0.992

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	B	317	GLU	-1	-0.950	-0.983	2.485	-56.870	-52.405	1.240	-2.713	-2.992	-0.022
4	B	318	ARG	1	0.879	0.922	5.200	28.767	28.822	-0.001	-0.003	-0.051	0.000
5	B	319	ILE	0	0.109	0.065	8.616	0.101	0.101	0.000	0.000	0.000	0.000
6	B	320	VAL	0	-0.057	-0.023	11.447	1.089	1.089	0.000	0.000	0.000	0.000
7	B	321	PHE	0	0.055	0.020	13.474	1.179	1.179	0.000	0.000	0.000	0.000
8	B	322	ASN	0	-0.011	-0.002	16.070	-1.111	-1.111	0.000	0.000	0.000	0.000
9	B	323	PHE	0	0.103	0.036	14.816	0.387	0.387	0.000	0.000	0.000	0.000
10	B	324	ASN	0	-0.018	-0.009	19.507	0.778	0.778	0.000	0.000	0.000	0.000
11	B	325	LEU	0	-0.049	-0.025	22.252	0.558	0.558	0.000	0.000	0.000	0.000
12	B	326	ILE	0	-0.025	0.007	19.239	0.234	0.234	0.000	0.000	0.000	0.000
13	B	327	TYR	0	-0.058	-0.057	20.117	-0.131	-0.131	0.000	0.000	0.000	0.000
14	B	328	PRO	0	-0.059	-0.014	24.673	-0.060	-0.060	0.000	0.000	0.000	0.000
15	B	329	GLU	-1	-0.980	-0.997	26.711	-9.807	-9.807	0.000	0.000	0.000	0.000
16	B	330	ASN	0	-0.128	-0.069	24.401	-0.165	-0.165	0.000	0.000	0.000	0.000
17	B	331	ASP	-1	-0.833	-0.905	27.197	-10.506	-10.506	0.000	0.000	0.000	0.000
18	B	332	GLU	-1	-0.958	-0.989	28.729	-9.532	-9.532	0.000	0.000	0.000	0.000
19	B	333	GLU	-1	-0.920	-0.937	23.407	-13.638	-13.638	0.000	0.000	0.000	0.000
20	B	334	PHE	0	-0.015	0.009	25.825	0.285	0.285	0.000	0.000	0.000	0.000
21	B	335	ASN	0	0.001	-0.037	24.678	-0.370	-0.370	0.000	0.000	0.000	0.000
22	B	336	THR	0	-0.018	-0.020	22.540	0.088	0.088	0.000	0.000	0.000	0.000
23	B	337	GLU	-1	-0.873	-0.930	24.849	-12.225	-12.225	0.000	0.000	0.000	0.000
24	B	338	GLU	-1	-0.787	-0.862	28.479	-10.337	-10.337	0.000	0.000	0.000	0.000
25	B	339	ILE	0	0.048	0.026	24.054	0.292	0.292	0.000	0.000	0.000	0.000
26	B	340	LEU	0	-0.063	-0.031	27.991	0.328	0.328	0.000	0.000	0.000	0.000
27	B	341	ALA	0	-0.002	-0.011	29.395	0.356	0.356	0.000	0.000	0.000	0.000
28	B	342	MET	0	-0.031	-0.010	30.547	0.321	0.321	0.000	0.000	0.000	0.000
29	B	343	ILE	0	-0.034	-0.009	27.154	0.252	0.252	0.000	0.000	0.000	0.000
30	B	344	LYS	1	0.868	0.931	31.791	9.962	9.962	0.000	0.000	0.000	0.000
31	B	345	GLY	0	-0.001	0.012	34.842	0.287	0.287	0.000	0.000	0.000	0.000
32	B	346	LEU	0	-0.069	-0.046	36.209	0.275	0.275	0.000	0.000	0.000	0.000
33	B	347	TYR	0	-0.041	-0.030	32.457	0.199	0.199	0.000	0.000	0.000	0.000
34	B	348	LYS	1	0.923	0.968	35.867	7.714	7.714	0.000	0.000	0.000	0.000
35	B	349	VAL	0	0.045	0.021	38.997	0.168	0.168	0.000	0.000	0.000	0.000
36	B	350	GLN	0	-0.011	-0.003	41.773	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:315:LYS)