FMO DATABASE

FMODB ID: R95Z8

Calculation Name: 3RK3-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RK3

Chain ID: E

ChEMBL ID:

UniProt ID: O14810

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-196330.302613
FMO2-HF: Nuclear repulsion	176248.810004
FMO2-HF: Total energy	-20081.492609
FMO2-MP2: Total energy	-20140.346652

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(E:24:GLY)

Summations of interaction energy for fragment #1(E:24: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.
-6.446	-3.607	0.131	-1.482	-1.487	0.007

Interaction energy analysis for fragmet #1(E:24:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.005

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	E	26	LYS	1	0.941	0.957	3.275	-5.547	-2.777	0.132	-1.480	-1.421	0.007
4	E	27	LEU	0	0.080	0.057	5.792	-0.503	-0.434	-0.001	-0.002	-0.066	0.000
5	E	28	PRO	0	0.038	0.025	8.269	-0.161	-0.161	0.000	0.000	0.000	0.000
6	E	29	ASP	-1	-0.828	-0.933	11.223	0.761	0.761	0.000	0.000	0.000	0.000
7	E	30	ALA	0	-0.039	-0.015	12.764	-0.068	-0.068	0.000	0.000	0.000	0.000
8	E	31	ALA	0	0.034	0.020	14.543	-0.046	-0.046	0.000	0.000	0.000	0.000
9	E	32	LYS	1	0.883	0.940	12.872	-0.722	-0.722	0.000	0.000	0.000	0.000
10	E	33	LYS	1	0.997	1.005	13.555	-0.427	-0.427	0.000	0.000	0.000	0.000
11	E	34	PHE	0	-0.016	-0.002	18.926	-0.029	-0.029	0.000	0.000	0.000	0.000
12	E	35	GLU	-1	-0.939	-0.967	20.403	0.169	0.169	0.000	0.000	0.000	0.000
13	E	36	GLU	-1	-0.914	-0.969	20.304	0.248	0.248	0.000	0.000	0.000	0.000
14	E	37	ALA	0	-0.016	-0.008	23.185	-0.015	-0.015	0.000	0.000	0.000	0.000
15	E	38	GLN	0	-0.030	-0.013	24.723	-0.020	-0.020	0.000	0.000	0.000	0.000
16	E	39	GLU	-1	-0.821	-0.907	26.106	0.094	0.094	0.000	0.000	0.000	0.000
17	E	40	ALA	0	-0.012	0.003	27.638	-0.009	-0.009	0.000	0.000	0.000	0.000
18	E	41	LEU	0	-0.041	-0.027	28.401	-0.010	-0.010	0.000	0.000	0.000	0.000
19	E	42	ARG	1	0.858	0.920	28.814	-0.093	-0.093	0.000	0.000	0.000	0.000
20	E	43	GLN	0	0.026	0.013	29.574	-0.007	-0.007	0.000	0.000	0.000	0.000
21	E	44	ALA	0	-0.028	-0.012	33.626	-0.005	-0.005	0.000	0.000	0.000	0.000
22	E	45	GLU	-1	-0.813	-0.884	35.506	0.031	0.031	0.000	0.000	0.000	0.000
23	E	46	GLU	-1	-0.976	-0.975	35.570	0.057	0.057	0.000	0.000	0.000	0.000
24	E	47	GLU	-1	-0.824	-0.919	36.104	0.067	0.067	0.000	0.000	0.000	0.000
25	E	48	ARG	1	0.827	0.909	38.604	-0.041	-0.041	0.000	0.000	0.000	0.000
26	E	49	LYS	1	0.867	0.910	39.151	-0.041	-0.041	0.000	0.000	0.000	0.000
27	E	50	ALA	0	0.028	0.016	42.547	-0.002	-0.002	0.000	0.000	0.000	0.000
28	E	51	LYS	1	0.849	0.913	39.324	-0.059	-0.059	0.000	0.000	0.000	0.000
29	E	52	TYR	0	-0.022	-0.026	45.327	-0.002	-0.002	0.000	0.000	0.000	0.000
30	E	53	ALA	0	0.002	-0.004	47.250	-0.002	-0.002	0.000	0.000	0.000	0.000
31	E	54	LYS	1	0.938	0.985	47.141	-0.046	-0.046	0.000	0.000	0.000	0.000
32	E	55	MET	0	0.043	0.023	48.924	-0.001	-0.001	0.000	0.000	0.000	0.000
33	E	56	GLU	-1	-0.794	-0.851	51.669	0.021	0.021	0.000	0.000	0.000	0.000
34	E	57	ALA	0	0.037	0.015	53.484	-0.001	-0.001	0.000	0.000	0.000	0.000
35	E	58	GLU	-1	-0.909	-0.963	52.136	0.033	0.033	0.000	0.000	0.000	0.000
36	E	59	ARG	1	0.883	0.913	54.235	-0.025	-0.025	0.000	0.000	0.000	0.000
37	E	60	GLU	-1	-0.840	-0.912	57.566	0.018	0.018	0.000	0.000	0.000	0.000
38	E	61	ALA	0	0.017	0.014	59.058	-0.001	-0.001	0.000	0.000	0.000	0.000
39	E	62	VAL	0	-0.027	-0.008	59.339	-0.001	-0.001	0.000	0.000	0.000	0.000
40	E	63	ARG	1	0.783	0.890	57.438	-0.022	-0.022	0.000	0.000	0.000	0.000
41	E	64	GLN	0	0.006	-0.003	63.549	-0.001	-0.001	0.000	0.000	0.000	0.000
42	E	65	GLY	0	0.039	0.025	64.533	-0.001	-0.001	0.000	0.000	0.000	0.000
43	E	66	ILE	0	-0.066	-0.049	65.584	-0.001	-0.001	0.000	0.000	0.000	0.000
44	E	67	ARG	1	0.821	0.901	64.964	-0.019	-0.019	0.000	0.000	0.000	0.000
45	E	68	ASP	-1	-0.836	-0.912	68.932	0.018	0.018	0.000	0.000	0.000	0.000
46	E	69	LYS	1	0.837	0.933	69.552	-0.019	-0.019	0.000	0.000	0.000	0.000
47	E	70	TYR	0	-0.009	-0.011	70.415	0.000	0.000	0.000	0.000	0.000	0.000
48	E	71	GLY	0	0.015	0.021	74.017	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	72	ILE	0	-0.031	-0.008	72.182	-0.001	-0.001	0.000	0.000	0.000	0.000
50	E	73	LYS	1	0.962	0.980	71.936	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:24:GLY)