FMO DATABASE

FMODB ID: MV3JZ

Calculation Name: 3K2T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2T

Chain ID: A

ChEMBL ID:

UniProt ID: Q927Y2

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-290865.098523
FMO2-HF: Nuclear repulsion	268270.296233
FMO2-HF: Total energy	-22594.802289
FMO2-MP2: Total energy	-22660.295205

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:1:GLU)

Summations of interaction energy for fragment #1(A:1:GLU)

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.
12.433	17.137	0.408	-2.035	-3.078	0

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.960 / q_NPA : -0.988

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	3	VAL	0	-0.033	-0.005	3.818	-4.648	-3.061	-0.021	-0.808	-0.758	0.002
4	A	4	ARG	1	0.855	0.946	6.617	-23.855	-23.855	0.000	0.000	0.000	0.000
5	A	5	THR	0	0.031	0.004	10.366	0.026	0.026	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.939	0.998	12.243	-16.770	-16.770	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.014	-0.004	13.993	-0.206	-0.206	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.101	0.075	15.740	-0.378	-0.378	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.026	0.006	14.253	-0.074	-0.074	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.004	-0.024	9.431	1.235	1.235	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.732	0.836	9.491	-24.753	-24.753	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.052	0.031	11.389	0.819	0.819	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.039	-0.008	8.016	1.380	1.380	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.721	-0.864	12.875	17.174	17.174	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.047	-0.027	13.009	0.841	0.841	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.950	-0.986	13.059	19.207	19.207	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.804	-0.893	9.536	25.691	25.691	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.002	-0.007	8.317	2.441	2.441	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.008	0.000	8.878	0.997	0.997	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.002	0.016	6.514	0.500	0.500	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.015	-0.005	2.922	2.778	3.860	0.116	-0.493	-0.706	-0.006
22	A	22	MET	0	-0.066	-0.009	5.419	0.792	0.792	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.030	-0.027	8.001	-1.016	-1.016	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.047	-0.006	2.922	-1.315	-0.182	0.159	-0.325	-0.967	0.000
25	A	25	LEU	0	-0.060	-0.030	3.340	-0.206	0.687	0.155	-0.409	-0.640	0.004
26	A	26	GLY	0	-0.007	0.015	5.360	-2.003	-1.994	-0.001	0.000	-0.007	0.000
27	A	27	HIS	0	-0.040	-0.014	8.215	-2.874	-2.874	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.011	-0.020	10.714	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.003	-0.033	13.079	-0.878	-0.878	0.000	0.000	0.000	0.000
30	A	30	TYR	0	0.011	0.009	6.087	0.270	0.270	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.016	-0.009	11.674	-0.841	-0.841	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.029	-0.019	11.178	1.300	1.300	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.011	-0.001	12.967	-0.797	-0.797	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.814	-0.893	14.579	15.538	15.538	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.016	-0.012	16.267	-0.137	-0.137	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.910	-0.953	17.704	13.663	13.663	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.059	-0.055	20.826	-0.551	-0.551	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.067	-0.031	19.347	-0.138	-0.138	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.009	0.015	20.391	-0.177	-0.177	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.053	-0.034	16.922	0.770	0.770	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.062	0.038	16.650	-1.021	-1.021	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.027	-0.027	15.333	0.798	0.798	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.019	0.038	12.271	-0.844	-0.844	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.008	-0.019	14.315	0.332	0.332	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.023	0.012	14.852	-0.251	-0.251	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.886	0.960	17.147	-12.144	-12.144	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.978	0.966	20.598	-10.606	-10.606	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.901	-0.941	22.980	11.541	11.541	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.027	0.013	20.316	-0.132	-0.132	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.888	0.953	19.583	-10.657	-10.657	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.065	0.026	14.212	0.323	0.323	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.043	-0.020	18.266	-0.720	-0.720	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.001	-0.006	17.126	0.800	0.800	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.050	-0.018	19.004	-0.704	-0.704	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.865	-0.935	19.619	12.353	12.353	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.082	-0.036	21.415	-0.382	-0.382	0.000	0.000	0.000	0.000

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