FMO DATABASE

FMODB ID: 2N4ZR

Calculation Name: 2H8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8U

Chain ID: A

ChEMBL ID:

UniProt ID: P83346

Base Structure: X-ray

Registration Date: 2023-09-22

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-355546.261511
FMO2-HF: Nuclear repulsion	328600.059969
FMO2-HF: Total energy	-26946.201542
FMO2-MP2: Total energy	-27018.594112

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:ARG)

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

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.
-1.933	6.818	47.201	-23.019	-32.932	-0.207

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.919

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	CYS	0	-0.023	-0.004	2.724	-7.785	-5.324	6.872	-3.167	-6.166	-0.004
4	A	4	LEU	0	-0.029	-0.007	4.657	3.892	3.937	-0.001	-0.014	-0.030	0.000
5	A	5	ILE	0	-0.032	-0.024	8.285	-0.668	-0.668	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.957	0.971	10.729	17.207	17.207	0.000	0.000	0.000	0.000
7	A	7	TYR	0	0.045	0.003	12.406	-0.887	-0.887	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.031	-0.015	14.514	0.932	0.932	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.023	-0.002	17.237	-0.179	-0.179	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.040	0.036	19.592	0.247	0.247	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.009	0.011	18.785	0.063	0.063	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.802	-0.868	11.876	-24.852	-24.852	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.006	-0.006	12.998	1.238	1.238	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.007	-0.005	7.956	-1.135	-1.135	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.953	0.993	6.453	30.480	30.480	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.040	0.008	4.134	-5.367	-5.169	-0.001	-0.044	-0.153	0.000
17	A	17	CYS	0	-0.134	-0.036	2.364	-0.013	0.359	4.518	-1.512	-3.378	0.002
18	A	18	PRO	0	0.033	0.024	4.446	0.279	0.389	-0.001	-0.020	-0.089	0.000
19	A	19	SER	0	0.055	0.012	5.410	-3.795	-3.795	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.064	0.038	6.537	1.537	1.537	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.043	-0.031	4.906	-2.033	-2.033	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.072	0.023	2.238	-11.428	-6.998	2.692	-3.064	-4.058	-0.019
23	A	23	LEU	0	0.001	0.024	1.795	-41.950	-45.090	16.381	-6.365	-6.876	-0.091
24	A	25	LEU	0	0.008	-0.002	4.279	2.639	2.741	0.000	-0.033	-0.068	0.000
25	A	26	LYS	1	0.810	0.903	8.099	20.337	20.337	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.836	0.909	11.051	16.466	16.466	0.000	0.000	0.000	0.000
27	A	28	TRP	0	-0.007	-0.007	14.467	-0.450	-0.450	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.888	-0.945	18.192	-12.874	-12.874	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.024	-0.011	21.773	0.068	0.068	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.022	0.003	24.707	0.228	0.228	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.008	0.017	24.611	0.767	0.767	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.008	0.006	27.501	-0.054	-0.054	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.024	-0.014	27.398	0.274	0.274	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.005	0.000	25.708	0.005	0.005	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.945	0.976	21.145	13.262	13.262	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.825	-0.919	19.941	-13.106	-13.106	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.058	-0.024	14.686	-0.660	-0.660	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.969	0.997	12.994	18.061	18.061	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.880	0.938	10.000	20.174	20.174	0.000	0.000	0.000	0.000
40	A	41	GLY	0	-0.012	-0.015	8.120	1.759	1.759	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.002	0.001	4.889	4.872	4.872	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.037	0.018	5.407	-5.036	-5.036	0.000	0.000	0.000	0.000
43	A	45	THR	0	0.006	0.004	7.843	-1.239	-1.239	0.000	0.000	0.000	0.000
44	A	46	CYS	0	-0.011	-0.013	8.157	-0.680	-0.680	0.000	0.000	0.000	0.000
45	A	47	PRO	0	0.017	0.019	10.890	1.322	1.322	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.960	0.974	13.856	14.269	14.269	0.000	0.000	0.000	0.000
47	A	49	PRO	0	0.032	0.007	17.208	0.136	0.136	0.000	0.000	0.000	0.000
48	A	50	TRP	0	-0.024	-0.015	19.019	0.530	0.530	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.957	0.959	21.987	10.679	10.679	0.000	0.000	0.000	0.000
50	A	52	ASN	0	0.055	0.043	24.299	0.254	0.254	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.768	-0.869	18.804	-15.647	-15.647	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.003	0.006	16.661	0.026	0.026	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.018	-0.020	12.877	-0.705	-0.705	0.000	0.000	0.000	0.000
54	A	56	GLN	0	0.061	0.037	10.404	1.633	1.633	0.000	0.000	0.000	0.000
55	A	58	CYS	0	-0.042	0.009	4.810	4.782	5.006	-0.001	-0.015	-0.208	0.000
56	A	59	ALA	0	0.079	0.032	3.116	-6.914	-5.860	0.118	-0.330	-0.842	0.002
57	A	60	LYS	1	0.964	0.976	2.967	31.447	33.724	1.566	-1.116	-2.727	-0.005
58	A	61	ASP	-1	-0.739	-0.886	1.768	-103.479	-103.094	15.040	-7.375	-8.049	-0.091
59	A	62	LYS	1	0.803	0.876	3.526	34.458	34.691	0.018	0.036	-0.288	-0.001
60	A	64	ASN	0	-0.017	-0.003	6.239	1.342	1.342	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.011	0.009	7.922	3.338	3.338	0.000	0.000	0.000	0.000

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