FMO DATABASE

FMODB ID: VQV11

Calculation Name: 2H3R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H3R

Chain ID: B

ChEMBL ID:

UniProt ID: P88989

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-454137.730915
FMO2-HF: Nuclear repulsion	419479.007365
FMO2-HF: Total energy	-34658.723551
FMO2-MP2: Total energy	-34759.092399

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:8:LYS)

Summations of interaction energy for fragment #1(B:8: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.
-65.936	-67.982	35.581	-17.573	-15.963	-0.186

Interaction energy analysis for fragmet #1(B:8:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.909 / q_NPA : 0.925

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

Sort

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	10	TYR	0	0.036	0.018	3.701	-0.493	1.195	0.005	-0.700	-0.993	0.003
4	B	11	GLU	-1	-0.789	-0.887	1.764	-121.413	-119.659	17.766	-10.153	-9.367	-0.120
5	B	12	GLU	-1	-0.828	-0.873	1.683	-108.349	-114.461	17.809	-6.462	-5.235	-0.069
6	B	13	MET	0	0.011	0.005	5.023	7.818	7.957	-0.001	-0.011	-0.127	0.000
7	B	14	VAL	0	0.007	0.008	8.006	3.664	3.664	0.000	0.000	0.000	0.000
8	B	15	LYS	1	0.835	0.885	3.085	70.538	71.023	0.002	-0.247	-0.241	0.000
9	B	16	GLU	-1	-0.825	-0.873	8.566	-25.331	-25.331	0.000	0.000	0.000	0.000
10	B	17	VAL	0	-0.004	-0.003	10.515	2.958	2.958	0.000	0.000	0.000	0.000
11	B	18	GLU	-1	-0.779	-0.883	12.182	-18.277	-18.277	0.000	0.000	0.000	0.000
12	B	19	ARG	1	0.845	0.898	8.051	31.870	31.870	0.000	0.000	0.000	0.000
13	B	20	LEU	0	0.059	0.031	13.685	1.904	1.904	0.000	0.000	0.000	0.000
14	B	21	LYS	1	0.767	0.881	15.799	20.572	20.572	0.000	0.000	0.000	0.000
15	B	22	LEU	0	-0.008	-0.005	16.036	1.357	1.357	0.000	0.000	0.000	0.000
16	B	23	GLU	-1	-0.897	-0.930	18.007	-15.554	-15.554	0.000	0.000	0.000	0.000
17	B	24	ASN	0	-0.029	-0.038	19.431	1.643	1.643	0.000	0.000	0.000	0.000
18	B	25	LYS	1	0.926	0.970	21.714	13.837	13.837	0.000	0.000	0.000	0.000
19	B	26	THR	0	-0.015	-0.017	21.978	0.844	0.844	0.000	0.000	0.000	0.000
20	B	27	LEU	0	0.009	-0.003	22.825	0.689	0.689	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.908	0.957	25.713	12.467	12.467	0.000	0.000	0.000	0.000
22	B	29	GLN	0	0.035	0.028	27.350	0.685	0.685	0.000	0.000	0.000	0.000
23	B	30	LYS	1	0.986	0.996	25.329	12.548	12.548	0.000	0.000	0.000	0.000
24	B	31	VAL	0	0.034	0.024	29.643	0.336	0.336	0.000	0.000	0.000	0.000
25	B	32	LYS	1	0.876	0.927	31.416	10.224	10.224	0.000	0.000	0.000	0.000
26	B	33	SER	0	-0.079	-0.033	32.646	0.287	0.287	0.000	0.000	0.000	0.000
27	B	34	SER	0	-0.048	-0.015	34.084	0.323	0.323	0.000	0.000	0.000	0.000
28	B	42	SER	0	0.041	0.010	36.362	0.019	0.019	0.000	0.000	0.000	0.000
29	B	43	ILE	0	-0.015	-0.011	29.914	-0.177	-0.177	0.000	0.000	0.000	0.000
30	B	44	LEU	0	0.032	0.034	30.309	-0.018	-0.018	0.000	0.000	0.000	0.000
31	B	45	THR	0	0.018	-0.006	28.767	-0.485	-0.485	0.000	0.000	0.000	0.000
32	B	46	ALA	0	0.020	0.002	25.033	0.114	0.114	0.000	0.000	0.000	0.000
33	B	47	ALA	0	0.078	0.032	26.916	0.065	0.065	0.000	0.000	0.000	0.000
34	B	48	LYS	1	0.936	0.971	29.316	9.055	9.055	0.000	0.000	0.000	0.000
35	B	49	ARG	1	0.887	0.914	23.545	12.786	12.786	0.000	0.000	0.000	0.000
36	B	50	GLU	-1	-0.770	-0.856	25.150	-11.875	-11.875	0.000	0.000	0.000	0.000
37	B	51	SER	0	-0.038	-0.008	29.496	0.324	0.324	0.000	0.000	0.000	0.000
38	B	52	ILE	0	0.015	0.006	32.920	0.297	0.297	0.000	0.000	0.000	0.000
39	B	53	ILE	0	0.047	0.027	28.411	0.236	0.236	0.000	0.000	0.000	0.000
40	B	54	VAL	0	0.017	0.018	29.650	0.146	0.146	0.000	0.000	0.000	0.000
41	B	55	SER	0	-0.028	-0.007	32.044	0.246	0.246	0.000	0.000	0.000	0.000
42	B	56	SER	0	0.023	-0.009	34.339	0.248	0.248	0.000	0.000	0.000	0.000
43	B	57	SER	0	-0.015	-0.022	31.443	0.064	0.064	0.000	0.000	0.000	0.000
44	B	58	ARG	1	0.931	0.969	32.540	9.028	9.028	0.000	0.000	0.000	0.000
45	B	59	ALA	0	0.015	0.023	36.140	0.184	0.184	0.000	0.000	0.000	0.000
46	B	60	LEU	0	0.041	0.008	34.795	0.155	0.155	0.000	0.000	0.000	0.000
47	B	61	GLY	0	0.017	0.013	36.234	0.075	0.075	0.000	0.000	0.000	0.000
48	B	62	ALA	0	0.004	-0.001	36.837	0.135	0.135	0.000	0.000	0.000	0.000
49	B	63	VAL	0	-0.021	-0.005	40.462	0.192	0.192	0.000	0.000	0.000	0.000
50	B	64	ALA	0	0.011	0.003	37.636	0.137	0.137	0.000	0.000	0.000	0.000
51	B	65	MET	0	0.019	-0.004	38.626	0.078	0.078	0.000	0.000	0.000	0.000
52	B	66	ARG	1	0.907	0.959	40.888	6.941	6.941	0.000	0.000	0.000	0.000
53	B	67	LYS	1	0.763	0.853	41.694	7.377	7.377	0.000	0.000	0.000	0.000
54	B	68	ILE	0	0.009	0.004	37.527	0.061	0.061	0.000	0.000	0.000	0.000
55	B	69	GLU	-1	-0.799	-0.875	41.969	-6.391	-6.391	0.000	0.000	0.000	0.000
56	B	70	ALA	0	-0.009	0.001	44.740	0.134	0.134	0.000	0.000	0.000	0.000
57	B	71	LYS	1	0.844	0.900	41.805	7.261	7.261	0.000	0.000	0.000	0.000
58	B	72	VAL	0	0.003	0.002	42.277	0.048	0.048	0.000	0.000	0.000	0.000
59	B	73	ARG	1	0.845	0.895	45.116	6.262	6.262	0.000	0.000	0.000	0.000
60	B	74	SER	0	-0.048	-0.017	48.669	0.099	0.099	0.000	0.000	0.000	0.000
61	B	75	ARG	1	0.890	0.931	41.813	6.960	6.960	0.000	0.000	0.000	0.000
62	B	76	ALA	0	0.029	0.016	48.209	0.030	0.030	0.000	0.000	0.000	0.000
63	B	77	ALA	0	-0.022	-0.003	49.512	0.085	0.085	0.000	0.000	0.000	0.000
64	B	78	LYS	1	0.928	0.955	52.282	5.719	5.719	0.000	0.000	0.000	0.000
65	B	79	ALA	0	-0.025	0.013	50.544	0.053	0.053	0.000	0.000	0.000	0.000
66	B	80	VAL	0	-0.004	-0.011	52.698	0.040	0.040	0.000	0.000	0.000	0.000
67	B	81	THR	0	-0.034	-0.018	53.655	0.044	0.044	0.000	0.000	0.000	0.000
68	B	82	GLU	-1	-0.876	-0.945	50.126	-5.845	-5.845	0.000	0.000	0.000	0.000
69	B	83	GLN	0	-0.003	0.007	48.473	-0.152	-0.152	0.000	0.000	0.000	0.000
70	B	84	GLU	-1	-0.812	-0.890	47.832	-5.775	-5.775	0.000	0.000	0.000	0.000
71	B	85	LEU	0	0.033	0.009	47.181	-0.119	-0.119	0.000	0.000	0.000	0.000
72	B	86	THR	0	-0.030	-0.035	43.639	-0.171	-0.171	0.000	0.000	0.000	0.000
73	B	87	SER	0	-0.041	-0.022	43.375	-0.223	-0.223	0.000	0.000	0.000	0.000
74	B	88	LEU	0	-0.048	-0.015	43.339	-0.142	-0.142	0.000	0.000	0.000	0.000
75	B	89	LEU	0	-0.012	-0.029	41.875	-0.131	-0.131	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.011	0.025	37.531	-0.178	-0.178	0.000	0.000	0.000	0.000
77	B	91	SER	0	0.007	-0.009	37.147	-0.184	-0.184	0.000	0.000	0.000	0.000
78	B	92	LEU	0	-0.030	-0.003	38.094	-0.025	-0.025	0.000	0.000	0.000	0.000
79	B	93	THR	0	-0.008	0.007	35.799	-0.184	-0.184	0.000	0.000	0.000	0.000
80	B	94	LEU	0	-0.039	-0.025	37.374	0.262	0.262	0.000	0.000	0.000	0.000
81	B	95	ARG	1	0.964	0.994	37.032	7.566	7.566	0.000	0.000	0.000	0.000
82	B	96	VAL	0	0.002	0.000	36.370	0.234	0.234	0.000	0.000	0.000	0.000
83	B	97	ASP	-1	-0.824	-0.908	37.392	-7.684	-7.684	0.000	0.000	0.000	0.000
84	B	98	VAL	0	-0.024	-0.006	37.099	0.203	0.203	0.000	0.000	0.000	0.000
85	B	99	SER	0	0.004	-0.029	38.729	-0.247	-0.247	0.000	0.000	0.000	0.000
86	B	100	MET	0	0.006	-0.008	38.105	0.051	0.051	0.000	0.000	0.000	0.000
87	B	101	GLU	-1	-0.880	-0.892	40.767	-7.195	-7.195	0.000	0.000	0.000	0.000
88	B	102	GLU	-1	-0.878	-0.916	42.992	-6.896	-6.896	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:8:LYS)