FMO DATABASE

FMODB ID: YV9K2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-453812.106298
FMO2-HF: Nuclear repulsion	419153.841296
FMO2-HF: Total energy	-34658.265002
FMO2-MP2: Total energy	-34758.688462

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.
-26.844	-21.901	21.228	-14.124	-12.043	-0.122

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 : 0.951 / q_NPA : 0.956

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	10	TYR	0	0.037	0.018	3.287	-1.428	1.085	0.056	-1.114	-1.454	0.009
4	B	11	GLU	-1	-0.848	-0.932	2.411	-71.137	-65.854	3.955	-4.761	-4.477	-0.041
5	B	12	GLU	-1	-0.826	-0.890	1.690	-110.512	-113.800	17.219	-8.122	-5.808	-0.090
6	B	13	MET	0	0.016	0.017	5.135	7.160	7.298	-0.001	-0.009	-0.127	0.000
7	B	14	VAL	0	0.007	0.005	7.269	3.431	3.431	0.000	0.000	0.000	0.000
8	B	15	LYS	1	0.854	0.920	3.383	65.106	65.403	-0.001	-0.118	-0.177	0.000
9	B	16	GLU	-1	-0.844	-0.901	8.760	-25.591	-25.591	0.000	0.000	0.000	0.000
10	B	17	VAL	0	-0.017	-0.012	10.373	2.862	2.862	0.000	0.000	0.000	0.000
11	B	18	GLU	-1	-0.814	-0.900	12.462	-17.179	-17.179	0.000	0.000	0.000	0.000
12	B	19	ARG	1	0.874	0.922	7.720	32.385	32.385	0.000	0.000	0.000	0.000
13	B	20	LEU	0	0.057	0.023	13.676	1.850	1.850	0.000	0.000	0.000	0.000
14	B	21	LYS	1	0.794	0.902	15.989	19.714	19.714	0.000	0.000	0.000	0.000
15	B	22	LEU	0	-0.038	-0.016	16.069	1.296	1.296	0.000	0.000	0.000	0.000
16	B	23	GLU	-1	-0.917	-0.956	17.883	-15.775	-15.775	0.000	0.000	0.000	0.000
17	B	24	ASN	0	-0.030	-0.041	19.115	1.658	1.658	0.000	0.000	0.000	0.000
18	B	25	LYS	1	0.949	0.990	21.713	13.562	13.562	0.000	0.000	0.000	0.000
19	B	26	THR	0	0.011	0.003	22.239	0.837	0.837	0.000	0.000	0.000	0.000
20	B	27	LEU	0	0.017	0.005	22.474	0.693	0.693	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.900	0.948	25.547	12.411	12.411	0.000	0.000	0.000	0.000
22	B	29	GLN	0	0.009	0.005	27.334	0.596	0.596	0.000	0.000	0.000	0.000
23	B	30	LYS	1	0.974	0.973	25.620	12.372	12.372	0.000	0.000	0.000	0.000
24	B	31	VAL	0	0.016	0.012	29.628	0.313	0.313	0.000	0.000	0.000	0.000
25	B	32	LYS	1	0.878	0.946	31.207	10.171	10.171	0.000	0.000	0.000	0.000
26	B	33	SER	0	-0.073	-0.014	33.250	0.323	0.323	0.000	0.000	0.000	0.000
27	B	34	SER	0	-0.007	0.004	34.704	0.124	0.124	0.000	0.000	0.000	0.000
28	B	42	SER	0	0.034	0.006	36.396	0.013	0.013	0.000	0.000	0.000	0.000
29	B	43	ILE	0	-0.019	-0.007	29.956	-0.161	-0.161	0.000	0.000	0.000	0.000
30	B	44	LEU	0	0.043	0.036	30.097	0.091	0.091	0.000	0.000	0.000	0.000
31	B	45	THR	0	0.013	-0.010	29.233	-0.471	-0.471	0.000	0.000	0.000	0.000
32	B	46	ALA	0	0.016	-0.004	24.886	0.077	0.077	0.000	0.000	0.000	0.000
33	B	47	ALA	0	0.078	0.030	26.737	0.031	0.031	0.000	0.000	0.000	0.000
34	B	48	LYS	1	0.964	0.998	28.665	8.906	8.906	0.000	0.000	0.000	0.000
35	B	49	ARG	1	0.937	0.946	24.191	12.258	12.258	0.000	0.000	0.000	0.000
36	B	50	GLU	-1	-0.854	-0.914	25.796	-11.518	-11.518	0.000	0.000	0.000	0.000
37	B	51	SER	0	-0.014	0.000	28.807	0.262	0.262	0.000	0.000	0.000	0.000
38	B	52	ILE	0	0.025	0.006	32.417	0.252	0.252	0.000	0.000	0.000	0.000
39	B	53	ILE	0	0.043	0.035	28.357	0.230	0.230	0.000	0.000	0.000	0.000
40	B	54	VAL	0	0.029	0.033	29.454	0.178	0.178	0.000	0.000	0.000	0.000
41	B	55	SER	0	-0.039	-0.010	31.929	0.256	0.256	0.000	0.000	0.000	0.000
42	B	56	SER	0	0.015	-0.027	34.405	0.228	0.228	0.000	0.000	0.000	0.000
43	B	57	SER	0	-0.023	-0.032	31.517	0.074	0.074	0.000	0.000	0.000	0.000
44	B	58	ARG	1	0.938	0.977	32.745	8.857	8.857	0.000	0.000	0.000	0.000
45	B	59	ALA	0	0.003	0.024	35.883	0.181	0.181	0.000	0.000	0.000	0.000
46	B	60	LEU	0	0.052	0.012	34.825	0.145	0.145	0.000	0.000	0.000	0.000
47	B	61	GLY	0	0.017	0.010	36.130	0.076	0.076	0.000	0.000	0.000	0.000
48	B	62	ALA	0	0.012	-0.003	36.702	0.140	0.140	0.000	0.000	0.000	0.000
49	B	63	VAL	0	-0.033	-0.004	40.034	0.217	0.217	0.000	0.000	0.000	0.000
50	B	64	ALA	0	0.030	0.004	37.411	0.145	0.145	0.000	0.000	0.000	0.000
51	B	65	MET	0	-0.016	-0.026	38.208	0.029	0.029	0.000	0.000	0.000	0.000
52	B	66	ARG	1	0.957	0.996	40.449	6.885	6.885	0.000	0.000	0.000	0.000
53	B	67	LYS	1	0.774	0.854	41.673	7.370	7.370	0.000	0.000	0.000	0.000
54	B	68	ILE	0	0.017	0.017	37.614	0.081	0.081	0.000	0.000	0.000	0.000
55	B	69	GLU	-1	-0.810	-0.880	42.148	-6.340	-6.340	0.000	0.000	0.000	0.000
56	B	70	ALA	0	-0.016	-0.007	44.810	0.144	0.144	0.000	0.000	0.000	0.000
57	B	71	LYS	1	0.891	0.925	42.198	7.206	7.206	0.000	0.000	0.000	0.000
58	B	72	VAL	0	0.015	0.006	42.399	0.061	0.061	0.000	0.000	0.000	0.000
59	B	73	ARG	1	0.873	0.911	45.312	6.214	6.214	0.000	0.000	0.000	0.000
60	B	74	SER	0	-0.053	-0.010	48.826	0.091	0.091	0.000	0.000	0.000	0.000
61	B	75	ARG	1	0.864	0.924	42.289	6.954	6.954	0.000	0.000	0.000	0.000
62	B	76	ALA	0	0.010	0.015	48.447	-0.012	-0.012	0.000	0.000	0.000	0.000
63	B	77	ALA	0	0.001	0.008	49.908	0.093	0.093	0.000	0.000	0.000	0.000
64	B	78	LYS	1	0.907	0.940	53.060	5.699	5.699	0.000	0.000	0.000	0.000
65	B	79	ALA	0	-0.021	0.010	50.696	0.037	0.037	0.000	0.000	0.000	0.000
66	B	80	VAL	0	0.008	-0.001	52.783	0.040	0.040	0.000	0.000	0.000	0.000
67	B	81	THR	0	-0.020	-0.001	53.684	0.030	0.030	0.000	0.000	0.000	0.000
68	B	82	GLU	-1	-0.867	-0.948	50.380	-5.826	-5.826	0.000	0.000	0.000	0.000
69	B	83	GLN	0	-0.008	0.003	48.849	-0.159	-0.159	0.000	0.000	0.000	0.000
70	B	84	GLU	-1	-0.840	-0.914	48.254	-5.776	-5.776	0.000	0.000	0.000	0.000
71	B	85	LEU	0	0.041	0.009	47.011	-0.106	-0.106	0.000	0.000	0.000	0.000
72	B	86	THR	0	-0.017	-0.017	43.895	-0.176	-0.176	0.000	0.000	0.000	0.000
73	B	87	SER	0	-0.047	-0.030	43.677	-0.211	-0.211	0.000	0.000	0.000	0.000
74	B	88	LEU	0	-0.033	-0.009	43.418	-0.166	-0.166	0.000	0.000	0.000	0.000
75	B	89	LEU	0	-0.043	-0.038	41.986	-0.137	-0.137	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.017	0.029	38.073	-0.234	-0.234	0.000	0.000	0.000	0.000
77	B	91	SER	0	0.028	-0.007	37.094	-0.167	-0.167	0.000	0.000	0.000	0.000
78	B	92	LEU	0	-0.037	0.008	38.232	-0.062	-0.062	0.000	0.000	0.000	0.000
79	B	93	THR	0	0.007	-0.001	36.156	-0.247	-0.247	0.000	0.000	0.000	0.000
80	B	94	LEU	0	-0.050	-0.036	37.691	0.260	0.260	0.000	0.000	0.000	0.000
81	B	95	ARG	1	0.975	0.997	37.394	7.646	7.646	0.000	0.000	0.000	0.000
82	B	96	VAL	0	-0.026	-0.026	36.694	0.256	0.256	0.000	0.000	0.000	0.000
83	B	97	ASP	-1	-0.863	-0.913	37.366	-7.894	-7.894	0.000	0.000	0.000	0.000
84	B	98	VAL	0	-0.030	-0.010	36.625	0.206	0.206	0.000	0.000	0.000	0.000
85	B	99	SER	0	0.007	-0.014	38.164	-0.277	-0.277	0.000	0.000	0.000	0.000
86	B	100	MET	0	0.002	-0.016	37.637	0.065	0.065	0.000	0.000	0.000	0.000
87	B	101	GLU	-1	-0.908	-0.923	40.345	-7.213	-7.213	0.000	0.000	0.000	0.000
88	B	102	GLU	-1	-0.889	-0.920	42.534	-6.917	-6.917	0.000	0.000	0.000	0.000

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