FMO DATABASE

FMODB ID: 5366Z

Calculation Name: 2WVR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WVR

Chain ID: B

ChEMBL ID:

UniProt ID: Q9H211

Base Structure: X-ray

Registration Date: 2023-06-20

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356248.872331
FMO2-HF: Nuclear repulsion	324962.971347
FMO2-HF: Total energy	-31285.900983
FMO2-MP2: Total energy	-31377.520098

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:86:PHE)

Summations of interaction energy for fragment #1(B:86:PHE)

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.
-5.287	-1.391	2.934	-2.657	-4.173	0.005

Interaction energy analysis for fragmet #1(B:86:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.020

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	88	LEU	0	-0.018	-0.013	3.116	-3.880	0.260	0.014	-2.007	-2.146	0.004
4	B	89	MET	0	-0.030	-0.001	1.892	-0.649	-1.044	2.921	-0.643	-1.883	0.001
5	B	90	ILE	0	-0.020	0.000	4.961	-0.029	-0.029	0.000	0.000	0.000	0.000
6	B	91	LYS	1	0.850	0.914	7.724	0.264	0.264	0.000	0.000	0.000	0.000
7	B	92	GLU	-1	-0.812	-0.885	11.094	-0.006	-0.006	0.000	0.000	0.000	0.000
8	B	93	ASN	0	-0.076	-0.057	11.208	0.024	0.024	0.000	0.000	0.000	0.000
9	B	94	PRO	0	0.036	0.032	7.292	-0.073	-0.073	0.000	0.000	0.000	0.000
10	B	95	SER	0	-0.041	-0.044	4.532	-0.346	-0.195	-0.001	-0.007	-0.144	0.000
11	B	96	SER	0	0.008	-0.002	6.579	0.110	0.110	0.000	0.000	0.000	0.000
12	B	97	GLN	0	-0.005	-0.041	6.085	-0.049	-0.049	0.000	0.000	0.000	0.000
13	B	98	TYR	0	0.089	0.066	6.183	0.048	0.048	0.000	0.000	0.000	0.000
14	B	99	TRP	0	0.044	0.016	7.608	0.108	0.108	0.000	0.000	0.000	0.000
15	B	100	LYS	1	0.936	0.981	10.591	-0.193	-0.193	0.000	0.000	0.000	0.000
16	B	101	GLU	-1	-0.938	-0.959	9.156	0.580	0.580	0.000	0.000	0.000	0.000
17	B	102	VAL	0	-0.013	-0.018	10.989	-0.025	-0.025	0.000	0.000	0.000	0.000
18	B	103	ALA	0	-0.026	-0.014	13.266	-0.040	-0.040	0.000	0.000	0.000	0.000
19	B	104	GLU	-1	-0.733	-0.809	14.931	0.221	0.221	0.000	0.000	0.000	0.000
20	B	105	LYS	1	0.944	0.963	14.216	-0.525	-0.525	0.000	0.000	0.000	0.000
21	B	106	ARG	1	0.943	0.972	16.680	-0.326	-0.326	0.000	0.000	0.000	0.000
22	B	107	ARG	1	0.893	0.929	19.215	-0.221	-0.221	0.000	0.000	0.000	0.000
23	B	108	LYS	1	0.858	0.904	17.448	-0.330	-0.330	0.000	0.000	0.000	0.000
24	B	109	ALA	0	0.021	0.010	21.078	-0.018	-0.018	0.000	0.000	0.000	0.000
25	B	110	LEU	0	0.005	-0.007	22.858	-0.015	-0.015	0.000	0.000	0.000	0.000
26	B	111	TYR	0	-0.003	0.005	24.980	-0.015	-0.015	0.000	0.000	0.000	0.000
27	B	112	GLU	-1	-0.823	-0.909	24.954	0.170	0.170	0.000	0.000	0.000	0.000
28	B	113	ALA	0	-0.014	0.006	27.019	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	114	LEU	0	0.010	-0.008	28.699	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	115	LYS	1	0.812	0.903	28.435	-0.166	-0.166	0.000	0.000	0.000	0.000
31	B	116	GLU	-1	-0.796	-0.890	30.672	0.125	0.125	0.000	0.000	0.000	0.000
32	B	117	ASN	0	0.000	-0.003	31.946	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	118	GLU	-1	-0.890	-0.923	35.087	0.080	0.080	0.000	0.000	0.000	0.000
34	B	119	LYS	1	0.799	0.894	34.416	-0.125	-0.125	0.000	0.000	0.000	0.000
35	B	120	LEU	0	0.012	0.001	35.252	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	121	HIS	0	-0.026	-0.015	38.072	-0.007	-0.007	0.000	0.000	0.000	0.000
37	B	122	LYS	1	0.897	0.941	40.116	-0.084	-0.084	0.000	0.000	0.000	0.000
38	B	123	GLU	-1	-0.857	-0.909	39.382	0.091	0.091	0.000	0.000	0.000	0.000
39	B	124	ILE	0	-0.028	-0.032	40.536	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	125	GLU	-1	-0.872	-0.920	44.058	0.061	0.061	0.000	0.000	0.000	0.000
41	B	126	GLN	0	-0.034	-0.016	45.000	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	127	LYS	1	0.836	0.889	42.161	-0.084	-0.084	0.000	0.000	0.000	0.000
43	B	128	ASP	-1	-0.869	-0.932	48.106	0.059	0.059	0.000	0.000	0.000	0.000
44	B	129	ASN	0	-0.093	-0.056	50.209	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	130	GLU	-1	-0.873	-0.906	50.542	0.053	0.053	0.000	0.000	0.000	0.000
46	B	131	ILE	0	-0.014	-0.014	49.594	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	132	ALA	0	-0.036	-0.015	53.325	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	133	ARG	1	0.868	0.912	53.282	-0.052	-0.052	0.000	0.000	0.000	0.000
49	B	134	LEU	0	0.043	0.025	54.064	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	135	LYS	1	0.910	0.957	56.262	-0.047	-0.047	0.000	0.000	0.000	0.000
51	B	136	LYS	1	0.781	0.886	58.956	-0.039	-0.039	0.000	0.000	0.000	0.000
52	B	137	GLU	-1	-0.787	-0.904	60.397	0.040	0.040	0.000	0.000	0.000	0.000
53	B	138	ASN	0	-0.035	-0.017	59.311	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	139	LYS	1	0.826	0.895	62.966	-0.032	-0.032	0.000	0.000	0.000	0.000
55	B	140	GLU	-1	-0.831	-0.906	65.337	0.034	0.034	0.000	0.000	0.000	0.000
56	B	141	LEU	0	-0.008	-0.003	64.263	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	142	ALA	0	-0.013	-0.002	66.957	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	143	GLU	-1	-0.825	-0.888	68.703	0.029	0.029	0.000	0.000	0.000	0.000
59	B	144	VAL	0	-0.048	-0.041	70.637	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	145	ALA	0	-0.084	-0.041	69.837	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	146	GLU	-1	-0.966	-0.979	71.981	0.027	0.027	0.000	0.000	0.000	0.000
62	B	147	HIS	0	-0.028	-0.014	74.406	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	148	VAL	0	0.016	-0.002	74.183	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	149	GLN	0	-0.013	0.010	77.101	0.000	0.000	0.000	0.000	0.000	0.000
65	B	150	TYR	0	0.040	0.008	79.305	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	151	MET	0	-0.040	-0.022	78.712	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	152	ALA	0	-0.011	-0.012	80.055	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	153	GLU	-1	-0.840	-0.900	82.036	0.021	0.021	0.000	0.000	0.000	0.000
69	B	154	LEU	0	-0.070	-0.026	84.826	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	155	ILE	0	-0.012	-0.024	82.480	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	156	GLU	-1	-0.942	-0.966	86.225	0.019	0.019	0.000	0.000	0.000	0.000
72	B	157	ARG	1	0.901	0.952	87.922	-0.019	-0.019	0.000	0.000	0.000	0.000
73	B	158	LEU	0	-0.087	-0.040	88.365	0.000	0.000	0.000	0.000	0.000	0.000
74	B	159	ASN	0	-0.037	0.004	89.943	-0.001	-0.001	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:86:PHE)