FMO DATABASE

FMODB ID: YY8G2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-356268.494227
FMO2-HF: Nuclear repulsion	324982.086372
FMO2-HF: Total energy	-31286.407855
FMO2-MP2: Total energy	-31377.933337

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.
-7.25	-2.796	2.672	-2.572	-4.552	0.004

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 : 0.036 / q_NPA : -0.005

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	88	LEU	0	-0.039	-0.018	3.248	-3.757	-0.702	0.065	-1.346	-1.774	0.006
4	B	89	MET	0	-0.029	-0.007	2.209	-2.012	-0.830	2.608	-1.204	-2.585	-0.002
5	B	90	ILE	0	-0.047	-0.004	4.868	-0.182	0.035	-0.001	-0.022	-0.193	0.000
6	B	91	LYS	1	0.849	0.905	7.782	0.381	0.381	0.000	0.000	0.000	0.000
7	B	92	GLU	-1	-0.797	-0.871	11.099	-0.096	-0.096	0.000	0.000	0.000	0.000
8	B	93	ASN	0	-0.066	-0.055	11.296	0.026	0.026	0.000	0.000	0.000	0.000
9	B	94	PRO	0	0.045	0.040	7.256	-0.066	-0.066	0.000	0.000	0.000	0.000
10	B	95	SER	0	-0.016	-0.044	4.992	-0.350	-0.350	0.000	0.000	0.000	0.000
11	B	96	SER	0	0.006	-0.013	6.979	0.065	0.065	0.000	0.000	0.000	0.000
12	B	97	GLN	0	0.014	-0.007	5.569	-0.105	-0.105	0.000	0.000	0.000	0.000
13	B	98	TYR	0	0.048	0.043	6.316	0.030	0.030	0.000	0.000	0.000	0.000
14	B	99	TRP	0	0.001	-0.004	7.841	0.027	0.027	0.000	0.000	0.000	0.000
15	B	100	LYS	1	0.853	0.927	10.425	-0.385	-0.385	0.000	0.000	0.000	0.000
16	B	101	GLU	-1	-0.812	-0.901	9.414	0.479	0.479	0.000	0.000	0.000	0.000
17	B	102	VAL	0	-0.026	-0.009	10.936	-0.024	-0.024	0.000	0.000	0.000	0.000
18	B	103	ALA	0	-0.008	-0.002	13.230	-0.046	-0.046	0.000	0.000	0.000	0.000
19	B	104	GLU	-1	-0.740	-0.819	14.883	0.243	0.243	0.000	0.000	0.000	0.000
20	B	105	LYS	1	0.917	0.952	13.995	-0.578	-0.578	0.000	0.000	0.000	0.000
21	B	106	ARG	1	0.958	0.978	16.652	-0.346	-0.346	0.000	0.000	0.000	0.000
22	B	107	ARG	1	0.881	0.915	19.163	-0.241	-0.241	0.000	0.000	0.000	0.000
23	B	108	LYS	1	0.856	0.906	17.424	-0.351	-0.351	0.000	0.000	0.000	0.000
24	B	109	ALA	0	0.015	0.006	20.852	-0.018	-0.018	0.000	0.000	0.000	0.000
25	B	110	LEU	0	0.016	0.011	22.603	-0.016	-0.016	0.000	0.000	0.000	0.000
26	B	111	TYR	0	0.003	0.009	24.822	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	112	GLU	-1	-0.804	-0.892	24.842	0.179	0.179	0.000	0.000	0.000	0.000
28	B	113	ALA	0	0.018	0.017	26.723	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	114	LEU	0	-0.010	-0.006	28.516	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	115	LYS	1	0.819	0.901	28.202	-0.178	-0.178	0.000	0.000	0.000	0.000
31	B	116	GLU	-1	-0.800	-0.899	30.957	0.128	0.128	0.000	0.000	0.000	0.000
32	B	117	ASN	0	-0.044	-0.035	31.737	-0.014	-0.014	0.000	0.000	0.000	0.000
33	B	118	GLU	-1	-0.885	-0.927	34.727	0.087	0.087	0.000	0.000	0.000	0.000
34	B	119	LYS	1	0.789	0.898	35.070	-0.128	-0.128	0.000	0.000	0.000	0.000
35	B	120	LEU	0	-0.008	-0.011	34.875	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	121	HIS	0	-0.001	-0.007	37.671	-0.007	-0.007	0.000	0.000	0.000	0.000
37	B	122	LYS	1	0.904	0.948	39.763	-0.091	-0.091	0.000	0.000	0.000	0.000
38	B	123	GLU	-1	-0.847	-0.916	39.189	0.097	0.097	0.000	0.000	0.000	0.000
39	B	124	ILE	0	-0.027	-0.013	40.725	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	125	GLU	-1	-0.893	-0.936	44.210	0.064	0.064	0.000	0.000	0.000	0.000
41	B	126	GLN	0	-0.036	-0.016	44.756	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	127	LYS	1	0.840	0.902	41.945	-0.089	-0.089	0.000	0.000	0.000	0.000
43	B	128	ASP	-1	-0.864	-0.940	47.984	0.061	0.061	0.000	0.000	0.000	0.000
44	B	129	ASN	0	-0.073	-0.046	50.244	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	130	GLU	-1	-0.863	-0.907	50.775	0.055	0.055	0.000	0.000	0.000	0.000
46	B	131	ILE	0	-0.010	-0.010	49.458	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	132	ALA	0	-0.037	-0.020	53.451	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	133	ARG	1	0.849	0.921	53.685	-0.055	-0.055	0.000	0.000	0.000	0.000
49	B	134	LEU	0	0.038	0.015	53.847	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	135	LYS	1	0.922	0.965	56.795	-0.047	-0.047	0.000	0.000	0.000	0.000
51	B	136	LYS	1	0.781	0.889	59.128	-0.041	-0.041	0.000	0.000	0.000	0.000
52	B	137	GLU	-1	-0.808	-0.921	60.591	0.041	0.041	0.000	0.000	0.000	0.000
53	B	138	ASN	0	-0.036	-0.020	58.807	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	139	LYS	1	0.778	0.879	62.849	-0.033	-0.033	0.000	0.000	0.000	0.000
55	B	140	GLU	-1	-0.838	-0.911	65.502	0.035	0.035	0.000	0.000	0.000	0.000
56	B	141	LEU	0	0.010	-0.003	64.022	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	142	ALA	0	-0.016	-0.003	66.983	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	143	GLU	-1	-0.799	-0.876	68.680	0.030	0.030	0.000	0.000	0.000	0.000
59	B	144	VAL	0	-0.037	-0.020	70.831	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	145	ALA	0	-0.041	-0.020	69.964	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	146	GLU	-1	-0.949	-0.981	72.079	0.027	0.027	0.000	0.000	0.000	0.000
62	B	147	HIS	0	-0.029	-0.013	74.523	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	148	VAL	0	-0.021	-0.005	74.267	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	149	GLN	0	-0.022	-0.021	77.056	0.000	0.000	0.000	0.000	0.000	0.000
65	B	150	TYR	0	0.047	0.020	79.495	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	151	MET	0	-0.021	-0.020	79.069	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	152	ALA	0	-0.003	0.004	80.255	0.000	0.000	0.000	0.000	0.000	0.000
68	B	153	GLU	-1	-0.835	-0.907	82.245	0.021	0.021	0.000	0.000	0.000	0.000
69	B	154	LEU	0	-0.099	-0.047	84.926	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	155	ILE	0	-0.014	-0.017	82.313	0.000	0.000	0.000	0.000	0.000	0.000
71	B	156	GLU	-1	-0.956	-0.971	86.261	0.020	0.020	0.000	0.000	0.000	0.000
72	B	157	ARG	1	0.905	0.953	87.690	-0.020	-0.020	0.000	0.000	0.000	0.000
73	B	158	LEU	0	-0.066	-0.029	88.419	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	159	ASN	0	-0.053	-0.005	89.819	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:86:PHE)