FMO DATABASE

FMODB ID: 7G79K

Calculation Name: 2YAD-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: F

ChEMBL ID:

UniProt ID: P11686

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:

Apendix: None

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-474885.963241
FMO2-HF: Nuclear repulsion	444132.480312
FMO2-HF: Total energy	-30753.482929
FMO2-MP2: Total energy	-30838.644273

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(F:89:VAL)

Summations of interaction energy for fragment #1(F:89:VAL)

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.
-3.287	-0.178	2.594	-1.796	-3.906	-0.005

Interaction energy analysis for fragmet #1(F:89:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.017

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	F	91	THR	0	-0.031	-0.013	3.440	-2.292	-0.370	0.025	-0.945	-1.002	-0.001
4	F	92	ALA	0	0.018	0.011	5.116	0.296	0.380	-0.001	-0.002	-0.081	0.000
5	F	93	THR	0	-0.005	0.010	7.095	-0.096	-0.096	0.000	0.000	0.000	0.000
6	F	94	PHE	0	-0.022	-0.017	8.411	0.040	0.040	0.000	0.000	0.000	0.000
7	F	95	SER	0	0.040	0.022	13.458	-0.006	-0.006	0.000	0.000	0.000	0.000
8	F	96	ILE	0	-0.041	-0.026	16.369	-0.010	-0.010	0.000	0.000	0.000	0.000
9	F	97	GLY	0	0.015	0.017	19.217	0.004	0.004	0.000	0.000	0.000	0.000
10	F	98	SER	0	-0.006	-0.011	22.866	0.005	0.005	0.000	0.000	0.000	0.000
11	F	99	THR	0	-0.029	-0.027	23.575	0.009	0.009	0.000	0.000	0.000	0.000
12	F	100	GLY	0	0.019	0.029	20.589	0.001	0.001	0.000	0.000	0.000	0.000
13	F	101	LEU	0	-0.026	-0.015	16.483	0.011	0.011	0.000	0.000	0.000	0.000
14	F	102	VAL	0	-0.003	-0.006	11.636	-0.021	-0.021	0.000	0.000	0.000	0.000
15	F	103	VAL	0	0.007	0.008	9.401	0.036	0.036	0.000	0.000	0.000	0.000
16	F	104	TYR	0	-0.058	-0.049	6.476	-0.011	-0.011	0.000	0.000	0.000	0.000
17	F	105	ASP	-1	-0.839	-0.936	6.078	-0.980	-0.980	0.000	0.000	0.000	0.000
18	F	106	TYR	0	0.024	-0.011	2.325	-1.022	-0.315	2.572	-0.810	-2.468	-0.004
19	F	107	GLN	0	-0.024	0.005	4.431	-0.177	0.112	-0.001	-0.036	-0.252	0.000
20	F	108	GLN	0	-0.020	-0.017	5.334	0.283	0.390	-0.001	-0.003	-0.103	0.000
21	F	109	LEU	0	-0.030	-0.004	7.319	0.210	0.210	0.000	0.000	0.000	0.000
22	F	110	LEU	0	-0.044	-0.036	8.843	0.184	0.184	0.000	0.000	0.000	0.000
23	F	111	ILE	0	0.004	0.006	9.356	-0.057	-0.057	0.000	0.000	0.000	0.000
24	F	112	ALA	0	-0.007	0.003	11.662	0.033	0.033	0.000	0.000	0.000	0.000
25	F	113	TYR	0	0.002	-0.005	14.100	0.013	0.013	0.000	0.000	0.000	0.000
26	F	114	LYS	1	0.924	0.961	16.710	0.050	0.050	0.000	0.000	0.000	0.000
27	F	115	PRO	0	0.019	0.017	19.540	0.009	0.009	0.000	0.000	0.000	0.000
28	F	116	ALA	0	0.058	0.029	22.315	0.009	0.009	0.000	0.000	0.000	0.000
29	F	117	PRO	0	-0.004	-0.005	24.065	-0.005	-0.005	0.000	0.000	0.000	0.000
30	F	118	GLY	0	0.013	0.012	25.038	0.000	0.000	0.000	0.000	0.000	0.000
31	F	119	THR	0	-0.003	-0.006	24.733	-0.005	-0.005	0.000	0.000	0.000	0.000
32	F	148	CYS	0	-0.086	-0.026	23.891	0.005	0.005	0.000	0.000	0.000	0.000
33	F	121	CYS	0	-0.062	-0.046	17.196	0.002	0.002	0.000	0.000	0.000	0.000
34	F	122	TYR	0	0.039	0.026	19.098	-0.001	-0.001	0.000	0.000	0.000	0.000
35	F	123	ILE	0	-0.021	-0.017	15.171	-0.020	-0.020	0.000	0.000	0.000	0.000
36	F	124	MET	0	0.020	0.022	15.089	0.016	0.016	0.000	0.000	0.000	0.000
37	F	125	LYS	1	0.934	0.979	12.791	0.471	0.471	0.000	0.000	0.000	0.000
38	F	126	ILE	0	-0.043	-0.016	7.943	0.044	0.044	0.000	0.000	0.000	0.000
39	F	127	ALA	0	0.040	0.017	11.551	-0.055	-0.055	0.000	0.000	0.000	0.000
40	F	128	PRO	0	0.016	-0.011	9.071	-0.014	-0.014	0.000	0.000	0.000	0.000
41	F	129	GLU	-1	-0.892	-0.940	10.032	-0.625	-0.625	0.000	0.000	0.000	0.000
42	F	130	SER	0	-0.073	-0.042	11.988	0.093	0.093	0.000	0.000	0.000	0.000
43	F	131	ILE	0	0.006	0.018	6.238	0.011	0.011	0.000	0.000	0.000	0.000
44	F	132	PRO	0	-0.034	0.003	10.225	0.043	0.043	0.000	0.000	0.000	0.000
45	F	133	SER	0	0.093	0.036	11.114	-0.016	-0.016	0.000	0.000	0.000	0.000
46	F	134	LEU	0	0.092	0.040	12.578	0.003	0.003	0.000	0.000	0.000	0.000
47	F	135	GLU	-1	-0.821	-0.886	13.845	-0.088	-0.088	0.000	0.000	0.000	0.000
48	F	136	ALA	0	-0.017	0.000	15.404	0.014	0.014	0.000	0.000	0.000	0.000
49	F	137	LEU	0	-0.002	0.006	13.119	0.008	0.008	0.000	0.000	0.000	0.000
50	F	138	THR	0	0.021	-0.006	16.345	0.017	0.017	0.000	0.000	0.000	0.000
51	F	139	ARG	1	0.819	0.885	19.187	0.125	0.125	0.000	0.000	0.000	0.000
52	F	140	LYS	1	0.866	0.945	17.593	0.232	0.232	0.000	0.000	0.000	0.000
53	F	141	VAL	0	0.022	-0.009	18.778	0.003	0.003	0.000	0.000	0.000	0.000
54	F	142	HIS	0	0.014	0.023	21.377	0.008	0.008	0.000	0.000	0.000	0.000
55	F	143	ASN	0	-0.041	-0.039	23.850	0.012	0.012	0.000	0.000	0.000	0.000
56	F	144	PHE	0	-0.038	-0.034	22.266	-0.005	-0.005	0.000	0.000	0.000	0.000
57	F	145	GLN	0	-0.043	-0.004	25.069	0.000	0.000	0.000	0.000	0.000	0.000
58	F	146	MET	0	-0.080	-0.023	19.418	-0.005	-0.005	0.000	0.000	0.000	0.000
59	F	147	GLU	-1	-0.854	-0.936	23.945	-0.071	-0.071	0.000	0.000	0.000	0.000
60	F	181	LEU	0	0.012	-0.003	14.660	-0.004	-0.004	0.000	0.000	0.000	0.000
61	F	182	GLY	0	0.094	0.049	11.859	-0.066	-0.066	0.000	0.000	0.000	0.000
62	F	183	MET	0	0.007	0.006	12.624	0.026	0.026	0.000	0.000	0.000	0.000
63	F	184	ALA	0	0.048	0.037	10.269	0.016	0.016	0.000	0.000	0.000	0.000
64	F	185	VAL	0	0.055	0.019	11.127	0.012	0.012	0.000	0.000	0.000	0.000
65	F	186	SER	0	-0.024	-0.034	13.640	0.015	0.015	0.000	0.000	0.000	0.000
66	F	187	THR	0	-0.046	-0.028	15.652	0.021	0.021	0.000	0.000	0.000	0.000
67	F	188	LEU	0	-0.017	-0.001	14.764	0.006	0.006	0.000	0.000	0.000	0.000
68	F	190	GLY	0	0.040	0.043	19.218	-0.003	-0.003	0.000	0.000	0.000	0.000
69	F	191	GLU	-1	-0.974	-0.995	21.671	-0.001	-0.001	0.000	0.000	0.000	0.000
70	F	192	VAL	0	-0.038	-0.001	22.337	0.003	0.003	0.000	0.000	0.000	0.000
71	F	193	PRO	0	-0.015	0.002	23.892	-0.007	-0.007	0.000	0.000	0.000	0.000
72	F	194	LEU	0	-0.006	-0.010	19.757	-0.008	-0.008	0.000	0.000	0.000	0.000
73	F	195	TYR	0	0.011	0.004	21.833	0.004	0.004	0.000	0.000	0.000	0.000
74	F	196	TYR	0	0.025	0.015	18.100	-0.021	-0.021	0.000	0.000	0.000	0.000
75	F	197	ILE	0	-0.007	-0.006	19.398	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:89:VAL)