FMO DATABASE

FMODB ID: J3G59

Calculation Name: 2YAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: A

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	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-472395.305907
FMO2-HF: Nuclear repulsion	441645.067245
FMO2-HF: Total energy	-30750.238662
FMO2-MP2: Total energy	-30835.269178

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(A:90:THR)

Summations of interaction energy for fragment #1(A:90:THR)

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.
-4.063	2.019	2.9	-3.722	-5.259	0.003

Interaction energy analysis for fragmet #1(A:90:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.027

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	A	92	ALA	0	0.019	0.016	3.867	-0.856	2.382	-0.007	-1.803	-1.429	0.005
4	A	93	THR	0	0.000	0.012	5.947	-0.131	-0.131	0.000	0.000	0.000	0.000
5	A	94	PHE	0	-0.027	-0.015	8.085	0.002	0.002	0.000	0.000	0.000	0.000
6	A	95	SER	0	0.052	0.025	12.576	0.031	0.031	0.000	0.000	0.000	0.000
7	A	96	ILE	0	-0.038	-0.024	16.102	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	97	GLY	0	0.008	0.006	18.707	0.021	0.021	0.000	0.000	0.000	0.000
9	A	98	SER	0	0.005	-0.002	21.684	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	99	THR	0	-0.037	-0.030	22.659	0.013	0.013	0.000	0.000	0.000	0.000
11	A	100	GLY	0	0.021	0.035	20.023	0.011	0.011	0.000	0.000	0.000	0.000
12	A	101	LEU	0	-0.021	-0.013	15.582	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	102	VAL	0	-0.007	-0.005	11.568	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	103	VAL	0	0.009	0.007	8.626	0.034	0.034	0.000	0.000	0.000	0.000
15	A	104	TYR	0	-0.054	-0.050	6.728	0.028	0.028	0.000	0.000	0.000	0.000
16	A	105	ASP	-1	-0.836	-0.934	4.546	-3.087	-2.998	-0.001	-0.023	-0.064	0.000
17	A	106	TYR	0	0.011	-0.019	2.402	-0.676	0.975	0.845	-0.649	-1.847	0.002
18	A	107	GLN	0	-0.044	-0.003	1.977	-1.358	-0.485	2.046	-1.189	-1.730	-0.003
19	A	108	GLN	0	0.027	0.002	3.613	0.846	1.077	0.017	-0.058	-0.189	-0.001
20	A	109	LEU	0	-0.010	-0.003	6.423	0.397	0.397	0.000	0.000	0.000	0.000
21	A	110	LEU	0	-0.032	-0.009	8.155	0.375	0.375	0.000	0.000	0.000	0.000
22	A	111	ILE	0	0.003	0.006	9.121	-0.263	-0.263	0.000	0.000	0.000	0.000
23	A	112	ALA	0	0.011	0.009	11.766	0.121	0.121	0.000	0.000	0.000	0.000
24	A	113	TYR	0	0.002	-0.003	13.664	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	114	LYS	1	0.919	0.957	16.583	0.067	0.067	0.000	0.000	0.000	0.000
26	A	115	PRO	0	0.011	0.017	19.137	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	116	ALA	0	0.054	0.022	21.877	0.007	0.007	0.000	0.000	0.000	0.000
28	A	117	PRO	0	-0.009	-0.007	22.911	0.002	0.002	0.000	0.000	0.000	0.000
29	A	118	GLY	0	0.025	0.017	23.742	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	119	THR	0	0.003	-0.006	24.142	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	120	CYS	0	-0.088	-0.031	22.770	0.013	0.013	0.000	0.000	0.000	0.000
32	A	121	CYS	0	-0.066	-0.047	15.480	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	122	TYR	0	0.039	0.024	18.669	0.010	0.010	0.000	0.000	0.000	0.000
34	A	123	ILE	0	-0.010	-0.001	13.700	-0.053	-0.053	0.000	0.000	0.000	0.000
35	A	124	MET	0	-0.019	-0.009	14.535	0.049	0.049	0.000	0.000	0.000	0.000
36	A	125	LYS	1	0.897	0.945	10.981	0.510	0.510	0.000	0.000	0.000	0.000
37	A	126	ILE	0	-0.028	-0.013	8.687	0.038	0.038	0.000	0.000	0.000	0.000
38	A	127	ALA	0	0.029	0.015	12.078	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	128	PRO	0	0.006	-0.016	10.145	-0.085	-0.085	0.000	0.000	0.000	0.000
40	A	129	DGL	-1	-0.946	-0.962	11.297	-0.469	-0.469	0.000	0.000	0.000	0.000
41	A	130	SER	0	-0.025	-0.022	13.758	0.055	0.055	0.000	0.000	0.000	0.000
42	A	131	ILE	0	-0.011	0.013	8.036	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	132	PRO	0	0.010	0.016	12.237	0.051	0.051	0.000	0.000	0.000	0.000
44	A	133	SER	0	0.075	0.030	12.449	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	134	LEU	0	0.091	0.038	12.849	0.025	0.025	0.000	0.000	0.000	0.000
46	A	135	GLU	-1	-0.864	-0.910	14.354	-0.267	-0.267	0.000	0.000	0.000	0.000
47	A	136	ALA	0	-0.030	-0.013	17.003	0.042	0.042	0.000	0.000	0.000	0.000
48	A	137	LEU	0	0.000	0.003	13.637	0.043	0.043	0.000	0.000	0.000	0.000
49	A	138	THR	0	0.025	-0.003	17.236	0.045	0.045	0.000	0.000	0.000	0.000
50	A	139	ARG	1	0.902	0.939	19.445	0.338	0.338	0.000	0.000	0.000	0.000
51	A	140	LYS	1	0.903	0.967	17.947	0.395	0.395	0.000	0.000	0.000	0.000
52	A	141	VAL	0	0.018	-0.001	18.993	0.022	0.022	0.000	0.000	0.000	0.000
53	A	142	HIS	0	0.001	0.003	21.937	0.030	0.030	0.000	0.000	0.000	0.000
54	A	143	ASN	0	-0.025	-0.027	24.998	0.019	0.019	0.000	0.000	0.000	0.000
55	A	144	PHE	0	-0.056	-0.030	24.614	0.008	0.008	0.000	0.000	0.000	0.000
56	A	145	GLN	0	-0.004	0.019	26.638	0.016	0.016	0.000	0.000	0.000	0.000
57	A	146	MET	0	-0.064	-0.012	21.777	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	147	GLU	-1	-0.894	-0.970	23.867	-0.131	-0.131	0.000	0.000	0.000	0.000
59	A	149	DSN	0	-0.030	-0.008	26.787	0.017	0.017	0.000	0.000	0.000	0.000
60	A	181	LEU	0	-0.012	-0.015	11.221	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	182	GLY	0	0.067	0.043	8.193	0.120	0.120	0.000	0.000	0.000	0.000
62	A	183	MET	0	0.029	0.010	8.743	-0.075	-0.075	0.000	0.000	0.000	0.000
63	A	184	ALA	0	0.032	0.028	7.808	-0.079	-0.079	0.000	0.000	0.000	0.000
64	A	185	VAL	0	0.036	0.008	9.043	-0.078	-0.078	0.000	0.000	0.000	0.000
65	A	186	SER	0	-0.001	-0.014	11.589	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	187	THR	0	-0.042	-0.025	12.629	0.011	0.011	0.000	0.000	0.000	0.000
67	A	188	LEU	0	-0.021	0.002	13.765	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	190	GLY	0	0.043	0.046	17.388	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	191	GLU	-1	-0.968	-0.992	19.154	0.056	0.056	0.000	0.000	0.000	0.000
70	A	192	VAL	0	-0.049	-0.006	20.718	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	193	PRO	0	0.001	0.002	21.793	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	194	LEU	0	-0.008	-0.002	17.406	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	195	TYR	0	0.013	-0.002	20.491	0.014	0.014	0.000	0.000	0.000	0.000
74	A	196	TYR	0	0.014	0.001	15.865	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	197	ILE	0	-0.012	-0.006	19.152	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:90:THR)