FMO DATABASE

FMODB ID: N1QYQ

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	OptH
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	-472222.279395
FMO2-HF: Nuclear repulsion	441472.221889
FMO2-HF: Total energy	-30750.057507
FMO2-MP2: Total energy	-30835.054961

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.
-4.187	2.118	2.514	-3.666	-5.151	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 : 0.050 / q_NPA : 0.024

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	A	92	ALA	0	0.029	0.020	3.884	-0.682	2.393	-0.015	-1.720	-1.341	0.005
4	A	93	THR	0	-0.025	-0.003	6.105	-0.194	-0.194	0.000	0.000	0.000	0.000
5	A	94	PHE	0	0.012	0.008	8.361	0.004	0.004	0.000	0.000	0.000	0.000
6	A	95	SER	0	0.039	0.017	12.718	0.029	0.029	0.000	0.000	0.000	0.000
7	A	96	ILE	0	-0.032	-0.021	16.234	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	97	GLY	0	0.005	0.007	18.820	0.022	0.022	0.000	0.000	0.000	0.000
9	A	98	SER	0	0.005	-0.005	21.821	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	99	THR	0	-0.045	-0.034	22.785	0.014	0.014	0.000	0.000	0.000	0.000
11	A	100	GLY	0	0.021	0.039	20.146	0.010	0.010	0.000	0.000	0.000	0.000
12	A	101	LEU	0	-0.021	-0.016	15.623	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	102	VAL	0	-0.017	-0.010	12.549	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	103	VAL	0	0.001	0.006	8.584	0.037	0.037	0.000	0.000	0.000	0.000
15	A	104	TYR	0	-0.046	-0.034	6.815	0.047	0.047	0.000	0.000	0.000	0.000
16	A	105	ASP	-1	-0.843	-0.931	4.727	-2.954	-2.866	-0.001	-0.019	-0.067	0.000
17	A	106	TYR	0	0.014	-0.018	2.517	-0.836	1.087	0.644	-0.735	-1.832	0.002
18	A	107	GLN	0	-0.049	-0.006	2.011	-1.569	-0.576	1.869	-1.139	-1.722	-0.003
19	A	108	GLN	0	0.027	-0.003	3.608	0.794	1.020	0.017	-0.053	-0.189	-0.001
20	A	109	LEU	0	-0.020	-0.002	6.409	0.386	0.386	0.000	0.000	0.000	0.000
21	A	110	LEU	0	-0.031	-0.012	8.139	0.383	0.383	0.000	0.000	0.000	0.000
22	A	111	ILE	0	-0.002	0.001	9.101	-0.276	-0.276	0.000	0.000	0.000	0.000
23	A	112	ALA	0	0.010	0.010	11.746	0.128	0.128	0.000	0.000	0.000	0.000
24	A	113	TYR	0	0.017	-0.004	13.647	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	114	LYS	1	0.951	0.977	16.652	0.083	0.083	0.000	0.000	0.000	0.000
26	A	115	PRO	0	0.014	0.023	19.234	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	116	ALA	0	0.061	0.029	21.978	0.008	0.008	0.000	0.000	0.000	0.000
28	A	117	PRO	0	-0.024	-0.013	22.901	0.001	0.001	0.000	0.000	0.000	0.000
29	A	118	GLY	0	0.028	0.018	23.738	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	119	THR	0	0.002	-0.008	24.132	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	120	CYS	0	-0.096	-0.044	22.763	0.012	0.012	0.000	0.000	0.000	0.000
32	A	121	CYS	0	-0.073	-0.056	15.473	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	122	TYR	0	0.032	0.030	18.645	0.010	0.010	0.000	0.000	0.000	0.000
34	A	123	ILE	0	-0.005	-0.001	13.604	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	124	MET	0	-0.030	-0.011	14.554	0.053	0.053	0.000	0.000	0.000	0.000
36	A	125	LYS	1	0.911	0.957	11.054	0.522	0.522	0.000	0.000	0.000	0.000
37	A	126	ILE	0	-0.031	-0.018	8.856	0.041	0.041	0.000	0.000	0.000	0.000
38	A	127	ALA	0	0.032	0.016	12.091	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	128	PRO	0	0.011	-0.016	10.242	-0.090	-0.090	0.000	0.000	0.000	0.000
40	A	129	DGL	-1	-0.951	-0.967	11.304	-0.481	-0.481	0.000	0.000	0.000	0.000
41	A	130	SER	0	-0.014	-0.010	13.863	0.047	0.047	0.000	0.000	0.000	0.000
42	A	131	ILE	0	-0.020	0.006	8.286	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	132	PRO	0	0.004	0.012	12.254	0.052	0.052	0.000	0.000	0.000	0.000
44	A	133	SER	0	0.067	0.020	12.424	-0.090	-0.090	0.000	0.000	0.000	0.000
45	A	134	LEU	0	0.097	0.043	12.866	0.024	0.024	0.000	0.000	0.000	0.000
46	A	135	GLU	-1	-0.917	-0.951	14.396	-0.285	-0.285	0.000	0.000	0.000	0.000
47	A	136	ALA	0	-0.047	-0.026	17.032	0.045	0.045	0.000	0.000	0.000	0.000
48	A	137	LEU	0	0.004	0.007	13.772	0.043	0.043	0.000	0.000	0.000	0.000
49	A	138	THR	0	0.028	-0.003	17.254	0.046	0.046	0.000	0.000	0.000	0.000
50	A	139	ARG	1	0.953	0.983	19.496	0.353	0.353	0.000	0.000	0.000	0.000
51	A	140	LYS	1	0.896	0.966	18.203	0.393	0.393	0.000	0.000	0.000	0.000
52	A	141	VAL	0	0.028	0.001	19.037	0.023	0.023	0.000	0.000	0.000	0.000
53	A	142	HIS	0	0.009	0.013	21.979	0.031	0.031	0.000	0.000	0.000	0.000
54	A	143	ASN	0	-0.036	-0.038	25.032	0.021	0.021	0.000	0.000	0.000	0.000
55	A	144	PHE	0	-0.067	-0.034	24.639	0.008	0.008	0.000	0.000	0.000	0.000
56	A	145	GLN	0	0.008	0.021	26.656	0.014	0.014	0.000	0.000	0.000	0.000
57	A	146	MET	0	-0.072	-0.017	21.828	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	147	GLU	-1	-0.899	-0.973	23.947	-0.133	-0.133	0.000	0.000	0.000	0.000
59	A	149	DSN	0	0.003	0.014	26.771	0.013	0.013	0.000	0.000	0.000	0.000
60	A	181	LEU	0	0.002	-0.011	11.218	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	182	GLY	0	0.062	0.041	8.195	0.121	0.121	0.000	0.000	0.000	0.000
62	A	183	MET	0	0.030	0.009	8.736	-0.078	-0.078	0.000	0.000	0.000	0.000
63	A	184	ALA	0	0.020	0.017	7.849	-0.059	-0.059	0.000	0.000	0.000	0.000
64	A	185	VAL	0	0.040	0.012	9.323	-0.068	-0.068	0.000	0.000	0.000	0.000
65	A	186	SER	0	0.002	-0.013	11.591	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	187	THR	0	-0.044	-0.022	12.731	0.012	0.012	0.000	0.000	0.000	0.000
67	A	188	LEU	0	-0.039	-0.011	13.761	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	190	GLY	0	0.045	0.048	17.394	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	191	GLU	-1	-0.962	-0.991	19.155	0.052	0.052	0.000	0.000	0.000	0.000
70	A	192	VAL	0	-0.062	-0.007	20.674	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	193	PRO	0	-0.006	0.001	21.786	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	194	LEU	0	0.001	-0.002	17.464	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	195	TYR	0	0.027	0.000	20.474	0.014	0.014	0.000	0.000	0.000	0.000
74	A	196	TYR	0	0.006	0.000	15.786	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	197	ILE	0	-0.010	-0.011	19.133	0.004	0.004	0.000	0.000	0.000	0.000

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