FMO DATABASE

FMODB ID: GNG31

Calculation Name: 2YAD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: B

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496943.746819
FMO2-HF: Nuclear repulsion	465394.116305
FMO2-HF: Total energy	-31549.630513
FMO2-MP2: Total energy	-31637.189808

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:89:VAL)

Summations of interaction energy for fragment #1(B: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.
-4.821	0.299	2.363	-2.455	-5.027	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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	B	91	THR	0	-0.024	-0.020	2.299	-1.309	0.477	1.015	-0.929	-1.871	0.001
4	B	92	ALA	0	0.024	0.014	4.793	0.123	0.147	-0.001	-0.009	-0.014	0.000
5	B	93	THR	0	-0.018	-0.001	8.569	-0.014	-0.014	0.000	0.000	0.000	0.000
6	B	94	PHE	0	-0.024	-0.009	11.295	0.047	0.047	0.000	0.000	0.000	0.000
7	B	95	SER	0	0.044	0.020	14.950	-0.019	-0.019	0.000	0.000	0.000	0.000
8	B	96	ILE	0	-0.031	-0.025	17.889	0.016	0.016	0.000	0.000	0.000	0.000
9	B	97	GLY	0	0.001	0.010	20.673	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	98	SER	0	-0.014	-0.013	24.379	0.000	0.000	0.000	0.000	0.000	0.000
11	B	99	THR	0	-0.028	-0.035	23.378	0.001	0.001	0.000	0.000	0.000	0.000
12	B	100	GLY	0	0.016	0.035	20.539	-0.015	-0.015	0.000	0.000	0.000	0.000
13	B	101	LEU	0	-0.028	-0.012	15.650	-0.004	-0.004	0.000	0.000	0.000	0.000
14	B	102	VAL	0	0.000	-0.010	12.633	0.006	0.006	0.000	0.000	0.000	0.000
15	B	103	VAL	0	0.006	0.007	7.719	-0.028	-0.028	0.000	0.000	0.000	0.000
16	B	104	TYR	0	-0.055	-0.047	8.814	0.045	0.045	0.000	0.000	0.000	0.000
17	B	105	ASP	-1	-0.813	-0.921	3.890	-1.804	-1.231	0.014	-0.204	-0.383	-0.001
18	B	106	TYR	0	0.014	-0.022	5.351	0.134	0.134	0.000	0.000	0.000	0.000
19	B	107	GLN	0	-0.032	0.002	2.427	-3.107	-0.760	1.337	-1.269	-2.415	-0.008
20	B	108	GLN	0	-0.016	-0.023	4.162	-0.093	0.064	-0.001	-0.020	-0.136	0.000
21	B	109	LEU	0	-0.009	0.004	6.106	0.033	0.033	0.000	0.000	0.000	0.000
22	B	110	LEU	0	-0.031	-0.006	8.126	0.030	0.030	0.000	0.000	0.000	0.000
23	B	111	ILE	0	0.017	0.008	9.047	-0.048	-0.048	0.000	0.000	0.000	0.000
24	B	112	ALA	0	0.000	0.013	11.237	0.026	0.026	0.000	0.000	0.000	0.000
25	B	113	TYR	0	0.016	-0.003	12.751	-0.014	-0.014	0.000	0.000	0.000	0.000
26	B	114	LYS	1	0.920	0.961	15.994	0.286	0.286	0.000	0.000	0.000	0.000
27	B	115	PRO	0	0.032	0.024	18.303	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	116	ALA	0	0.060	0.032	21.804	0.008	0.008	0.000	0.000	0.000	0.000
29	B	117	PRO	0	0.000	0.002	21.514	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	118	GLY	0	0.029	0.015	22.238	0.013	0.013	0.000	0.000	0.000	0.000
31	B	119	THR	0	-0.018	-0.017	22.617	0.008	0.008	0.000	0.000	0.000	0.000
32	B	120	CYS	0	-0.104	-0.053	20.779	0.001	0.001	0.000	0.000	0.000	0.000
33	B	121	CYS	0	-0.070	-0.046	13.058	0.042	0.042	0.000	0.000	0.000	0.000
34	B	122	TYR	0	0.040	0.031	17.399	0.013	0.013	0.000	0.000	0.000	0.000
35	B	123	ILE	0	-0.008	-0.007	12.362	-0.029	-0.029	0.000	0.000	0.000	0.000
36	B	124	MET	0	-0.007	0.008	14.095	0.051	0.051	0.000	0.000	0.000	0.000
37	B	125	LYS	1	0.874	0.937	10.504	0.097	0.097	0.000	0.000	0.000	0.000
38	B	126	ILE	0	-0.040	-0.023	10.426	0.009	0.009	0.000	0.000	0.000	0.000
39	B	127	ALA	0	0.028	0.012	13.469	0.012	0.012	0.000	0.000	0.000	0.000
40	B	128	PRO	0	-0.014	-0.014	12.875	-0.011	-0.011	0.000	0.000	0.000	0.000
41	B	129	GLU	-1	-0.880	-0.938	13.876	0.249	0.249	0.000	0.000	0.000	0.000
42	B	130	SER	0	-0.072	-0.042	16.561	-0.008	-0.008	0.000	0.000	0.000	0.000
43	B	131	ILE	0	0.014	0.017	11.113	-0.037	-0.037	0.000	0.000	0.000	0.000
44	B	132	PRO	0	-0.020	0.009	14.342	0.007	0.007	0.000	0.000	0.000	0.000
45	B	133	SER	0	0.085	0.032	15.719	-0.022	-0.022	0.000	0.000	0.000	0.000
46	B	134	LEU	0	0.103	0.040	15.820	-0.008	-0.008	0.000	0.000	0.000	0.000
47	B	135	GLU	-1	-0.832	-0.888	18.006	-0.060	-0.060	0.000	0.000	0.000	0.000
48	B	136	ALA	0	-0.007	-0.004	19.735	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	137	LEU	0	-0.001	0.003	15.129	0.000	0.000	0.000	0.000	0.000	0.000
50	B	138	THR	0	0.005	-0.011	19.174	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	139	ARG	1	0.820	0.892	21.852	0.055	0.055	0.000	0.000	0.000	0.000
52	B	140	LYS	1	0.924	0.975	18.189	0.096	0.096	0.000	0.000	0.000	0.000
53	B	141	VAL	0	0.030	0.006	20.016	0.000	0.000	0.000	0.000	0.000	0.000
54	B	142	HIS	0	0.009	0.010	22.648	0.001	0.001	0.000	0.000	0.000	0.000
55	B	143	ASN	0	-0.055	-0.045	25.870	0.002	0.002	0.000	0.000	0.000	0.000
56	B	144	PHE	0	-0.029	-0.029	23.437	0.004	0.004	0.000	0.000	0.000	0.000
57	B	145	GLN	0	-0.020	0.016	25.855	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	146	MET	0	-0.066	-0.015	20.065	-0.009	-0.009	0.000	0.000	0.000	0.000
59	B	147	GLU	-1	-0.871	-0.956	23.626	-0.117	-0.117	0.000	0.000	0.000	0.000
60	B	149	SER	0	-0.012	0.015	25.372	0.002	0.002	0.000	0.000	0.000	0.000
61	B	180	PHE	0	0.000	-0.010	10.456	0.012	0.012	0.000	0.000	0.000	0.000
62	B	181	LEU	0	0.016	0.017	8.169	-0.048	-0.048	0.000	0.000	0.000	0.000
63	B	182	GLY	0	0.082	0.043	4.482	-0.131	-0.080	-0.001	-0.008	-0.042	0.000
64	B	183	MET	0	0.025	0.003	4.005	0.187	0.369	0.000	-0.016	-0.166	0.000
65	B	184	ALA	0	0.033	0.023	5.713	0.225	0.225	0.000	0.000	0.000	0.000
66	B	185	VAL	0	0.039	0.015	7.008	0.161	0.161	0.000	0.000	0.000	0.000
67	B	186	SER	0	0.009	-0.005	8.876	0.149	0.149	0.000	0.000	0.000	0.000
68	B	187	THR	0	-0.055	-0.033	10.153	0.090	0.090	0.000	0.000	0.000	0.000
69	B	188	LEU	0	-0.017	0.005	11.643	0.067	0.067	0.000	0.000	0.000	0.000
70	B	190	GLY	0	0.046	0.045	14.854	0.027	0.027	0.000	0.000	0.000	0.000
71	B	191	GLU	-1	-0.968	-0.995	16.341	-0.217	-0.217	0.000	0.000	0.000	0.000
72	B	192	VAL	0	-0.050	-0.008	18.236	0.023	0.023	0.000	0.000	0.000	0.000
73	B	193	PRO	0	-0.008	0.006	19.246	-0.014	-0.014	0.000	0.000	0.000	0.000
74	B	194	LEU	0	-0.002	-0.007	14.903	-0.011	-0.011	0.000	0.000	0.000	0.000
75	B	195	TYR	0	0.000	-0.007	18.547	0.016	0.016	0.000	0.000	0.000	0.000
76	B	196	TYR	0	0.022	0.007	13.944	-0.009	-0.009	0.000	0.000	0.000	0.000
77	B	197	ILE	0	-0.028	-0.013	18.543	0.015	0.015	0.000	0.000	0.000	0.000

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