FMO DATABASE

FMODB ID: K9ZL3

Calculation Name: 5D0Q-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: G

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-375984.046147
FMO2-HF: Nuclear repulsion	344385.562567
FMO2-HF: Total energy	-31598.483579
FMO2-MP2: Total energy	-31688.274557

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(G:29:SER)

Summations of interaction energy for fragment #1(G:29:SER)

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.
-9.211	-4.2	2.856	-3.196	-4.673	-0.01

Interaction energy analysis for fragmet #1(G:29:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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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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	G	31	TYR	0	0.045	0.006	2.434	-4.873	-1.427	1.403	-2.272	-2.578	-0.013
4	G	32	LYS	1	0.937	0.981	2.346	-1.712	-0.917	1.452	-0.603	-1.644	0.002
5	G	33	ARG	1	0.936	0.975	3.674	-3.372	-2.602	0.001	-0.321	-0.451	0.001
6	G	34	GLN	0	0.037	0.037	7.630	0.109	0.109	0.000	0.000	0.000	0.000
7	G	35	VAL	0	0.078	0.039	9.789	-0.035	-0.035	0.000	0.000	0.000	0.000
8	G	36	SER	0	-0.033	-0.022	11.525	0.077	0.077	0.000	0.000	0.000	0.000
9	G	37	GLY	0	0.037	0.023	12.986	-0.052	-0.052	0.000	0.000	0.000	0.000
10	G	38	ASP	-1	-0.913	-0.966	14.244	0.351	0.351	0.000	0.000	0.000	0.000
11	G	39	GLU	-1	-0.795	-0.909	14.647	0.500	0.500	0.000	0.000	0.000	0.000
12	G	40	ALA	0	0.039	0.030	18.115	-0.021	-0.021	0.000	0.000	0.000	0.000
13	G	41	TYR	0	-0.010	-0.006	17.838	-0.018	-0.018	0.000	0.000	0.000	0.000
14	G	42	LEU	0	-0.038	-0.030	18.934	-0.012	-0.012	0.000	0.000	0.000	0.000
15	G	43	GLU	-1	-0.981	-0.979	22.590	0.190	0.190	0.000	0.000	0.000	0.000
16	G	44	ALA	0	-0.039	-0.007	25.205	-0.014	-0.014	0.000	0.000	0.000	0.000
17	G	45	ALA	0	-0.008	-0.007	27.862	-0.003	-0.003	0.000	0.000	0.000	0.000
18	G	46	PRO	0	-0.005	0.000	31.502	0.002	0.002	0.000	0.000	0.000	0.000
19	G	47	LEU	0	0.006	-0.010	32.723	-0.006	-0.006	0.000	0.000	0.000	0.000
20	G	48	ALA	0	-0.046	-0.014	35.249	-0.002	-0.002	0.000	0.000	0.000	0.000
21	G	49	GLU	-1	-0.879	-0.951	38.449	0.069	0.069	0.000	0.000	0.000	0.000
22	G	50	LEU	0	-0.055	-0.010	41.339	-0.002	-0.002	0.000	0.000	0.000	0.000
23	G	51	HIS	0	-0.010	-0.013	44.094	-0.003	-0.003	0.000	0.000	0.000	0.000
24	G	52	ALA	0	-0.007	-0.002	48.008	-0.001	-0.001	0.000	0.000	0.000	0.000
25	G	53	PRO	0	-0.008	-0.013	51.218	-0.001	-0.001	0.000	0.000	0.000	0.000
26	G	54	ALA	0	0.009	0.004	54.214	0.000	0.000	0.000	0.000	0.000	0.000
27	G	55	GLY	0	-0.020	-0.007	57.793	0.000	0.000	0.000	0.000	0.000	0.000
28	G	56	MET	0	-0.018	-0.007	54.202	0.000	0.000	0.000	0.000	0.000	0.000
29	G	57	ILE	0	-0.001	-0.003	51.710	0.001	0.001	0.000	0.000	0.000	0.000
30	G	58	LEU	0	0.009	0.013	48.185	-0.001	-0.001	0.000	0.000	0.000	0.000
31	G	59	PRO	0	0.002	-0.006	48.068	0.000	0.000	0.000	0.000	0.000	0.000
32	G	60	VAL	0	0.014	0.000	44.920	0.002	0.002	0.000	0.000	0.000	0.000
33	G	61	THR	0	0.010	-0.003	39.884	-0.001	-0.001	0.000	0.000	0.000	0.000
34	G	62	SER	0	-0.044	-0.008	42.993	-0.001	-0.001	0.000	0.000	0.000	0.000
35	G	63	GLY	0	-0.013	0.003	43.017	0.000	0.000	0.000	0.000	0.000	0.000
36	G	64	ASP	-1	-0.905	-0.961	37.597	0.073	0.073	0.000	0.000	0.000	0.000
37	G	65	TYR	0	-0.047	-0.033	34.421	0.001	0.001	0.000	0.000	0.000	0.000
38	G	66	ALA	0	0.045	0.041	36.272	0.001	0.001	0.000	0.000	0.000	0.000
39	G	67	ILE	0	-0.022	-0.017	30.593	0.004	0.004	0.000	0.000	0.000	0.000
40	G	68	PRO	0	-0.015	-0.005	33.138	-0.002	-0.002	0.000	0.000	0.000	0.000
41	G	69	VAL	0	0.022	0.020	32.992	0.007	0.007	0.000	0.000	0.000	0.000
42	G	70	THR	0	0.003	-0.008	29.616	0.001	0.001	0.000	0.000	0.000	0.000
43	G	71	ASN	0	-0.005	-0.015	29.956	0.001	0.001	0.000	0.000	0.000	0.000
44	G	72	GLY	0	-0.009	0.055	26.923	0.006	0.006	0.000	0.000	0.000	0.000
45	G	73	SER	0	0.027	-0.023	24.815	-0.006	-0.006	0.000	0.000	0.000	0.000
46	G	74	GLY	0	-0.029	-0.024	22.166	-0.001	-0.001	0.000	0.000	0.000	0.000
47	G	75	ALA	0	-0.029	-0.014	16.567	0.000	0.000	0.000	0.000	0.000	0.000
48	G	76	VAL	0	0.063	0.022	18.270	-0.006	-0.006	0.000	0.000	0.000	0.000
49	G	77	GLY	0	0.041	0.031	16.717	0.020	0.020	0.000	0.000	0.000	0.000
50	G	78	LYS	1	0.724	0.848	10.594	-0.549	-0.549	0.000	0.000	0.000	0.000
51	G	79	ALA	0	-0.029	-0.010	11.763	0.064	0.064	0.000	0.000	0.000	0.000
52	G	80	LEU	0	-0.020	-0.004	13.583	0.017	0.017	0.000	0.000	0.000	0.000
53	G	81	ASP	-1	-0.787	-0.879	10.929	0.679	0.679	0.000	0.000	0.000	0.000
54	G	82	ILE	0	-0.017	-0.006	11.221	-0.050	-0.050	0.000	0.000	0.000	0.000
55	G	83	ARG	1	0.811	0.888	8.470	-0.696	-0.696	0.000	0.000	0.000	0.000
56	G	84	PRO	0	0.036	0.024	12.509	-0.010	-0.010	0.000	0.000	0.000	0.000
57	G	85	PRO	0	-0.031	-0.009	15.663	0.011	0.011	0.000	0.000	0.000	0.000
58	G	86	ALA	0	-0.008	-0.007	16.736	-0.025	-0.025	0.000	0.000	0.000	0.000
59	G	87	GLN	0	0.056	0.021	18.508	0.017	0.017	0.000	0.000	0.000	0.000
60	G	88	PRO	0	-0.038	-0.006	20.507	-0.016	-0.016	0.000	0.000	0.000	0.000
61	G	189	ALA	0	0.029	0.016	18.393	-0.002	-0.002	0.000	0.000	0.000	0.000
62	G	190	ASP	-1	-0.858	-0.913	17.021	0.290	0.290	0.000	0.000	0.000	0.000
63	G	191	ALA	0	0.060	0.011	19.830	0.007	0.007	0.000	0.000	0.000	0.000
64	G	192	ALA	0	0.024	0.008	18.956	-0.005	-0.005	0.000	0.000	0.000	0.000
65	G	193	SER	0	-0.053	-0.051	15.566	0.037	0.037	0.000	0.000	0.000	0.000
66	G	194	MET	0	-0.022	-0.006	17.050	0.008	0.008	0.000	0.000	0.000	0.000
67	G	195	GLN	0	-0.015	0.000	19.825	-0.015	-0.015	0.000	0.000	0.000	0.000
68	G	196	ARG	1	0.920	0.950	13.152	-0.369	-0.369	0.000	0.000	0.000	0.000
69	G	197	TYR	0	-0.022	-0.021	10.017	0.041	0.041	0.000	0.000	0.000	0.000
70	G	198	SER	0	0.027	0.012	16.442	-0.027	-0.027	0.000	0.000	0.000	0.000
71	G	199	THR	0	-0.022	-0.014	18.358	-0.027	-0.027	0.000	0.000	0.000	0.000
72	G	200	GLU	-1	-0.977	-0.977	13.390	0.252	0.252	0.000	0.000	0.000	0.000
73	G	201	MET	0	-0.008	0.001	16.955	-0.021	-0.021	0.000	0.000	0.000	0.000
74	G	202	MET	0	0.076	0.039	19.983	-0.021	-0.021	0.000	0.000	0.000	0.000
75	G	203	ASN	0	-0.029	-0.026	18.271	-0.022	-0.022	0.000	0.000	0.000	0.000
76	G	204	VAL	0	-0.021	-0.007	18.921	-0.010	-0.010	0.000	0.000	0.000	0.000
77	G	205	ILE	0	-0.041	-0.022	21.559	-0.015	-0.015	0.000	0.000	0.000	0.000
78	G	206	SER	0	-0.008	-0.008	24.196	-0.009	-0.009	0.000	0.000	0.000	0.000
79	G	207	ALA	0	0.007	0.016	22.629	-0.005	-0.005	0.000	0.000	0.000	0.000
80	G	208	GLY	0	-0.017	-0.014	24.674	-0.009	-0.009	0.000	0.000	0.000	0.000
81	G	209	LEU	0	-0.068	-0.037	26.604	-0.005	-0.005	0.000	0.000	0.000	0.000
82	G	210	ASP	-1	-0.918	-0.961	27.884	0.011	0.011	0.000	0.000	0.000	0.000
83	G	211	LYS	1	0.914	0.982	26.104	-0.001	-0.001	0.000	0.000	0.000	0.000
84	G	212	SER	0	-0.050	-0.031	29.656	-0.004	-0.004	0.000	0.000	0.000	0.000
85	G	213	ALA	0	0.026	0.027	32.402	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:29:SER)