FMO DATABASE

FMODB ID: 6Y29Z

Calculation Name: 4GMQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GMQ

Chain ID: A

ChEMBL ID:

UniProt ID: G0RYD6

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-602370.345965
FMO2-HF: Nuclear repulsion	568927.556159
FMO2-HF: Total energy	-33442.789806
FMO2-MP2: Total energy	-33543.172034

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:355:ASN)

Summations of interaction energy for fragment #1(A:355:ASN)

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.
-53.234	-52.826	19.302	-8.507	-11.202	0.076

Interaction energy analysis for fragmet #1(A:355:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / 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	357	VAL	0	0.094	0.052	2.324	1.212	2.864	3.056	-1.634	-3.073	0.007
4	A	358	LYS	1	0.891	0.936	1.971	-38.525	-40.301	16.221	-6.768	-7.677	0.068
5	A	359	LYS	1	0.943	0.967	3.841	-6.718	-6.186	0.025	-0.105	-0.452	0.001
6	A	360	ASN	0	0.062	0.035	6.125	-0.768	-0.768	0.000	0.000	0.000	0.000
7	A	361	LYS	1	0.992	0.997	5.625	-2.991	-2.991	0.000	0.000	0.000	0.000
8	A	362	ARG	1	0.899	0.955	7.807	-4.542	-4.542	0.000	0.000	0.000	0.000
9	A	363	VAL	0	0.032	0.026	10.345	-0.340	-0.340	0.000	0.000	0.000	0.000
10	A	364	LEU	0	-0.015	0.011	10.982	-0.211	-0.211	0.000	0.000	0.000	0.000
11	A	365	ARG	1	0.845	0.883	10.725	-1.710	-1.710	0.000	0.000	0.000	0.000
12	A	366	GLY	0	0.002	0.010	14.169	-0.133	-0.133	0.000	0.000	0.000	0.000
13	A	367	SER	0	0.017	0.001	16.003	-0.183	-0.183	0.000	0.000	0.000	0.000
14	A	368	VAL	0	0.034	0.013	18.067	-0.094	-0.094	0.000	0.000	0.000	0.000
15	A	369	LYS	1	0.849	0.921	18.869	-0.897	-0.897	0.000	0.000	0.000	0.000
16	A	370	GLU	-1	-0.887	-0.925	20.165	0.770	0.770	0.000	0.000	0.000	0.000
17	A	371	ALA	0	-0.023	-0.006	22.011	-0.064	-0.064	0.000	0.000	0.000	0.000
18	A	372	ASN	0	-0.043	-0.031	24.196	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	373	TYR	0	0.006	-0.020	20.447	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	374	PHE	0	-0.030	-0.032	22.098	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	375	VAL	0	-0.022	0.001	27.374	-0.038	-0.038	0.000	0.000	0.000	0.000
22	A	376	GLU	-1	-0.861	-0.928	30.318	0.338	0.338	0.000	0.000	0.000	0.000
23	A	377	GLY	0	-0.039	-0.010	33.111	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	378	GLU	-1	-0.954	-0.974	30.515	0.402	0.402	0.000	0.000	0.000	0.000
25	A	379	ALA	0	0.006	0.007	27.169	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	380	SER	0	0.023	0.003	28.650	0.012	0.012	0.000	0.000	0.000	0.000
27	A	381	ALA	0	0.058	0.008	27.267	0.022	0.022	0.000	0.000	0.000	0.000
28	A	382	ALA	0	0.021	0.013	26.961	0.019	0.019	0.000	0.000	0.000	0.000
29	A	383	THR	0	0.005	0.015	27.200	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	384	ILE	0	0.011	0.005	22.537	0.024	0.024	0.000	0.000	0.000	0.000
31	A	385	ASP	-1	-0.889	-0.937	22.881	0.431	0.431	0.000	0.000	0.000	0.000
32	A	386	ALA	0	-0.004	-0.011	23.173	0.013	0.013	0.000	0.000	0.000	0.000
33	A	387	VAL	0	0.006	-0.003	21.347	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	388	LEU	0	-0.012	-0.007	17.563	0.059	0.059	0.000	0.000	0.000	0.000
35	A	389	ASN	0	-0.038	-0.026	18.536	0.059	0.059	0.000	0.000	0.000	0.000
36	A	390	ASP	-1	-0.769	-0.857	20.134	0.305	0.305	0.000	0.000	0.000	0.000
37	A	391	VAL	0	0.000	-0.006	15.224	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	392	ASP	-1	-0.801	-0.880	14.580	1.100	1.100	0.000	0.000	0.000	0.000
39	A	393	LEU	0	-0.010	0.011	15.634	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	394	VAL	0	0.037	0.017	16.019	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	395	ILE	0	-0.034	-0.025	10.817	0.019	0.019	0.000	0.000	0.000	0.000
42	A	396	THR	0	-0.109	-0.063	12.489	-0.127	-0.127	0.000	0.000	0.000	0.000
43	A	397	LYS	1	0.807	0.911	14.286	-0.202	-0.202	0.000	0.000	0.000	0.000
44	A	398	ILE	0	-0.048	-0.013	12.033	-0.056	-0.056	0.000	0.000	0.000	0.000
45	A	399	ASP	-1	-0.807	-0.893	10.003	-0.546	-0.546	0.000	0.000	0.000	0.000
46	A	400	ALA	0	-0.042	-0.056	6.170	0.338	0.338	0.000	0.000	0.000	0.000
47	A	401	ASP	-1	-0.896	-0.940	7.839	-0.517	-0.517	0.000	0.000	0.000	0.000
48	A	402	GLU	-1	-0.726	-0.847	11.020	0.081	0.081	0.000	0.000	0.000	0.000
49	A	403	ILE	0	-0.028	-0.017	7.711	0.403	0.403	0.000	0.000	0.000	0.000
50	A	404	ALA	0	-0.038	-0.026	9.205	0.302	0.302	0.000	0.000	0.000	0.000
51	A	405	ALA	0	0.017	0.007	10.552	0.059	0.059	0.000	0.000	0.000	0.000
52	A	406	LEU	0	-0.034	0.010	13.450	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	407	ALA	0	0.012	-0.013	10.975	0.042	0.042	0.000	0.000	0.000	0.000
54	A	408	GLY	0	-0.032	-0.020	12.988	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	409	LYS	1	0.837	0.912	15.201	-0.399	-0.399	0.000	0.000	0.000	0.000
56	A	410	LEU	0	0.015	0.004	15.350	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	411	ASN	0	-0.070	-0.046	14.341	0.070	0.070	0.000	0.000	0.000	0.000
58	A	412	GLY	0	0.005	0.010	16.561	-0.088	-0.088	0.000	0.000	0.000	0.000
59	A	413	LEU	0	-0.011	0.015	19.884	-0.058	-0.058	0.000	0.000	0.000	0.000
60	A	414	THR	0	-0.007	-0.015	21.714	0.043	0.043	0.000	0.000	0.000	0.000
61	A	415	VAL	0	0.022	0.027	24.493	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	416	ALA	0	0.067	0.024	25.452	0.016	0.016	0.000	0.000	0.000	0.000
63	A	417	ASP	-1	-0.864	-0.945	25.709	0.336	0.336	0.000	0.000	0.000	0.000
64	A	418	GLU	-1	-0.969	-0.973	24.786	0.384	0.384	0.000	0.000	0.000	0.000
65	A	419	ILE	0	0.008	-0.002	20.461	0.002	0.002	0.000	0.000	0.000	0.000
66	A	420	LYS	1	0.839	0.925	22.308	-0.341	-0.341	0.000	0.000	0.000	0.000
67	A	421	ASN	0	0.000	-0.004	24.579	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	422	VAL	0	0.015	0.019	19.571	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	423	TRP	0	0.000	-0.022	15.098	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	424	LYS	1	0.878	0.944	21.336	-0.306	-0.306	0.000	0.000	0.000	0.000
71	A	425	GLU	-1	-0.925	-0.932	22.799	0.124	0.124	0.000	0.000	0.000	0.000
72	A	426	GLU	-1	-0.810	-0.891	17.435	0.240	0.240	0.000	0.000	0.000	0.000
73	A	427	VAL	0	0.011	-0.011	20.768	-0.040	-0.040	0.000	0.000	0.000	0.000
74	A	428	SER	0	-0.006	-0.008	22.462	-0.044	-0.044	0.000	0.000	0.000	0.000
75	A	429	ARG	1	0.770	0.863	16.656	-0.101	-0.101	0.000	0.000	0.000	0.000
76	A	430	LEU	0	-0.034	-0.024	17.651	-0.047	-0.047	0.000	0.000	0.000	0.000
77	A	431	VAL	0	-0.003	-0.003	21.751	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	432	GLY	0	-0.001	0.008	25.299	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	433	ALA	0	-0.050	-0.023	21.862	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	434	GLY	0	-0.003	0.006	23.424	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	435	LYS	1	0.791	0.891	15.835	0.177	0.177	0.000	0.000	0.000	0.000
82	A	436	LEU	0	-0.040	-0.003	20.241	0.018	0.018	0.000	0.000	0.000	0.000
83	A	437	LYS	1	0.894	0.928	23.320	0.021	0.021	0.000	0.000	0.000	0.000
84	A	438	GLU	-1	-0.918	-0.971	26.816	0.080	0.080	0.000	0.000	0.000	0.000
85	A	439	GLY	0	0.002	0.011	29.142	0.015	0.015	0.000	0.000	0.000	0.000
86	A	440	ASP	-1	-0.866	-0.930	23.299	0.090	0.090	0.000	0.000	0.000	0.000
87	A	441	ILE	0	-0.057	-0.021	21.213	0.034	0.034	0.000	0.000	0.000	0.000
88	A	442	LYS	1	0.884	0.939	24.562	-0.341	-0.341	0.000	0.000	0.000	0.000
89	A	443	ALA	0	0.007	0.004	25.961	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	444	LEU	0	-0.024	-0.017	20.089	0.006	0.006	0.000	0.000	0.000	0.000
91	A	445	VAL	0	0.035	0.009	24.395	0.007	0.007	0.000	0.000	0.000	0.000
92	A	446	ALA	0	-0.039	-0.003	26.820	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:355:ASN)