FMO DATABASE

FMODB ID: 767LK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-600333.118593
FMO2-HF: Nuclear repulsion	566890.799493
FMO2-HF: Total energy	-33442.3191
FMO2-MP2: Total energy	-33542.708782

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.
-41.922	-36.425	8.093	-4.899	-8.693	0.046

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 : 0.047 / q_NPA : 0.009

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	357	VAL	0	0.118	0.064	2.443	0.707	2.639	2.476	-1.526	-2.882	0.010
4	A	358	LYS	1	0.904	0.962	2.177	-23.443	-20.671	5.600	-3.156	-5.217	0.035
5	A	359	LYS	1	0.927	0.945	3.931	-8.492	-7.699	0.017	-0.217	-0.594	0.001
6	A	360	ASN	0	0.085	0.045	5.936	-0.929	-0.929	0.000	0.000	0.000	0.000
7	A	361	LYS	1	0.989	1.001	5.741	-4.045	-4.045	0.000	0.000	0.000	0.000
8	A	362	ARG	1	0.891	0.948	6.900	-5.114	-5.114	0.000	0.000	0.000	0.000
9	A	363	VAL	0	0.028	0.031	9.964	-0.362	-0.362	0.000	0.000	0.000	0.000
10	A	364	LEU	0	0.008	0.020	11.252	-0.225	-0.225	0.000	0.000	0.000	0.000
11	A	365	ARG	1	0.897	0.945	9.793	-1.937	-1.937	0.000	0.000	0.000	0.000
12	A	366	GLY	0	-0.004	0.001	13.884	-0.158	-0.158	0.000	0.000	0.000	0.000
13	A	367	SER	0	0.014	0.009	15.661	-0.186	-0.186	0.000	0.000	0.000	0.000
14	A	368	VAL	0	0.058	0.022	18.032	-0.103	-0.103	0.000	0.000	0.000	0.000
15	A	369	LYS	1	0.917	0.966	19.056	-0.911	-0.911	0.000	0.000	0.000	0.000
16	A	370	GLU	-1	-0.946	-0.965	19.817	0.733	0.733	0.000	0.000	0.000	0.000
17	A	371	ALA	0	-0.014	-0.002	21.549	-0.066	-0.066	0.000	0.000	0.000	0.000
18	A	372	ASN	0	-0.044	-0.032	23.913	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	373	TYR	0	-0.034	-0.039	20.706	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	374	PHE	0	-0.041	-0.034	22.257	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	375	VAL	0	-0.022	0.008	27.516	-0.039	-0.039	0.000	0.000	0.000	0.000
22	A	376	GLU	-1	-0.894	-0.944	30.216	0.350	0.350	0.000	0.000	0.000	0.000
23	A	377	GLY	0	-0.033	-0.016	32.900	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	378	GLU	-1	-0.950	-0.968	30.278	0.407	0.407	0.000	0.000	0.000	0.000
25	A	379	ALA	0	0.017	0.016	27.101	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	380	SER	0	0.039	0.018	28.964	0.015	0.015	0.000	0.000	0.000	0.000
27	A	381	ALA	0	0.068	0.013	27.324	0.026	0.026	0.000	0.000	0.000	0.000
28	A	382	ALA	0	0.001	0.002	27.074	0.020	0.020	0.000	0.000	0.000	0.000
29	A	383	THR	0	0.009	0.010	26.982	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	384	ILE	0	0.004	-0.005	22.427	0.029	0.029	0.000	0.000	0.000	0.000
31	A	385	ASP	-1	-0.908	-0.948	22.983	0.488	0.488	0.000	0.000	0.000	0.000
32	A	386	ALA	0	-0.016	-0.011	23.199	0.013	0.013	0.000	0.000	0.000	0.000
33	A	387	VAL	0	0.028	0.005	21.363	0.005	0.005	0.000	0.000	0.000	0.000
34	A	388	LEU	0	0.002	-0.013	17.315	0.061	0.061	0.000	0.000	0.000	0.000
35	A	389	ASN	0	0.010	0.013	18.577	0.078	0.078	0.000	0.000	0.000	0.000
36	A	390	ASP	-1	-0.759	-0.876	19.909	0.388	0.388	0.000	0.000	0.000	0.000
37	A	391	VAL	0	-0.029	-0.018	15.219	0.017	0.017	0.000	0.000	0.000	0.000
38	A	392	ASP	-1	-0.870	-0.943	15.032	1.088	1.088	0.000	0.000	0.000	0.000
39	A	393	LEU	0	-0.025	-0.006	15.653	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	394	VAL	0	0.054	0.031	16.037	-0.059	-0.059	0.000	0.000	0.000	0.000
41	A	395	ILE	0	-0.037	-0.023	10.897	0.070	0.070	0.000	0.000	0.000	0.000
42	A	396	THR	0	-0.139	-0.077	12.855	-0.083	-0.083	0.000	0.000	0.000	0.000
43	A	397	LYS	1	0.893	0.950	14.524	-0.277	-0.277	0.000	0.000	0.000	0.000
44	A	398	ILE	0	-0.053	-0.004	12.526	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	399	ASP	-1	-0.821	-0.910	10.832	-0.155	-0.155	0.000	0.000	0.000	0.000
46	A	400	ALA	0	-0.055	-0.060	6.888	0.318	0.318	0.000	0.000	0.000	0.000
47	A	401	ASP	-1	-0.894	-0.935	8.709	-0.272	-0.272	0.000	0.000	0.000	0.000
48	A	402	GLU	-1	-0.820	-0.920	11.615	0.247	0.247	0.000	0.000	0.000	0.000
49	A	403	ILE	0	-0.039	-0.023	8.174	0.375	0.375	0.000	0.000	0.000	0.000
50	A	404	ALA	0	-0.043	-0.028	9.395	0.238	0.238	0.000	0.000	0.000	0.000
51	A	405	ALA	0	-0.005	0.000	10.744	0.017	0.017	0.000	0.000	0.000	0.000
52	A	406	LEU	0	-0.003	0.005	13.962	0.011	0.011	0.000	0.000	0.000	0.000
53	A	407	ALA	0	0.011	-0.018	11.268	0.035	0.035	0.000	0.000	0.000	0.000
54	A	408	GLY	0	-0.038	-0.022	13.287	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	409	LYS	1	0.931	0.966	15.392	-0.460	-0.460	0.000	0.000	0.000	0.000
56	A	410	LEU	0	0.023	0.017	15.489	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	411	ASN	0	-0.093	-0.051	13.237	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	412	GLY	0	0.016	0.013	16.786	-0.091	-0.091	0.000	0.000	0.000	0.000
59	A	413	LEU	0	-0.015	0.014	19.646	-0.061	-0.061	0.000	0.000	0.000	0.000
60	A	414	THR	0	0.023	0.000	21.661	0.040	0.040	0.000	0.000	0.000	0.000
61	A	415	VAL	0	0.010	0.019	24.372	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	416	ALA	0	0.076	0.029	25.513	0.017	0.017	0.000	0.000	0.000	0.000
63	A	417	ASP	-1	-0.869	-0.944	25.964	0.363	0.363	0.000	0.000	0.000	0.000
64	A	418	GLU	-1	-0.985	-0.988	25.037	0.414	0.414	0.000	0.000	0.000	0.000
65	A	419	ILE	0	0.003	-0.006	20.652	0.010	0.010	0.000	0.000	0.000	0.000
66	A	420	LYS	1	0.888	0.942	22.461	-0.364	-0.364	0.000	0.000	0.000	0.000
67	A	421	ASN	0	-0.027	-0.022	24.609	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	422	VAL	0	-0.002	0.017	19.522	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	423	TRP	0	0.001	-0.020	15.365	0.000	0.000	0.000	0.000	0.000	0.000
70	A	424	LYS	1	0.890	0.952	21.482	-0.342	-0.342	0.000	0.000	0.000	0.000
71	A	425	GLU	-1	-0.941	-0.952	22.991	0.208	0.208	0.000	0.000	0.000	0.000
72	A	426	GLU	-1	-0.797	-0.890	17.133	0.378	0.378	0.000	0.000	0.000	0.000
73	A	427	VAL	0	-0.010	-0.015	21.065	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	428	SER	0	0.000	0.002	22.850	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	429	ARG	1	0.755	0.878	17.404	-0.258	-0.258	0.000	0.000	0.000	0.000
76	A	430	LEU	0	-0.025	-0.027	18.215	-0.046	-0.046	0.000	0.000	0.000	0.000
77	A	431	VAL	0	-0.006	0.000	22.417	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	432	GLY	0	0.003	0.009	25.935	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	433	ALA	0	-0.063	-0.023	22.877	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	434	GLY	0	-0.013	-0.003	24.659	-0.032	-0.032	0.000	0.000	0.000	0.000
81	A	435	LYS	1	0.869	0.925	17.946	0.023	0.023	0.000	0.000	0.000	0.000
82	A	436	LEU	0	-0.026	-0.008	20.970	0.018	0.018	0.000	0.000	0.000	0.000
83	A	437	LYS	1	0.897	0.933	24.216	-0.063	-0.063	0.000	0.000	0.000	0.000
84	A	438	GLU	-1	-0.917	-0.963	27.479	0.133	0.133	0.000	0.000	0.000	0.000
85	A	439	GLY	0	-0.015	-0.005	29.041	0.018	0.018	0.000	0.000	0.000	0.000
86	A	440	ASP	-1	-0.890	-0.924	24.507	0.167	0.167	0.000	0.000	0.000	0.000
87	A	441	ILE	0	-0.072	-0.024	21.475	0.035	0.035	0.000	0.000	0.000	0.000
88	A	442	LYS	1	0.871	0.957	24.724	-0.401	-0.401	0.000	0.000	0.000	0.000
89	A	443	ALA	0	-0.023	-0.024	26.023	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	444	LEU	0	-0.047	-0.029	20.195	0.001	0.001	0.000	0.000	0.000	0.000
91	A	445	VAL	0	0.029	0.005	24.577	0.014	0.014	0.000	0.000	0.000	0.000
92	A	446	ALA	0	-0.004	0.015	26.988	-0.017	-0.017	0.000	0.000	0.000	0.000

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