FMO DATABASE

FMODB ID: 6Y3RZ

Calculation Name: 3Q9V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q9V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRR8

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737439.809775
FMO2-HF: Nuclear repulsion	698944.12437
FMO2-HF: Total energy	-38495.685405
FMO2-MP2: Total energy	-38609.393647

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:124:GLU)

Summations of interaction energy for fragment #1(A:124:GLU)

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.
-42.708	-38.698	0.025	-1.964	-2.069	0.007

Interaction energy analysis for fragmet #1(A:124:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.964

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	126	LEU	0	-0.008	-0.001	3.367	2.183	5.802	0.028	-1.927	-1.719	0.007
4	A	127	SER	0	0.008	-0.016	5.752	-1.733	-1.733	0.000	0.000	0.000	0.000
5	A	128	MET	0	-0.066	-0.030	8.680	-0.774	-0.774	0.000	0.000	0.000	0.000
6	A	129	GLY	0	0.023	0.006	12.157	-1.240	-1.240	0.000	0.000	0.000	0.000
7	A	130	ASP	-1	-0.823	-0.892	13.093	17.086	17.086	0.000	0.000	0.000	0.000
8	A	131	LEU	0	-0.012	0.004	13.163	-0.262	-0.262	0.000	0.000	0.000	0.000
9	A	132	THR	0	0.026	0.022	7.031	1.517	1.517	0.000	0.000	0.000	0.000
10	A	133	LEU	0	-0.015	0.005	8.026	-1.637	-1.637	0.000	0.000	0.000	0.000
11	A	134	ASP	-1	-0.761	-0.876	4.653	36.846	36.945	-0.001	-0.022	-0.076	0.000
12	A	135	PRO	0	-0.010	-0.027	4.513	-2.191	-2.052	-0.001	-0.011	-0.127	0.000
13	A	136	GLN	0	-0.022	0.001	4.462	-3.761	-3.608	-0.001	-0.004	-0.147	0.000
14	A	137	LYS	1	0.880	0.917	5.029	-36.966	-36.966	0.000	0.000	0.000	0.000
15	A	138	ARG	1	0.786	0.904	8.591	-18.963	-18.963	0.000	0.000	0.000	0.000
16	A	139	LEU	0	0.036	0.035	9.178	-1.002	-1.002	0.000	0.000	0.000	0.000
17	A	140	VAL	0	-0.019	-0.026	9.735	1.415	1.415	0.000	0.000	0.000	0.000
18	A	141	THR	0	0.005	0.016	12.007	-0.693	-0.693	0.000	0.000	0.000	0.000
19	A	142	TYR	0	-0.022	-0.035	13.498	0.633	0.633	0.000	0.000	0.000	0.000
20	A	143	LYS	1	0.839	0.894	15.396	-15.284	-15.284	0.000	0.000	0.000	0.000
21	A	144	GLY	0	-0.013	0.001	13.854	-0.499	-0.499	0.000	0.000	0.000	0.000
22	A	145	GLU	-1	-0.875	-0.919	14.911	14.752	14.752	0.000	0.000	0.000	0.000
23	A	146	GLU	-1	-0.853	-0.919	14.710	17.315	17.315	0.000	0.000	0.000	0.000
24	A	147	LEU	0	0.000	0.010	15.845	-0.982	-0.982	0.000	0.000	0.000	0.000
25	A	148	ARG	1	0.845	0.903	16.848	-13.983	-13.983	0.000	0.000	0.000	0.000
26	A	149	LEU	0	-0.017	-0.001	15.629	-0.774	-0.774	0.000	0.000	0.000	0.000
27	A	150	SER	0	-0.006	-0.023	18.505	0.169	0.169	0.000	0.000	0.000	0.000
28	A	151	PRO	0	0.048	0.004	16.989	0.478	0.478	0.000	0.000	0.000	0.000
29	A	152	LYS	1	0.889	0.933	16.984	-12.375	-12.375	0.000	0.000	0.000	0.000
30	A	153	GLU	-1	-0.756	-0.839	18.723	12.460	12.460	0.000	0.000	0.000	0.000
31	A	154	PHE	0	0.024	0.011	9.519	0.232	0.232	0.000	0.000	0.000	0.000
32	A	155	ASP	-1	-0.805	-0.885	14.315	15.751	15.751	0.000	0.000	0.000	0.000
33	A	156	ILE	0	-0.015	-0.017	15.346	0.289	0.289	0.000	0.000	0.000	0.000
34	A	157	LEU	0	0.010	0.005	14.676	0.113	0.113	0.000	0.000	0.000	0.000
35	A	158	ALA	0	0.021	0.002	10.980	0.679	0.679	0.000	0.000	0.000	0.000
36	A	159	LEU	0	-0.033	-0.007	12.423	0.838	0.838	0.000	0.000	0.000	0.000
37	A	160	LEU	0	-0.024	-0.022	15.001	0.140	0.140	0.000	0.000	0.000	0.000
38	A	161	ILE	0	-0.024	-0.010	10.672	-0.222	-0.222	0.000	0.000	0.000	0.000
39	A	162	ARG	1	0.921	0.975	11.202	-17.413	-17.413	0.000	0.000	0.000	0.000
40	A	163	GLN	0	0.017	0.024	12.864	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	164	PRO	0	0.053	0.031	13.961	-1.155	-1.155	0.000	0.000	0.000	0.000
42	A	165	GLY	0	-0.063	-0.032	16.746	-0.340	-0.340	0.000	0.000	0.000	0.000
43	A	166	ARG	1	0.835	0.909	19.157	-14.328	-14.328	0.000	0.000	0.000	0.000
44	A	167	VAL	0	-0.056	-0.037	21.061	0.090	0.090	0.000	0.000	0.000	0.000
45	A	168	TYR	0	0.009	-0.006	16.321	-0.232	-0.232	0.000	0.000	0.000	0.000
46	A	169	SER	0	0.026	0.000	23.294	-0.350	-0.350	0.000	0.000	0.000	0.000
47	A	170	ARG	1	0.879	0.886	25.469	-8.779	-8.779	0.000	0.000	0.000	0.000
48	A	171	GLN	0	0.046	0.016	26.468	0.230	0.230	0.000	0.000	0.000	0.000
49	A	172	GLU	-1	-0.775	-0.855	22.184	12.260	12.260	0.000	0.000	0.000	0.000
50	A	173	ILE	0	0.004	-0.002	21.216	0.336	0.336	0.000	0.000	0.000	0.000
51	A	174	GLY	0	0.033	-0.001	22.430	0.176	0.176	0.000	0.000	0.000	0.000
52	A	175	GLN	0	-0.064	-0.034	22.814	-0.410	-0.410	0.000	0.000	0.000	0.000
53	A	176	GLU	-1	-0.906	-0.954	18.659	13.429	13.429	0.000	0.000	0.000	0.000
54	A	177	ILE	0	-0.068	-0.027	17.426	0.410	0.410	0.000	0.000	0.000	0.000
55	A	178	TRP	0	0.015	-0.010	20.223	0.111	0.111	0.000	0.000	0.000	0.000
56	A	179	GLN	0	-0.020	-0.003	20.238	-0.618	-0.618	0.000	0.000	0.000	0.000
57	A	180	GLY	0	0.032	0.013	24.344	-0.308	-0.308	0.000	0.000	0.000	0.000
58	A	181	ARG	1	0.876	0.959	25.712	-10.346	-10.346	0.000	0.000	0.000	0.000
59	A	182	LEU	0	-0.051	-0.026	26.399	0.049	0.049	0.000	0.000	0.000	0.000
60	A	183	PRO	0	0.023	0.023	30.264	-0.066	-0.066	0.000	0.000	0.000	0.000
61	A	184	GLU	-1	-0.874	-0.944	33.899	7.616	7.616	0.000	0.000	0.000	0.000
62	A	185	GLY	0	0.006	0.004	35.702	-0.144	-0.144	0.000	0.000	0.000	0.000
63	A	186	SER	0	-0.074	-0.026	32.006	0.073	0.073	0.000	0.000	0.000	0.000
64	A	187	ASN	0	0.027	0.002	32.193	0.178	0.178	0.000	0.000	0.000	0.000
65	A	188	VAL	0	0.042	0.022	26.446	0.194	0.194	0.000	0.000	0.000	0.000
66	A	189	VAL	0	0.044	0.028	24.808	0.253	0.253	0.000	0.000	0.000	0.000
67	A	190	ASP	-1	-0.755	-0.831	26.167	9.673	9.673	0.000	0.000	0.000	0.000
68	A	191	VAL	0	0.030	0.018	28.214	0.132	0.132	0.000	0.000	0.000	0.000
69	A	192	HIS	0	-0.006	-0.008	22.920	0.285	0.285	0.000	0.000	0.000	0.000
70	A	193	MET	0	-0.033	-0.006	21.416	0.446	0.446	0.000	0.000	0.000	0.000
71	A	194	ALA	0	-0.030	-0.012	24.763	0.194	0.194	0.000	0.000	0.000	0.000
72	A	195	ASN	0	-0.011	-0.020	25.011	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	196	LEU	0	0.008	0.009	18.552	0.187	0.187	0.000	0.000	0.000	0.000
74	A	197	ARG	1	0.826	0.882	22.415	-10.502	-10.502	0.000	0.000	0.000	0.000
75	A	198	ALA	0	-0.023	-0.009	24.484	0.046	0.046	0.000	0.000	0.000	0.000
76	A	199	LYS	1	0.866	0.909	21.587	-12.145	-12.145	0.000	0.000	0.000	0.000
77	A	200	LEU	0	-0.019	-0.007	18.354	0.252	0.252	0.000	0.000	0.000	0.000
78	A	201	ARG	1	0.891	0.945	21.961	-10.083	-10.083	0.000	0.000	0.000	0.000
79	A	202	ASP	-1	-0.940	-0.953	24.321	11.174	11.174	0.000	0.000	0.000	0.000
80	A	203	LEU	0	-0.001	0.011	18.965	0.037	0.037	0.000	0.000	0.000	0.000
81	A	204	ASP	-1	-0.843	-0.932	21.776	11.748	11.748	0.000	0.000	0.000	0.000
82	A	205	GLY	0	0.002	-0.010	21.289	0.199	0.199	0.000	0.000	0.000	0.000
83	A	206	TYR	0	-0.105	-0.061	22.053	-0.318	-0.318	0.000	0.000	0.000	0.000
84	A	207	GLY	0	-0.060	-0.037	24.230	0.161	0.161	0.000	0.000	0.000	0.000
85	A	208	LEU	0	0.017	0.034	18.811	0.048	0.048	0.000	0.000	0.000	0.000
86	A	209	LEU	0	0.057	0.034	21.368	0.174	0.174	0.000	0.000	0.000	0.000
87	A	210	ARG	1	0.876	0.945	22.851	-12.038	-12.038	0.000	0.000	0.000	0.000
88	A	211	THR	0	0.015	0.015	25.502	0.231	0.231	0.000	0.000	0.000	0.000
89	A	212	VAL	0	-0.013	-0.004	27.016	-0.254	-0.254	0.000	0.000	0.000	0.000
90	A	213	ARG	1	0.948	0.979	29.618	-8.229	-8.229	0.000	0.000	0.000	0.000
91	A	214	GLY	0	0.100	0.058	32.616	0.060	0.060	0.000	0.000	0.000	0.000
92	A	215	VAL	0	-0.045	-0.033	29.536	-0.222	-0.222	0.000	0.000	0.000	0.000
93	A	216	GLY	0	0.020	0.003	27.135	0.078	0.078	0.000	0.000	0.000	0.000
94	A	217	TYR	0	-0.065	-0.051	23.773	-0.261	-0.261	0.000	0.000	0.000	0.000
95	A	218	ALA	0	0.057	0.044	21.587	0.253	0.253	0.000	0.000	0.000	0.000
96	A	219	LEU	0	0.023	0.020	15.555	-0.454	-0.454	0.000	0.000	0.000	0.000
97	A	220	ARG	1	0.934	0.958	18.615	-13.674	-13.674	0.000	0.000	0.000	0.000
98	A	221	GLY	0	0.089	0.047	17.123	-0.358	-0.358	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:124:GLU)