FMO DATABASE

FMODB ID: ZVG5N

Calculation Name: 2B9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B9C

Chain ID: A

ChEMBL ID:

UniProt ID: P04692

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-708829.388193
FMO2-HF: Nuclear repulsion	653688.596307
FMO2-HF: Total energy	-55140.791886
FMO2-MP2: Total energy	-55302.236015

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:98:GLU)

Summations of interaction energy for fragment #1(A:98: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.
24.23	28.089	0.081	-1.838	-2.1	0.012

Interaction energy analysis for fragmet #1(A:98:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.950 / q_NPA : -0.984

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	100	ASP	-1	-0.837	-0.909	3.174	21.842	25.390	0.081	-1.708	-1.920	0.011
4	A	101	ARG	1	0.882	0.925	4.170	-33.525	-33.214	0.000	-0.130	-0.180	0.001
5	A	102	ALA	0	0.028	0.007	6.105	-2.841	-2.841	0.000	0.000	0.000	0.000
6	A	103	GLN	0	-0.045	-0.030	8.657	-3.120	-3.120	0.000	0.000	0.000	0.000
7	A	104	GLU	-1	-0.828	-0.892	10.657	18.880	18.880	0.000	0.000	0.000	0.000
8	A	105	ARG	1	0.922	0.963	9.654	-23.439	-23.439	0.000	0.000	0.000	0.000
9	A	106	LEU	0	-0.009	-0.009	12.801	-0.640	-0.640	0.000	0.000	0.000	0.000
10	A	107	ALA	0	0.084	0.010	15.561	-0.847	-0.847	0.000	0.000	0.000	0.000
11	A	108	THR	0	-0.083	-0.023	14.821	-0.525	-0.525	0.000	0.000	0.000	0.000
12	A	109	ALA	0	-0.049	-0.048	17.543	-0.631	-0.631	0.000	0.000	0.000	0.000
13	A	110	LEU	0	0.033	0.035	19.356	-0.351	-0.351	0.000	0.000	0.000	0.000
14	A	111	GLN	0	0.053	0.032	20.725	-0.343	-0.343	0.000	0.000	0.000	0.000
15	A	112	LYS	1	0.890	0.938	21.607	-12.252	-12.252	0.000	0.000	0.000	0.000
16	A	113	LEU	0	-0.047	-0.022	23.493	-0.145	-0.145	0.000	0.000	0.000	0.000
17	A	114	GLU	-1	-0.868	-0.932	25.221	9.973	9.973	0.000	0.000	0.000	0.000
18	A	115	GLU	-1	-0.967	-0.973	26.287	9.921	9.921	0.000	0.000	0.000	0.000
19	A	116	ALA	0	-0.124	-0.071	27.647	-0.371	-0.371	0.000	0.000	0.000	0.000
20	A	117	GLU	-1	-0.932	-0.953	29.311	9.360	9.360	0.000	0.000	0.000	0.000
21	A	118	LYS	1	1.046	1.019	31.047	-8.542	-8.542	0.000	0.000	0.000	0.000
22	A	119	ALA	0	-0.047	-0.031	32.420	-0.272	-0.272	0.000	0.000	0.000	0.000
23	A	120	ALA	0	-0.005	0.015	33.321	-0.283	-0.283	0.000	0.000	0.000	0.000
24	A	121	ASP	-1	-0.825	-0.927	35.192	7.630	7.630	0.000	0.000	0.000	0.000
25	A	122	GLU	-1	-0.911	-0.963	36.990	7.370	7.370	0.000	0.000	0.000	0.000
26	A	123	SER	0	-0.228	-0.094	37.954	-0.270	-0.270	0.000	0.000	0.000	0.000
27	A	124	GLU	-1	-0.863	-0.937	39.796	7.083	7.083	0.000	0.000	0.000	0.000
28	A	125	ARG	1	0.955	0.975	41.616	-7.072	-7.072	0.000	0.000	0.000	0.000
29	A	126	GLY	0	-0.122	-0.073	42.819	-0.184	-0.184	0.000	0.000	0.000	0.000
30	A	127	MET	0	0.050	0.040	41.611	-0.141	-0.141	0.000	0.000	0.000	0.000
31	A	128	LYS	1	0.964	0.958	45.283	-6.331	-6.331	0.000	0.000	0.000	0.000
32	A	129	VAL	0	-0.152	-0.088	47.578	-0.176	-0.176	0.000	0.000	0.000	0.000
33	A	130	ILE	0	0.017	-0.009	45.984	-0.132	-0.132	0.000	0.000	0.000	0.000
34	A	131	GLU	-1	-0.821	-0.858	49.800	5.957	5.957	0.000	0.000	0.000	0.000
35	A	132	SER	0	0.030	-0.007	51.438	-0.147	-0.147	0.000	0.000	0.000	0.000
36	A	133	ARG	1	0.847	0.922	51.150	-6.017	-6.017	0.000	0.000	0.000	0.000
37	A	134	ALA	0	0.076	0.053	53.160	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	135	GLN	0	-0.017	-0.001	54.766	-0.154	-0.154	0.000	0.000	0.000	0.000
39	A	136	LYS	1	0.870	0.928	57.525	-5.284	-5.284	0.000	0.000	0.000	0.000
40	A	137	ASP	-1	-0.871	-0.959	57.154	5.274	5.274	0.000	0.000	0.000	0.000
41	A	138	GLU	-1	-0.914	-0.934	59.228	5.086	5.086	0.000	0.000	0.000	0.000
42	A	139	GLU	-1	-0.969	-0.987	60.955	4.755	4.755	0.000	0.000	0.000	0.000
43	A	140	LYS	1	0.825	0.924	63.371	-4.665	-4.665	0.000	0.000	0.000	0.000
44	A	141	MET	0	0.024	-0.002	61.903	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	142	GLU	-1	-0.827	-0.886	64.628	4.714	4.714	0.000	0.000	0.000	0.000
46	A	143	ILE	0	-0.048	-0.017	67.279	-0.098	-0.098	0.000	0.000	0.000	0.000
47	A	144	GLN	0	-0.057	-0.043	65.801	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	145	GLU	-1	-0.908	-0.969	67.387	4.544	4.544	0.000	0.000	0.000	0.000
49	A	146	ILE	0	-0.088	-0.047	70.803	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	147	GLN	0	0.083	0.044	71.652	0.004	0.004	0.000	0.000	0.000	0.000
51	A	148	LEU	0	-0.017	0.006	71.452	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	149	LYN	0	-0.026	-0.031	73.563	-0.061	-0.061	0.000	0.000	0.000	0.000
53	A	150	GLU	-1	-0.944	-0.947	76.668	4.013	4.013	0.000	0.000	0.000	0.000
54	A	151	ALA	0	-0.026	-0.033	77.477	-0.055	-0.055	0.000	0.000	0.000	0.000
55	A	152	LYS	1	0.885	0.956	74.627	-4.220	-4.220	0.000	0.000	0.000	0.000
56	A	153	HIS	0	0.081	0.027	80.143	-0.052	-0.052	0.000	0.000	0.000	0.000
57	A	154	ILE	0	-0.018	-0.005	82.610	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	155	ALA	0	-0.005	0.009	83.004	-0.053	-0.053	0.000	0.000	0.000	0.000
59	A	156	GLU	-1	-0.930	-0.980	82.460	3.784	3.784	0.000	0.000	0.000	0.000
60	A	157	ASP	-1	-1.033	-1.017	85.996	3.505	3.505	0.000	0.000	0.000	0.000
61	A	158	ALA	0	-0.026	-0.014	88.073	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	159	ASP	-1	-0.863	-0.944	86.833	3.595	3.595	0.000	0.000	0.000	0.000
63	A	160	ARG	1	0.944	0.985	86.798	-3.636	-3.636	0.000	0.000	0.000	0.000
64	A	161	LYS	1	0.943	0.968	91.473	-3.495	-3.495	0.000	0.000	0.000	0.000
65	A	162	TYR	0	-0.052	-0.003	93.216	-0.052	-0.052	0.000	0.000	0.000	0.000
66	A	163	GLU	-1	-0.905	-0.965	93.458	3.332	3.332	0.000	0.000	0.000	0.000
67	A	164	GLU	-1	-1.014	-1.000	96.207	3.261	3.261	0.000	0.000	0.000	0.000
68	A	165	VAL	0	-0.075	-0.065	97.954	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	166	ALA	0	0.096	0.061	98.323	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	167	ARG	1	0.916	0.962	100.252	-3.114	-3.114	0.000	0.000	0.000	0.000
71	A	168	LYS	1	0.928	0.939	101.007	-3.176	-3.176	0.000	0.000	0.000	0.000
72	A	169	LEU	0	0.006	-0.006	101.807	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	170	VAL	0	0.024	0.041	104.132	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	171	ILE	0	-0.032	-0.004	106.355	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	172	ILE	0	-0.049	-0.013	107.688	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	173	GLU	-1	-0.848	-0.937	108.796	2.882	2.882	0.000	0.000	0.000	0.000
77	A	174	SER	0	0.036	0.047	110.619	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	175	ASP	-1	-1.031	-1.036	112.437	2.815	2.815	0.000	0.000	0.000	0.000
79	A	176	LEU	0	-0.022	-0.023	112.857	-0.028	-0.028	0.000	0.000	0.000	0.000
80	A	177	GLU	-1	-0.924	-0.969	113.076	2.793	2.793	0.000	0.000	0.000	0.000
81	A	178	ARG	1	0.937	0.969	115.366	-2.795	-2.795	0.000	0.000	0.000	0.000
82	A	179	ALA	0	-0.138	-0.045	118.196	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	180	GLU	-1	-0.837	-0.951	117.409	2.716	2.716	0.000	0.000	0.000	0.000
84	A	181	GLU	-1	-0.901	-0.927	120.885	2.612	2.612	0.000	0.000	0.000	0.000
85	A	182	ARG	1	0.854	0.923	121.712	-2.634	-2.634	0.000	0.000	0.000	0.000
86	A	183	ALA	0	-0.082	-0.024	123.722	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	184	GLU	-1	-0.875	-0.951	124.723	2.508	2.508	0.000	0.000	0.000	0.000
88	A	185	LEU	0	0.056	0.033	126.512	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	186	SER	0	-0.101	-0.087	128.410	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	187	GLU	-1	-0.985	-0.977	127.065	2.518	2.518	0.000	0.000	0.000	0.000
91	A	188	GLY	0	0.056	0.028	130.888	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	189	LYS	1	0.906	0.961	132.700	-2.368	-2.368	0.000	0.000	0.000	0.000
93	A	190	CYS	0	-0.022	-0.027	133.341	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	191	ALA	0	0.058	0.045	135.313	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	192	GLU	-1	-0.960	-0.984	136.950	2.322	2.322	0.000	0.000	0.000	0.000
96	A	193	LEU	0	-0.050	-0.036	138.000	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	194	GLU	-1	-0.958	-0.968	138.692	2.312	2.312	0.000	0.000	0.000	0.000
98	A	195	GLU	-1	-0.926	-0.947	141.453	2.239	2.239	0.000	0.000	0.000	0.000
99	A	196	GLU	-1	-0.966	-0.999	143.127	2.218	2.218	0.000	0.000	0.000	0.000
100	A	197	LEU	0	-0.016	-0.006	143.734	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	198	LYS	1	0.918	0.941	145.510	-2.219	-2.219	0.000	0.000	0.000	0.000
102	A	199	THR	0	-0.004	0.002	147.403	-0.021	-0.021	0.000	0.000	0.000	0.000
103	A	200	VAL	0	-0.024	0.001	148.906	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	201	THR	0	0.000	-0.016	149.458	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	202	ASN	0	0.003	0.014	150.399	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	203	ASN	0	-0.049	-0.024	152.966	-0.027	-0.027	0.000	0.000	0.000	0.000
107	A	204	LEU	0	-0.027	-0.028	153.951	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	205	LYS	1	0.966	1.004	156.126	-2.042	-2.042	0.000	0.000	0.000	0.000
109	A	206	SER	0	-0.021	-0.008	157.997	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	207	LEU	0	-0.025	-0.024	158.921	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	208	GLU	-1	-0.875	-0.964	159.149	2.015	2.015	0.000	0.000	0.000	0.000
112	A	209	ASP	-1	-0.895	-0.911	161.938	1.982	1.982	0.000	0.000	0.000	0.000
113	A	210	LYS	1	0.832	0.932	164.055	-1.977	-1.977	0.000	0.000	0.000	0.000
114	A	211	VAL	0	0.024	-0.005	163.735	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	212	GLU	-1	-0.947	-0.970	166.709	1.920	1.920	0.000	0.000	0.000	0.000
116	A	213	GLU	-1	-0.864	-0.950	168.336	1.895	1.895	0.000	0.000	0.000	0.000
117	A	214	LEU	0	-0.024	-0.019	168.760	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	215	LEU	0	-0.007	-0.016	168.671	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	216	SER	0	0.009	0.028	172.495	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	217	LYS	1	0.860	0.923	173.265	-1.886	-1.886	0.000	0.000	0.000	0.000
121	A	218	ASN	0	-0.013	-0.013	174.706	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	219	TYR	0	0.044	0.024	176.406	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	220	HIS	0	-0.058	-0.042	177.994	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	221	LEU	0	0.028	0.029	178.703	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	222	GLU	-1	-0.865	-0.923	179.072	1.794	1.794	0.000	0.000	0.000	0.000
126	A	223	ASN	0	-0.122	-0.049	181.865	-0.015	-0.015	0.000	0.000	0.000	0.000
127	A	224	GLU	-1	-0.837	-0.936	183.944	1.729	1.729	0.000	0.000	0.000	0.000
128	A	225	VAL	0	0.003	0.006	184.035	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	226	ALA	0	-0.019	-0.020	186.276	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	227	ARG	1	0.819	0.911	188.111	-1.727	-1.727	0.000	0.000	0.000	0.000
131	A	228	LEU	0	-0.024	-0.013	188.939	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	229	LYS	1	0.978	0.994	186.732	-1.738	-1.738	0.000	0.000	0.000	0.000
133	A	230	LYS	1	0.897	0.948	192.459	-1.686	-1.686	0.000	0.000	0.000	0.000
134	A	231	LEU	0	0.001	0.016	195.245	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	232	VAL	0	0.018	0.008	195.066	0.009	0.009	0.000	0.000	0.000	0.000
136	A	233	GLY	0	-0.033	-0.002	197.897	-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:98:GLU)