FMO DATABASE

FMODB ID: R8KG8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-708636.855008
FMO2-HF: Nuclear repulsion	653492.576904
FMO2-HF: Total energy	-55144.278105
FMO2-MP2: Total energy	-55305.251446

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.
24.7	28.705	0.089	-1.876	-2.219	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 : -0.953 / 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	-0.839	-0.912	3.137	21.874	25.548	0.089	-1.743	-2.020	0.011
4	A	101	ARG	1	0.906	0.938	4.173	-33.546	-33.215	0.000	-0.133	-0.199	0.001
5	A	102	ALA	0	0.029	0.005	6.105	-2.955	-2.955	0.000	0.000	0.000	0.000
6	A	103	GLN	0	-0.045	-0.030	8.660	-3.271	-3.271	0.000	0.000	0.000	0.000
7	A	104	GLU	-1	-0.780	-0.855	10.657	19.294	19.294	0.000	0.000	0.000	0.000
8	A	105	ARG	1	0.835	0.914	10.414	-22.933	-22.933	0.000	0.000	0.000	0.000
9	A	106	LEU	0	-0.012	-0.008	12.801	-0.619	-0.619	0.000	0.000	0.000	0.000
10	A	107	ALA	0	0.085	0.014	15.561	-0.826	-0.826	0.000	0.000	0.000	0.000
11	A	108	THR	0	-0.065	-0.030	15.388	-0.638	-0.638	0.000	0.000	0.000	0.000
12	A	109	ALA	0	-0.041	-0.039	17.535	-0.631	-0.631	0.000	0.000	0.000	0.000
13	A	110	LEU	0	0.026	0.032	19.356	-0.347	-0.347	0.000	0.000	0.000	0.000
14	A	111	GLN	0	0.000	0.008	20.725	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	112	LYS	1	0.881	0.932	21.686	-12.323	-12.323	0.000	0.000	0.000	0.000
16	A	113	LEU	0	-0.036	-0.019	23.461	-0.170	-0.170	0.000	0.000	0.000	0.000
17	A	114	GLU	-1	-0.871	-0.933	25.221	10.002	10.002	0.000	0.000	0.000	0.000
18	A	115	GLU	-1	-0.914	-0.950	25.996	10.023	10.023	0.000	0.000	0.000	0.000
19	A	116	ALA	0	-0.111	-0.063	27.646	-0.373	-0.373	0.000	0.000	0.000	0.000
20	A	117	GLU	-1	-0.932	-0.949	29.311	9.364	9.364	0.000	0.000	0.000	0.000
21	A	118	LYS	1	0.982	0.990	31.047	-8.436	-8.436	0.000	0.000	0.000	0.000
22	A	119	ALA	0	-0.025	-0.021	32.362	-0.289	-0.289	0.000	0.000	0.000	0.000
23	A	120	ALA	0	0.005	0.027	33.317	-0.286	-0.286	0.000	0.000	0.000	0.000
24	A	121	ASP	-1	-0.814	-0.911	35.192	7.568	7.568	0.000	0.000	0.000	0.000
25	A	122	GLU	-1	-0.931	-0.967	36.997	7.269	7.269	0.000	0.000	0.000	0.000
26	A	123	SER	0	-0.155	-0.078	38.047	-0.215	-0.215	0.000	0.000	0.000	0.000
27	A	124	GLU	-1	-0.853	-0.928	39.799	6.992	6.992	0.000	0.000	0.000	0.000
28	A	125	ARG	1	0.893	0.939	41.616	-7.235	-7.235	0.000	0.000	0.000	0.000
29	A	126	GLY	0	-0.120	-0.072	42.823	-0.179	-0.179	0.000	0.000	0.000	0.000
30	A	127	MET	0	0.039	0.037	42.221	-0.137	-0.137	0.000	0.000	0.000	0.000
31	A	128	LYS	1	0.969	0.959	45.283	-6.372	-6.372	0.000	0.000	0.000	0.000
32	A	129	VAL	0	-0.149	-0.081	47.478	-0.173	-0.173	0.000	0.000	0.000	0.000
33	A	130	ILE	0	0.016	-0.015	46.177	-0.130	-0.130	0.000	0.000	0.000	0.000
34	A	131	GLU	-1	-0.822	-0.861	49.798	5.969	5.969	0.000	0.000	0.000	0.000
35	A	132	SER	0	0.014	-0.008	51.438	-0.141	-0.141	0.000	0.000	0.000	0.000
36	A	133	ARG	1	0.871	0.936	50.707	-6.027	-6.027	0.000	0.000	0.000	0.000
37	A	134	ALA	0	0.064	0.047	53.144	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	135	GLN	0	0.000	-0.001	54.347	-0.158	-0.158	0.000	0.000	0.000	0.000
39	A	136	LYS	1	0.805	0.885	57.600	-5.130	-5.130	0.000	0.000	0.000	0.000
40	A	137	ASP	-1	-0.896	-0.965	57.592	5.269	5.269	0.000	0.000	0.000	0.000
41	A	138	GLU	-1	-0.909	-0.936	59.229	5.139	5.139	0.000	0.000	0.000	0.000
42	A	139	GLU	-1	-0.899	-0.942	60.961	4.802	4.802	0.000	0.000	0.000	0.000
43	A	140	LYS	1	0.854	0.942	63.370	-4.662	-4.662	0.000	0.000	0.000	0.000
44	A	141	MET	0	0.040	0.006	61.858	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	142	GLU	-1	-0.868	-0.910	64.983	4.637	4.637	0.000	0.000	0.000	0.000
46	A	143	ILE	0	-0.040	-0.018	67.287	-0.094	-0.094	0.000	0.000	0.000	0.000
47	A	144	GLN	0	-0.060	-0.039	65.706	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	145	GLU	-1	-0.913	-0.969	68.188	4.493	4.493	0.000	0.000	0.000	0.000
49	A	146	ILE	0	-0.076	-0.046	70.812	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	147	GLN	0	0.072	0.040	71.834	0.008	0.008	0.000	0.000	0.000	0.000
51	A	148	LEU	0	-0.025	0.002	71.223	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	149	LYN	0	0.028	0.010	73.240	-0.068	-0.068	0.000	0.000	0.000	0.000
53	A	150	GLU	-1	-0.930	-0.936	76.677	4.011	4.011	0.000	0.000	0.000	0.000
54	A	151	ALA	0	-0.020	-0.030	77.388	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	152	LYS	1	0.857	0.920	74.007	-4.249	-4.249	0.000	0.000	0.000	0.000
56	A	153	HIS	0	0.061	0.018	80.151	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	154	ILE	0	-0.026	-0.008	82.623	-0.057	-0.057	0.000	0.000	0.000	0.000
58	A	155	ALA	0	0.011	0.014	82.927	-0.052	-0.052	0.000	0.000	0.000	0.000
59	A	156	GLU	-1	-0.813	-0.891	83.066	3.733	3.733	0.000	0.000	0.000	0.000
60	A	157	ASP	-1	-0.881	-0.941	86.004	3.495	3.495	0.000	0.000	0.000	0.000
61	A	158	ALA	0	-0.023	0.007	88.088	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	159	ASP	-1	-0.865	-0.948	87.149	3.588	3.588	0.000	0.000	0.000	0.000
63	A	160	ARG	1	0.759	0.872	86.553	-3.661	-3.661	0.000	0.000	0.000	0.000
64	A	161	LYS	1	0.830	0.894	90.724	-3.531	-3.531	0.000	0.000	0.000	0.000
65	A	162	TYR	0	-0.039	0.000	93.092	-0.053	-0.053	0.000	0.000	0.000	0.000
66	A	163	GLU	-1	-0.868	-0.958	93.688	3.318	3.318	0.000	0.000	0.000	0.000
67	A	164	GLU	-1	-0.958	-0.950	96.215	3.226	3.226	0.000	0.000	0.000	0.000
68	A	165	VAL	0	-0.081	-0.081	97.967	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	166	ALA	0	0.093	0.058	98.412	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	167	ARG	1	0.921	0.971	100.260	-3.119	-3.119	0.000	0.000	0.000	0.000
71	A	168	LYS	1	0.838	0.889	100.133	-3.213	-3.213	0.000	0.000	0.000	0.000
72	A	169	LEU	0	0.012	0.005	101.743	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	170	VAL	0	0.021	0.030	104.004	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	171	ILE	0	-0.031	0.013	106.312	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	172	ILE	0	-0.054	-0.011	107.854	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	173	GLU	-1	-0.806	-0.949	108.746	2.895	2.895	0.000	0.000	0.000	0.000
77	A	174	SER	0	0.000	0.045	110.626	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	175	ASP	-1	-0.985	-1.017	112.450	2.798	2.798	0.000	0.000	0.000	0.000
79	A	176	LEU	0	-0.008	0.000	113.124	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	177	GLU	-1	-0.934	-0.980	113.690	2.789	2.789	0.000	0.000	0.000	0.000
81	A	178	ARG	1	0.903	0.943	113.777	-2.820	-2.820	0.000	0.000	0.000	0.000
82	A	179	ALA	0	-0.137	-0.056	118.203	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	180	GLU	-1	-0.866	-0.960	117.661	2.711	2.711	0.000	0.000	0.000	0.000
84	A	181	GLU	-1	-0.912	-0.918	120.893	2.617	2.617	0.000	0.000	0.000	0.000
85	A	182	ARG	1	0.857	0.918	121.464	-2.643	-2.643	0.000	0.000	0.000	0.000
86	A	183	ALA	0	-0.057	-0.023	123.682	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	184	GLU	-1	-0.872	-0.943	124.745	2.511	2.511	0.000	0.000	0.000	0.000
88	A	185	LEU	0	0.052	0.028	126.221	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	186	SER	0	-0.091	-0.054	128.426	-0.026	-0.026	0.000	0.000	0.000	0.000
90	A	187	GLU	-1	-0.969	-0.980	127.232	2.512	2.512	0.000	0.000	0.000	0.000
91	A	188	GLY	0	0.049	0.019	130.895	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	189	LYS	1	0.839	0.918	132.709	-2.360	-2.360	0.000	0.000	0.000	0.000
93	A	190	CYS	0	-0.060	-0.046	132.955	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	191	ALA	0	0.050	0.046	135.244	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	192	GLU	-1	-0.898	-0.952	136.936	2.329	2.329	0.000	0.000	0.000	0.000
96	A	193	LEU	0	-0.037	-0.031	137.659	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	194	GLU	-1	-0.947	-0.964	138.350	2.309	2.309	0.000	0.000	0.000	0.000
98	A	195	GLU	-1	-0.925	-0.944	141.468	2.231	2.231	0.000	0.000	0.000	0.000
99	A	196	GLU	-1	-0.969	-0.998	143.134	2.229	2.229	0.000	0.000	0.000	0.000
100	A	197	LEU	0	-0.012	-0.007	143.914	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	198	LYS	1	0.925	0.961	145.423	-2.226	-2.226	0.000	0.000	0.000	0.000
102	A	199	THR	0	-0.026	-0.010	147.017	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	200	VAL	0	-0.011	0.003	148.815	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	201	THR	0	0.003	-0.020	149.379	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	202	ASN	0	-0.003	0.008	150.569	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	203	ASN	0	-0.025	-0.009	153.404	-0.024	-0.024	0.000	0.000	0.000	0.000
107	A	204	LEU	0	-0.039	-0.031	153.807	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	205	LYS	1	0.846	0.917	156.134	-2.028	-2.028	0.000	0.000	0.000	0.000
109	A	206	SER	0	0.003	0.001	157.843	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	207	LEU	0	-0.050	-0.032	158.972	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	208	GLU	-1	-0.894	-0.969	159.071	2.011	2.011	0.000	0.000	0.000	0.000
112	A	209	ASP	-1	-0.802	-0.842	161.945	1.988	1.988	0.000	0.000	0.000	0.000
113	A	210	LYS	1	0.866	0.938	164.068	-1.976	-1.976	0.000	0.000	0.000	0.000
114	A	211	VAL	0	0.027	-0.008	163.994	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	212	GLU	-1	-0.938	-0.958	166.717	1.922	1.922	0.000	0.000	0.000	0.000
116	A	213	GLU	-1	-0.817	-0.904	168.343	1.895	1.895	0.000	0.000	0.000	0.000
117	A	214	LEU	0	-0.021	-0.016	168.361	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	215	LEU	0	0.017	-0.007	168.880	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	216	SER	0	-0.013	0.010	172.503	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	217	LYS	1	0.792	0.879	172.330	-1.895	-1.895	0.000	0.000	0.000	0.000
121	A	218	ASN	0	-0.004	-0.009	174.672	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	219	TYR	0	0.016	0.010	176.347	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	220	HIS	0	-0.035	-0.028	178.001	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	221	LEU	0	0.023	0.022	178.526	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	222	GLU	-1	-0.854	-0.918	179.840	1.787	1.787	0.000	0.000	0.000	0.000
126	A	223	ASN	0	-0.126	-0.055	181.929	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	224	GLU	-1	-0.845	-0.933	183.952	1.728	1.728	0.000	0.000	0.000	0.000
128	A	225	VAL	0	0.004	0.003	183.871	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	226	ALA	0	-0.033	-0.030	186.282	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	227	ARG	1	0.822	0.917	188.119	-1.727	-1.727	0.000	0.000	0.000	0.000
131	A	228	LEU	0	-0.006	-0.008	188.986	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	229	LYS	1	0.982	1.000	186.380	-1.742	-1.742	0.000	0.000	0.000	0.000
133	A	230	LYS	1	0.896	0.945	192.467	-1.687	-1.687	0.000	0.000	0.000	0.000
134	A	231	LEU	0	0.009	0.025	195.253	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	232	VAL	0	0.004	-0.002	195.048	0.009	0.009	0.000	0.000	0.000	0.000
136	A	233	GLY	0	-0.026	0.003	197.905	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:98:GLU)