FMO DATABASE

FMODB ID: 39Y4L

Calculation Name: 2A61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A61

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZG9

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	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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1225882.884521
FMO2-HF: Nuclear repulsion	1169106.331635
FMO2-HF: Total energy	-56776.552886
FMO2-MP2: Total energy	-56944.562437

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
89.255	92.817	6.057	-3.856	-5.765	0.014

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.033 / q_NPA : 1.012

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	7	PRO	0	0.019	-0.003	2.366	-0.857	0.432	3.906	-2.235	-2.961	0.010
4	A	8	PHE	0	0.052	0.020	2.363	-3.634	-1.970	2.143	-1.397	-2.410	0.003
5	A	9	GLU	-1	-0.823	-0.883	3.584	-28.837	-28.228	0.008	-0.224	-0.394	0.001
6	A	10	ARG	1	0.945	0.967	5.429	30.845	30.845	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.074	0.045	7.158	1.599	1.599	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.013	0.004	6.957	1.406	1.406	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.847	0.910	8.822	26.178	26.178	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.919	-0.968	11.421	-16.458	-16.458	0.000	0.000	0.000	0.000
11	A	15	ILE	0	0.008	0.009	11.499	1.104	1.104	0.000	0.000	0.000	0.000
12	A	16	CYS	0	-0.052	-0.038	12.525	0.956	0.956	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.022	-0.008	15.346	0.910	0.910	0.000	0.000	0.000	0.000
14	A	18	MET	0	0.046	0.017	16.575	0.986	0.986	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.034	0.025	17.919	0.688	0.688	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.883	0.945	19.478	14.166	14.166	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.031	-0.023	21.213	0.594	0.594	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.821	-0.904	22.997	-9.793	-9.793	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.040	0.013	24.244	0.419	0.419	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.822	0.879	24.323	11.895	11.895	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.842	0.924	26.676	10.526	10.526	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.037	0.024	29.774	0.271	0.271	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.036	-0.013	29.145	0.200	0.200	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.913	0.961	32.786	8.435	8.435	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.902	-0.946	34.953	-7.962	-7.962	0.000	0.000	0.000	0.000
26	A	30	PHE	0	-0.059	-0.032	35.063	0.184	0.184	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.016	0.023	37.227	0.131	0.131	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.049	-0.007	32.950	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	33	THR	0	0.014	-0.011	33.112	-0.252	-0.252	0.000	0.000	0.000	0.000
30	A	34	PRO	0	0.032	-0.013	27.573	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.059	0.038	28.898	-0.178	-0.178	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.017	0.001	30.389	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	37	PHE	0	0.066	0.023	26.104	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.848	-0.906	25.846	-11.941	-11.941	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.031	-0.014	28.290	-0.118	-0.118	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.012	0.002	31.269	0.028	0.028	0.000	0.000	0.000	0.000
37	A	41	GLN	0	0.017	0.002	23.990	0.082	0.082	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.834	0.944	23.847	12.193	12.193	0.000	0.000	0.000	0.000
39	A	43	ILE	0	-0.016	-0.007	28.592	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	44	TYR	0	-0.004	0.000	29.169	0.032	0.032	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.032	-0.013	25.828	0.010	0.010	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.874	-0.939	25.603	-11.949	-11.949	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.022	0.028	29.876	0.171	0.171	0.000	0.000	0.000	0.000
44	A	48	PRO	0	-0.006	-0.023	33.284	-0.132	-0.132	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.884	0.957	28.890	10.360	10.360	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.869	0.943	34.739	8.645	8.645	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.032	0.005	34.955	-0.288	-0.288	0.000	0.000	0.000	0.000
48	A	52	GLY	0	-0.054	-0.051	34.948	-0.160	-0.160	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.812	-0.905	31.188	-9.810	-9.810	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.018	0.010	30.142	-0.388	-0.388	0.000	0.000	0.000	0.000
51	A	55	SER	0	-0.092	-0.050	30.657	-0.184	-0.184	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.010	-0.002	26.874	-0.207	-0.207	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.010	0.001	25.093	-0.416	-0.416	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.060	-0.038	25.685	-0.362	-0.362	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.042	0.041	26.756	-0.303	-0.303	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.032	-0.006	27.722	0.146	0.146	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.060	0.031	31.199	0.100	0.100	0.000	0.000	0.000	0.000
58	A	62	LYS	1	1.018	0.994	34.570	8.922	8.922	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.035	0.027	37.042	0.022	0.022	0.000	0.000	0.000	0.000
60	A	64	THR	0	0.014	0.007	33.880	0.094	0.094	0.000	0.000	0.000	0.000
61	A	65	VAL	0	0.017	0.017	33.740	0.073	0.073	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.023	-0.009	36.237	0.154	0.154	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.022	-0.016	39.576	0.167	0.167	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.060	-0.039	33.378	0.128	0.128	0.000	0.000	0.000	0.000
65	A	69	VAL	0	0.066	0.025	36.676	0.024	0.024	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.987	1.002	38.848	7.285	7.285	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.947	0.978	37.636	8.202	8.202	0.000	0.000	0.000	0.000
68	A	72	LEU	0	0.006	0.017	35.328	0.058	0.058	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.815	-0.889	40.012	-7.285	-7.285	0.000	0.000	0.000	0.000
70	A	74	ALA	0	-0.036	-0.009	42.954	0.130	0.130	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.905	-0.949	41.853	-7.079	-7.079	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.009	0.016	43.326	0.008	0.008	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.003	0.002	37.662	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.028	-0.017	36.124	-0.227	-0.227	0.000	0.000	0.000	0.000
75	A	79	THR	0	0.043	0.019	39.981	0.227	0.227	0.000	0.000	0.000	0.000
76	A	80	ARG	1	0.824	0.894	41.244	6.974	6.974	0.000	0.000	0.000	0.000
77	A	81	THR	0	0.028	0.010	41.864	0.207	0.207	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.007	0.002	43.487	-0.160	-0.160	0.000	0.000	0.000	0.000
79	A	83	ASP	-1	-0.768	-0.892	42.007	-7.747	-7.747	0.000	0.000	0.000	0.000
80	A	84	PRO	0	-0.042	-0.014	43.184	0.147	0.147	0.000	0.000	0.000	0.000
81	A	85	ALA	0	-0.008	-0.005	43.641	0.152	0.152	0.000	0.000	0.000	0.000
82	A	86	ASP	-1	-0.875	-0.940	44.213	-7.053	-7.053	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.962	0.967	46.171	6.156	6.156	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.906	0.960	46.127	6.871	6.871	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.030	0.015	41.918	-0.110	-0.110	0.000	0.000	0.000	0.000
86	A	90	TYR	0	-0.034	-0.034	41.317	0.145	0.145	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.022	-0.012	36.758	-0.216	-0.216	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.038	-0.021	37.108	0.228	0.228	0.000	0.000	0.000	0.000
89	A	93	VAL	0	0.021	-0.010	37.258	-0.248	-0.248	0.000	0.000	0.000	0.000
90	A	94	ILE	0	0.008	0.017	34.007	0.104	0.104	0.000	0.000	0.000	0.000
91	A	95	THR	0	-0.024	-0.029	37.848	0.083	0.083	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.890	0.919	36.938	7.735	7.735	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.909	0.958	39.019	7.036	7.036	0.000	0.000	0.000	0.000
94	A	98	GLY	0	-0.004	-0.012	36.980	-0.120	-0.120	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.889	-0.958	34.644	-8.490	-8.490	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.898	-0.949	34.259	-7.632	-7.632	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.062	-0.008	32.464	-0.126	-0.126	0.000	0.000	0.000	0.000
98	A	102	ILE	0	-0.051	-0.027	28.866	-0.248	-0.248	0.000	0.000	0.000	0.000
99	A	103	GLU	-1	-0.809	-0.905	29.985	-8.609	-8.609	0.000	0.000	0.000	0.000
100	A	104	LYS	1	1.026	1.012	31.548	7.735	7.735	0.000	0.000	0.000	0.000
101	A	105	VAL	0	-0.076	-0.029	26.570	-0.174	-0.174	0.000	0.000	0.000	0.000
102	A	106	ILE	0	-0.035	-0.027	26.317	-0.378	-0.378	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.869	-0.915	27.338	-8.636	-8.636	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.887	0.957	27.555	9.268	9.268	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.881	0.929	19.615	12.427	12.427	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.894	-0.942	24.572	-10.154	-10.154	0.000	0.000	0.000	0.000
107	A	111	ASN	0	0.050	0.023	26.485	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.072	-0.038	20.911	-0.057	-0.057	0.000	0.000	0.000	0.000
109	A	113	ILE	0	-0.008	-0.015	20.041	-0.216	-0.216	0.000	0.000	0.000	0.000
110	A	114	GLU	-1	-0.914	-0.951	23.471	-9.146	-9.146	0.000	0.000	0.000	0.000
111	A	115	LYS	1	0.943	0.966	26.417	9.168	9.168	0.000	0.000	0.000	0.000
112	A	116	ILE	0	-0.010	0.012	19.682	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	117	THR	0	-0.041	-0.039	21.677	0.042	0.042	0.000	0.000	0.000	0.000
114	A	118	SER	0	-0.016	-0.007	23.477	0.195	0.195	0.000	0.000	0.000	0.000
115	A	119	ASP	-1	-0.947	-0.960	23.940	-9.824	-9.824	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.115	-0.051	18.718	-0.111	-0.111	0.000	0.000	0.000	0.000
117	A	121	GLY	0	0.055	0.041	22.621	0.049	0.049	0.000	0.000	0.000	0.000
118	A	122	LYS	1	0.997	0.991	23.905	8.744	8.744	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.903	-0.957	23.281	-10.498	-10.498	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.976	0.979	18.709	11.404	11.404	0.000	0.000	0.000	0.000
121	A	125	SER	0	0.037	0.006	19.430	-0.640	-0.640	0.000	0.000	0.000	0.000
122	A	126	SER	0	-0.033	-0.013	20.263	-0.253	-0.253	0.000	0.000	0.000	0.000
123	A	127	LYS	1	0.954	0.987	17.701	11.165	11.165	0.000	0.000	0.000	0.000
124	A	128	ILE	0	-0.002	0.002	14.973	-0.638	-0.638	0.000	0.000	0.000	0.000
125	A	129	LEU	0	-0.007	-0.008	15.918	-0.696	-0.696	0.000	0.000	0.000	0.000
126	A	130	ASP	-1	-0.903	-0.957	17.846	-12.843	-12.843	0.000	0.000	0.000	0.000
127	A	131	TYR	0	0.000	0.000	12.493	-0.429	-0.429	0.000	0.000	0.000	0.000
128	A	132	LEU	0	-0.027	-0.011	12.693	-1.175	-1.175	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.943	0.977	14.522	11.828	11.828	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.907	-0.947	13.876	-17.155	-17.155	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.046	-0.022	8.080	-1.070	-1.070	0.000	0.000	0.000	0.000
132	A	136	LYS	1	0.855	0.899	11.824	13.581	13.581	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.054	0.034	14.477	-0.077	-0.077	0.000	0.000	0.000	0.000
134	A	138	VAL	0	-0.052	-0.030	10.884	-0.125	-0.125	0.000	0.000	0.000	0.000
135	A	139	MET	0	-0.034	-0.031	8.828	-0.632	-0.632	0.000	0.000	0.000	0.000
136	A	140	GLU	-1	-0.814	-0.895	12.641	-15.341	-15.341	0.000	0.000	0.000	0.000
137	A	141	ARG	1	0.907	0.969	14.711	19.425	19.425	0.000	0.000	0.000	0.000
138	A	142	ASN	0	-0.075	-0.054	11.177	-0.501	-0.501	0.000	0.000	0.000	0.000
139	A	143	PHE	0	-0.012	0.004	12.972	-0.843	-0.843	0.000	0.000	0.000	0.000
140	A	144	SER	0	0.015	0.020	14.702	0.066	0.066	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.942	0.990	9.312	30.913	30.913	0.000	0.000	0.000	0.000
142	A	146	GLN	0	-0.017	-0.012	13.461	0.174	0.174	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)