FMO DATABASE

FMODB ID: 85Y1Y

Calculation Name: 3SIR-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SIR

Chain ID: D

ChEMBL ID:

UniProt ID: O01382

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:

Apendix: None

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	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1885977.730225
FMO2-HF: Nuclear repulsion	1815041.953659
FMO2-HF: Total energy	-70935.776566
FMO2-MP2: Total energy	-71138.048791

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(D:10:ALA)

Summations of interaction energy for fragment #1(D:10:ALA)

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.
-7.036	-4.118	2.545	-2.158	-3.305	-0.003

Interaction energy analysis for fragmet #1(D:10:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.013

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	D	12	GLU	-1	-0.812	-0.887	3.367	-1.391	1.035	-0.016	-1.074	-1.336	-0.002
4	D	13	TYR	0	-0.033	-0.043	4.184	0.157	0.309	0.000	-0.032	-0.120	0.000
5	D	14	ASN	0	-0.003	-0.008	6.151	-0.223	-0.223	0.000	0.000	0.000	0.000
6	D	15	MET	0	-0.043	-0.013	7.280	0.075	0.075	0.000	0.000	0.000	0.000
7	D	16	ARG	1	0.941	0.951	9.865	0.038	0.038	0.000	0.000	0.000	0.000
8	D	17	HIS	0	0.014	0.028	9.754	-0.019	-0.019	0.000	0.000	0.000	0.000
9	D	18	LYS	1	0.872	0.941	13.720	-0.162	-0.162	0.000	0.000	0.000	0.000
10	D	19	ASN	0	0.031	0.007	17.414	-0.029	-0.029	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.815	0.890	14.772	0.008	0.008	0.000	0.000	0.000	0.000
12	D	21	GLY	0	0.053	0.022	17.046	0.018	0.018	0.000	0.000	0.000	0.000
13	D	22	MET	0	-0.044	-0.013	19.268	-0.019	-0.019	0.000	0.000	0.000	0.000
14	D	23	ALA	0	0.008	0.000	21.595	0.004	0.004	0.000	0.000	0.000	0.000
15	D	24	LEU	0	-0.008	-0.003	24.101	-0.009	-0.009	0.000	0.000	0.000	0.000
16	D	25	ILE	0	0.020	0.018	26.797	-0.001	-0.001	0.000	0.000	0.000	0.000
17	D	26	PHE	0	0.015	-0.005	27.742	-0.001	-0.001	0.000	0.000	0.000	0.000
18	D	27	ASN	0	-0.061	-0.044	31.895	-0.006	-0.006	0.000	0.000	0.000	0.000
19	D	28	HIS	0	0.047	0.028	35.104	0.002	0.002	0.000	0.000	0.000	0.000
20	D	43	ASN	0	0.061	0.010	36.664	0.002	0.002	0.000	0.000	0.000	0.000
21	D	44	VAL	0	0.080	0.034	36.847	0.000	0.000	0.000	0.000	0.000	0.000
22	D	45	ASP	-1	-0.765	-0.870	33.266	0.001	0.001	0.000	0.000	0.000	0.000
23	D	46	CYS	0	-0.036	-0.006	32.287	0.001	0.001	0.000	0.000	0.000	0.000
24	D	47	GLU	-1	-0.848	-0.877	32.521	0.010	0.010	0.000	0.000	0.000	0.000
25	D	48	ASN	0	-0.001	-0.006	31.165	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	49	LEU	0	0.062	0.044	25.730	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	50	THR	0	0.004	-0.025	27.405	0.003	0.003	0.000	0.000	0.000	0.000
28	D	51	ARG	1	0.789	0.874	28.412	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	52	VAL	0	0.022	-0.004	24.365	0.000	0.000	0.000	0.000	0.000	0.000
30	D	53	LEU	0	0.003	-0.001	22.045	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	54	LYS	1	0.876	0.931	23.553	-0.028	-0.028	0.000	0.000	0.000	0.000
32	D	55	GLN	0	-0.016	0.002	25.084	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	56	LEU	0	-0.060	-0.019	19.893	-0.006	-0.006	0.000	0.000	0.000	0.000
34	D	57	ASP	-1	-0.814	-0.885	19.740	0.000	0.000	0.000	0.000	0.000	0.000
35	D	58	PHE	0	-0.020	-0.018	18.055	0.012	0.012	0.000	0.000	0.000	0.000
36	D	59	GLU	-1	-0.832	-0.908	22.095	0.039	0.039	0.000	0.000	0.000	0.000
37	D	60	VAL	0	-0.065	-0.028	24.927	0.006	0.006	0.000	0.000	0.000	0.000
38	D	61	THR	0	-0.040	-0.004	27.269	-0.004	-0.004	0.000	0.000	0.000	0.000
39	D	62	VAL	0	0.016	-0.006	29.703	0.001	0.001	0.000	0.000	0.000	0.000
40	D	63	TYR	0	0.018	0.011	29.094	-0.002	-0.002	0.000	0.000	0.000	0.000
41	D	64	LYS	1	0.899	0.924	33.951	-0.024	-0.024	0.000	0.000	0.000	0.000
42	D	65	ASP	-1	-0.771	-0.862	37.260	0.039	0.039	0.000	0.000	0.000	0.000
43	D	66	CYS	0	0.033	0.033	36.953	0.002	0.002	0.000	0.000	0.000	0.000
44	D	67	ARG	1	0.842	0.899	34.502	-0.045	-0.045	0.000	0.000	0.000	0.000
45	D	68	TYR	0	-0.014	-0.023	35.128	0.005	0.005	0.000	0.000	0.000	0.000
46	D	69	LYS	1	0.921	0.953	35.420	-0.043	-0.043	0.000	0.000	0.000	0.000
47	D	70	ASP	-1	-0.773	-0.880	34.923	0.053	0.053	0.000	0.000	0.000	0.000
48	D	71	ILE	0	-0.012	0.027	30.052	0.004	0.004	0.000	0.000	0.000	0.000
49	D	72	LEU	0	-0.035	-0.014	30.144	0.006	0.006	0.000	0.000	0.000	0.000
50	D	73	ARG	1	0.973	0.986	30.019	-0.054	-0.054	0.000	0.000	0.000	0.000
51	D	74	THR	0	-0.021	-0.026	29.870	0.004	0.004	0.000	0.000	0.000	0.000
52	D	75	ILE	0	-0.037	-0.028	25.284	0.005	0.005	0.000	0.000	0.000	0.000
53	D	76	GLU	-1	-0.925	-0.948	26.230	0.102	0.102	0.000	0.000	0.000	0.000
54	D	77	TYR	0	-0.022	-0.022	27.130	0.009	0.009	0.000	0.000	0.000	0.000
55	D	78	SER	0	-0.019	-0.030	25.024	0.005	0.005	0.000	0.000	0.000	0.000
56	D	79	ALA	0	-0.017	-0.004	22.487	0.011	0.011	0.000	0.000	0.000	0.000
57	D	80	SER	0	-0.026	-0.002	22.499	0.017	0.017	0.000	0.000	0.000	0.000
58	D	81	GLN	0	-0.029	0.003	23.497	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	82	ASN	0	0.049	0.029	19.999	0.040	0.040	0.000	0.000	0.000	0.000
60	D	83	HIS	0	0.037	0.004	17.350	-0.025	-0.025	0.000	0.000	0.000	0.000
61	D	84	SER	0	-0.015	-0.030	15.765	0.031	0.031	0.000	0.000	0.000	0.000
62	D	85	ASP	-1	-0.869	-0.914	15.266	0.199	0.199	0.000	0.000	0.000	0.000
63	D	86	SER	0	-0.043	-0.021	16.389	-0.033	-0.033	0.000	0.000	0.000	0.000
64	D	87	ASP	-1	-0.771	-0.874	12.741	0.158	0.158	0.000	0.000	0.000	0.000
65	D	88	CYS	0	-0.109	-0.045	12.369	0.035	0.035	0.000	0.000	0.000	0.000
66	D	89	ILE	0	0.024	0.025	14.889	-0.011	-0.011	0.000	0.000	0.000	0.000
67	D	90	LEU	0	-0.007	-0.001	17.993	-0.004	-0.004	0.000	0.000	0.000	0.000
68	D	91	VAL	0	-0.002	-0.005	20.677	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	92	ALA	0	-0.001	0.003	23.909	-0.004	-0.004	0.000	0.000	0.000	0.000
70	D	93	ILE	0	-0.007	-0.002	26.692	0.000	0.000	0.000	0.000	0.000	0.000
71	D	94	LEU	0	0.015	0.010	29.917	-0.005	-0.005	0.000	0.000	0.000	0.000
72	D	95	SER	0	0.018	0.005	32.788	0.002	0.002	0.000	0.000	0.000	0.000
73	D	114	ILE	0	0.011	-0.013	26.708	0.000	0.000	0.000	0.000	0.000	0.000
74	D	115	TRP	0	0.055	0.019	22.065	0.006	0.006	0.000	0.000	0.000	0.000
75	D	116	SER	0	0.001	-0.006	22.096	0.019	0.019	0.000	0.000	0.000	0.000
76	D	117	PHE	0	0.021	0.007	23.229	0.012	0.012	0.000	0.000	0.000	0.000
77	D	118	PHE	0	0.053	0.009	18.917	0.006	0.006	0.000	0.000	0.000	0.000
78	D	119	THR	0	-0.043	0.000	17.855	0.039	0.039	0.000	0.000	0.000	0.000
79	D	120	ALA	0	0.036	-0.002	14.736	0.002	0.002	0.000	0.000	0.000	0.000
80	D	121	ASN	0	-0.010	-0.009	16.415	0.033	0.033	0.000	0.000	0.000	0.000
81	D	122	HIS	0	-0.002	-0.002	19.770	0.002	0.002	0.000	0.000	0.000	0.000
82	D	123	CYS	0	-0.031	-0.009	19.393	-0.015	-0.015	0.000	0.000	0.000	0.000
83	D	124	PRO	0	0.080	0.043	15.967	0.022	0.022	0.000	0.000	0.000	0.000
84	D	125	SER	0	-0.043	-0.027	14.821	0.052	0.052	0.000	0.000	0.000	0.000
85	D	126	LEU	0	-0.049	-0.023	14.051	0.014	0.014	0.000	0.000	0.000	0.000
86	D	127	ALA	0	0.038	0.036	12.834	-0.026	-0.026	0.000	0.000	0.000	0.000
87	D	128	GLY	0	-0.009	0.000	8.747	0.084	0.084	0.000	0.000	0.000	0.000
88	D	129	LYS	1	0.794	0.911	8.168	-0.286	-0.286	0.000	0.000	0.000	0.000
89	D	130	PRO	0	0.005	0.001	10.280	-0.024	-0.024	0.000	0.000	0.000	0.000
90	D	131	LYS	1	0.860	0.945	12.866	-0.412	-0.412	0.000	0.000	0.000	0.000
91	D	132	LEU	0	-0.033	-0.008	15.170	-0.014	-0.014	0.000	0.000	0.000	0.000
92	D	133	PHE	0	0.006	-0.006	18.631	-0.003	-0.003	0.000	0.000	0.000	0.000
93	D	134	PHE	0	0.010	0.002	20.694	-0.012	-0.012	0.000	0.000	0.000	0.000
94	D	135	ILE	0	0.003	0.006	25.101	0.004	0.004	0.000	0.000	0.000	0.000
95	D	136	GLN	0	0.011	0.028	28.364	-0.008	-0.008	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.005	-0.004	31.572	0.001	0.001	0.000	0.000	0.000	0.000
97	D	170	ALA	0	0.006	-0.007	12.968	-0.018	-0.018	0.000	0.000	0.000	0.000
98	D	171	ASP	-1	-0.824	-0.893	9.966	0.746	0.746	0.000	0.000	0.000	0.000
99	D	172	PHE	0	-0.006	-0.003	12.879	-0.034	-0.034	0.000	0.000	0.000	0.000
100	D	173	LEU	0	0.002	-0.005	16.085	-0.018	-0.018	0.000	0.000	0.000	0.000
101	D	174	ILE	0	-0.009	0.004	18.033	0.002	0.002	0.000	0.000	0.000	0.000
102	D	175	ALA	0	0.022	0.022	21.826	-0.013	-0.013	0.000	0.000	0.000	0.000
103	D	176	TYR	0	0.036	0.009	23.806	0.008	0.008	0.000	0.000	0.000	0.000
104	D	177	SER	0	-0.007	0.019	27.420	-0.006	-0.006	0.000	0.000	0.000	0.000
105	D	178	THR	0	-0.003	-0.011	30.731	0.005	0.005	0.000	0.000	0.000	0.000
106	D	179	VAL	0	-0.014	-0.003	34.332	-0.004	-0.004	0.000	0.000	0.000	0.000
107	D	180	PRO	0	-0.016	-0.023	36.977	0.002	0.002	0.000	0.000	0.000	0.000
108	D	181	GLY	0	0.039	0.013	40.665	0.001	0.001	0.000	0.000	0.000	0.000
109	D	182	PHE	0	0.023	0.041	42.818	0.000	0.000	0.000	0.000	0.000	0.000
110	D	183	TYR	0	-0.019	-0.015	44.535	-0.001	-0.001	0.000	0.000	0.000	0.000
111	D	184	SER	0	0.017	0.010	40.035	0.000	0.000	0.000	0.000	0.000	0.000
112	D	185	TRP	0	0.055	-0.005	42.402	0.002	0.002	0.000	0.000	0.000	0.000
113	D	186	ARG	1	0.917	0.989	42.006	-0.005	-0.005	0.000	0.000	0.000	0.000
114	D	187	ASN	0	-0.014	-0.021	38.648	-0.001	-0.001	0.000	0.000	0.000	0.000
115	D	188	THR	0	0.023	0.007	42.327	-0.001	-0.001	0.000	0.000	0.000	0.000
116	D	189	THR	0	0.025	0.027	41.763	0.000	0.000	0.000	0.000	0.000	0.000
117	D	190	ARG	1	0.878	0.951	37.891	0.012	0.012	0.000	0.000	0.000	0.000
118	D	191	GLY	0	0.061	0.019	35.309	0.002	0.002	0.000	0.000	0.000	0.000
119	D	192	SER	0	-0.030	-0.034	33.731	-0.002	-0.002	0.000	0.000	0.000	0.000
120	D	193	TRP	0	0.068	0.027	34.015	0.001	0.001	0.000	0.000	0.000	0.000
121	D	194	PHE	0	0.047	0.031	26.274	-0.004	-0.004	0.000	0.000	0.000	0.000
122	D	195	MET	0	0.018	0.021	28.157	-0.003	-0.003	0.000	0.000	0.000	0.000
123	D	196	GLN	0	0.001	-0.011	30.085	-0.004	-0.004	0.000	0.000	0.000	0.000
124	D	197	SER	0	0.033	0.012	29.414	-0.004	-0.004	0.000	0.000	0.000	0.000
125	D	198	LEU	0	-0.016	-0.009	23.451	-0.006	-0.006	0.000	0.000	0.000	0.000
126	D	199	CYS	0	-0.044	-0.023	25.646	-0.002	-0.002	0.000	0.000	0.000	0.000
127	D	200	ALA	0	0.030	0.023	27.068	-0.004	-0.004	0.000	0.000	0.000	0.000
128	D	201	GLU	-1	-0.762	-0.870	24.056	-0.079	-0.079	0.000	0.000	0.000	0.000
129	D	202	LEU	0	-0.002	-0.023	20.880	-0.007	-0.007	0.000	0.000	0.000	0.000
130	D	203	ALA	0	-0.057	-0.026	23.390	-0.003	-0.003	0.000	0.000	0.000	0.000
131	D	204	ALA	0	-0.027	-0.001	25.118	0.001	0.001	0.000	0.000	0.000	0.000
132	D	205	ASN	0	-0.064	-0.061	21.798	-0.011	-0.011	0.000	0.000	0.000	0.000
133	D	206	GLY	0	0.019	0.030	20.092	-0.015	-0.015	0.000	0.000	0.000	0.000
134	D	207	LYS	1	0.817	0.888	17.647	0.028	0.028	0.000	0.000	0.000	0.000
135	D	208	ARG	1	0.863	0.951	17.317	0.083	0.083	0.000	0.000	0.000	0.000
136	D	209	LEU	0	0.003	0.001	17.250	-0.029	-0.029	0.000	0.000	0.000	0.000
137	D	210	ASP	-1	-0.834	-0.893	13.113	-0.263	-0.263	0.000	0.000	0.000	0.000
138	D	211	ILE	0	0.004	-0.008	14.472	0.024	0.024	0.000	0.000	0.000	0.000
139	D	212	LEU	0	0.008	0.009	13.769	0.031	0.031	0.000	0.000	0.000	0.000
140	D	213	THR	0	-0.009	-0.008	17.168	0.027	0.027	0.000	0.000	0.000	0.000
141	D	214	LEU	0	-0.012	0.000	18.626	0.021	0.021	0.000	0.000	0.000	0.000
142	D	215	LEU	0	0.005	-0.024	19.414	0.015	0.015	0.000	0.000	0.000	0.000
143	D	216	THR	0	0.006	-0.005	20.590	0.010	0.010	0.000	0.000	0.000	0.000
144	D	217	PHE	0	0.011	-0.007	21.865	0.008	0.008	0.000	0.000	0.000	0.000
145	D	218	VAL	0	-0.057	-0.020	24.373	0.009	0.009	0.000	0.000	0.000	0.000
146	D	219	CYS	0	-0.052	-0.017	25.961	0.008	0.008	0.000	0.000	0.000	0.000
147	D	220	GLN	0	0.002	-0.007	27.344	-0.002	-0.002	0.000	0.000	0.000	0.000
148	D	221	ARG	1	0.871	0.923	28.423	0.063	0.063	0.000	0.000	0.000	0.000
149	D	222	VAL	0	-0.035	-0.021	30.393	0.004	0.004	0.000	0.000	0.000	0.000
150	D	223	ALA	0	-0.027	0.000	31.870	0.003	0.003	0.000	0.000	0.000	0.000
151	D	224	VAL	0	-0.093	-0.040	32.957	0.002	0.002	0.000	0.000	0.000	0.000
152	D	225	ASP	-1	-0.845	-0.915	35.070	-0.035	-0.035	0.000	0.000	0.000	0.000
153	D	226	PHE	0	-0.125	-0.058	33.760	0.006	0.006	0.000	0.000	0.000	0.000
154	D	241	GLN	0	0.006	-0.014	34.450	-0.002	-0.002	0.000	0.000	0.000	0.000
155	D	242	ILE	0	0.032	0.025	29.321	0.000	0.000	0.000	0.000	0.000	0.000
156	D	243	PRO	0	-0.035	-0.026	26.809	0.004	0.004	0.000	0.000	0.000	0.000
157	D	244	CYS	0	-0.005	-0.013	26.257	-0.007	-0.007	0.000	0.000	0.000	0.000
158	D	245	ILE	0	-0.016	-0.007	20.587	0.010	0.010	0.000	0.000	0.000	0.000
159	D	246	THR	0	0.002	0.009	21.248	-0.008	-0.008	0.000	0.000	0.000	0.000
160	D	247	THR	0	-0.003	-0.011	15.231	0.031	0.031	0.000	0.000	0.000	0.000
161	D	248	MET	0	0.027	0.015	14.955	-0.015	-0.015	0.000	0.000	0.000	0.000
162	D	249	LEU	0	-0.031	-0.005	11.441	0.085	0.085	0.000	0.000	0.000	0.000
163	D	250	THR	0	-0.028	-0.024	8.138	0.043	0.043	0.000	0.000	0.000	0.000
164	D	251	ARG	1	0.883	0.940	2.148	-6.752	-6.412	2.561	-1.052	-1.849	-0.001
165	D	252	ILE	0	0.026	0.025	7.282	0.184	0.184	0.000	0.000	0.000	0.000
166	D	253	LEU	0	0.012	0.022	8.365	0.022	0.022	0.000	0.000	0.000	0.000
167	D	254	ARG	1	0.890	0.911	10.036	0.440	0.440	0.000	0.000	0.000	0.000
168	D	255	PHE	0	0.002	0.009	12.097	0.020	0.020	0.000	0.000	0.000	0.000
169	D	256	SER	0	-0.014	-0.017	11.681	-0.017	-0.017	0.000	0.000	0.000	0.000
170	D	257	ASP	-1	-0.823	-0.890	14.313	-0.009	-0.009	0.000	0.000	0.000	0.000
171	D	258	LYS	1	0.808	0.874	15.065	-0.056	-0.056	0.000	0.000	0.000	0.000
172	D	259	GLN	0	0.014	0.027	17.168	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:ALA)