FMO DATABASE

FMODB ID: JL589

Calculation Name: 3SIR-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SIR

Chain ID: C

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	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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1715029.804821
FMO2-HF: Nuclear repulsion	1648049.532056
FMO2-HF: Total energy	-66980.272765
FMO2-MP2: Total energy	-67169.685177

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(C:10:ALA)

Summations of interaction energy for fragment #1(C: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.
-0.446	2.82	2.384	-2.412	-3.238	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.017

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	C	12	GLU	-1	-0.857	-0.921	2.713	-1.887	0.709	0.096	-1.271	-1.421	-0.001
4	C	13	TYR	0	-0.148	-0.148	3.631	-0.197	0.248	0.030	-0.201	-0.274	-0.001
5	C	14	ASN	0	0.004	-0.009	6.117	0.099	0.099	0.000	0.000	0.000	0.000
6	C	15	MET	0	-0.058	-0.012	7.305	0.034	0.034	0.000	0.000	0.000	0.000
7	C	16	ARG	1	0.945	0.956	10.498	0.127	0.127	0.000	0.000	0.000	0.000
8	C	17	HIS	0	-0.037	0.003	10.033	0.066	0.066	0.000	0.000	0.000	0.000
9	C	18	LYS	1	0.949	0.985	14.000	0.068	0.068	0.000	0.000	0.000	0.000
10	C	19	ASN	0	-0.001	-0.017	17.540	0.004	0.004	0.000	0.000	0.000	0.000
11	C	20	ARG	1	0.949	0.991	14.515	0.220	0.220	0.000	0.000	0.000	0.000
12	C	21	GLY	0	0.030	0.005	16.673	-0.025	-0.025	0.000	0.000	0.000	0.000
13	C	22	MET	0	-0.011	0.014	19.131	0.002	0.002	0.000	0.000	0.000	0.000
14	C	23	ALA	0	0.020	0.011	20.923	-0.020	-0.020	0.000	0.000	0.000	0.000
15	C	24	LEU	0	-0.031	-0.008	23.342	0.014	0.014	0.000	0.000	0.000	0.000
16	C	25	ILE	0	0.013	0.009	26.263	-0.007	-0.007	0.000	0.000	0.000	0.000
17	C	26	PHE	0	0.016	0.006	26.975	0.010	0.010	0.000	0.000	0.000	0.000
18	C	27	ASN	0	0.038	0.017	31.295	-0.009	-0.009	0.000	0.000	0.000	0.000
19	C	28	HIS	0	-0.036	-0.003	34.411	0.006	0.006	0.000	0.000	0.000	0.000
20	C	43	ASN	0	0.021	-0.014	36.715	-0.003	-0.003	0.000	0.000	0.000	0.000
21	C	44	VAL	0	0.119	0.050	36.173	-0.001	-0.001	0.000	0.000	0.000	0.000
22	C	45	ASP	-1	-0.847	-0.924	32.655	-0.104	-0.104	0.000	0.000	0.000	0.000
23	C	46	CYS	0	0.014	0.015	31.652	-0.004	-0.004	0.000	0.000	0.000	0.000
24	C	47	GLU	-1	-0.922	-0.893	32.035	-0.079	-0.079	0.000	0.000	0.000	0.000
25	C	48	ASN	0	-0.054	-0.035	31.471	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	49	LEU	0	0.059	0.020	25.347	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	50	THR	0	-0.028	-0.083	27.217	-0.007	-0.007	0.000	0.000	0.000	0.000
28	C	51	ARG	1	0.904	0.956	27.869	0.088	0.088	0.000	0.000	0.000	0.000
29	C	52	VAL	0	0.027	0.017	24.308	-0.002	-0.002	0.000	0.000	0.000	0.000
30	C	53	LEU	0	-0.002	-0.016	22.201	-0.010	-0.010	0.000	0.000	0.000	0.000
31	C	54	LYS	1	0.954	0.971	23.364	0.091	0.091	0.000	0.000	0.000	0.000
32	C	55	GLN	0	-0.038	-0.013	24.986	0.011	0.011	0.000	0.000	0.000	0.000
33	C	56	LEU	0	-0.118	-0.042	19.015	-0.004	-0.004	0.000	0.000	0.000	0.000
34	C	57	ASP	-1	-0.927	-0.970	19.839	-0.144	-0.144	0.000	0.000	0.000	0.000
35	C	58	PHE	0	-0.050	-0.025	17.666	-0.008	-0.008	0.000	0.000	0.000	0.000
36	C	59	GLU	-1	-0.945	-0.974	21.884	-0.085	-0.085	0.000	0.000	0.000	0.000
37	C	60	VAL	0	-0.074	-0.026	24.619	-0.003	-0.003	0.000	0.000	0.000	0.000
38	C	61	THR	0	-0.022	-0.008	26.680	0.012	0.012	0.000	0.000	0.000	0.000
39	C	62	VAL	0	0.017	0.002	28.984	-0.006	-0.006	0.000	0.000	0.000	0.000
40	C	63	TYR	0	-0.002	-0.015	28.935	0.009	0.009	0.000	0.000	0.000	0.000
41	C	64	LYS	1	0.942	0.951	33.601	0.067	0.067	0.000	0.000	0.000	0.000
42	C	65	ASP	-1	-0.801	-0.887	36.660	-0.063	-0.063	0.000	0.000	0.000	0.000
43	C	66	CYS	0	-0.031	-0.025	37.754	-0.002	-0.002	0.000	0.000	0.000	0.000
44	C	67	ARG	1	0.927	0.954	38.820	0.056	0.056	0.000	0.000	0.000	0.000
45	C	68	TYR	0	0.113	0.051	35.259	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	69	LYS	1	0.924	0.954	34.179	0.062	0.062	0.000	0.000	0.000	0.000
47	C	70	ASP	-1	-0.844	-0.929	34.317	-0.073	-0.073	0.000	0.000	0.000	0.000
48	C	71	ILE	0	-0.013	0.016	30.217	-0.003	-0.003	0.000	0.000	0.000	0.000
49	C	72	LEU	0	-0.031	-0.017	29.411	-0.006	-0.006	0.000	0.000	0.000	0.000
50	C	73	ARG	1	0.982	0.991	29.510	0.069	0.069	0.000	0.000	0.000	0.000
51	C	74	THR	0	-0.038	-0.021	29.190	0.000	0.000	0.000	0.000	0.000	0.000
52	C	75	ILE	0	-0.020	-0.003	24.814	-0.005	-0.005	0.000	0.000	0.000	0.000
53	C	76	GLU	-1	-0.894	-0.945	25.575	-0.097	-0.097	0.000	0.000	0.000	0.000
54	C	77	TYR	0	-0.015	-0.011	26.416	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	78	SER	0	0.037	-0.003	23.731	0.002	0.002	0.000	0.000	0.000	0.000
56	C	79	ALA	0	-0.109	-0.053	21.884	-0.008	-0.008	0.000	0.000	0.000	0.000
57	C	80	SER	0	0.006	-0.010	22.568	0.002	0.002	0.000	0.000	0.000	0.000
58	C	81	GLN	0	-0.058	0.017	22.904	0.004	0.004	0.000	0.000	0.000	0.000
59	C	82	ASN	0	0.041	0.027	19.597	-0.022	-0.022	0.000	0.000	0.000	0.000
60	C	83	HIS	1	0.877	0.912	17.231	0.167	0.167	0.000	0.000	0.000	0.000
61	C	84	SER	0	0.026	-0.002	15.588	-0.021	-0.021	0.000	0.000	0.000	0.000
62	C	85	ASP	-1	-0.925	-0.953	14.897	-0.090	-0.090	0.000	0.000	0.000	0.000
63	C	86	SER	0	-0.080	-0.051	16.051	0.004	0.004	0.000	0.000	0.000	0.000
64	C	87	ASP	-1	-0.775	-0.880	12.626	-0.255	-0.255	0.000	0.000	0.000	0.000
65	C	88	CYS	0	-0.095	-0.047	12.121	-0.064	-0.064	0.000	0.000	0.000	0.000
66	C	89	ILE	0	-0.011	-0.001	14.513	0.041	0.041	0.000	0.000	0.000	0.000
67	C	90	LEU	0	-0.003	0.015	17.826	-0.025	-0.025	0.000	0.000	0.000	0.000
68	C	91	VAL	0	0.015	0.012	20.232	0.024	0.024	0.000	0.000	0.000	0.000
69	C	92	ALA	0	0.012	0.000	23.307	-0.012	-0.012	0.000	0.000	0.000	0.000
70	C	93	ILE	0	-0.034	-0.009	26.003	0.011	0.011	0.000	0.000	0.000	0.000
71	C	94	LEU	0	0.001	0.000	28.859	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	95	SER	0	0.008	0.005	32.010	0.008	0.008	0.000	0.000	0.000	0.000
73	C	113	ASN	0	0.083	0.026	27.607	-0.006	-0.006	0.000	0.000	0.000	0.000
74	C	114	ILE	0	0.002	0.023	25.427	-0.004	-0.004	0.000	0.000	0.000	0.000
75	C	115	TRP	0	0.051	0.024	21.490	-0.004	-0.004	0.000	0.000	0.000	0.000
76	C	116	SER	0	-0.064	-0.062	21.541	-0.010	-0.010	0.000	0.000	0.000	0.000
77	C	117	PHE	0	0.053	0.013	23.046	0.004	0.004	0.000	0.000	0.000	0.000
78	C	118	PHE	0	0.016	-0.006	18.500	-0.002	-0.002	0.000	0.000	0.000	0.000
79	C	119	THR	0	-0.037	0.004	17.458	-0.029	-0.029	0.000	0.000	0.000	0.000
80	C	120	ALA	0	0.035	0.006	14.151	0.011	0.011	0.000	0.000	0.000	0.000
81	C	121	ASN	0	0.003	0.002	15.921	0.016	0.016	0.000	0.000	0.000	0.000
82	C	122	HIS	0	-0.006	0.001	19.075	0.005	0.005	0.000	0.000	0.000	0.000
83	C	123	CYS	0	-0.017	0.012	18.481	0.007	0.007	0.000	0.000	0.000	0.000
84	C	124	PRO	0	0.075	0.037	16.002	-0.027	-0.027	0.000	0.000	0.000	0.000
85	C	125	SER	0	-0.026	-0.012	14.798	-0.020	-0.020	0.000	0.000	0.000	0.000
86	C	126	LEU	0	-0.068	-0.043	13.797	-0.012	-0.012	0.000	0.000	0.000	0.000
87	C	127	ALA	0	0.085	0.053	12.449	-0.012	-0.012	0.000	0.000	0.000	0.000
88	C	128	GLY	0	-0.010	0.004	8.292	0.006	0.006	0.000	0.000	0.000	0.000
89	C	129	LYS	1	0.803	0.907	7.837	0.163	0.163	0.000	0.000	0.000	0.000
90	C	130	PRO	0	0.018	0.019	9.623	0.024	0.024	0.000	0.000	0.000	0.000
91	C	131	LYS	1	0.841	0.921	12.293	0.481	0.481	0.000	0.000	0.000	0.000
92	C	132	LEU	0	-0.012	-0.007	14.691	-0.005	-0.005	0.000	0.000	0.000	0.000
93	C	133	PHE	0	-0.016	-0.012	17.933	0.037	0.037	0.000	0.000	0.000	0.000
94	C	134	PHE	0	0.010	-0.005	19.900	-0.007	-0.007	0.000	0.000	0.000	0.000
95	C	135	ILE	0	0.006	0.005	24.301	0.014	0.014	0.000	0.000	0.000	0.000
96	C	136	GLN	0	0.063	0.033	27.496	-0.006	-0.006	0.000	0.000	0.000	0.000
97	C	137	ALA	0	0.035	0.015	30.622	0.007	0.007	0.000	0.000	0.000	0.000
98	C	138	CYS	0	0.012	0.012	33.018	0.003	0.003	0.000	0.000	0.000	0.000
99	C	139	GLN	0	0.017	0.016	36.012	-0.005	-0.005	0.000	0.000	0.000	0.000
100	C	168	VAL	0	-0.016	-0.046	17.857	-0.003	-0.003	0.000	0.000	0.000	0.000
101	C	169	HIS	0	0.029	0.029	14.591	-0.011	-0.011	0.000	0.000	0.000	0.000
102	C	170	ALA	0	0.053	0.016	11.165	-0.014	-0.014	0.000	0.000	0.000	0.000
103	C	171	ASP	-1	-0.769	-0.808	9.299	-0.876	-0.876	0.000	0.000	0.000	0.000
104	C	172	PHE	0	-0.012	-0.002	12.153	0.055	0.055	0.000	0.000	0.000	0.000
105	C	173	LEU	0	0.027	0.006	15.210	-0.047	-0.047	0.000	0.000	0.000	0.000
106	C	174	ILE	0	-0.007	-0.001	17.303	0.025	0.025	0.000	0.000	0.000	0.000
107	C	175	ALA	0	0.006	0.019	21.088	0.001	0.001	0.000	0.000	0.000	0.000
108	C	176	TYR	0	-0.002	-0.010	23.043	0.013	0.013	0.000	0.000	0.000	0.000
109	C	177	SER	0	0.029	0.018	26.676	0.004	0.004	0.000	0.000	0.000	0.000
110	C	178	THR	0	-0.005	-0.006	30.052	0.003	0.003	0.000	0.000	0.000	0.000
111	C	179	VAL	0	-0.024	0.001	33.654	0.000	0.000	0.000	0.000	0.000	0.000
112	C	180	PRO	0	0.004	-0.001	36.204	0.003	0.003	0.000	0.000	0.000	0.000
113	C	192	SER	0	0.043	0.017	32.860	0.000	0.000	0.000	0.000	0.000	0.000
114	C	193	TRP	0	0.104	0.040	33.760	-0.006	-0.006	0.000	0.000	0.000	0.000
115	C	194	PHE	0	0.059	0.093	25.570	-0.007	-0.007	0.000	0.000	0.000	0.000
116	C	195	MET	0	0.020	0.028	29.216	-0.009	-0.009	0.000	0.000	0.000	0.000
117	C	196	GLN	0	0.013	0.003	29.581	-0.002	-0.002	0.000	0.000	0.000	0.000
118	C	197	SER	0	-0.072	-0.118	29.056	0.001	0.001	0.000	0.000	0.000	0.000
119	C	198	LEU	0	-0.027	-0.006	23.044	-0.010	-0.010	0.000	0.000	0.000	0.000
120	C	199	CYS	0	-0.056	-0.018	25.306	-0.010	-0.010	0.000	0.000	0.000	0.000
121	C	200	ALA	0	0.051	0.026	26.539	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	201	GLU	-1	-0.819	-0.926	23.574	-0.178	-0.178	0.000	0.000	0.000	0.000
123	C	202	LEU	0	0.021	0.002	20.705	-0.010	-0.010	0.000	0.000	0.000	0.000
124	C	203	ALA	0	-0.040	-0.007	22.722	-0.002	-0.002	0.000	0.000	0.000	0.000
125	C	204	ALA	0	-0.050	-0.005	25.186	0.010	0.010	0.000	0.000	0.000	0.000
126	C	205	ASN	0	-0.023	-0.033	21.300	0.009	0.009	0.000	0.000	0.000	0.000
127	C	206	GLY	0	0.019	0.009	19.884	-0.019	-0.019	0.000	0.000	0.000	0.000
128	C	207	LYS	1	0.924	0.952	17.537	0.147	0.147	0.000	0.000	0.000	0.000
129	C	208	ARG	1	0.855	0.932	16.940	0.126	0.126	0.000	0.000	0.000	0.000
130	C	209	LEU	0	0.021	0.016	16.742	-0.010	-0.010	0.000	0.000	0.000	0.000
131	C	210	ASP	-1	-0.892	-0.952	12.474	-0.560	-0.560	0.000	0.000	0.000	0.000
132	C	211	ILE	0	0.012	-0.004	13.631	0.043	0.043	0.000	0.000	0.000	0.000
133	C	212	LEU	0	0.023	0.009	13.643	0.044	0.044	0.000	0.000	0.000	0.000
134	C	213	THR	0	0.010	0.013	16.748	0.065	0.065	0.000	0.000	0.000	0.000
135	C	214	LEU	0	0.015	0.017	18.477	0.033	0.033	0.000	0.000	0.000	0.000
136	C	215	LEU	0	-0.005	-0.008	18.209	0.030	0.030	0.000	0.000	0.000	0.000
137	C	216	THR	0	0.022	0.012	20.794	0.026	0.026	0.000	0.000	0.000	0.000
138	C	217	PHE	0	-0.027	-0.020	22.398	0.020	0.020	0.000	0.000	0.000	0.000
139	C	218	VAL	0	-0.046	-0.011	24.076	0.018	0.018	0.000	0.000	0.000	0.000
140	C	219	CYS	0	-0.054	-0.025	25.302	0.009	0.009	0.000	0.000	0.000	0.000
141	C	220	GLN	0	0.013	0.001	26.826	0.004	0.004	0.000	0.000	0.000	0.000
142	C	221	ARG	1	0.852	0.941	28.128	0.139	0.139	0.000	0.000	0.000	0.000
143	C	222	VAL	0	0.039	0.017	29.948	0.007	0.007	0.000	0.000	0.000	0.000
144	C	223	ALA	0	-0.028	-0.006	31.531	0.007	0.007	0.000	0.000	0.000	0.000
145	C	224	VAL	0	-0.125	-0.051	32.883	0.007	0.007	0.000	0.000	0.000	0.000
146	C	225	ASP	-1	-0.959	-0.974	34.756	-0.087	-0.087	0.000	0.000	0.000	0.000
147	C	241	GLN	0	0.001	-0.009	33.812	-0.004	-0.004	0.000	0.000	0.000	0.000
148	C	242	ILE	0	0.036	0.019	28.189	-0.002	-0.002	0.000	0.000	0.000	0.000
149	C	243	PRO	0	-0.079	-0.037	26.626	-0.002	-0.002	0.000	0.000	0.000	0.000
150	C	244	CYS	0	-0.008	-0.010	26.063	-0.007	-0.007	0.000	0.000	0.000	0.000
151	C	245	ILE	0	0.033	0.006	19.643	-0.005	-0.005	0.000	0.000	0.000	0.000
152	C	246	THR	0	-0.027	-0.013	20.562	-0.009	-0.009	0.000	0.000	0.000	0.000
153	C	247	THR	0	-0.002	-0.008	14.613	-0.017	-0.017	0.000	0.000	0.000	0.000
154	C	248	MET	0	0.028	0.035	13.992	0.029	0.029	0.000	0.000	0.000	0.000
155	C	249	LEU	0	-0.053	-0.017	10.635	-0.058	-0.058	0.000	0.000	0.000	0.000
156	C	250	THR	0	0.005	-0.010	6.884	-0.083	-0.083	0.000	0.000	0.000	0.000
157	C	251	ARG	1	0.844	0.933	2.004	0.941	1.166	2.258	-0.940	-1.543	0.000
158	C	252	ILE	0	0.041	0.024	6.937	0.482	0.482	0.000	0.000	0.000	0.000
159	C	253	LEU	0	-0.013	-0.006	8.353	-0.002	-0.002	0.000	0.000	0.000	0.000
160	C	254	ARG	1	0.955	0.971	10.056	0.618	0.618	0.000	0.000	0.000	0.000
161	C	255	PHE	0	0.011	0.011	12.018	-0.009	-0.009	0.000	0.000	0.000	0.000
162	C	256	SER	0	0.029	0.018	10.909	0.051	0.051	0.000	0.000	0.000	0.000

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