FMO DATABASE

FMODB ID: N9YRQ

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1887176.078942
FMO2-HF: Nuclear repulsion	1816239.053624
FMO2-HF: Total energy	-70937.025318
FMO2-MP2: Total energy	-71139.14969

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.
-10.894	-7.201	2.214	-2.494	-3.413	0.007

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 : 0.026 / q_NPA : -0.003

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	-0.831	-0.888	2.958	-1.128	1.087	0.038	-1.086	-1.167	-0.001
4	D	13	TYR	0	-0.030	-0.048	3.442	0.018	0.525	0.039	-0.231	-0.315	-0.001
5	D	14	ASN	0	-0.008	-0.009	5.653	-0.277	-0.277	0.000	0.000	0.000	0.000
6	D	15	MET	0	-0.024	-0.002	6.921	0.031	0.031	0.000	0.000	0.000	0.000
7	D	16	ARG	1	0.933	0.954	9.013	-0.217	-0.217	0.000	0.000	0.000	0.000
8	D	17	HIS	0	0.015	0.026	9.199	-0.041	-0.041	0.000	0.000	0.000	0.000
9	D	18	LYS	1	0.872	0.931	13.318	-0.224	-0.224	0.000	0.000	0.000	0.000
10	D	19	ASN	0	0.030	0.017	16.839	-0.034	-0.034	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.781	0.860	14.262	-0.105	-0.105	0.000	0.000	0.000	0.000
12	D	21	GLY	0	0.054	0.012	15.959	0.034	0.034	0.000	0.000	0.000	0.000
13	D	22	MET	0	-0.039	-0.005	18.498	-0.024	-0.024	0.000	0.000	0.000	0.000
14	D	23	ALA	0	0.007	0.006	21.019	0.008	0.008	0.000	0.000	0.000	0.000
15	D	24	LEU	0	-0.028	-0.014	23.397	-0.011	-0.011	0.000	0.000	0.000	0.000
16	D	25	ILE	0	0.025	0.009	26.172	-0.002	-0.002	0.000	0.000	0.000	0.000
17	D	26	PHE	0	-0.001	-0.008	27.564	-0.002	-0.002	0.000	0.000	0.000	0.000
18	D	27	ASN	0	-0.061	-0.051	31.632	-0.006	-0.006	0.000	0.000	0.000	0.000
19	D	28	HIS	0	0.016	0.014	34.617	0.000	0.000	0.000	0.000	0.000	0.000
20	D	43	ASN	0	0.084	0.031	36.852	0.001	0.001	0.000	0.000	0.000	0.000
21	D	44	VAL	0	0.038	0.021	35.868	0.002	0.002	0.000	0.000	0.000	0.000
22	D	45	ASP	-1	-0.764	-0.860	32.497	0.022	0.022	0.000	0.000	0.000	0.000
23	D	46	CYS	0	0.024	0.032	31.421	0.003	0.003	0.000	0.000	0.000	0.000
24	D	47	GLU	-1	-0.864	-0.889	31.382	0.033	0.033	0.000	0.000	0.000	0.000
25	D	48	ASN	0	-0.032	-0.025	30.975	0.000	0.000	0.000	0.000	0.000	0.000
26	D	49	LEU	0	0.057	0.028	24.995	0.001	0.001	0.000	0.000	0.000	0.000
27	D	50	THR	0	0.002	-0.028	26.902	0.006	0.006	0.000	0.000	0.000	0.000
28	D	51	ARG	1	0.758	0.860	28.051	-0.029	-0.029	0.000	0.000	0.000	0.000
29	D	52	VAL	0	0.045	0.022	24.031	0.002	0.002	0.000	0.000	0.000	0.000
30	D	53	LEU	0	-0.002	-0.009	21.497	0.003	0.003	0.000	0.000	0.000	0.000
31	D	54	LYS	1	0.846	0.915	22.980	-0.063	-0.063	0.000	0.000	0.000	0.000
32	D	55	GLN	0	-0.017	-0.005	24.439	0.002	0.002	0.000	0.000	0.000	0.000
33	D	56	LEU	0	-0.028	-0.007	19.369	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	57	ASP	-1	-0.801	-0.873	19.079	0.094	0.094	0.000	0.000	0.000	0.000
35	D	58	PHE	0	-0.015	-0.015	17.532	0.017	0.017	0.000	0.000	0.000	0.000
36	D	59	GLU	-1	-0.802	-0.876	21.437	0.070	0.070	0.000	0.000	0.000	0.000
37	D	60	VAL	0	-0.056	-0.040	24.015	0.006	0.006	0.000	0.000	0.000	0.000
38	D	61	THR	0	-0.033	-0.003	26.520	-0.008	-0.008	0.000	0.000	0.000	0.000
39	D	62	VAL	0	0.020	0.000	29.175	0.000	0.000	0.000	0.000	0.000	0.000
40	D	63	TYR	0	0.046	0.021	28.868	-0.005	-0.005	0.000	0.000	0.000	0.000
41	D	64	LYS	1	0.876	0.922	33.756	-0.039	-0.039	0.000	0.000	0.000	0.000
42	D	65	ASP	-1	-0.757	-0.848	36.930	0.046	0.046	0.000	0.000	0.000	0.000
43	D	66	CYS	0	0.060	0.047	37.068	0.002	0.002	0.000	0.000	0.000	0.000
44	D	67	ARG	1	0.793	0.863	34.610	-0.056	-0.056	0.000	0.000	0.000	0.000
45	D	68	TYR	0	0.002	-0.020	35.213	0.005	0.005	0.000	0.000	0.000	0.000
46	D	69	LYS	1	0.937	0.963	35.576	-0.043	-0.043	0.000	0.000	0.000	0.000
47	D	70	ASP	-1	-0.770	-0.873	34.809	0.060	0.060	0.000	0.000	0.000	0.000
48	D	71	ILE	0	-0.004	0.026	29.773	0.005	0.005	0.000	0.000	0.000	0.000
49	D	72	LEU	0	-0.031	-0.008	30.244	0.007	0.007	0.000	0.000	0.000	0.000
50	D	73	ARG	1	0.943	0.960	30.086	-0.056	-0.056	0.000	0.000	0.000	0.000
51	D	74	THR	0	-0.013	-0.018	29.506	0.003	0.003	0.000	0.000	0.000	0.000
52	D	75	ILE	0	-0.034	-0.001	25.015	0.007	0.007	0.000	0.000	0.000	0.000
53	D	76	GLU	-1	-0.913	-0.949	26.195	0.100	0.100	0.000	0.000	0.000	0.000
54	D	77	TYR	0	-0.010	-0.002	27.211	0.009	0.009	0.000	0.000	0.000	0.000
55	D	78	SER	0	-0.021	-0.027	25.065	0.007	0.007	0.000	0.000	0.000	0.000
56	D	79	ALA	0	-0.014	-0.015	22.358	0.014	0.014	0.000	0.000	0.000	0.000
57	D	80	SER	0	-0.018	-0.010	22.444	0.018	0.018	0.000	0.000	0.000	0.000
58	D	81	GLN	0	-0.025	0.000	23.584	-0.004	-0.004	0.000	0.000	0.000	0.000
59	D	82	ASN	0	0.007	0.004	19.792	0.043	0.043	0.000	0.000	0.000	0.000
60	D	83	HIS	0	0.035	0.005	16.980	-0.020	-0.020	0.000	0.000	0.000	0.000
61	D	84	SER	0	0.011	-0.007	15.374	0.048	0.048	0.000	0.000	0.000	0.000
62	D	85	ASP	-1	-0.854	-0.913	14.679	0.271	0.271	0.000	0.000	0.000	0.000
63	D	86	SER	0	-0.015	-0.005	15.696	-0.034	-0.034	0.000	0.000	0.000	0.000
64	D	87	ASP	-1	-0.753	-0.858	11.835	0.324	0.324	0.000	0.000	0.000	0.000
65	D	88	CYS	0	-0.107	-0.038	11.802	0.055	0.055	0.000	0.000	0.000	0.000
66	D	89	ILE	0	0.020	0.019	14.382	-0.021	-0.021	0.000	0.000	0.000	0.000
67	D	90	LEU	0	-0.007	0.006	17.719	-0.001	-0.001	0.000	0.000	0.000	0.000
68	D	91	VAL	0	0.003	0.005	20.324	-0.005	-0.005	0.000	0.000	0.000	0.000
69	D	92	ALA	0	0.008	-0.001	23.695	-0.005	-0.005	0.000	0.000	0.000	0.000
70	D	93	ILE	0	-0.007	-0.007	26.370	0.000	0.000	0.000	0.000	0.000	0.000
71	D	94	LEU	0	0.006	0.004	29.711	-0.005	-0.005	0.000	0.000	0.000	0.000
72	D	95	SER	0	0.032	0.028	32.503	0.000	0.000	0.000	0.000	0.000	0.000
73	D	114	ILE	0	0.002	-0.016	26.674	-0.002	-0.002	0.000	0.000	0.000	0.000
74	D	115	TRP	0	0.061	0.021	22.122	0.012	0.012	0.000	0.000	0.000	0.000
75	D	116	SER	0	0.004	0.000	22.496	0.018	0.018	0.000	0.000	0.000	0.000
76	D	117	PHE	0	0.025	0.010	23.779	0.009	0.009	0.000	0.000	0.000	0.000
77	D	118	PHE	0	0.051	0.015	19.173	0.008	0.008	0.000	0.000	0.000	0.000
78	D	119	THR	0	-0.025	-0.016	18.268	0.039	0.039	0.000	0.000	0.000	0.000
79	D	120	ALA	0	0.025	-0.002	15.186	0.009	0.009	0.000	0.000	0.000	0.000
80	D	121	ASN	0	-0.006	-0.006	17.031	0.031	0.031	0.000	0.000	0.000	0.000
81	D	122	HIS	0	0.004	0.016	20.367	-0.003	-0.003	0.000	0.000	0.000	0.000
82	D	123	CYS	0	-0.010	0.007	19.175	-0.006	-0.006	0.000	0.000	0.000	0.000
83	D	124	PRO	0	0.064	0.033	16.755	0.040	0.040	0.000	0.000	0.000	0.000
84	D	125	SER	0	-0.042	-0.012	15.470	0.064	0.064	0.000	0.000	0.000	0.000
85	D	126	LEU	0	-0.010	-0.016	14.186	0.021	0.021	0.000	0.000	0.000	0.000
86	D	127	ALA	0	0.011	0.001	13.417	0.006	0.006	0.000	0.000	0.000	0.000
87	D	128	GLY	0	-0.023	-0.002	9.287	0.103	0.103	0.000	0.000	0.000	0.000
88	D	129	LYS	1	0.761	0.890	8.379	-0.283	-0.283	0.000	0.000	0.000	0.000
89	D	130	PRO	0	0.001	-0.011	9.770	-0.073	-0.073	0.000	0.000	0.000	0.000
90	D	131	LYS	1	0.825	0.934	12.598	-0.444	-0.444	0.000	0.000	0.000	0.000
91	D	132	LEU	0	-0.022	-0.007	14.899	-0.024	-0.024	0.000	0.000	0.000	0.000
92	D	133	PHE	0	0.000	-0.002	18.277	-0.003	-0.003	0.000	0.000	0.000	0.000
93	D	134	PHE	0	0.020	0.007	19.846	-0.012	-0.012	0.000	0.000	0.000	0.000
94	D	135	ILE	0	-0.005	-0.006	24.718	0.002	0.002	0.000	0.000	0.000	0.000
95	D	136	GLN	0	-0.016	0.008	28.126	-0.007	-0.007	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.038	0.009	31.424	0.000	0.000	0.000	0.000	0.000	0.000
97	D	170	ALA	0	0.017	-0.002	12.729	-0.016	-0.016	0.000	0.000	0.000	0.000
98	D	171	ASP	-1	-0.807	-0.878	10.111	0.781	0.781	0.000	0.000	0.000	0.000
99	D	172	PHE	0	0.001	0.009	12.802	-0.021	-0.021	0.000	0.000	0.000	0.000
100	D	173	LEU	0	0.003	-0.001	15.884	-0.023	-0.023	0.000	0.000	0.000	0.000
101	D	174	ILE	0	-0.019	-0.015	17.703	0.009	0.009	0.000	0.000	0.000	0.000
102	D	175	ALA	0	0.018	0.021	21.498	-0.014	-0.014	0.000	0.000	0.000	0.000
103	D	176	TYR	0	0.006	0.000	23.671	0.007	0.007	0.000	0.000	0.000	0.000
104	D	177	SER	0	-0.011	-0.003	27.305	-0.006	-0.006	0.000	0.000	0.000	0.000
105	D	178	THR	0	-0.018	-0.013	30.559	0.004	0.004	0.000	0.000	0.000	0.000
106	D	179	VAL	0	0.008	0.007	34.277	-0.004	-0.004	0.000	0.000	0.000	0.000
107	D	180	PRO	0	0.010	-0.011	36.612	0.001	0.001	0.000	0.000	0.000	0.000
108	D	181	GLY	0	0.017	0.011	40.386	0.001	0.001	0.000	0.000	0.000	0.000
109	D	182	PHE	0	0.021	0.018	41.795	0.001	0.001	0.000	0.000	0.000	0.000
110	D	183	TYR	0	0.018	-0.003	44.536	-0.001	-0.001	0.000	0.000	0.000	0.000
111	D	184	SER	0	-0.026	0.002	39.337	0.000	0.000	0.000	0.000	0.000	0.000
112	D	185	TRP	0	0.027	0.002	41.685	0.002	0.002	0.000	0.000	0.000	0.000
113	D	186	ARG	1	0.920	0.977	41.651	-0.014	-0.014	0.000	0.000	0.000	0.000
114	D	187	ASN	0	0.011	-0.003	38.275	-0.002	-0.002	0.000	0.000	0.000	0.000
115	D	188	THR	0	0.027	0.004	41.988	0.000	0.000	0.000	0.000	0.000	0.000
116	D	189	THR	0	-0.021	-0.012	41.783	-0.001	-0.001	0.000	0.000	0.000	0.000
117	D	190	ARG	1	0.939	0.979	37.407	-0.004	-0.004	0.000	0.000	0.000	0.000
118	D	191	GLY	0	0.047	0.019	34.619	0.001	0.001	0.000	0.000	0.000	0.000
119	D	192	SER	0	-0.026	-0.032	32.951	-0.004	-0.004	0.000	0.000	0.000	0.000
120	D	193	TRP	0	0.068	0.029	33.741	0.002	0.002	0.000	0.000	0.000	0.000
121	D	194	PHE	0	0.045	0.031	25.639	-0.003	-0.003	0.000	0.000	0.000	0.000
122	D	195	MET	0	0.012	0.012	27.813	0.000	0.000	0.000	0.000	0.000	0.000
123	D	196	GLN	0	-0.024	-0.024	29.759	0.000	0.000	0.000	0.000	0.000	0.000
124	D	197	SER	0	0.017	-0.001	28.902	-0.002	-0.002	0.000	0.000	0.000	0.000
125	D	198	LEU	0	-0.026	-0.014	23.069	-0.003	-0.003	0.000	0.000	0.000	0.000
126	D	199	CYS	0	-0.054	-0.033	25.352	0.003	0.003	0.000	0.000	0.000	0.000
127	D	200	ALA	0	0.014	0.011	27.024	0.000	0.000	0.000	0.000	0.000	0.000
128	D	201	GLU	-1	-0.756	-0.860	23.569	-0.031	-0.031	0.000	0.000	0.000	0.000
129	D	202	LEU	0	-0.016	-0.020	20.533	-0.002	-0.002	0.000	0.000	0.000	0.000
130	D	203	ALA	0	0.007	0.001	23.004	0.002	0.002	0.000	0.000	0.000	0.000
131	D	204	ALA	0	-0.014	0.015	24.999	-0.001	-0.001	0.000	0.000	0.000	0.000
132	D	205	ASN	0	-0.045	-0.048	21.159	-0.008	-0.008	0.000	0.000	0.000	0.000
133	D	206	GLY	0	0.022	0.032	19.485	-0.009	-0.009	0.000	0.000	0.000	0.000
134	D	207	LYS	1	0.794	0.887	16.979	-0.048	-0.048	0.000	0.000	0.000	0.000
135	D	208	ARG	1	0.819	0.915	16.604	0.029	0.029	0.000	0.000	0.000	0.000
136	D	209	LEU	0	0.004	0.000	16.096	-0.022	-0.022	0.000	0.000	0.000	0.000
137	D	210	ASP	-1	-0.828	-0.885	12.751	-0.147	-0.147	0.000	0.000	0.000	0.000
138	D	211	ILE	0	0.012	-0.016	14.065	0.009	0.009	0.000	0.000	0.000	0.000
139	D	212	LEU	0	0.006	0.008	13.933	0.016	0.016	0.000	0.000	0.000	0.000
140	D	213	THR	0	0.004	-0.021	16.400	0.018	0.018	0.000	0.000	0.000	0.000
141	D	214	LEU	0	-0.014	0.006	18.174	0.013	0.013	0.000	0.000	0.000	0.000
142	D	215	LEU	0	-0.005	-0.019	19.051	0.009	0.009	0.000	0.000	0.000	0.000
143	D	216	THR	0	0.000	-0.005	20.580	0.004	0.004	0.000	0.000	0.000	0.000
144	D	217	PHE	0	0.009	0.001	21.013	0.004	0.004	0.000	0.000	0.000	0.000
145	D	218	VAL	0	-0.067	-0.022	23.959	0.006	0.006	0.000	0.000	0.000	0.000
146	D	219	CYS	0	-0.029	-0.018	25.498	0.005	0.005	0.000	0.000	0.000	0.000
147	D	220	GLN	0	0.018	0.009	27.019	-0.002	-0.002	0.000	0.000	0.000	0.000
148	D	221	ARG	1	0.858	0.915	28.033	0.026	0.026	0.000	0.000	0.000	0.000
149	D	222	VAL	0	-0.033	-0.023	29.901	0.002	0.002	0.000	0.000	0.000	0.000
150	D	223	ALA	0	-0.044	-0.017	31.538	0.002	0.002	0.000	0.000	0.000	0.000
151	D	224	VAL	0	-0.063	-0.021	32.659	-0.001	-0.001	0.000	0.000	0.000	0.000
152	D	225	ASP	-1	-0.834	-0.886	34.591	-0.015	-0.015	0.000	0.000	0.000	0.000
153	D	226	PHE	0	-0.161	-0.096	33.282	0.004	0.004	0.000	0.000	0.000	0.000
154	D	241	GLN	0	0.014	-0.012	34.360	-0.001	-0.001	0.000	0.000	0.000	0.000
155	D	242	ILE	0	0.038	0.037	29.318	0.002	0.002	0.000	0.000	0.000	0.000
156	D	243	PRO	0	-0.032	-0.028	26.402	0.003	0.003	0.000	0.000	0.000	0.000
157	D	244	CYS	0	0.015	0.011	25.889	-0.008	-0.008	0.000	0.000	0.000	0.000
158	D	245	ILE	0	-0.015	-0.010	20.240	0.011	0.011	0.000	0.000	0.000	0.000
159	D	246	THR	0	-0.036	-0.014	21.345	-0.009	-0.009	0.000	0.000	0.000	0.000
160	D	247	THR	0	0.022	-0.007	15.293	0.029	0.029	0.000	0.000	0.000	0.000
161	D	248	MET	0	0.036	0.025	14.932	-0.024	-0.024	0.000	0.000	0.000	0.000
162	D	249	LEU	0	-0.047	-0.010	11.148	0.077	0.077	0.000	0.000	0.000	0.000
163	D	250	THR	0	-0.025	-0.025	7.623	0.032	0.032	0.000	0.000	0.000	0.000
164	D	251	ARG	1	0.835	0.932	2.671	-10.335	-9.364	2.137	-1.177	-1.931	0.009
165	D	252	ILE	0	0.050	0.027	7.369	0.156	0.156	0.000	0.000	0.000	0.000
166	D	253	LEU	0	0.008	0.004	7.941	0.108	0.108	0.000	0.000	0.000	0.000
167	D	254	ARG	1	0.894	0.920	9.493	0.182	0.182	0.000	0.000	0.000	0.000
168	D	255	PHE	0	0.001	0.007	11.898	0.038	0.038	0.000	0.000	0.000	0.000
169	D	256	SER	0	-0.030	-0.018	11.130	-0.022	-0.022	0.000	0.000	0.000	0.000
170	D	257	ASP	-1	-0.781	-0.867	13.691	0.080	0.080	0.000	0.000	0.000	0.000
171	D	258	LYS	1	0.776	0.853	14.349	-0.187	-0.187	0.000	0.000	0.000	0.000
172	D	259	GLN	0	0.007	0.017	16.803	0.003	0.003	0.000	0.000	0.000	0.000

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