FMO DATABASE

FMODB ID: G63M1

Calculation Name: 3SIR-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-1884902.084125
FMO2-HF: Nuclear repulsion	1813968.485254
FMO2-HF: Total energy	-70933.59887
FMO2-MP2: Total energy	-71136.013004

3D Structure Molmil

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.
1.076	3.109	3.485	-2.119	-3.399	-0.005

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 : 0.000 / q_NPA : -0.020

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	-0.848	-0.898	3.211	-1.451	0.826	-0.014	-0.969	-1.294	-0.001
4	D	13	TYR	0	-0.067	-0.086	4.014	-0.329	-0.140	0.001	-0.059	-0.131	0.000
5	D	14	ASN	0	-0.013	-0.008	6.090	0.138	0.138	0.000	0.000	0.000	0.000
6	D	15	MET	0	-0.037	-0.008	7.163	0.050	0.050	0.000	0.000	0.000	0.000
7	D	16	ARG	1	0.927	0.933	10.442	0.250	0.250	0.000	0.000	0.000	0.000
8	D	17	HIS	0	0.026	0.038	10.270	0.067	0.067	0.000	0.000	0.000	0.000
9	D	18	LYS	1	0.941	0.984	13.645	0.125	0.125	0.000	0.000	0.000	0.000
10	D	19	ASN	0	0.047	0.012	17.288	0.017	0.017	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.860	0.934	14.411	0.223	0.223	0.000	0.000	0.000	0.000
12	D	21	GLY	0	0.078	0.034	16.904	-0.028	-0.028	0.000	0.000	0.000	0.000
13	D	22	MET	0	-0.041	-0.012	19.243	0.015	0.015	0.000	0.000	0.000	0.000
14	D	23	ALA	0	0.008	-0.003	21.571	-0.015	-0.015	0.000	0.000	0.000	0.000
15	D	24	LEU	0	-0.002	-0.002	24.077	0.013	0.013	0.000	0.000	0.000	0.000
16	D	25	ILE	0	0.015	0.016	26.755	-0.004	-0.004	0.000	0.000	0.000	0.000
17	D	26	PHE	0	0.008	-0.007	27.488	0.009	0.009	0.000	0.000	0.000	0.000
18	D	27	ASN	0	-0.058	-0.049	31.833	0.000	0.000	0.000	0.000	0.000	0.000
19	D	28	HIS	0	0.041	0.029	35.040	0.004	0.004	0.000	0.000	0.000	0.000
20	D	43	ASN	0	0.036	-0.001	37.226	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	44	VAL	0	0.066	0.020	36.755	-0.001	-0.001	0.000	0.000	0.000	0.000
22	D	45	ASP	-1	-0.818	-0.877	33.062	-0.084	-0.084	0.000	0.000	0.000	0.000
23	D	46	CYS	0	-0.025	0.007	32.098	-0.006	-0.006	0.000	0.000	0.000	0.000
24	D	47	GLU	-1	-0.953	-0.961	32.337	-0.070	-0.070	0.000	0.000	0.000	0.000
25	D	48	ASN	0	0.034	0.015	30.950	0.000	0.000	0.000	0.000	0.000	0.000
26	D	49	LEU	0	0.063	0.026	25.426	-0.005	-0.005	0.000	0.000	0.000	0.000
27	D	50	THR	0	0.023	0.005	27.232	-0.008	-0.008	0.000	0.000	0.000	0.000
28	D	51	ARG	1	0.871	0.930	28.255	0.074	0.074	0.000	0.000	0.000	0.000
29	D	52	VAL	0	0.016	-0.002	24.028	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	53	LEU	0	0.000	-0.004	22.146	-0.006	-0.006	0.000	0.000	0.000	0.000
31	D	54	LYS	1	0.975	0.988	23.407	0.086	0.086	0.000	0.000	0.000	0.000
32	D	55	GLN	0	-0.009	0.007	24.964	-0.004	-0.004	0.000	0.000	0.000	0.000
33	D	56	LEU	0	-0.097	-0.036	19.689	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	57	ASP	-1	-0.876	-0.946	19.645	-0.160	-0.160	0.000	0.000	0.000	0.000
35	D	58	PHE	0	-0.064	-0.035	17.990	-0.009	-0.009	0.000	0.000	0.000	0.000
36	D	59	GLU	-1	-0.930	-0.961	21.947	-0.093	-0.093	0.000	0.000	0.000	0.000
37	D	60	VAL	0	-0.048	-0.022	24.775	-0.005	-0.005	0.000	0.000	0.000	0.000
38	D	61	THR	0	-0.041	-0.006	27.100	0.009	0.009	0.000	0.000	0.000	0.000
39	D	62	VAL	0	0.022	-0.003	29.678	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	63	TYR	0	0.004	0.003	29.218	0.005	0.005	0.000	0.000	0.000	0.000
41	D	64	LYS	1	0.952	0.951	33.909	0.062	0.062	0.000	0.000	0.000	0.000
42	D	65	ASP	-1	-0.823	-0.877	37.212	-0.066	-0.066	0.000	0.000	0.000	0.000
43	D	66	CYS	0	0.052	-0.001	36.884	-0.003	-0.003	0.000	0.000	0.000	0.000
44	D	67	ARG	1	0.870	0.942	34.183	0.077	0.077	0.000	0.000	0.000	0.000
45	D	68	TYR	0	-0.025	-0.039	35.229	-0.005	-0.005	0.000	0.000	0.000	0.000
46	D	69	LYS	1	0.895	0.942	35.325	0.061	0.061	0.000	0.000	0.000	0.000
47	D	70	ASP	-1	-0.789	-0.884	34.832	-0.072	-0.072	0.000	0.000	0.000	0.000
48	D	71	ILE	0	-0.017	0.054	30.194	-0.003	-0.003	0.000	0.000	0.000	0.000
49	D	72	LEU	0	-0.017	-0.005	30.044	-0.005	-0.005	0.000	0.000	0.000	0.000
50	D	73	ARG	1	1.009	1.006	29.930	0.069	0.069	0.000	0.000	0.000	0.000
51	D	74	THR	0	-0.028	-0.060	29.989	0.000	0.000	0.000	0.000	0.000	0.000
52	D	75	ILE	0	-0.038	-0.019	25.203	-0.005	-0.005	0.000	0.000	0.000	0.000
53	D	76	GLU	-1	-0.943	-0.960	26.156	-0.100	-0.100	0.000	0.000	0.000	0.000
54	D	77	TYR	0	-0.032	-0.030	27.059	-0.003	-0.003	0.000	0.000	0.000	0.000
55	D	78	SER	0	0.027	-0.026	24.860	-0.002	-0.002	0.000	0.000	0.000	0.000
56	D	79	ALA	0	-0.053	-0.018	22.425	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	80	SER	0	-0.013	0.003	22.438	-0.006	-0.006	0.000	0.000	0.000	0.000
58	D	81	GLN	0	-0.032	0.016	23.297	0.007	0.007	0.000	0.000	0.000	0.000
59	D	82	ASN	0	0.033	0.020	19.904	-0.025	-0.025	0.000	0.000	0.000	0.000
60	D	83	HIS	0	0.042	0.003	17.458	0.009	0.009	0.000	0.000	0.000	0.000
61	D	84	SER	0	-0.025	-0.042	15.776	-0.032	-0.032	0.000	0.000	0.000	0.000
62	D	85	ASP	-1	-0.957	-0.956	15.306	-0.154	-0.154	0.000	0.000	0.000	0.000
63	D	86	SER	0	-0.055	-0.031	16.415	0.010	0.010	0.000	0.000	0.000	0.000
64	D	87	ASP	-1	-0.771	-0.911	12.660	-0.329	-0.329	0.000	0.000	0.000	0.000
65	D	88	CYS	0	-0.150	-0.057	12.364	-0.059	-0.059	0.000	0.000	0.000	0.000
66	D	89	ILE	0	0.022	0.022	14.867	0.036	0.036	0.000	0.000	0.000	0.000
67	D	90	LEU	0	0.011	0.003	17.939	-0.024	-0.024	0.000	0.000	0.000	0.000
68	D	91	VAL	0	-0.008	-0.006	20.626	0.019	0.019	0.000	0.000	0.000	0.000
69	D	92	ALA	0	0.000	-0.001	23.842	-0.005	-0.005	0.000	0.000	0.000	0.000
70	D	93	ILE	0	-0.017	-0.002	26.623	0.009	0.009	0.000	0.000	0.000	0.000
71	D	94	LEU	0	0.027	0.010	29.836	-0.001	-0.001	0.000	0.000	0.000	0.000
72	D	95	SER	0	0.015	0.010	32.712	0.005	0.005	0.000	0.000	0.000	0.000
73	D	114	ILE	0	0.016	-0.008	26.499	0.000	0.000	0.000	0.000	0.000	0.000
74	D	115	TRP	0	0.055	0.017	22.253	-0.011	-0.011	0.000	0.000	0.000	0.000
75	D	116	SER	0	-0.023	-0.014	21.967	-0.016	-0.016	0.000	0.000	0.000	0.000
76	D	117	PHE	0	0.042	0.012	23.108	-0.003	-0.003	0.000	0.000	0.000	0.000
77	D	118	PHE	0	0.043	0.012	18.821	-0.004	-0.004	0.000	0.000	0.000	0.000
78	D	119	THR	0	-0.034	0.002	17.744	-0.030	-0.030	0.000	0.000	0.000	0.000
79	D	120	ALA	0	0.046	0.000	14.595	0.004	0.004	0.000	0.000	0.000	0.000
80	D	121	ASN	0	0.001	-0.004	16.297	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	122	HIS	0	-0.010	-0.001	19.656	0.004	0.004	0.000	0.000	0.000	0.000
82	D	123	CYS	0	-0.045	-0.016	19.136	0.006	0.006	0.000	0.000	0.000	0.000
83	D	124	PRO	0	0.084	0.044	15.887	-0.025	-0.025	0.000	0.000	0.000	0.000
84	D	125	SER	0	-0.024	-0.011	14.766	-0.031	-0.031	0.000	0.000	0.000	0.000
85	D	126	LEU	0	-0.036	-0.025	13.987	-0.023	-0.023	0.000	0.000	0.000	0.000
86	D	127	ALA	0	0.035	0.041	12.742	0.009	0.009	0.000	0.000	0.000	0.000
87	D	128	GLY	0	-0.007	0.006	8.642	-0.013	-0.013	0.000	0.000	0.000	0.000
88	D	129	LYS	1	0.832	0.936	8.083	0.197	0.197	0.000	0.000	0.000	0.000
89	D	130	PRO	0	-0.002	0.003	10.048	0.048	0.048	0.000	0.000	0.000	0.000
90	D	131	LYS	1	0.837	0.924	12.785	0.449	0.449	0.000	0.000	0.000	0.000
91	D	132	LEU	0	-0.048	-0.014	15.042	0.005	0.005	0.000	0.000	0.000	0.000
92	D	133	PHE	0	0.006	0.002	18.548	0.026	0.026	0.000	0.000	0.000	0.000
93	D	134	PHE	0	0.018	-0.001	20.655	-0.001	-0.001	0.000	0.000	0.000	0.000
94	D	135	ILE	0	0.005	0.010	25.016	0.009	0.009	0.000	0.000	0.000	0.000
95	D	136	GLN	0	0.043	0.056	28.267	-0.001	-0.001	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.006	-0.003	31.480	0.006	0.006	0.000	0.000	0.000	0.000
97	D	170	ALA	0	0.017	-0.005	12.371	0.012	0.012	0.000	0.000	0.000	0.000
98	D	171	ASP	-1	-0.802	-0.842	9.965	-0.835	-0.835	0.000	0.000	0.000	0.000
99	D	172	PHE	0	-0.007	-0.004	12.739	0.033	0.033	0.000	0.000	0.000	0.000
100	D	173	LEU	0	0.030	0.004	15.949	-0.027	-0.027	0.000	0.000	0.000	0.000
101	D	174	ILE	0	-0.011	0.010	17.912	0.013	0.013	0.000	0.000	0.000	0.000
102	D	175	ALA	0	0.022	0.016	21.708	0.005	0.005	0.000	0.000	0.000	0.000
103	D	176	TYR	0	0.045	0.010	23.702	0.007	0.007	0.000	0.000	0.000	0.000
104	D	177	SER	0	-0.004	0.023	27.309	0.004	0.004	0.000	0.000	0.000	0.000
105	D	178	THR	0	-0.029	-0.024	30.627	0.001	0.001	0.000	0.000	0.000	0.000
106	D	179	VAL	0	0.014	0.017	34.224	0.002	0.002	0.000	0.000	0.000	0.000
107	D	180	PRO	0	-0.016	-0.029	36.881	0.002	0.002	0.000	0.000	0.000	0.000
108	D	181	GLY	0	0.035	0.016	40.567	0.000	0.000	0.000	0.000	0.000	0.000
109	D	182	PHE	0	0.032	0.045	42.715	-0.001	-0.001	0.000	0.000	0.000	0.000
110	D	183	TYR	0	-0.030	-0.019	44.398	0.001	0.001	0.000	0.000	0.000	0.000
111	D	184	SER	0	0.017	0.005	39.990	0.000	0.000	0.000	0.000	0.000	0.000
112	D	185	TRP	0	0.084	0.016	42.345	0.000	0.000	0.000	0.000	0.000	0.000
113	D	186	ARG	1	0.907	0.976	41.857	0.041	0.041	0.000	0.000	0.000	0.000
114	D	187	ASN	0	-0.025	-0.024	38.571	0.004	0.004	0.000	0.000	0.000	0.000
115	D	188	THR	0	0.014	0.005	42.133	0.000	0.000	0.000	0.000	0.000	0.000
116	D	189	THR	0	0.028	0.028	41.582	-0.003	-0.003	0.000	0.000	0.000	0.000
117	D	190	ARG	1	0.871	0.942	37.715	0.052	0.052	0.000	0.000	0.000	0.000
118	D	191	GLY	0	0.065	0.001	35.130	0.001	0.001	0.000	0.000	0.000	0.000
119	D	192	SER	0	-0.013	-0.046	33.823	0.004	0.004	0.000	0.000	0.000	0.000
120	D	193	TRP	0	0.040	0.016	33.826	-0.006	-0.006	0.000	0.000	0.000	0.000
121	D	194	PHE	0	0.042	0.041	26.068	-0.003	-0.003	0.000	0.000	0.000	0.000
122	D	195	MET	0	0.026	0.024	28.015	-0.009	-0.009	0.000	0.000	0.000	0.000
123	D	196	GLN	0	-0.015	-0.015	29.907	-0.002	-0.002	0.000	0.000	0.000	0.000
124	D	197	SER	0	0.028	-0.012	29.044	0.001	0.001	0.000	0.000	0.000	0.000
125	D	198	LEU	0	-0.003	0.006	23.188	-0.006	-0.006	0.000	0.000	0.000	0.000
126	D	199	CYS	0	-0.038	-0.012	25.482	-0.007	-0.007	0.000	0.000	0.000	0.000
127	D	200	ALA	0	0.028	0.022	26.923	-0.002	-0.002	0.000	0.000	0.000	0.000
128	D	201	GLU	-1	-0.850	-0.943	23.923	-0.115	-0.115	0.000	0.000	0.000	0.000
129	D	202	LEU	0	-0.018	-0.026	20.886	-0.008	-0.008	0.000	0.000	0.000	0.000
130	D	203	ALA	0	-0.070	-0.036	23.265	-0.005	-0.005	0.000	0.000	0.000	0.000
131	D	204	ALA	0	-0.028	-0.002	25.002	0.010	0.010	0.000	0.000	0.000	0.000
132	D	205	ASN	0	-0.060	-0.037	21.711	0.009	0.009	0.000	0.000	0.000	0.000
133	D	206	GLY	0	0.024	0.031	19.990	-0.017	-0.017	0.000	0.000	0.000	0.000
134	D	207	LYS	1	0.931	0.958	17.579	0.124	0.124	0.000	0.000	0.000	0.000
135	D	208	ARG	1	0.879	0.946	17.257	0.087	0.087	0.000	0.000	0.000	0.000
136	D	209	LEU	0	-0.004	-0.002	17.148	-0.003	-0.003	0.000	0.000	0.000	0.000
137	D	210	ASP	-1	-0.820	-0.917	12.938	-0.362	-0.362	0.000	0.000	0.000	0.000
138	D	211	ILE	0	0.002	-0.004	14.327	0.036	0.036	0.000	0.000	0.000	0.000
139	D	212	LEU	0	0.030	0.013	13.855	0.040	0.040	0.000	0.000	0.000	0.000
140	D	213	THR	0	-0.042	0.030	16.963	0.045	0.045	0.000	0.000	0.000	0.000
141	D	214	LEU	0	0.014	0.009	18.481	0.024	0.024	0.000	0.000	0.000	0.000
142	D	215	LEU	0	-0.001	-0.027	19.106	0.022	0.022	0.000	0.000	0.000	0.000
143	D	216	THR	0	-0.006	-0.029	20.503	0.019	0.019	0.000	0.000	0.000	0.000
144	D	217	PHE	0	0.006	-0.010	22.611	0.015	0.015	0.000	0.000	0.000	0.000
145	D	218	VAL	0	-0.040	-0.009	24.218	0.011	0.011	0.000	0.000	0.000	0.000
146	D	219	CYS	0	-0.057	-0.024	25.790	0.006	0.006	0.000	0.000	0.000	0.000
147	D	220	GLN	0	0.012	0.003	27.272	0.004	0.004	0.000	0.000	0.000	0.000
148	D	221	ARG	1	0.952	0.971	29.129	0.084	0.084	0.000	0.000	0.000	0.000
149	D	222	VAL	0	-0.026	-0.006	30.141	0.005	0.005	0.000	0.000	0.000	0.000
150	D	223	ALA	0	-0.035	-0.011	31.868	0.004	0.004	0.000	0.000	0.000	0.000
151	D	224	VAL	0	-0.103	-0.056	33.170	0.005	0.005	0.000	0.000	0.000	0.000
152	D	225	ASP	-1	-0.885	-0.927	34.986	-0.056	-0.056	0.000	0.000	0.000	0.000
153	D	226	PHE	0	-0.074	-0.023	33.755	0.000	0.000	0.000	0.000	0.000	0.000
154	D	241	GLN	0	0.006	-0.015	34.156	-0.001	-0.001	0.000	0.000	0.000	0.000
155	D	242	ILE	0	0.015	0.014	28.365	-0.003	-0.003	0.000	0.000	0.000	0.000
156	D	243	PRO	0	-0.046	-0.023	26.701	-0.001	-0.001	0.000	0.000	0.000	0.000
157	D	244	CYS	0	-0.010	-0.018	26.655	-0.001	-0.001	0.000	0.000	0.000	0.000
158	D	245	ILE	0	0.004	-0.001	20.319	-0.008	-0.008	0.000	0.000	0.000	0.000
159	D	246	THR	0	-0.015	0.001	20.775	0.004	0.004	0.000	0.000	0.000	0.000
160	D	247	THR	0	-0.009	-0.012	14.926	-0.037	-0.037	0.000	0.000	0.000	0.000
161	D	248	MET	0	0.017	0.006	14.394	0.036	0.036	0.000	0.000	0.000	0.000
162	D	249	LEU	0	-0.029	-0.004	11.387	-0.049	-0.049	0.000	0.000	0.000	0.000
163	D	250	THR	0	-0.027	-0.039	7.290	-0.062	-0.062	0.000	0.000	0.000	0.000
164	D	251	ARG	1	0.904	0.954	2.254	2.251	1.818	3.498	-1.091	-1.974	-0.004
165	D	252	ILE	0	0.020	0.027	7.284	0.396	0.396	0.000	0.000	0.000	0.000
166	D	253	LEU	0	0.029	0.024	8.193	-0.139	-0.139	0.000	0.000	0.000	0.000
167	D	254	ARG	1	0.926	0.933	10.003	0.504	0.504	0.000	0.000	0.000	0.000
168	D	255	PHE	0	-0.020	-0.001	11.987	-0.028	-0.028	0.000	0.000	0.000	0.000
169	D	256	SER	0	0.010	-0.015	11.810	0.032	0.032	0.000	0.000	0.000	0.000
170	D	257	ASP	-1	-0.910	-0.937	14.261	-0.134	-0.134	0.000	0.000	0.000	0.000
171	D	258	LYS	1	0.881	0.943	15.041	0.195	0.195	0.000	0.000	0.000	0.000
172	D	259	GLN	0	0.005	0.026	16.426	0.002	0.002	0.000	0.000	0.000	0.000

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