FMO DATABASE

FMODB ID: R9G88

Calculation Name: 1SND-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SND

Chain ID: A

ChEMBL ID:

UniProt ID: P00644

Base Structure: X-ray

Registration Date: 2023-09-19

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1067894.118042
FMO2-HF: Nuclear repulsion	1016759.690599
FMO2-HF: Total energy	-51134.427444
FMO2-MP2: Total energy	-51284.310648

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:7:LEU)

Summations of interaction energy for fragment #1(A:7:LEU)

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.
-21.091	-10.901	6.194	-6.006	-10.375	-0.051

Interaction energy analysis for fragmet #1(A:7:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.089 / q_NPA : -0.050

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	9	LYS	1	0.939	0.974	3.813	1.968	3.505	-0.023	-0.644	-0.869	0.003
4	A	10	GLU	-1	-0.853	-0.925	6.489	0.844	0.844	0.000	0.000	0.000	0.000
5	A	11	PRO	0	0.044	0.029	9.465	-0.115	-0.115	0.000	0.000	0.000	0.000
6	A	12	ALA	0	-0.025	-0.018	12.876	0.119	0.119	0.000	0.000	0.000	0.000
7	A	13	THR	0	-0.006	0.006	14.658	-0.052	-0.052	0.000	0.000	0.000	0.000
8	A	14	LEU	0	0.011	0.012	18.258	0.030	0.030	0.000	0.000	0.000	0.000
9	A	15	ILE	0	-0.038	-0.005	19.666	0.027	0.027	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.989	0.977	21.351	0.087	0.087	0.000	0.000	0.000	0.000
11	A	17	ALA	0	0.037	0.042	20.568	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	18	ILE	0	-0.096	-0.060	20.738	0.026	0.026	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.684	-0.844	20.820	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.038	0.024	20.088	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.832	-0.895	16.313	-0.176	-0.176	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.027	-0.030	15.821	0.011	0.011	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.017	0.004	15.925	0.005	0.005	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.906	0.969	16.780	0.040	0.040	0.000	0.000	0.000	0.000
19	A	25	LEU	0	0.004	-0.014	13.469	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	26	MET	0	0.025	0.015	17.390	0.059	0.059	0.000	0.000	0.000	0.000
21	A	27	TYR	0	-0.017	-0.028	9.883	0.033	0.033	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.947	0.975	11.788	-0.513	-0.513	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.018	0.019	16.502	0.027	0.027	0.000	0.000	0.000	0.000
24	A	30	GLN	0	0.000	-0.008	18.450	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	31	PRO	0	-0.022	-0.011	18.371	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	32	MET	0	0.020	0.016	14.663	0.052	0.052	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.014	-0.004	17.400	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	34	PHE	0	-0.012	-0.013	10.875	0.046	0.046	0.000	0.000	0.000	0.000
29	A	35	ARG	1	0.863	0.943	13.275	0.099	0.099	0.000	0.000	0.000	0.000
30	A	36	LEU	0	-0.014	-0.009	11.253	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.004	-0.004	5.809	0.118	0.118	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.019	0.008	6.103	-0.167	-0.167	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.018	0.003	9.876	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.905	-0.954	13.026	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	41	THR	0	-0.005	-0.016	16.582	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	42	PRO	0	-0.017	0.021	18.977	0.023	0.023	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.917	-0.976	21.581	-0.073	-0.073	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.096	-0.081	23.988	0.011	0.011	0.000	0.000	0.000	0.000
39	A	45	LYS	1	0.843	0.920	24.820	0.083	0.083	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.088	0.069	24.547	0.017	0.017	0.000	0.000	0.000	0.000
41	A	47	PRO	0	-0.021	-0.022	25.100	0.006	0.006	0.000	0.000	0.000	0.000
42	A	48	LYS	1	0.913	0.951	28.129	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	49	LYS	1	0.864	0.938	26.077	0.050	0.050	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.035	0.035	29.468	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.013	-0.006	28.519	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.846	-0.911	24.566	-0.075	-0.075	0.000	0.000	0.000	0.000
47	A	53	LYS	1	0.968	0.973	28.483	0.088	0.088	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.019	-0.006	25.114	0.001	0.001	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.025	0.035	24.596	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	56	PRO	0	0.002	-0.020	24.971	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.867	-0.933	25.568	-0.147	-0.147	0.000	0.000	0.000	0.000
52	A	58	ALA	0	0.055	0.027	20.502	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.027	-0.005	21.434	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	60	ALA	0	-0.013	-0.016	23.090	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.018	-0.013	17.539	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	62	THR	0	0.005	-0.020	17.416	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.861	0.931	19.514	0.141	0.141	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.969	0.990	22.359	0.229	0.229	0.000	0.000	0.000	0.000
59	A	65	MET	0	-0.042	0.005	14.883	0.002	0.002	0.000	0.000	0.000	0.000
60	A	66	VAL	0	-0.030	-0.027	17.070	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.868	-0.942	19.141	-0.175	-0.175	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.095	-0.045	22.024	0.031	0.031	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.022	0.015	17.960	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.915	0.949	19.916	0.381	0.381	0.000	0.000	0.000	0.000
65	A	71	LYS	1	0.915	0.954	16.033	0.503	0.503	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.020	0.017	13.911	-0.065	-0.065	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.964	-0.988	9.845	-1.093	-1.093	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.027	-0.002	8.138	-0.074	-0.074	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.831	-0.910	2.342	-14.303	-11.374	3.208	-2.475	-3.661	-0.033
70	A	76	PHE	0	-0.025	-0.013	3.547	-0.408	0.037	0.005	-0.098	-0.352	0.000
71	A	77	ASP	-1	-0.777	-0.885	2.424	-0.667	2.303	2.390	-2.221	-3.139	-0.021
72	A	78	LYS	1	0.934	0.943	2.854	-3.248	-2.172	0.143	-0.256	-0.963	0.001
73	A	79	GLY	0	0.019	0.010	4.362	-0.700	-0.636	0.000	-0.024	-0.040	0.000
74	A	80	GLN	0	-0.040	-0.003	7.434	-0.154	-0.154	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.903	0.942	5.492	-3.290	-3.290	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.010	-0.004	10.023	-0.100	-0.100	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.756	-0.880	13.703	0.170	0.170	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.960	0.967	16.372	-0.141	-0.141	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.071	-0.032	19.522	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	86	GLY	0	0.008	0.010	18.850	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	87	ARG	1	0.823	0.929	15.774	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	88	GLY	0	0.059	0.032	12.693	0.073	0.073	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.021	-0.016	9.462	-0.125	-0.125	0.000	0.000	0.000	0.000
84	A	90	ALA	0	-0.016	-0.021	6.969	0.164	0.164	0.000	0.000	0.000	0.000
85	A	91	TYR	0	0.024	0.010	2.610	-0.962	0.137	0.472	-0.288	-1.283	-0.001
86	A	92	ILE	0	0.026	0.003	7.344	-0.169	-0.169	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.084	-0.062	4.700	0.329	0.399	-0.001	0.000	-0.068	0.000
88	A	94	ALA	0	0.045	0.013	11.373	0.117	0.117	0.000	0.000	0.000	0.000
89	A	95	ASP	-1	-0.845	-0.923	15.067	-0.480	-0.480	0.000	0.000	0.000	0.000
90	A	96	GLY	0	-0.005	-0.002	12.223	0.022	0.022	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.949	0.969	11.649	0.391	0.391	0.000	0.000	0.000	0.000
92	A	98	MET	0	0.017	0.034	5.773	0.203	0.203	0.000	0.000	0.000	0.000
93	A	99	VAL	0	0.061	0.000	10.643	0.122	0.122	0.000	0.000	0.000	0.000
94	A	100	ASN	0	-0.027	-0.023	9.363	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.864	-0.953	10.254	-0.596	-0.596	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.005	0.009	12.067	0.099	0.099	0.000	0.000	0.000	0.000
97	A	103	LEU	0	-0.012	-0.012	15.054	0.064	0.064	0.000	0.000	0.000	0.000
98	A	104	VAL	0	-0.014	-0.003	12.890	0.054	0.054	0.000	0.000	0.000	0.000
99	A	105	ARG	1	0.911	0.975	15.938	0.427	0.427	0.000	0.000	0.000	0.000
100	A	106	GLN	0	-0.056	-0.032	17.627	0.017	0.017	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.008	0.009	19.675	0.031	0.031	0.000	0.000	0.000	0.000
102	A	108	LEU	0	-0.058	-0.032	19.728	0.030	0.030	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.000	-0.008	16.106	0.011	0.011	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.947	0.983	17.030	0.116	0.116	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.025	0.017	11.408	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	112	ALA	0	0.002	0.012	12.361	0.042	0.042	0.000	0.000	0.000	0.000
107	A	113	TYR	0	-0.019	-0.002	13.647	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	120	THR	0	0.029	0.003	10.819	0.045	0.045	0.000	0.000	0.000	0.000
109	A	121	HIS	0	0.010	0.004	13.833	-0.046	-0.046	0.000	0.000	0.000	0.000
110	A	122	GLU	-1	-0.904	-0.966	8.127	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	123	GLN	0	0.044	0.018	12.497	0.008	0.008	0.000	0.000	0.000	0.000
112	A	124	HIS	0	-0.003	-0.001	14.977	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	125	LEU	0	0.051	0.008	12.484	0.000	0.000	0.000	0.000	0.000	0.000
114	A	126	ARG	1	0.862	0.925	8.204	-0.094	-0.094	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.953	0.998	14.841	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	128	SER	0	0.015	-0.005	18.293	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.844	-0.895	12.307	0.184	0.184	0.000	0.000	0.000	0.000
118	A	130	ALA	0	-0.036	-0.025	16.685	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.002	-0.004	18.497	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	132	ALA	0	0.040	0.023	18.756	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.888	0.942	13.736	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	134	LYS	1	0.913	0.963	19.815	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	135	GLU	-1	-0.952	-0.978	23.087	0.066	0.066	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.944	0.977	22.863	-0.036	-0.036	0.000	0.000	0.000	0.000
125	A	137	LEU	0	0.023	0.019	22.300	0.012	0.012	0.000	0.000	0.000	0.000
126	A	138	ASN	0	0.017	0.009	21.040	0.016	0.016	0.000	0.000	0.000	0.000
127	A	139	ILE	0	0.018	0.015	15.023	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	140	TRP	0	-0.048	-0.025	13.320	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	141	SER	0	-0.047	-0.018	19.921	-0.036	-0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LEU)