FMO DATABASE

FMODB ID: K9LG3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1070239.800813
FMO2-HF: Nuclear repulsion	1019104.073776
FMO2-HF: Total energy	-51135.727036
FMO2-MP2: Total energy	-51285.552136

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.
-13.361	-4.781	3.954	-4.089	-8.445	-0.027

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 : -0.043 / q_NPA : -0.029

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	0.808	0.912	3.869	1.120	2.536	-0.018	-0.633	-0.766	0.002
4	A	10	GLU	-1	-0.776	-0.863	6.646	0.544	0.544	0.000	0.000	0.000	0.000
5	A	11	PRO	0	0.018	0.010	9.843	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	12	ALA	0	-0.013	-0.015	13.255	0.084	0.084	0.000	0.000	0.000	0.000
7	A	13	THR	0	0.013	0.017	15.127	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	14	LEU	0	0.016	0.016	18.770	0.016	0.016	0.000	0.000	0.000	0.000
9	A	15	ILE	0	-0.040	-0.006	19.999	0.022	0.022	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.964	0.961	21.149	0.098	0.098	0.000	0.000	0.000	0.000
11	A	17	ALA	0	0.049	0.049	20.245	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	18	ILE	0	-0.064	-0.035	20.510	0.023	0.023	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.722	-0.822	20.534	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.045	0.029	19.781	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.722	-0.807	16.169	-0.145	-0.145	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.034	-0.046	15.497	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.022	0.004	15.786	0.004	0.004	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.916	0.967	16.726	0.058	0.058	0.000	0.000	0.000	0.000
19	A	25	LEU	0	0.048	0.018	13.642	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	26	MET	0	0.012	0.009	17.662	0.044	0.044	0.000	0.000	0.000	0.000
21	A	27	TYR	0	-0.009	-0.035	10.091	0.015	0.015	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.819	0.894	11.022	-0.156	-0.156	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.037	0.034	16.402	0.027	0.027	0.000	0.000	0.000	0.000
24	A	30	GLN	0	-0.012	-0.017	18.461	0.023	0.023	0.000	0.000	0.000	0.000
25	A	31	PRO	0	-0.024	-0.022	18.471	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	32	MET	0	0.020	0.022	14.593	0.033	0.033	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.032	-0.027	17.136	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	34	PHE	0	0.000	0.004	10.464	0.031	0.031	0.000	0.000	0.000	0.000
29	A	35	ARG	1	0.764	0.861	12.725	0.123	0.123	0.000	0.000	0.000	0.000
30	A	36	LEU	0	-0.013	-0.005	10.778	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.006	-0.001	5.140	0.112	0.112	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.009	-0.004	6.024	-0.086	-0.086	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.016	0.014	9.307	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.841	-0.898	12.365	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	41	THR	0	-0.008	-0.031	15.953	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	42	PRO	0	-0.014	0.023	18.802	0.019	0.019	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.900	-0.955	20.554	-0.079	-0.079	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.064	-0.080	23.577	0.006	0.006	0.000	0.000	0.000	0.000
39	A	45	LYS	1	0.847	0.905	24.782	0.095	0.095	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.109	0.070	23.755	0.012	0.012	0.000	0.000	0.000	0.000
41	A	47	PRO	0	-0.009	-0.017	24.719	0.005	0.005	0.000	0.000	0.000	0.000
42	A	48	LYS	1	0.896	0.939	27.588	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	49	LYS	1	0.798	0.901	25.044	0.049	0.049	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.028	0.032	29.505	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.047	-0.026	28.185	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.804	-0.879	24.768	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	53	LYS	1	0.962	0.970	28.082	0.075	0.075	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.028	-0.002	24.901	0.003	0.003	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.035	0.041	24.051	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	56	PRO	0	0.019	-0.009	24.397	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.881	-0.936	25.561	-0.120	-0.120	0.000	0.000	0.000	0.000
52	A	58	ALA	0	0.048	0.021	20.306	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.026	-0.039	20.925	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	60	ALA	0	-0.041	-0.018	22.529	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.016	0.000	17.069	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	62	THR	0	0.002	-0.017	16.938	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.813	0.884	18.978	0.128	0.128	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.959	0.984	21.802	0.182	0.182	0.000	0.000	0.000	0.000
59	A	65	MET	0	-0.036	-0.001	14.193	0.006	0.006	0.000	0.000	0.000	0.000
60	A	66	VAL	0	0.002	-0.009	16.707	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.853	-0.914	18.569	-0.155	-0.155	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.085	-0.041	21.423	0.027	0.027	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.045	0.006	17.596	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.867	0.914	19.701	0.339	0.339	0.000	0.000	0.000	0.000
65	A	71	LYS	1	0.939	0.972	15.571	0.422	0.422	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.014	0.015	14.217	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.864	-0.919	9.700	-1.087	-1.087	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.033	-0.007	8.897	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.789	-0.883	2.781	-6.168	-4.409	0.387	-0.702	-1.444	-0.005
70	A	76	PHE	0	-0.006	0.003	4.347	-0.496	-0.045	0.000	-0.086	-0.365	0.000
71	A	77	ASP	-1	-0.736	-0.862	2.485	-1.331	1.767	2.529	-2.273	-3.352	-0.021
72	A	78	LYS	1	0.930	0.970	2.889	-2.938	-2.126	0.106	-0.004	-0.914	-0.001
73	A	79	GLY	0	-0.018	0.003	4.525	-0.631	-0.581	-0.001	-0.017	-0.032	0.000
74	A	80	GLN	0	-0.078	-0.037	6.648	-0.249	-0.249	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.945	0.938	4.871	-2.626	-2.626	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.027	-0.025	9.644	-0.104	-0.104	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.750	-0.858	13.263	0.095	0.095	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.953	0.968	15.968	-0.087	-0.087	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.056	-0.028	19.007	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	86	GLY	0	0.009	0.014	18.196	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	87	ARG	1	0.748	0.862	15.416	0.019	0.019	0.000	0.000	0.000	0.000
82	A	88	GLY	0	0.053	0.026	12.440	0.052	0.052	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.053	-0.024	9.302	-0.085	-0.085	0.000	0.000	0.000	0.000
84	A	90	ALA	0	0.024	-0.004	6.278	0.099	0.099	0.000	0.000	0.000	0.000
85	A	91	TYR	0	0.025	0.007	2.407	-0.682	0.242	0.952	-0.373	-1.504	-0.002
86	A	92	ILE	0	0.023	0.011	6.867	-0.105	-0.105	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.056	-0.061	4.629	0.277	0.347	-0.001	-0.001	-0.068	0.000
88	A	94	ALA	0	0.033	0.012	11.085	0.087	0.087	0.000	0.000	0.000	0.000
89	A	95	ASP	-1	-0.854	-0.934	14.761	-0.379	-0.379	0.000	0.000	0.000	0.000
90	A	96	GLY	0	0.020	0.018	11.996	0.026	0.026	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.945	0.975	11.434	0.323	0.323	0.000	0.000	0.000	0.000
92	A	98	MET	0	0.017	0.026	5.288	0.152	0.152	0.000	0.000	0.000	0.000
93	A	99	VAL	0	0.035	-0.017	10.199	0.099	0.099	0.000	0.000	0.000	0.000
94	A	100	ASN	0	-0.002	-0.015	8.830	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.879	-0.947	10.122	-0.455	-0.455	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.039	0.018	11.805	0.082	0.082	0.000	0.000	0.000	0.000
97	A	103	LEU	0	-0.026	-0.011	14.765	0.052	0.052	0.000	0.000	0.000	0.000
98	A	104	VAL	0	-0.018	-0.002	13.173	0.041	0.041	0.000	0.000	0.000	0.000
99	A	105	ARG	1	0.895	0.952	15.692	0.317	0.317	0.000	0.000	0.000	0.000
100	A	106	GLN	0	-0.037	-0.016	17.382	0.021	0.021	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.010	0.004	19.523	0.022	0.022	0.000	0.000	0.000	0.000
102	A	108	LEU	0	-0.063	-0.028	19.680	0.021	0.021	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.007	-0.007	15.607	0.004	0.004	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.933	0.969	16.654	0.107	0.107	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.033	0.014	11.200	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	112	ALA	0	0.008	0.017	11.954	0.033	0.033	0.000	0.000	0.000	0.000
107	A	113	TYR	0	-0.032	-0.025	13.416	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	120	THR	0	0.021	-0.009	10.314	0.043	0.043	0.000	0.000	0.000	0.000
109	A	121	HIS	0	0.018	0.017	13.783	-0.040	-0.040	0.000	0.000	0.000	0.000
110	A	122	GLU	-1	-0.845	-0.907	8.739	0.008	0.008	0.000	0.000	0.000	0.000
111	A	123	GLN	0	0.050	0.020	12.336	0.008	0.008	0.000	0.000	0.000	0.000
112	A	124	HIS	0	0.036	0.018	15.003	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	125	LEU	0	0.014	0.016	12.563	0.006	0.006	0.000	0.000	0.000	0.000
114	A	126	ARG	1	0.819	0.874	8.675	-0.124	-0.124	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.963	0.989	14.730	-0.030	-0.030	0.000	0.000	0.000	0.000
116	A	128	SER	0	-0.023	-0.023	18.007	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.804	-0.884	12.553	0.136	0.136	0.000	0.000	0.000	0.000
118	A	130	ALA	0	-0.002	-0.001	16.879	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.019	-0.009	18.688	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	132	ALA	0	0.075	0.037	18.904	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.800	0.907	13.098	-0.070	-0.070	0.000	0.000	0.000	0.000
122	A	134	LYS	1	0.870	0.931	19.995	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	135	GLU	-1	-0.891	-0.941	23.349	0.076	0.076	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.870	0.934	22.784	-0.061	-0.061	0.000	0.000	0.000	0.000
125	A	137	LEU	0	0.039	0.025	22.124	0.011	0.011	0.000	0.000	0.000	0.000
126	A	138	ASN	0	0.002	-0.006	21.168	0.013	0.013	0.000	0.000	0.000	0.000
127	A	139	ILE	0	0.040	0.032	15.339	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	140	TRP	0	-0.010	0.000	13.418	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	141	SER	0	-0.046	-0.025	20.228	-0.046	-0.046	0.000	0.000	0.000	0.000

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