FMO DATABASE

FMODB ID: QYGVY

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	OptHSide
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	-1068332.408549
FMO2-HF: Nuclear repulsion	1017197.08128
FMO2-HF: Total energy	-51135.327268
FMO2-MP2: Total energy	-51285.176411

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.
-14.386	-5.379	4.223	-4.451	-8.777	-0.029

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 : -0.068 / q_NPA : -0.042

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	0.827	0.916	3.813	1.025	2.602	-0.023	-0.665	-0.889	0.002
4	A	10	GLU	-1	-0.792	-0.875	6.487	0.941	0.941	0.000	0.000	0.000	0.000
5	A	11	PRO	0	0.024	0.024	9.446	-0.109	-0.109	0.000	0.000	0.000	0.000
6	A	12	ALA	0	-0.020	-0.016	12.861	0.093	0.093	0.000	0.000	0.000	0.000
7	A	13	THR	0	0.002	0.007	14.655	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	14	LEU	0	0.008	0.016	18.261	0.021	0.021	0.000	0.000	0.000	0.000
9	A	15	ILE	0	-0.032	-0.004	19.681	0.023	0.023	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.974	0.969	21.366	0.077	0.077	0.000	0.000	0.000	0.000
11	A	17	ALA	0	0.042	0.043	20.528	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	18	ILE	0	-0.073	-0.047	20.675	0.022	0.022	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.710	-0.826	20.749	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.043	0.025	20.151	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.763	-0.843	16.499	-0.158	-0.158	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.028	-0.048	15.719	0.003	0.003	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.025	0.008	15.885	0.009	0.009	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.909	0.969	16.713	0.032	0.032	0.000	0.000	0.000	0.000
19	A	25	LEU	0	0.008	-0.010	13.532	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	26	MET	0	0.027	0.017	17.394	0.047	0.047	0.000	0.000	0.000	0.000
21	A	27	TYR	0	-0.021	-0.048	10.110	0.004	0.004	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.896	0.940	11.126	-0.462	-0.462	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.023	0.023	16.462	0.022	0.022	0.000	0.000	0.000	0.000
24	A	30	GLN	0	-0.011	-0.011	18.416	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	PRO	0	-0.009	-0.008	18.347	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	32	MET	0	0.009	0.009	14.883	0.045	0.045	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.021	-0.011	17.395	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	34	PHE	0	-0.008	-0.008	10.406	0.037	0.037	0.000	0.000	0.000	0.000
29	A	35	ARG	1	0.792	0.885	13.154	0.125	0.125	0.000	0.000	0.000	0.000
30	A	36	LEU	0	-0.010	-0.008	11.160	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.029	-0.002	5.538	0.095	0.095	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.030	0.006	6.151	-0.102	-0.102	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.019	0.004	9.839	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.875	-0.925	13.064	-0.087	-0.087	0.000	0.000	0.000	0.000
35	A	41	THR	0	0.027	-0.002	16.656	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	42	PRO	0	-0.030	0.019	19.053	0.019	0.019	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.901	-0.971	21.256	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.059	-0.049	24.052	0.011	0.011	0.000	0.000	0.000	0.000
39	A	45	LYS	1	0.852	0.905	24.804	0.084	0.084	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.090	0.066	24.291	0.013	0.013	0.000	0.000	0.000	0.000
41	A	47	PRO	0	-0.032	-0.024	25.200	0.006	0.006	0.000	0.000	0.000	0.000
42	A	48	LYS	1	0.915	0.953	28.053	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	49	LYS	1	0.794	0.888	25.392	0.058	0.058	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.034	0.036	29.457	0.000	0.000	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.013	-0.008	28.555	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.818	-0.893	25.072	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	53	LYS	1	0.967	0.973	28.544	0.083	0.083	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.013	-0.008	25.409	0.001	0.001	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.027	0.035	24.711	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	56	PRO	0	0.016	-0.013	25.114	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.872	-0.937	25.775	-0.127	-0.127	0.000	0.000	0.000	0.000
52	A	58	ALA	0	0.052	0.026	20.720	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.023	-0.034	21.502	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	60	ALA	0	-0.048	-0.021	23.182	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.017	-0.012	17.616	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	62	THR	0	0.010	-0.011	17.593	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.830	0.900	19.632	0.120	0.120	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.973	0.995	22.500	0.186	0.186	0.000	0.000	0.000	0.000
59	A	65	MET	0	-0.039	0.004	14.879	0.005	0.005	0.000	0.000	0.000	0.000
60	A	66	VAL	0	-0.020	-0.028	17.116	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.854	-0.915	19.340	-0.145	-0.145	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.088	-0.044	22.252	0.026	0.026	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.046	0.008	17.915	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.892	0.936	19.891	0.330	0.330	0.000	0.000	0.000	0.000
65	A	71	LYS	1	0.940	0.970	15.908	0.386	0.386	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.004	0.011	13.948	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.868	-0.931	9.950	-1.049	-1.049	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.042	-0.007	8.469	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.816	-0.886	2.860	-6.867	-5.314	0.367	-0.533	-1.387	-0.003
70	A	76	PHE	0	-0.004	-0.006	3.546	-0.404	0.076	0.005	-0.107	-0.378	0.000
71	A	77	ASP	-1	-0.748	-0.863	2.416	-2.337	0.860	3.315	-2.707	-3.804	-0.028
72	A	78	LYS	1	0.944	0.972	2.761	-2.566	-1.452	0.363	-0.181	-1.296	0.000
73	A	79	GLY	0	-0.017	-0.005	4.079	-0.501	-0.407	0.003	-0.038	-0.059	0.000
74	A	80	GLN	0	-0.077	-0.034	6.948	-0.101	-0.101	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.939	0.940	5.193	-2.760	-2.760	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.012	-0.008	9.704	-0.073	-0.073	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.740	-0.864	13.397	0.095	0.095	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.959	0.966	16.177	-0.086	-0.086	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.068	-0.032	19.326	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	GLY	0	0.003	0.008	18.785	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	87	ARG	1	0.788	0.908	15.683	0.018	0.018	0.000	0.000	0.000	0.000
82	A	88	GLY	0	0.049	0.027	12.683	0.055	0.055	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.023	-0.014	9.341	-0.095	-0.095	0.000	0.000	0.000	0.000
84	A	90	ALA	0	-0.013	-0.022	6.857	0.092	0.092	0.000	0.000	0.000	0.000
85	A	91	TYR	0	0.037	0.010	2.907	-0.669	0.323	0.193	-0.220	-0.964	0.000
86	A	92	ILE	0	0.020	0.006	7.324	-0.135	-0.135	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.070	-0.071	5.022	0.406	0.406	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.038	0.010	11.597	0.099	0.099	0.000	0.000	0.000	0.000
89	A	95	ASP	-1	-0.830	-0.926	15.270	-0.375	-0.375	0.000	0.000	0.000	0.000
90	A	96	GLY	0	0.001	0.001	12.195	0.024	0.024	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.954	0.977	11.968	0.321	0.321	0.000	0.000	0.000	0.000
92	A	98	MET	0	0.009	0.030	5.767	0.184	0.184	0.000	0.000	0.000	0.000
93	A	99	VAL	0	0.062	0.000	10.862	0.099	0.099	0.000	0.000	0.000	0.000
94	A	100	ASN	0	-0.019	-0.020	9.457	0.003	0.003	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.869	-0.948	10.390	-0.499	-0.499	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.006	0.008	12.162	0.085	0.085	0.000	0.000	0.000	0.000
97	A	103	LEU	0	-0.023	-0.016	15.180	0.055	0.055	0.000	0.000	0.000	0.000
98	A	104	VAL	0	-0.009	-0.004	13.181	0.044	0.044	0.000	0.000	0.000	0.000
99	A	105	ARG	1	0.908	0.972	16.015	0.348	0.348	0.000	0.000	0.000	0.000
100	A	106	GLN	0	-0.048	-0.026	17.698	0.023	0.023	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.006	0.011	19.779	0.025	0.025	0.000	0.000	0.000	0.000
102	A	108	LEU	0	-0.067	-0.035	19.876	0.025	0.025	0.000	0.000	0.000	0.000
103	A	109	ALA	0	-0.001	-0.011	16.172	0.008	0.008	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.944	0.980	17.092	0.112	0.112	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.031	0.019	11.420	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	112	ALA	0	-0.009	0.009	12.203	0.036	0.036	0.000	0.000	0.000	0.000
107	A	113	TYR	0	-0.026	-0.016	13.537	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	120	THR	0	0.018	-0.007	10.431	0.037	0.037	0.000	0.000	0.000	0.000
109	A	121	HIS	0	0.015	0.018	13.827	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	122	GLU	-1	-0.829	-0.910	8.350	-0.051	-0.051	0.000	0.000	0.000	0.000
111	A	123	GLN	0	0.036	0.016	12.359	0.009	0.009	0.000	0.000	0.000	0.000
112	A	124	HIS	0	0.012	0.002	14.793	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	125	LEU	0	0.042	0.003	12.712	0.002	0.002	0.000	0.000	0.000	0.000
114	A	126	ARG	1	0.809	0.882	8.316	-0.042	-0.042	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.956	0.994	14.720	0.003	0.003	0.000	0.000	0.000	0.000
116	A	128	SER	0	0.010	-0.004	18.200	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.807	-0.872	12.363	0.076	0.076	0.000	0.000	0.000	0.000
118	A	130	ALA	0	-0.015	-0.011	16.856	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.003	-0.009	18.463	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	132	ALA	0	0.052	0.032	18.876	0.000	0.000	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.823	0.908	13.161	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	134	LYS	1	0.851	0.923	19.985	0.006	0.006	0.000	0.000	0.000	0.000
123	A	135	GLU	-1	-0.910	-0.944	23.217	0.043	0.043	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.941	0.978	22.930	-0.019	-0.019	0.000	0.000	0.000	0.000
125	A	137	LEU	0	0.035	0.021	22.517	0.010	0.010	0.000	0.000	0.000	0.000
126	A	138	ASN	0	0.022	0.012	21.074	0.008	0.008	0.000	0.000	0.000	0.000
127	A	139	ILE	0	0.025	0.028	15.022	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	140	TRP	0	-0.033	-0.026	13.260	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	141	SER	0	-0.066	-0.033	19.985	-0.034	-0.034	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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