FMO DATABASE

FMODB ID: 2NN9R

Calculation Name: 5SV2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5SV2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WF91

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1238707.721458
FMO2-HF: Nuclear repulsion	1185159.000874
FMO2-HF: Total energy	-53548.720584
FMO2-MP2: Total energy	-53707.137282

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-4.862	-2.014	1.972	-2.038	-2.781	0.001

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.004

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	4	ARG	1	0.798	0.896	3.619	-3.033	-0.853	0.004	-1.192	-0.992	0.004
4	A	5	TYR	0	0.020	-0.025	4.737	0.486	0.601	-0.001	-0.007	-0.106	0.000
5	A	6	LEU	0	-0.009	0.007	8.998	0.006	0.006	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.012	-0.004	12.727	0.070	0.070	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.031	0.022	14.223	0.039	0.039	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.846	0.891	17.695	0.136	0.136	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.022	0.005	19.869	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.053	0.040	16.161	0.014	0.014	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.015	0.004	17.994	0.004	0.004	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.067	-0.056	18.799	0.014	0.014	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.834	0.907	20.362	0.149	0.149	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.046	0.026	17.837	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	HIS	0	0.002	0.012	19.047	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.006	-0.004	21.503	0.015	0.015	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.024	0.001	20.241	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.035	0.018	18.785	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.007	0.004	16.774	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.848	0.920	15.480	0.100	0.100	0.000	0.000	0.000	0.000
21	A	22	HIS	0	0.002	0.003	14.602	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.817	0.906	6.715	0.550	0.550	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.001	-0.015	10.699	-0.082	-0.082	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.802	-0.898	11.425	-0.238	-0.238	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.008	0.010	9.574	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.020	-0.014	5.730	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.049	-0.010	8.006	-0.191	-0.191	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.837	-0.906	10.311	-0.094	-0.094	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.790	0.885	5.608	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.041	0.040	5.928	-0.395	-0.395	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.013	-0.012	2.227	-1.375	-0.822	1.969	-0.839	-1.683	-0.003
32	A	33	LEU	0	-0.011	0.003	5.923	0.153	0.153	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.031	0.012	9.539	0.001	0.001	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.822	0.911	11.445	0.396	0.396	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.029	0.039	15.236	0.017	0.017	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.077	0.028	18.198	0.006	0.006	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.031	0.015	21.593	0.004	0.004	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.006	-0.010	17.448	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.782	-0.874	19.115	-0.259	-0.259	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.035	-0.014	21.538	0.012	0.012	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.806	-0.901	21.065	-0.163	-0.163	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.021	0.017	20.649	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.024	0.026	23.329	0.007	0.007	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.037	-0.027	26.356	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.052	-0.021	25.287	0.007	0.007	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.034	-0.010	27.706	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.875	0.920	27.823	0.104	0.104	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.007	-0.004	32.582	0.005	0.005	0.000	0.000	0.000	0.000
49	A	50	ARG	1	1.005	0.992	32.440	0.059	0.059	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.769	-0.853	32.036	-0.079	-0.079	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.777	-0.864	28.809	-0.106	-0.106	0.000	0.000	0.000	0.000
52	A	53	HIS	0	0.034	0.019	27.620	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.783	0.860	26.988	0.070	0.070	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.003	0.008	25.813	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.000	-0.001	23.616	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.008	0.001	22.217	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.060	-0.044	21.995	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	59	TYR	0	0.042	0.016	17.168	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.838	0.902	17.301	0.251	0.251	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.840	0.917	16.818	0.118	0.118	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.899	-0.949	16.578	-0.207	-0.207	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.020	-0.004	14.214	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.057	-0.028	11.971	-0.067	-0.067	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.804	-0.886	9.847	-0.543	-0.543	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.061	-0.032	11.901	0.036	0.036	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.019	0.008	12.082	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.006	-0.008	14.995	0.019	0.019	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.017	0.005	18.465	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	70	PRO	0	-0.024	0.006	19.822	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.844	-0.941	22.738	-0.044	-0.044	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.018	-0.006	22.887	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.022	-0.005	21.831	0.003	0.003	0.000	0.000	0.000	0.000
73	A	74	TRP	0	-0.018	-0.007	24.438	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.000	0.013	28.006	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.817	0.868	20.917	0.014	0.014	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.003	-0.014	25.300	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.016	-0.014	26.096	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.838	-0.920	26.239	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.009	-0.006	22.071	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.039	-0.024	26.212	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.904	-0.933	29.253	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.026	0.010	27.460	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.063	-0.039	25.717	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.035	-0.041	29.659	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.919	-0.951	33.452	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.894	0.947	28.126	0.028	0.028	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.019	0.000	33.192	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.048	0.000	27.880	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	90	HIS	0	0.025	0.045	29.776	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.911	0.955	31.354	0.034	0.034	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.041	-0.022	28.746	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.039	-0.013	24.680	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.770	0.862	24.703	0.100	0.100	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.075	0.029	25.927	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	PRO	0	0.010	-0.017	24.845	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.748	-0.858	21.686	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.020	0.014	21.184	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.004	0.006	22.146	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.044	-0.022	17.507	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.013	0.007	17.290	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.079	0.047	17.365	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.032	-0.022	16.413	0.010	0.010	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.011	-0.017	13.254	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.812	-0.870	13.423	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.033	-0.021	15.204	0.053	0.053	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.088	-0.044	12.231	0.013	0.013	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.001	0.015	11.137	0.012	0.012	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.057	-0.020	7.911	0.126	0.126	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.017	-0.008	7.034	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.009	0.008	10.059	-0.115	-0.115	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.044	-0.005	9.377	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.007	-0.019	12.787	0.006	0.006	0.000	0.000	0.000	0.000
113	A	114	TYR	0	-0.053	-0.037	16.366	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.825	-0.922	19.235	-0.091	-0.091	0.000	0.000	0.000	0.000
115	A	116	GLN	0	0.045	0.026	20.566	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.759	-0.876	22.577	-0.070	-0.070	0.000	0.000	0.000	0.000
117	A	118	PHE	0	0.010	0.000	17.495	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.836	-0.898	17.206	-0.099	-0.099	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.807	0.895	19.813	0.073	0.073	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.024	0.024	19.888	0.008	0.008	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.055	0.041	17.013	0.010	0.010	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.069	-0.033	18.789	0.014	0.014	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.072	-0.026	21.782	0.008	0.008	0.000	0.000	0.000	0.000
124	A	125	THR	0	0.010	-0.030	18.534	0.009	0.009	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.815	0.913	18.309	0.019	0.019	0.000	0.000	0.000	0.000
126	A	127	GLN	0	0.018	0.035	14.528	0.022	0.022	0.000	0.000	0.000	0.000
127	A	128	PRO	0	0.017	0.009	10.007	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.013	-0.021	12.170	-0.035	-0.035	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.789	-0.863	8.310	-0.406	-0.406	0.000	0.000	0.000	0.000
130	A	131	TRP	0	-0.049	-0.028	12.192	-0.027	-0.027	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.018	-0.019	13.096	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.005	-0.003	14.135	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.042	0.015	16.370	0.005	0.005	0.000	0.000	0.000	0.000
134	A	135	PRO	0	0.021	0.025	17.979	0.004	0.004	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.027	-0.012	20.980	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)