FMO DATABASE

FMODB ID: ZYKVN

Calculation Name: 2YV4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YV4

Chain ID: A

ChEMBL ID:

UniProt ID: O73972

Base Structure: X-ray

Registration Date: 2023-06-19

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-793869.218187
FMO2-HF: Nuclear repulsion	754186.174646
FMO2-HF: Total energy	-39683.043541
FMO2-MP2: Total energy	-39800.45889

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:236:ALA)

Summations of interaction energy for fragment #1(A:236: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.
-7.132	-4.944	0.054	-0.958	-1.282	0.003

Interaction energy analysis for fragmet #1(A:236:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.021

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	238	ASN	0	-0.052	-0.033	3.826	-0.248	1.398	-0.015	-0.781	-0.849	0.003
4	A	239	ALA	0	0.019	0.033	6.354	0.606	0.606	0.000	0.000	0.000	0.000
5	A	240	GLU	-1	-0.862	-0.912	7.375	-0.617	-0.617	0.000	0.000	0.000	0.000
6	A	241	VAL	0	-0.001	-0.007	6.391	0.053	0.053	0.000	0.000	0.000	0.000
7	A	242	ILE	0	-0.010	-0.012	9.424	0.172	0.172	0.000	0.000	0.000	0.000
8	A	243	VAL	0	0.003	0.010	11.723	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	244	VAL	0	-0.015	0.002	14.232	0.020	0.020	0.000	0.000	0.000	0.000
10	A	245	GLU	-1	-0.903	-0.963	18.007	0.108	0.108	0.000	0.000	0.000	0.000
11	A	246	GLY	0	0.030	0.014	19.993	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	247	PRO	0	-0.001	0.003	23.682	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	248	ARG	1	0.967	0.954	24.829	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	249	GLU	-1	-0.905	-0.934	25.893	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	250	LYS	1	0.910	0.935	26.892	0.003	0.003	0.000	0.000	0.000	0.000
16	A	251	VAL	0	0.000	0.010	20.938	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	252	LYS	1	0.796	0.878	23.209	0.070	0.070	0.000	0.000	0.000	0.000
18	A	253	GLY	0	0.005	0.014	24.979	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	254	LYS	1	0.870	0.916	21.780	0.081	0.081	0.000	0.000	0.000	0.000
20	A	255	ILE	0	0.004	-0.001	19.133	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	256	THR	0	-0.021	-0.023	21.693	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	257	GLU	-1	-0.878	-0.915	24.614	-0.112	-0.112	0.000	0.000	0.000	0.000
23	A	258	LEU	0	0.029	0.007	18.779	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	259	VAL	0	-0.002	0.014	19.837	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	260	LYS	1	0.936	0.971	21.585	0.124	0.124	0.000	0.000	0.000	0.000
26	A	261	GLU	-1	-0.899	-0.943	22.853	-0.170	-0.170	0.000	0.000	0.000	0.000
27	A	262	LEU	0	-0.066	-0.054	17.109	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	263	LYS	1	0.849	0.918	21.030	0.275	0.275	0.000	0.000	0.000	0.000
29	A	264	GLU	-1	-0.949	-0.956	23.107	-0.187	-0.187	0.000	0.000	0.000	0.000
30	A	265	ARG	1	0.873	0.936	18.714	0.276	0.276	0.000	0.000	0.000	0.000
31	A	266	GLY	0	-0.012	-0.001	22.528	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	267	LYS	1	0.761	0.880	15.065	0.540	0.540	0.000	0.000	0.000	0.000
33	A	268	LYS	1	0.847	0.924	16.955	0.620	0.620	0.000	0.000	0.000	0.000
34	A	269	VAL	0	-0.009	-0.026	16.115	-0.079	-0.079	0.000	0.000	0.000	0.000
35	A	270	GLY	0	0.036	0.006	14.926	0.032	0.032	0.000	0.000	0.000	0.000
36	A	271	VAL	0	-0.025	-0.006	15.058	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	272	ILE	0	-0.020	-0.009	10.790	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	273	GLY	0	0.035	-0.017	15.143	0.045	0.045	0.000	0.000	0.000	0.000
39	A	274	SER	0	-0.093	-0.091	18.263	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	275	GLU	-1	-0.846	-0.909	21.568	-0.106	-0.106	0.000	0.000	0.000	0.000
41	A	276	SER	0	0.032	0.012	21.027	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	277	TYR	0	0.037	-0.002	20.651	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	278	ASN	0	-0.055	-0.035	23.965	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	279	ALA	0	0.032	0.024	18.972	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	280	ASP	-1	-0.834	-0.908	19.244	-0.351	-0.351	0.000	0.000	0.000	0.000
46	A	281	GLU	-1	-0.788	-0.868	16.328	-0.525	-0.525	0.000	0.000	0.000	0.000
47	A	282	PHE	0	-0.027	-0.022	17.714	0.010	0.010	0.000	0.000	0.000	0.000
48	A	283	PHE	0	-0.008	-0.003	14.413	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	284	PHE	0	0.003	0.012	16.520	0.016	0.016	0.000	0.000	0.000	0.000
50	A	285	LEU	0	-0.013	0.004	14.516	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	286	GLY	0	0.034	0.010	16.379	0.036	0.036	0.000	0.000	0.000	0.000
52	A	287	SER	0	-0.111	-0.056	19.117	0.002	0.002	0.000	0.000	0.000	0.000
53	A	288	SER	0	0.005	-0.040	20.769	0.017	0.017	0.000	0.000	0.000	0.000
54	A	289	VAL	0	0.064	0.021	18.626	0.001	0.001	0.000	0.000	0.000	0.000
55	A	290	GLU	-1	-0.820	-0.896	17.668	0.165	0.165	0.000	0.000	0.000	0.000
56	A	291	GLU	-1	-0.756	-0.845	17.369	0.032	0.032	0.000	0.000	0.000	0.000
57	A	292	VAL	0	0.020	0.030	14.140	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	293	ALA	0	-0.020	-0.012	13.091	0.014	0.014	0.000	0.000	0.000	0.000
59	A	294	LYS	1	0.819	0.898	12.390	-0.031	-0.031	0.000	0.000	0.000	0.000
60	A	295	ASN	0	-0.018	-0.019	12.947	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	296	LEU	0	0.037	0.028	8.946	-0.109	-0.109	0.000	0.000	0.000	0.000
62	A	297	PHE	0	0.045	0.004	5.760	-0.151	-0.151	0.000	0.000	0.000	0.000
63	A	298	LYS	1	0.897	0.961	7.399	-0.107	-0.107	0.000	0.000	0.000	0.000
64	A	299	ALA	0	0.026	0.015	10.036	-0.135	-0.135	0.000	0.000	0.000	0.000
65	A	300	LEU	0	0.033	0.001	5.539	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	301	ARG	1	0.943	0.978	6.238	0.246	0.246	0.000	0.000	0.000	0.000
67	A	302	TYR	0	-0.097	-0.057	7.920	0.015	0.015	0.000	0.000	0.000	0.000
68	A	303	MET	0	0.007	0.009	9.945	0.055	0.055	0.000	0.000	0.000	0.000
69	A	304	ASP	-1	-0.786	-0.891	6.180	-3.844	-3.844	0.000	0.000	0.000	0.000
70	A	305	LYS	1	0.890	0.956	9.767	0.822	0.822	0.000	0.000	0.000	0.000
71	A	306	ALA	0	-0.037	-0.016	12.266	0.132	0.132	0.000	0.000	0.000	0.000
72	A	307	GLY	0	0.009	0.011	13.077	0.120	0.120	0.000	0.000	0.000	0.000
73	A	308	VAL	0	-0.070	-0.030	12.549	0.097	0.097	0.000	0.000	0.000	0.000
74	A	309	ASP	-1	-0.773	-0.854	12.058	-0.825	-0.825	0.000	0.000	0.000	0.000
75	A	310	VAL	0	-0.043	-0.035	11.995	-0.086	-0.086	0.000	0.000	0.000	0.000
76	A	311	VAL	0	0.020	0.002	9.869	0.045	0.045	0.000	0.000	0.000	0.000
77	A	312	ILE	0	0.002	0.001	11.944	0.054	0.054	0.000	0.000	0.000	0.000
78	A	313	ALA	0	-0.029	-0.020	11.721	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	314	GLU	-1	-0.761	-0.821	13.838	-0.054	-0.054	0.000	0.000	0.000	0.000
80	A	315	GLY	0	0.007	-0.013	16.953	0.026	0.026	0.000	0.000	0.000	0.000
81	A	316	VAL	0	-0.018	-0.005	17.928	0.009	0.009	0.000	0.000	0.000	0.000
82	A	317	GLU	-1	-0.869	-0.936	21.391	0.069	0.069	0.000	0.000	0.000	0.000
83	A	318	GLU	-1	-0.812	-0.919	23.667	0.028	0.028	0.000	0.000	0.000	0.000
84	A	319	ARG	1	0.874	0.919	23.855	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	320	GLY	0	0.054	0.034	22.223	0.011	0.011	0.000	0.000	0.000	0.000
86	A	321	LEU	0	-0.033	-0.007	19.064	0.029	0.029	0.000	0.000	0.000	0.000
87	A	322	GLY	0	0.082	0.040	17.273	0.018	0.018	0.000	0.000	0.000	0.000
88	A	323	LEU	0	0.005	0.017	16.260	0.028	0.028	0.000	0.000	0.000	0.000
89	A	324	ALA	0	-0.021	-0.009	16.025	0.066	0.066	0.000	0.000	0.000	0.000
90	A	325	VAL	0	-0.002	-0.005	11.995	0.087	0.087	0.000	0.000	0.000	0.000
91	A	326	MET	0	0.026	0.016	11.536	0.088	0.088	0.000	0.000	0.000	0.000
92	A	327	ASN	0	-0.020	-0.012	11.702	0.158	0.158	0.000	0.000	0.000	0.000
93	A	328	ARG	1	0.795	0.908	9.059	-0.669	-0.669	0.000	0.000	0.000	0.000
94	A	329	LEU	0	0.002	0.002	6.250	0.354	0.354	0.000	0.000	0.000	0.000
95	A	330	ARG	1	0.845	0.934	5.228	-3.475	-3.475	0.000	0.000	0.000	0.000
96	A	331	LYS	1	1.030	1.013	9.577	-1.024	-1.024	0.000	0.000	0.000	0.000
97	A	332	ALA	0	-0.028	-0.035	7.125	0.358	0.358	0.000	0.000	0.000	0.000
98	A	333	SER	0	-0.006	-0.005	3.252	0.661	1.193	0.070	-0.171	-0.430	0.000
99	A	334	GLY	0	0.027	0.022	4.800	-0.745	-0.735	-0.001	-0.006	-0.003	0.000
100	A	335	TYR	0	-0.009	0.002	7.066	-0.300	-0.300	0.000	0.000	0.000	0.000
101	A	336	LYS	1	0.870	0.936	9.601	0.331	0.331	0.000	0.000	0.000	0.000
102	A	337	ILE	0	0.029	0.016	13.279	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	338	VAL	0	-0.020	-0.012	15.906	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	339	LYS	1	0.985	1.000	18.978	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	340	ALA	0	-0.025	-0.013	22.105	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:236:ALA)