FMO DATABASE

FMODB ID: V5511

Calculation Name: 5M2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5M2Y

Chain ID: A

ChEMBL ID:

UniProt ID: B7LG64

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1098645.033954
FMO2-HF: Nuclear repulsion	1048430.391336
FMO2-HF: Total energy	-50214.642617
FMO2-MP2: Total energy	-50360.433774

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:316:SER)

Summations of interaction energy for fragment #1(A:316:SER)

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.
-9.411	-4.874	1.858	-2.44	-3.954	-0.015

Interaction energy analysis for fragmet #1(A:316:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.006

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	318	VAL	0	0.054	0.019	3.686	-2.068	-0.658	-0.004	-0.603	-0.803	0.001
4	A	319	VAL	0	-0.022	-0.005	5.999	0.760	0.760	0.000	0.000	0.000	0.000
5	A	320	PHE	0	-0.015	-0.003	9.157	-0.022	-0.022	0.000	0.000	0.000	0.000
6	A	321	ILE	0	-0.024	-0.018	11.371	0.066	0.066	0.000	0.000	0.000	0.000
7	A	322	GLU	-1	-0.836	-0.895	14.688	-0.342	-0.342	0.000	0.000	0.000	0.000
8	A	323	LEU	0	-0.004	-0.004	17.953	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	324	LYS	1	0.818	0.877	20.391	0.366	0.366	0.000	0.000	0.000	0.000
10	A	325	GLN	0	-0.001	0.002	24.110	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	326	LYS	1	0.845	0.902	26.390	0.312	0.312	0.000	0.000	0.000	0.000
12	A	327	GLY	0	0.037	0.021	29.734	0.001	0.001	0.000	0.000	0.000	0.000
13	A	328	VAL	0	0.026	0.007	29.709	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	329	MET	0	-0.009	0.018	26.439	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	330	TRP	0	0.028	0.003	22.241	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	331	GLU	-1	-0.839	-0.903	22.601	-0.346	-0.346	0.000	0.000	0.000	0.000
17	A	332	GLY	0	0.049	0.030	18.754	0.007	0.007	0.000	0.000	0.000	0.000
18	A	333	ALA	0	-0.026	-0.002	19.327	0.009	0.009	0.000	0.000	0.000	0.000
19	A	334	LEU	0	-0.043	-0.037	14.621	-0.085	-0.085	0.000	0.000	0.000	0.000
20	A	335	HIS	0	0.089	0.027	17.053	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	336	ASP	-1	-0.836	-0.883	11.855	-0.959	-0.959	0.000	0.000	0.000	0.000
22	A	337	ALA	0	0.013	-0.017	13.829	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	338	ARG	1	0.887	0.913	8.827	0.977	0.977	0.000	0.000	0.000	0.000
24	A	339	LEU	0	-0.031	-0.005	9.732	-0.191	-0.191	0.000	0.000	0.000	0.000
25	A	340	ARG	1	0.893	0.949	11.302	0.580	0.580	0.000	0.000	0.000	0.000
26	A	341	GLU	-1	-0.942	-0.960	9.569	-0.720	-0.720	0.000	0.000	0.000	0.000
27	A	342	GLY	0	-0.018	-0.008	9.018	0.027	0.027	0.000	0.000	0.000	0.000
28	A	343	ALA	0	-0.031	-0.010	7.314	-0.545	-0.545	0.000	0.000	0.000	0.000
29	A	344	ASP	-1	-0.829	-0.875	7.310	-1.958	-1.958	0.000	0.000	0.000	0.000
30	A	345	PHE	0	0.037	0.000	8.208	-0.357	-0.357	0.000	0.000	0.000	0.000
31	A	346	TRP	0	0.042	0.006	6.956	0.047	0.047	0.000	0.000	0.000	0.000
32	A	347	LEU	0	-0.005	0.005	12.120	0.003	0.003	0.000	0.000	0.000	0.000
33	A	348	SER	0	-0.028	-0.009	14.261	0.049	0.049	0.000	0.000	0.000	0.000
34	A	349	VAL	0	-0.015	-0.018	16.113	0.015	0.015	0.000	0.000	0.000	0.000
35	A	350	ARG	1	0.785	0.853	18.108	0.345	0.345	0.000	0.000	0.000	0.000
36	A	351	SER	0	0.022	-0.015	22.547	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	352	SER	0	0.075	0.054	26.155	0.007	0.007	0.000	0.000	0.000	0.000
38	A	353	MET	0	-0.082	-0.016	27.975	0.007	0.007	0.000	0.000	0.000	0.000
39	A	354	PRO	0	0.035	0.017	27.853	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	355	GLY	0	0.091	0.037	24.992	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	356	HIS	0	0.053	0.016	24.826	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	357	GLU	-1	-0.844	-0.898	26.745	-0.155	-0.155	0.000	0.000	0.000	0.000
43	A	358	LEU	0	0.028	0.002	22.945	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	359	GLN	0	-0.020	-0.009	21.436	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	360	THR	0	-0.043	-0.035	23.612	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	361	LYS	1	0.863	0.905	26.602	0.151	0.151	0.000	0.000	0.000	0.000
47	A	362	PHE	0	0.046	0.026	20.133	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	363	PRO	0	-0.021	-0.013	21.900	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	364	GLN	0	-0.044	-0.017	23.621	0.006	0.006	0.000	0.000	0.000	0.000
50	A	365	LEU	0	-0.033	-0.020	26.949	0.010	0.010	0.000	0.000	0.000	0.000
51	A	366	CYS	0	-0.065	-0.015	22.890	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	367	LYS	1	0.886	0.949	24.645	0.276	0.276	0.000	0.000	0.000	0.000
53	A	368	ALA	0	0.045	0.025	21.436	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	369	GLY	0	0.017	0.006	23.324	0.030	0.030	0.000	0.000	0.000	0.000
55	A	370	SER	0	-0.023	-0.021	24.291	-0.040	-0.040	0.000	0.000	0.000	0.000
56	A	371	PRO	0	-0.054	-0.029	22.426	0.010	0.010	0.000	0.000	0.000	0.000
57	A	372	ASP	-1	-0.887	-0.965	24.787	-0.329	-0.329	0.000	0.000	0.000	0.000
58	A	373	ASP	-1	-0.828	-0.874	27.521	-0.209	-0.209	0.000	0.000	0.000	0.000
59	A	374	VAL	0	-0.029	-0.012	30.706	0.003	0.003	0.000	0.000	0.000	0.000
60	A	375	SER	0	-0.074	-0.049	33.859	0.017	0.017	0.000	0.000	0.000	0.000
61	A	376	GLU	-1	-0.923	-0.970	36.200	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	377	VAL	0	-0.074	-0.026	35.923	0.006	0.006	0.000	0.000	0.000	0.000
63	A	378	VAL	0	0.029	0.014	35.155	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	379	ASN	0	-0.081	-0.061	31.567	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	380	VAL	0	0.044	0.048	30.144	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	381	ALA	0	-0.011	-0.004	27.790	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	382	LEU	0	-0.002	0.011	21.350	0.008	0.008	0.000	0.000	0.000	0.000
68	A	383	SER	0	-0.011	-0.008	24.714	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	384	GLY	0	0.006	-0.012	22.874	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	385	VAL	0	0.008	0.004	18.923	-0.054	-0.054	0.000	0.000	0.000	0.000
71	A	386	ILE	0	-0.032	-0.012	19.587	0.053	0.053	0.000	0.000	0.000	0.000
72	A	387	ILE	0	0.002	0.017	18.533	-0.066	-0.066	0.000	0.000	0.000	0.000
73	A	388	ARG	1	0.851	0.899	17.040	0.529	0.529	0.000	0.000	0.000	0.000
74	A	389	PRO	0	0.018	0.018	17.144	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	390	VAL	0	-0.036	-0.021	12.737	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	391	THR	0	0.002	-0.014	14.066	0.012	0.012	0.000	0.000	0.000	0.000
77	A	392	HIS	0	-0.007	0.003	9.503	0.022	0.022	0.000	0.000	0.000	0.000
78	A	393	VAL	0	0.030	0.031	7.081	-0.063	-0.063	0.000	0.000	0.000	0.000
79	A	394	PRO	0	-0.027	0.003	6.020	0.289	0.289	0.000	0.000	0.000	0.000
80	A	395	ALA	0	-0.006	-0.026	3.456	-1.461	-1.057	0.011	-0.115	-0.300	-0.001
81	A	396	ALA	0	-0.010	0.009	4.346	0.269	0.368	-0.001	-0.010	-0.088	0.000
82	A	397	ILE	0	0.019	0.010	6.776	-0.349	-0.349	0.000	0.000	0.000	0.000
83	A	398	PRO	0	-0.028	-0.022	9.454	0.176	0.176	0.000	0.000	0.000	0.000
84	A	399	LEU	0	0.030	0.026	12.588	-0.064	-0.064	0.000	0.000	0.000	0.000
85	A	400	ARG	1	0.887	0.933	15.056	0.230	0.230	0.000	0.000	0.000	0.000
86	A	401	LEU	0	0.027	0.019	18.066	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	402	GLU	-1	-0.905	-0.956	20.425	-0.123	-0.123	0.000	0.000	0.000	0.000
88	A	403	ASN	0	-0.027	-0.001	17.694	0.027	0.027	0.000	0.000	0.000	0.000
89	A	404	GLN	0	-0.020	0.002	18.749	0.009	0.009	0.000	0.000	0.000	0.000
90	A	405	TYR	0	0.019	0.001	13.264	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	406	PHE	0	0.027	0.001	15.428	0.062	0.062	0.000	0.000	0.000	0.000
92	A	407	ALA	0	0.000	0.014	13.096	-0.105	-0.105	0.000	0.000	0.000	0.000
93	A	408	LEU	0	-0.023	-0.022	13.438	0.142	0.142	0.000	0.000	0.000	0.000
94	A	409	ASP	-1	-0.842	-0.901	14.147	-0.709	-0.709	0.000	0.000	0.000	0.000
95	A	410	LEU	0	-0.023	-0.014	14.448	0.084	0.084	0.000	0.000	0.000	0.000
96	A	411	SER	0	0.052	0.029	16.931	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	412	THR	0	0.019	-0.014	18.427	-0.059	-0.059	0.000	0.000	0.000	0.000
98	A	413	ASP	-1	-0.889	-0.949	19.472	-0.388	-0.388	0.000	0.000	0.000	0.000
99	A	414	ALA	0	0.002	0.011	19.818	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	415	ALA	0	0.001	-0.005	15.716	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	416	ARG	1	0.833	0.907	16.966	0.516	0.516	0.000	0.000	0.000	0.000
102	A	417	ALA	0	0.082	0.048	19.800	0.008	0.008	0.000	0.000	0.000	0.000
103	A	418	MET	0	-0.022	-0.016	17.222	0.009	0.009	0.000	0.000	0.000	0.000
104	A	419	LEU	0	-0.058	-0.040	14.018	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	420	ASP	-1	-0.851	-0.914	18.194	-0.424	-0.424	0.000	0.000	0.000	0.000
106	A	421	ALA	0	-0.025	0.006	21.607	0.030	0.030	0.000	0.000	0.000	0.000
107	A	422	GLY	0	0.014	0.013	19.631	0.023	0.023	0.000	0.000	0.000	0.000
108	A	423	ARG	1	0.758	0.870	20.508	0.343	0.343	0.000	0.000	0.000	0.000
109	A	424	CYS	0	-0.004	0.014	18.104	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	425	THR	0	0.037	0.001	20.377	0.032	0.032	0.000	0.000	0.000	0.000
111	A	426	PHE	0	0.021	0.003	17.380	-0.015	-0.015	0.000	0.000	0.000	0.000
112	A	427	TYR	0	0.058	0.023	23.310	0.025	0.025	0.000	0.000	0.000	0.000
113	A	428	THR	0	0.005	-0.008	24.460	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	429	PRO	0	0.003	0.011	27.176	0.013	0.013	0.000	0.000	0.000	0.000
115	A	430	ALA	0	0.084	0.021	30.403	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	431	SER	0	-0.039	-0.013	32.594	0.002	0.002	0.000	0.000	0.000	0.000
117	A	432	LEU	0	-0.015	-0.008	26.057	0.003	0.003	0.000	0.000	0.000	0.000
118	A	433	GLY	0	0.016	0.020	29.165	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	434	ASP	-1	-0.945	-0.962	29.858	-0.185	-0.185	0.000	0.000	0.000	0.000
120	A	435	VAL	0	-0.055	-0.027	24.246	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	436	LYS	1	0.892	0.938	20.434	0.382	0.382	0.000	0.000	0.000	0.000
122	A	437	LEU	0	0.007	0.013	19.738	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	438	GLU	-1	-0.845	-0.889	15.640	-0.386	-0.386	0.000	0.000	0.000	0.000
124	A	439	LEU	0	0.030	0.026	13.486	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	440	PHE	0	-0.006	-0.005	9.155	0.060	0.060	0.000	0.000	0.000	0.000
126	A	441	ALA	0	0.031	0.022	8.336	0.074	0.074	0.000	0.000	0.000	0.000
127	A	442	VAL	0	-0.030	-0.014	2.474	-0.775	-0.530	1.134	-0.442	-0.937	-0.003
128	A	443	LEU	0	-0.018	-0.017	3.829	0.176	0.554	0.005	-0.080	-0.303	0.000
129	A	444	ARG	1	0.854	0.911	2.799	-3.855	-2.046	0.713	-1.173	-1.349	-0.012
130	A	445	THR	0	0.009	0.007	3.875	1.023	1.215	0.000	-0.017	-0.174	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:316:SER)