FMO DATABASE

FMODB ID: YZZK2

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	OptH
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	-1098753.837998
FMO2-HF: Nuclear repulsion	1048539.729291
FMO2-HF: Total energy	-50214.108706
FMO2-MP2: Total energy	-50359.863765

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.
-9.742	-4.469	0.951	-2.452	-3.773	-0.012

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 : 0.037 / q_NPA : -0.002

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	0.053	0.018	3.437	-2.344	-0.665	0.008	-0.788	-0.899	0.001
4	A	319	VAL	0	-0.030	-0.009	5.941	0.752	0.752	0.000	0.000	0.000	0.000
5	A	320	PHE	0	-0.015	0.000	8.985	-0.005	-0.005	0.000	0.000	0.000	0.000
6	A	321	ILE	0	-0.024	-0.016	11.700	0.061	0.061	0.000	0.000	0.000	0.000
7	A	322	GLU	-1	-0.871	-0.936	14.615	-0.375	-0.375	0.000	0.000	0.000	0.000
8	A	323	LEU	0	-0.014	-0.011	18.036	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	324	LYS	1	0.883	0.935	20.405	0.392	0.392	0.000	0.000	0.000	0.000
10	A	325	GLN	0	-0.001	0.003	24.101	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	326	LYS	1	0.862	0.922	26.455	0.339	0.339	0.000	0.000	0.000	0.000
12	A	327	GLY	0	0.033	0.019	29.778	0.003	0.003	0.000	0.000	0.000	0.000
13	A	328	VAL	0	0.018	0.003	29.852	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	329	MET	0	-0.006	0.017	26.476	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	330	TRP	0	0.037	0.009	22.348	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	331	GLU	-1	-0.877	-0.945	22.555	-0.380	-0.380	0.000	0.000	0.000	0.000
17	A	332	GLY	0	0.044	0.031	18.694	0.006	0.006	0.000	0.000	0.000	0.000
18	A	333	ALA	0	-0.031	-0.008	19.156	0.014	0.014	0.000	0.000	0.000	0.000
19	A	334	LEU	0	-0.053	-0.038	14.457	-0.095	-0.095	0.000	0.000	0.000	0.000
20	A	335	HIS	0	0.079	0.022	16.806	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	336	ASP	-1	-0.840	-0.888	12.335	-1.108	-1.108	0.000	0.000	0.000	0.000
22	A	337	ALA	0	-0.001	-0.030	13.869	-0.074	-0.074	0.000	0.000	0.000	0.000
23	A	338	ARG	1	0.885	0.921	9.002	1.278	1.278	0.000	0.000	0.000	0.000
24	A	339	LEU	0	-0.016	-0.002	9.655	-0.217	-0.217	0.000	0.000	0.000	0.000
25	A	340	ARG	1	0.937	0.971	11.263	0.676	0.676	0.000	0.000	0.000	0.000
26	A	341	GLU	-1	-0.962	-0.967	10.170	-0.844	-0.844	0.000	0.000	0.000	0.000
27	A	342	GLY	0	-0.043	-0.034	9.118	0.016	0.016	0.000	0.000	0.000	0.000
28	A	343	ALA	0	-0.016	-0.007	7.163	-0.627	-0.627	0.000	0.000	0.000	0.000
29	A	344	ASP	-1	-0.862	-0.907	7.327	-1.763	-1.763	0.000	0.000	0.000	0.000
30	A	345	PHE	0	0.030	-0.004	8.330	-0.371	-0.371	0.000	0.000	0.000	0.000
31	A	346	TRP	0	0.038	0.007	7.119	0.094	0.094	0.000	0.000	0.000	0.000
32	A	347	LEU	0	-0.009	0.001	12.429	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	348	SER	0	-0.031	-0.005	14.346	0.068	0.068	0.000	0.000	0.000	0.000
34	A	349	VAL	0	-0.004	-0.012	16.165	0.007	0.007	0.000	0.000	0.000	0.000
35	A	350	ARG	1	0.858	0.950	17.993	0.365	0.365	0.000	0.000	0.000	0.000
36	A	351	SER	0	0.018	-0.018	22.561	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	352	SER	0	0.071	0.052	26.182	0.008	0.008	0.000	0.000	0.000	0.000
38	A	353	MET	0	-0.077	-0.010	28.085	0.007	0.007	0.000	0.000	0.000	0.000
39	A	354	PRO	0	0.048	0.022	27.901	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	355	GLY	0	0.076	0.031	25.056	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	356	HIS	0	0.044	0.010	24.917	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	357	GLU	-1	-0.832	-0.913	26.845	-0.136	-0.136	0.000	0.000	0.000	0.000
43	A	358	LEU	0	0.031	0.000	22.707	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	359	GLN	0	-0.018	-0.010	21.307	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	360	THR	0	-0.034	-0.023	23.747	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	361	LYS	1	0.860	0.921	26.763	0.137	0.137	0.000	0.000	0.000	0.000
47	A	362	PHE	0	0.046	0.024	20.424	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	363	PRO	0	-0.026	-0.015	22.173	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	364	GLN	0	-0.037	-0.013	23.930	0.004	0.004	0.000	0.000	0.000	0.000
50	A	365	LEU	0	-0.060	-0.033	27.305	0.008	0.008	0.000	0.000	0.000	0.000
51	A	366	CYS	0	-0.056	-0.006	21.868	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	367	LYS	1	0.913	0.963	24.910	0.260	0.260	0.000	0.000	0.000	0.000
53	A	368	ALA	0	0.050	0.029	21.593	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	369	GLY	0	0.013	0.001	23.451	0.032	0.032	0.000	0.000	0.000	0.000
55	A	370	SER	0	-0.017	-0.023	24.306	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	371	PRO	0	-0.067	-0.035	22.228	0.010	0.010	0.000	0.000	0.000	0.000
57	A	372	ASP	-1	-0.899	-0.972	24.692	-0.353	-0.353	0.000	0.000	0.000	0.000
58	A	373	ASP	-1	-0.832	-0.872	27.380	-0.222	-0.222	0.000	0.000	0.000	0.000
59	A	374	VAL	0	-0.026	-0.013	30.606	0.002	0.002	0.000	0.000	0.000	0.000
60	A	375	SER	0	-0.081	-0.052	33.720	0.018	0.018	0.000	0.000	0.000	0.000
61	A	376	GLU	-1	-0.923	-0.970	36.114	-0.151	-0.151	0.000	0.000	0.000	0.000
62	A	377	VAL	0	-0.066	-0.024	35.641	0.007	0.007	0.000	0.000	0.000	0.000
63	A	378	VAL	0	0.027	0.010	35.149	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	379	ASN	0	-0.085	-0.059	31.622	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	380	VAL	0	0.039	0.044	30.131	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	381	ALA	0	-0.013	-0.004	27.866	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	382	LEU	0	0.000	0.010	21.306	0.008	0.008	0.000	0.000	0.000	0.000
68	A	383	SER	0	-0.031	-0.020	24.820	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	384	GLY	0	0.024	0.000	22.661	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	385	VAL	0	0.011	0.005	19.111	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	386	ILE	0	-0.031	-0.010	19.442	0.054	0.054	0.000	0.000	0.000	0.000
72	A	387	ILE	0	0.003	0.014	18.471	-0.061	-0.061	0.000	0.000	0.000	0.000
73	A	388	ARG	1	0.856	0.912	16.917	0.463	0.463	0.000	0.000	0.000	0.000
74	A	389	PRO	0	0.013	0.018	17.275	-0.063	-0.063	0.000	0.000	0.000	0.000
75	A	390	VAL	0	-0.034	-0.021	12.985	0.003	0.003	0.000	0.000	0.000	0.000
76	A	391	THR	0	0.002	-0.029	14.265	0.006	0.006	0.000	0.000	0.000	0.000
77	A	392	HIS	0	0.006	0.023	9.954	-0.055	-0.055	0.000	0.000	0.000	0.000
78	A	393	VAL	0	0.022	0.025	7.179	-0.042	-0.042	0.000	0.000	0.000	0.000
79	A	394	PRO	0	-0.021	0.007	5.847	0.233	0.233	0.000	0.000	0.000	0.000
80	A	395	ALA	0	-0.012	-0.029	3.461	-0.859	-0.506	0.009	-0.093	-0.269	0.000
81	A	396	ALA	0	-0.011	0.007	4.338	0.373	0.480	-0.001	-0.010	-0.096	0.000
82	A	397	ILE	0	0.012	0.007	6.597	-0.417	-0.417	0.000	0.000	0.000	0.000
83	A	398	PRO	0	-0.021	-0.018	9.322	0.208	0.208	0.000	0.000	0.000	0.000
84	A	399	LEU	0	0.035	0.028	12.880	-0.051	-0.051	0.000	0.000	0.000	0.000
85	A	400	ARG	1	0.879	0.929	14.944	0.258	0.258	0.000	0.000	0.000	0.000
86	A	401	LEU	0	0.028	0.019	17.994	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	402	GLU	-1	-0.911	-0.961	20.373	-0.106	-0.106	0.000	0.000	0.000	0.000
88	A	403	ASN	0	-0.025	-0.012	17.494	0.024	0.024	0.000	0.000	0.000	0.000
89	A	404	GLN	0	-0.002	0.011	18.844	0.014	0.014	0.000	0.000	0.000	0.000
90	A	405	TYR	0	0.017	0.002	13.346	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	406	PHE	0	0.021	0.000	15.569	0.068	0.068	0.000	0.000	0.000	0.000
92	A	407	ALA	0	0.005	0.014	13.048	-0.108	-0.108	0.000	0.000	0.000	0.000
93	A	408	LEU	0	-0.027	-0.023	13.682	0.132	0.132	0.000	0.000	0.000	0.000
94	A	409	ASP	-1	-0.845	-0.909	14.071	-0.656	-0.656	0.000	0.000	0.000	0.000
95	A	410	LEU	0	-0.024	-0.020	14.380	0.076	0.076	0.000	0.000	0.000	0.000
96	A	411	SER	0	0.052	0.031	16.741	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	412	THR	0	0.015	-0.018	18.319	-0.061	-0.061	0.000	0.000	0.000	0.000
98	A	413	ASP	-1	-0.871	-0.937	19.363	-0.388	-0.388	0.000	0.000	0.000	0.000
99	A	414	ALA	0	-0.009	0.005	19.629	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	415	ALA	0	-0.002	-0.007	15.625	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	416	ARG	1	0.844	0.917	16.645	0.571	0.571	0.000	0.000	0.000	0.000
102	A	417	ALA	0	0.086	0.050	19.662	0.002	0.002	0.000	0.000	0.000	0.000
103	A	418	MET	0	-0.026	-0.017	17.186	0.002	0.002	0.000	0.000	0.000	0.000
104	A	419	LEU	0	-0.062	-0.045	13.814	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	420	ASP	-1	-0.858	-0.920	17.954	-0.465	-0.465	0.000	0.000	0.000	0.000
106	A	421	ALA	0	-0.028	0.003	21.456	0.029	0.029	0.000	0.000	0.000	0.000
107	A	422	GLY	0	0.016	0.019	19.381	0.022	0.022	0.000	0.000	0.000	0.000
108	A	423	ARG	1	0.801	0.911	20.295	0.370	0.370	0.000	0.000	0.000	0.000
109	A	424	CYS	0	0.017	0.017	16.916	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	425	THR	0	0.012	0.000	20.324	0.032	0.032	0.000	0.000	0.000	0.000
111	A	426	PHE	0	0.030	0.005	17.485	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	427	TYR	0	0.056	0.019	23.432	0.023	0.023	0.000	0.000	0.000	0.000
113	A	428	THR	0	0.003	-0.013	24.618	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	429	PRO	0	0.001	0.013	27.406	0.012	0.012	0.000	0.000	0.000	0.000
115	A	430	ALA	0	0.089	0.020	30.680	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	431	SER	0	-0.056	-0.018	32.681	0.002	0.002	0.000	0.000	0.000	0.000
117	A	432	LEU	0	-0.015	-0.010	26.236	0.005	0.005	0.000	0.000	0.000	0.000
118	A	433	GLY	0	0.019	0.019	29.231	0.000	0.000	0.000	0.000	0.000	0.000
119	A	434	ASP	-1	-0.952	-0.964	29.532	-0.193	-0.193	0.000	0.000	0.000	0.000
120	A	435	VAL	0	-0.034	-0.016	24.235	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	436	LYS	1	0.900	0.944	20.656	0.402	0.402	0.000	0.000	0.000	0.000
122	A	437	LEU	0	-0.007	0.001	19.916	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	438	GLU	-1	-0.940	-0.982	15.757	-0.481	-0.481	0.000	0.000	0.000	0.000
124	A	439	LEU	0	0.033	0.023	13.487	0.001	0.001	0.000	0.000	0.000	0.000
125	A	440	PHE	0	0.004	0.001	9.285	0.022	0.022	0.000	0.000	0.000	0.000
126	A	441	ALA	0	0.029	0.018	8.354	0.108	0.108	0.000	0.000	0.000	0.000
127	A	442	VAL	0	-0.032	-0.014	2.701	-0.966	-0.351	0.295	-0.262	-0.648	-0.001
128	A	443	LEU	0	-0.026	-0.022	3.590	0.145	0.570	0.008	-0.124	-0.309	0.000
129	A	444	ARG	1	0.894	0.967	2.828	-4.326	-2.367	0.633	-1.164	-1.428	-0.012
130	A	445	THR	0	0.010	0.007	4.124	0.929	1.064	-0.001	-0.011	-0.124	0.000

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