FMO DATABASE

FMODB ID: 177GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1100339.536341
FMO2-HF: Nuclear repulsion	1050124.685214
FMO2-HF: Total energy	-50214.851127
FMO2-MP2: Total energy	-50360.737766

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.
-7.219	-3.825	3.12	-2.404	-4.11	-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 : 0.001 / q_NPA : -0.008

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	0.024	0.006	3.568	-2.681	-1.369	0.009	-0.553	-0.769	0.001
4	A	319	VAL	0	-0.013	0.001	6.123	0.828	0.828	0.000	0.000	0.000	0.000
5	A	320	PHE	0	-0.009	-0.009	9.344	-0.073	-0.073	0.000	0.000	0.000	0.000
6	A	321	ILE	0	-0.021	-0.010	11.575	0.077	0.077	0.000	0.000	0.000	0.000
7	A	322	GLU	-1	-0.836	-0.897	15.030	-0.363	-0.363	0.000	0.000	0.000	0.000
8	A	323	LEU	0	-0.006	-0.011	18.152	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	324	LYS	1	0.839	0.894	20.933	0.364	0.364	0.000	0.000	0.000	0.000
10	A	325	GLN	0	-0.023	-0.009	24.658	0.004	0.004	0.000	0.000	0.000	0.000
11	A	326	LYS	1	0.816	0.889	26.459	0.320	0.320	0.000	0.000	0.000	0.000
12	A	327	GLY	0	0.039	0.023	29.903	0.004	0.004	0.000	0.000	0.000	0.000
13	A	328	VAL	0	0.011	0.009	29.604	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	329	MET	0	0.001	0.028	26.447	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	330	TRP	0	0.043	0.007	22.469	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	331	GLU	-1	-0.810	-0.890	22.556	-0.330	-0.330	0.000	0.000	0.000	0.000
17	A	332	GLY	0	0.036	0.027	19.164	0.010	0.010	0.000	0.000	0.000	0.000
18	A	333	ALA	0	-0.015	0.005	19.503	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	334	LEU	0	-0.022	-0.026	14.417	-0.086	-0.086	0.000	0.000	0.000	0.000
20	A	335	HIS	0	0.077	0.020	16.397	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	336	ASP	-1	-0.831	-0.874	12.148	-0.721	-0.721	0.000	0.000	0.000	0.000
22	A	337	ALA	0	0.043	0.004	14.112	-0.064	-0.064	0.000	0.000	0.000	0.000
23	A	338	ARG	1	0.884	0.917	9.466	0.681	0.681	0.000	0.000	0.000	0.000
24	A	339	LEU	0	-0.047	-0.015	9.820	-0.176	-0.176	0.000	0.000	0.000	0.000
25	A	340	ARG	1	0.846	0.921	11.216	0.460	0.460	0.000	0.000	0.000	0.000
26	A	341	GLU	-1	-0.836	-0.891	9.137	-0.406	-0.406	0.000	0.000	0.000	0.000
27	A	342	GLY	0	-0.007	-0.009	9.348	0.126	0.126	0.000	0.000	0.000	0.000
28	A	343	ALA	0	-0.042	-0.009	6.970	-0.383	-0.383	0.000	0.000	0.000	0.000
29	A	344	ASP	-1	-0.833	-0.892	7.179	-1.769	-1.769	0.000	0.000	0.000	0.000
30	A	345	PHE	0	0.033	0.004	8.154	-0.412	-0.412	0.000	0.000	0.000	0.000
31	A	346	TRP	0	0.036	0.003	6.907	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	347	LEU	0	0.013	0.013	11.771	0.013	0.013	0.000	0.000	0.000	0.000
33	A	348	SER	0	-0.064	-0.032	14.314	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	349	VAL	0	-0.001	-0.010	16.000	0.037	0.037	0.000	0.000	0.000	0.000
35	A	350	ARG	1	0.804	0.862	18.839	0.428	0.428	0.000	0.000	0.000	0.000
36	A	351	SER	0	0.006	-0.032	22.848	0.003	0.003	0.000	0.000	0.000	0.000
37	A	352	SER	0	0.063	0.052	26.582	0.004	0.004	0.000	0.000	0.000	0.000
38	A	353	MET	0	-0.076	-0.018	27.904	0.007	0.007	0.000	0.000	0.000	0.000
39	A	354	PRO	0	0.042	0.019	27.899	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	355	GLY	0	0.082	0.041	25.133	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	356	HIS	0	0.063	0.022	24.680	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	357	GLU	-1	-0.842	-0.899	26.595	-0.211	-0.211	0.000	0.000	0.000	0.000
43	A	358	LEU	0	0.025	0.002	23.059	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	359	GLN	0	-0.023	-0.016	21.308	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	360	THR	0	-0.048	-0.034	23.148	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	361	LYS	1	0.874	0.909	25.965	0.206	0.206	0.000	0.000	0.000	0.000
47	A	362	PHE	0	0.035	0.026	19.864	0.006	0.006	0.000	0.000	0.000	0.000
48	A	363	PRO	0	0.000	-0.007	21.522	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	364	GLN	0	-0.037	-0.016	23.517	0.015	0.015	0.000	0.000	0.000	0.000
50	A	365	LEU	0	-0.019	-0.004	27.086	0.013	0.013	0.000	0.000	0.000	0.000
51	A	366	CYS	0	-0.054	-0.006	22.919	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	367	LYS	1	0.822	0.900	24.615	0.342	0.342	0.000	0.000	0.000	0.000
53	A	368	ALA	0	0.055	0.035	21.292	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	369	GLY	0	0.009	0.010	23.240	0.033	0.033	0.000	0.000	0.000	0.000
55	A	370	SER	0	-0.021	-0.016	24.270	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	371	PRO	0	-0.049	-0.026	22.120	0.010	0.010	0.000	0.000	0.000	0.000
57	A	372	ASP	-1	-0.876	-0.954	24.574	-0.306	-0.306	0.000	0.000	0.000	0.000
58	A	373	ASP	-1	-0.800	-0.860	27.122	-0.195	-0.195	0.000	0.000	0.000	0.000
59	A	374	VAL	0	-0.061	-0.037	30.534	0.002	0.002	0.000	0.000	0.000	0.000
60	A	375	SER	0	-0.069	-0.048	33.824	0.017	0.017	0.000	0.000	0.000	0.000
61	A	376	GLU	-1	-0.939	-0.974	36.244	-0.135	-0.135	0.000	0.000	0.000	0.000
62	A	377	VAL	0	-0.072	-0.023	35.840	0.004	0.004	0.000	0.000	0.000	0.000
63	A	378	VAL	0	0.025	0.006	35.002	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	379	ASN	0	-0.065	-0.051	31.498	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	380	VAL	0	0.042	0.043	29.971	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	381	ALA	0	0.007	0.002	27.853	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	382	LEU	0	-0.028	-0.009	21.357	0.011	0.011	0.000	0.000	0.000	0.000
68	A	383	SER	0	-0.011	-0.009	24.543	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	384	GLY	0	0.024	0.006	22.945	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	385	VAL	0	-0.005	0.000	18.854	-0.052	-0.052	0.000	0.000	0.000	0.000
71	A	386	ILE	0	-0.043	-0.022	19.329	0.054	0.054	0.000	0.000	0.000	0.000
72	A	387	ILE	0	0.008	0.011	18.339	-0.071	-0.071	0.000	0.000	0.000	0.000
73	A	388	ARG	1	0.845	0.898	16.410	0.626	0.626	0.000	0.000	0.000	0.000
74	A	389	PRO	0	0.005	0.009	16.644	-0.084	-0.084	0.000	0.000	0.000	0.000
75	A	390	VAL	0	-0.047	-0.028	12.481	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	391	THR	0	0.006	-0.015	14.274	0.020	0.020	0.000	0.000	0.000	0.000
77	A	392	HIS	0	-0.008	0.012	9.604	0.117	0.117	0.000	0.000	0.000	0.000
78	A	393	VAL	0	0.033	0.031	7.000	-0.053	-0.053	0.000	0.000	0.000	0.000
79	A	394	PRO	0	-0.040	-0.008	5.430	0.216	0.216	0.000	0.000	0.000	0.000
80	A	395	ALA	0	0.000	-0.015	3.270	-1.476	-1.060	0.023	-0.114	-0.325	0.000
81	A	396	ALA	0	-0.006	0.004	4.611	0.671	0.776	-0.001	-0.006	-0.098	0.000
82	A	397	ILE	0	0.018	0.015	6.731	-0.215	-0.215	0.000	0.000	0.000	0.000
83	A	398	PRO	0	-0.037	-0.031	9.790	0.192	0.192	0.000	0.000	0.000	0.000
84	A	399	LEU	0	0.045	0.036	12.377	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	400	ARG	1	0.888	0.932	15.077	0.419	0.419	0.000	0.000	0.000	0.000
86	A	401	LEU	0	0.019	0.016	18.432	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	402	GLU	-1	-0.910	-0.950	20.930	-0.211	-0.211	0.000	0.000	0.000	0.000
88	A	403	ASN	0	-0.023	0.006	17.677	0.047	0.047	0.000	0.000	0.000	0.000
89	A	404	GLN	0	-0.037	-0.012	18.932	0.012	0.012	0.000	0.000	0.000	0.000
90	A	405	TYR	0	0.026	0.001	13.583	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	406	PHE	0	0.015	-0.003	15.123	0.054	0.054	0.000	0.000	0.000	0.000
92	A	407	ALA	0	0.003	0.018	12.769	-0.096	-0.096	0.000	0.000	0.000	0.000
93	A	408	LEU	0	-0.025	-0.026	13.303	0.169	0.169	0.000	0.000	0.000	0.000
94	A	409	ASP	-1	-0.821	-0.885	14.180	-0.767	-0.767	0.000	0.000	0.000	0.000
95	A	410	LEU	0	-0.019	-0.016	14.470	0.077	0.077	0.000	0.000	0.000	0.000
96	A	411	SER	0	-0.016	-0.027	17.113	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	412	THR	0	0.017	-0.012	18.364	-0.054	-0.054	0.000	0.000	0.000	0.000
98	A	413	ASP	-1	-0.818	-0.887	19.398	-0.364	-0.364	0.000	0.000	0.000	0.000
99	A	414	ALA	0	0.010	0.014	20.042	0.000	0.000	0.000	0.000	0.000	0.000
100	A	415	ALA	0	-0.008	-0.009	15.623	-0.028	-0.028	0.000	0.000	0.000	0.000
101	A	416	ARG	1	0.820	0.902	17.290	0.405	0.405	0.000	0.000	0.000	0.000
102	A	417	ALA	0	0.073	0.039	19.577	0.007	0.007	0.000	0.000	0.000	0.000
103	A	418	MET	0	-0.027	-0.021	17.257	0.005	0.005	0.000	0.000	0.000	0.000
104	A	419	LEU	0	-0.047	-0.028	13.720	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	420	ASP	-1	-0.848	-0.910	17.848	-0.335	-0.335	0.000	0.000	0.000	0.000
106	A	421	ALA	0	-0.023	-0.003	21.320	0.028	0.028	0.000	0.000	0.000	0.000
107	A	422	GLY	0	0.007	0.011	19.193	0.013	0.013	0.000	0.000	0.000	0.000
108	A	423	ARG	1	0.788	0.886	20.223	0.320	0.320	0.000	0.000	0.000	0.000
109	A	424	CYS	0	-0.019	-0.001	18.192	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	425	THR	0	0.029	0.000	20.240	0.033	0.033	0.000	0.000	0.000	0.000
111	A	426	PHE	0	0.028	-0.001	17.570	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	427	TYR	0	0.073	0.023	23.336	0.024	0.024	0.000	0.000	0.000	0.000
113	A	428	THR	0	-0.008	-0.018	24.731	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	429	PRO	0	0.021	0.028	27.390	0.016	0.016	0.000	0.000	0.000	0.000
115	A	430	ALA	0	0.076	0.017	30.455	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	431	SER	0	-0.033	-0.011	32.568	0.001	0.001	0.000	0.000	0.000	0.000
117	A	432	LEU	0	-0.001	-0.003	25.786	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	433	GLY	0	0.010	0.031	28.701	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	434	ASP	-1	-0.936	-0.962	30.075	-0.226	-0.226	0.000	0.000	0.000	0.000
120	A	435	VAL	0	-0.056	-0.029	24.296	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	436	LYS	1	0.886	0.930	20.773	0.432	0.432	0.000	0.000	0.000	0.000
122	A	437	LEU	0	0.003	0.014	19.782	-0.027	-0.027	0.000	0.000	0.000	0.000
123	A	438	GLU	-1	-0.831	-0.882	15.872	-0.477	-0.477	0.000	0.000	0.000	0.000
124	A	439	LEU	0	0.025	0.016	13.521	-0.019	-0.019	0.000	0.000	0.000	0.000
125	A	440	PHE	0	-0.005	-0.006	9.030	0.058	0.058	0.000	0.000	0.000	0.000
126	A	441	ALA	0	0.042	0.026	8.609	0.085	0.085	0.000	0.000	0.000	0.000
127	A	442	VAL	0	-0.012	0.000	2.402	-0.337	-0.719	2.091	-0.597	-1.112	-0.001
128	A	443	LEU	0	-0.008	-0.009	3.886	0.409	0.680	0.001	-0.054	-0.218	0.000
129	A	444	ARG	1	0.872	0.925	2.524	-2.425	-0.874	0.998	-1.078	-1.471	-0.015
130	A	445	THR	0	0.020	0.016	4.859	0.413	0.534	-0.001	-0.002	-0.117	0.000

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