FMO DATABASE

FMODB ID: 17ZMZ

Calculation Name: 2DYQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYQ

Chain ID: A

ChEMBL ID:

UniProt ID: O95704

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1056429.77143
FMO2-HF: Nuclear repulsion	1005053.203509
FMO2-HF: Total energy	-51376.567922
FMO2-MP2: Total energy	-51519.45599

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:288:ALA)

Summations of interaction energy for fragment #1(A:288: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.
-3.53	-0.303	1.124	-2.045	-2.307	0.006

Interaction energy analysis for fragmet #1(A:288:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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	290	LYS	1	0.962	0.978	3.851	0.875	2.652	-0.025	-0.998	-0.754	0.002
4	A	291	TYR	0	0.010	-0.006	6.998	-0.229	-0.229	0.000	0.000	0.000	0.000
5	A	292	GLU	-1	-0.903	-0.926	10.280	-0.004	-0.004	0.000	0.000	0.000	0.000
6	A	293	ALA	0	-0.006	-0.007	13.478	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	294	LEU	0	-0.028	0.006	15.242	0.034	0.034	0.000	0.000	0.000	0.000
8	A	295	TYR	0	0.022	0.014	16.593	0.003	0.003	0.000	0.000	0.000	0.000
9	A	296	MET	0	-0.025	-0.018	18.229	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	297	GLY	0	-0.001	0.011	20.845	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	298	THR	0	-0.051	-0.042	20.766	0.020	0.020	0.000	0.000	0.000	0.000
12	A	299	LEU	0	0.024	0.012	22.793	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	300	PRO	0	-0.010	0.000	25.370	0.011	0.011	0.000	0.000	0.000	0.000
14	A	301	VAL	0	0.023	0.005	25.074	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	302	THR	0	0.026	0.000	28.049	0.004	0.004	0.000	0.000	0.000	0.000
16	A	303	LYS	1	0.922	0.971	28.293	-0.098	-0.098	0.000	0.000	0.000	0.000
17	A	304	ALA	0	0.037	0.015	24.204	0.001	0.001	0.000	0.000	0.000	0.000
18	A	305	MET	0	-0.022	-0.006	23.607	0.005	0.005	0.000	0.000	0.000	0.000
19	A	306	GLY	0	0.055	0.037	24.755	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	307	MET	0	0.016	0.010	22.322	0.010	0.010	0.000	0.000	0.000	0.000
21	A	308	ASP	-1	-0.849	-0.921	26.193	0.067	0.067	0.000	0.000	0.000	0.000
22	A	309	VAL	0	-0.013	-0.011	26.669	0.002	0.002	0.000	0.000	0.000	0.000
23	A	310	LEU	0	0.004	0.012	21.084	0.008	0.008	0.000	0.000	0.000	0.000
24	A	311	ASN	0	0.036	0.001	25.129	0.003	0.003	0.000	0.000	0.000	0.000
25	A	312	GLU	-1	-0.940	-0.944	27.221	0.095	0.095	0.000	0.000	0.000	0.000
26	A	313	ALA	0	0.084	0.046	25.387	0.000	0.000	0.000	0.000	0.000	0.000
27	A	314	ILE	0	0.005	-0.005	21.966	0.003	0.003	0.000	0.000	0.000	0.000
28	A	315	GLY	0	-0.051	-0.031	25.288	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	316	THR	0	-0.038	-0.027	28.789	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	317	LEU	0	-0.025	0.003	23.432	0.000	0.000	0.000	0.000	0.000	0.000
31	A	318	THR	0	-0.074	-0.049	26.671	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	319	ALA	0	-0.043	-0.018	27.945	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	320	ARG	1	0.928	0.965	26.866	-0.103	-0.103	0.000	0.000	0.000	0.000
34	A	321	GLY	0	0.009	0.011	31.163	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	322	ASP	-1	-0.820	-0.921	29.229	0.077	0.077	0.000	0.000	0.000	0.000
36	A	323	ARG	1	0.870	0.930	25.830	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	324	ASN	0	0.009	0.003	26.571	0.004	0.004	0.000	0.000	0.000	0.000
38	A	325	ALA	0	-0.089	-0.042	26.242	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	326	TRP	0	0.024	0.021	21.688	0.015	0.015	0.000	0.000	0.000	0.000
40	A	327	VAL	0	0.026	0.011	18.442	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	328	PRO	0	0.006	-0.003	17.922	0.017	0.017	0.000	0.000	0.000	0.000
42	A	329	THR	0	-0.069	-0.034	13.293	0.040	0.040	0.000	0.000	0.000	0.000
43	A	330	MET	0	0.039	0.019	8.416	-0.161	-0.161	0.000	0.000	0.000	0.000
44	A	331	LEU	0	-0.036	-0.033	8.764	0.180	0.180	0.000	0.000	0.000	0.000
45	A	332	SER	0	-0.031	-0.004	3.961	-0.435	-0.360	0.000	-0.028	-0.046	0.000
46	A	333	VAL	0	-0.012	-0.021	4.180	-0.347	-0.133	-0.001	-0.050	-0.164	0.000
47	A	334	SER	0	0.001	0.006	2.791	-0.856	0.487	1.092	-1.205	-1.231	0.002
48	A	335	ASP	-1	-0.862	-0.953	3.747	-2.025	-2.207	0.058	0.236	-0.112	0.002
49	A	336	SER	0	-0.089	-0.032	6.483	-0.515	-0.515	0.000	0.000	0.000	0.000
50	A	337	LEU	0	-0.046	-0.027	7.105	-0.477	-0.477	0.000	0.000	0.000	0.000
51	A	338	MET	0	0.023	0.028	6.739	1.093	1.093	0.000	0.000	0.000	0.000
52	A	339	THR	0	0.001	-0.012	7.876	-0.380	-0.380	0.000	0.000	0.000	0.000
53	A	340	ALA	0	0.032	0.024	8.926	0.008	0.008	0.000	0.000	0.000	0.000
54	A	341	HIS	0	0.032	0.019	8.440	0.151	0.151	0.000	0.000	0.000	0.000
55	A	342	PRO	0	0.046	0.016	12.059	-0.063	-0.063	0.000	0.000	0.000	0.000
56	A	343	ILE	0	0.011	0.002	13.976	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	344	GLN	0	0.031	0.035	14.956	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	345	ALA	0	-0.026	-0.025	16.541	0.006	0.006	0.000	0.000	0.000	0.000
59	A	346	GLU	-1	-0.921	-0.994	10.569	0.342	0.342	0.000	0.000	0.000	0.000
60	A	347	ALA	0	0.006	-0.002	11.864	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	348	SER	0	-0.041	-0.056	13.211	0.055	0.055	0.000	0.000	0.000	0.000
62	A	349	THR	0	-0.119	-0.041	16.734	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	350	GLU	-1	-0.797	-0.854	19.012	0.198	0.198	0.000	0.000	0.000	0.000
64	A	351	GLH	0	-0.081	-0.015	14.784	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	352	GLU	-1	-0.993	-1.012	14.079	0.436	0.436	0.000	0.000	0.000	0.000
66	A	353	PRO	0	-0.065	-0.047	11.574	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	354	LEU	0	0.033	0.038	13.893	-0.067	-0.067	0.000	0.000	0.000	0.000
68	A	355	TRP	0	-0.012	-0.025	12.419	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	356	GLN	0	0.009	0.006	12.196	0.221	0.221	0.000	0.000	0.000	0.000
70	A	357	CYS	0	-0.011	-0.007	12.306	-0.193	-0.193	0.000	0.000	0.000	0.000
71	A	358	PRO	0	0.006	0.007	11.779	0.199	0.199	0.000	0.000	0.000	0.000
72	A	359	VAL	0	0.071	0.028	8.509	-0.186	-0.186	0.000	0.000	0.000	0.000
73	A	360	ARG	1	0.931	0.956	11.889	-0.713	-0.713	0.000	0.000	0.000	0.000
74	A	361	LEU	0	-0.045	-0.021	14.922	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	362	VAL	0	-0.011	0.005	13.329	-0.053	-0.053	0.000	0.000	0.000	0.000
76	A	363	THR	0	-0.053	-0.041	16.509	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	364	PHE	0	-0.007	-0.005	19.519	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	365	ILE	0	-0.015	-0.005	14.356	0.038	0.038	0.000	0.000	0.000	0.000
79	A	366	GLY	0	0.024	0.009	17.810	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	367	VAL	0	0.014	0.033	18.520	0.019	0.019	0.000	0.000	0.000	0.000
81	A	368	GLY	0	0.025	0.016	20.374	0.003	0.003	0.000	0.000	0.000	0.000
82	A	369	ARG	1	0.816	0.893	23.809	-0.065	-0.065	0.000	0.000	0.000	0.000
83	A	370	ASP	-1	-0.837	-0.916	25.774	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	371	PRO	0	0.027	-0.005	22.692	0.010	0.010	0.000	0.000	0.000	0.000
85	A	372	HIS	0	0.004	0.013	21.088	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	373	THR	0	-0.049	-0.026	20.209	0.012	0.012	0.000	0.000	0.000	0.000
87	A	374	PHE	0	0.018	0.000	14.015	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	375	GLY	0	0.025	0.001	18.292	0.024	0.024	0.000	0.000	0.000	0.000
89	A	376	LEU	0	-0.042	-0.026	14.047	0.000	0.000	0.000	0.000	0.000	0.000
90	A	377	ILE	0	0.009	0.006	18.144	0.007	0.007	0.000	0.000	0.000	0.000
91	A	378	ALA	0	0.026	0.010	17.699	0.023	0.023	0.000	0.000	0.000	0.000
92	A	379	ASP	-1	-0.897	-0.951	19.675	0.205	0.205	0.000	0.000	0.000	0.000
93	A	380	LEU	0	0.014	0.011	20.505	0.028	0.028	0.000	0.000	0.000	0.000
94	A	381	GLY	0	0.015	0.014	22.688	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	382	ARG	1	0.907	0.951	25.193	-0.190	-0.190	0.000	0.000	0.000	0.000
96	A	383	GLN	0	-0.069	-0.056	26.799	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	384	SER	0	-0.002	0.000	27.091	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	385	PHE	0	0.031	0.029	24.129	0.019	0.019	0.000	0.000	0.000	0.000
99	A	386	GLN	0	0.001	0.019	21.670	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	387	CYS	0	-0.002	0.002	21.242	0.006	0.006	0.000	0.000	0.000	0.000
101	A	388	ALA	0	-0.016	0.004	17.794	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	389	ALA	0	0.045	0.019	19.036	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	390	PHE	0	-0.019	-0.013	15.030	0.027	0.027	0.000	0.000	0.000	0.000
104	A	391	TRP	0	0.041	0.028	18.247	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	392	CYS	0	-0.006	-0.011	16.377	0.009	0.009	0.000	0.000	0.000	0.000
106	A	393	GLN	0	0.027	0.001	18.279	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	394	PRO	0	-0.027	0.008	16.412	0.000	0.000	0.000	0.000	0.000	0.000
108	A	395	HIS	0	0.052	0.036	18.133	0.003	0.003	0.000	0.000	0.000	0.000
109	A	396	ALA	0	0.016	-0.012	16.544	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	397	GLY	0	0.005	0.003	15.690	0.017	0.017	0.000	0.000	0.000	0.000
111	A	398	GLY	0	0.000	-0.002	13.623	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	399	LEU	0	0.017	0.012	10.056	-0.087	-0.087	0.000	0.000	0.000	0.000
113	A	400	SER	0	0.021	0.002	11.059	0.051	0.051	0.000	0.000	0.000	0.000
114	A	401	GLU	-1	-0.943	-0.974	12.443	-0.149	-0.149	0.000	0.000	0.000	0.000
115	A	402	ALA	0	-0.031	-0.005	7.085	-0.031	-0.031	0.000	0.000	0.000	0.000
116	A	403	VAL	0	-0.003	-0.015	8.370	0.156	0.156	0.000	0.000	0.000	0.000
117	A	404	GLN	0	0.056	0.030	10.130	0.097	0.097	0.000	0.000	0.000	0.000
118	A	405	ALA	0	-0.008	-0.007	9.000	0.047	0.047	0.000	0.000	0.000	0.000
119	A	406	ALA	0	0.022	0.018	7.208	0.012	0.012	0.000	0.000	0.000	0.000
120	A	407	CYS	0	-0.035	-0.034	8.664	0.065	0.065	0.000	0.000	0.000	0.000
121	A	408	MET	0	-0.040	-0.013	12.266	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	409	VAL	0	0.015	0.016	8.878	0.005	0.005	0.000	0.000	0.000	0.000
123	A	410	GLN	0	0.015	0.009	11.080	0.105	0.105	0.000	0.000	0.000	0.000
124	A	411	TYR	0	-0.005	-0.010	12.487	-0.024	-0.024	0.000	0.000	0.000	0.000
125	A	412	GLN	0	0.001	-0.001	15.133	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	413	LYS	1	0.889	0.940	10.717	-0.507	-0.507	0.000	0.000	0.000	0.000
127	A	414	CYS	0	-0.087	-0.049	15.836	0.018	0.018	0.000	0.000	0.000	0.000
128	A	415	LEU	0	-0.049	0.012	18.464	-0.015	-0.015	0.000	0.000	0.000	0.000
129	A	416	VAL	0	-0.011	-0.004	19.777	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	417	ALA	0	-0.002	0.001	20.505	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:288:ALA)