FMO DATABASE

FMODB ID: K38Y3

Calculation Name: 2HY5-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HY5

Chain ID: C

ChEMBL ID:

UniProt ID: O87896

Base Structure: X-ray

Registration Date: 2023-03-13

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-738237.02036
FMO2-HF: Nuclear repulsion	700135.081536
FMO2-HF: Total energy	-38101.938824
FMO2-MP2: Total energy	-38214.333504

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(C:402:SER)

Summations of interaction energy for fragment #1(C:402: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.
-36.58	-36.322	17.533	-9.547	-8.245	-0.077

Interaction energy analysis for fragmet #1(C:402: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 : -0.041

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	C	404	LEU	0	0.055	0.025	3.873	1.024	2.252	-0.015	-0.565	-0.649	0.002
4	C	405	HIS	0	0.022	0.017	5.941	-1.480	-1.480	0.000	0.000	0.000	0.000
5	C	406	THR	0	-0.006	-0.001	9.424	-0.196	-0.196	0.000	0.000	0.000	0.000
6	C	407	VAL	0	-0.018	-0.009	12.850	-0.039	-0.039	0.000	0.000	0.000	0.000
7	C	408	ASN	0	0.005	-0.006	16.045	0.002	0.002	0.000	0.000	0.000	0.000
8	C	409	LYS	1	0.814	0.871	19.482	-0.316	-0.316	0.000	0.000	0.000	0.000
9	C	410	SER	0	0.054	0.046	21.090	0.057	0.057	0.000	0.000	0.000	0.000
10	C	411	PRO	0	0.060	0.027	21.271	0.002	0.002	0.000	0.000	0.000	0.000
11	C	412	PHE	0	-0.078	-0.056	23.030	-0.005	-0.005	0.000	0.000	0.000	0.000
12	C	413	GLU	-1	-0.899	-0.919	25.656	0.223	0.223	0.000	0.000	0.000	0.000
13	C	414	ARG	1	0.896	0.922	22.366	-0.285	-0.285	0.000	0.000	0.000	0.000
14	C	415	ASN	0	0.033	0.026	20.539	-0.010	-0.010	0.000	0.000	0.000	0.000
15	C	416	SER	0	-0.017	-0.011	18.311	0.067	0.067	0.000	0.000	0.000	0.000
16	C	417	LEU	0	0.053	0.036	16.177	0.103	0.103	0.000	0.000	0.000	0.000
17	C	418	GLU	-1	-0.867	-0.937	16.088	0.664	0.664	0.000	0.000	0.000	0.000
18	C	419	SER	0	-0.077	-0.056	16.581	0.049	0.049	0.000	0.000	0.000	0.000
19	C	420	CYS	0	-0.006	0.015	11.172	0.135	0.135	0.000	0.000	0.000	0.000
20	C	421	LEU	0	0.016	0.000	11.775	0.308	0.308	0.000	0.000	0.000	0.000
21	C	422	LYS	1	0.892	0.966	12.849	-0.651	-0.651	0.000	0.000	0.000	0.000
22	C	423	PHE	0	-0.036	-0.033	11.214	-0.088	-0.088	0.000	0.000	0.000	0.000
23	C	424	ALA	0	-0.011	0.019	7.745	0.346	0.346	0.000	0.000	0.000	0.000
24	C	425	THR	0	0.002	-0.013	4.536	-0.602	-0.536	-0.001	-0.008	-0.057	0.000
25	C	426	GLU	-1	-0.832	-0.926	6.367	2.671	2.671	0.000	0.000	0.000	0.000
26	C	427	GLY	0	-0.022	-0.006	4.520	1.214	1.298	-0.001	-0.010	-0.074	0.000
27	C	428	ALA	0	-0.054	-0.007	3.333	-0.291	0.805	0.134	-0.479	-0.751	0.004
28	C	429	SER	0	0.030	0.010	4.179	-3.259	-3.050	0.011	-0.051	-0.169	0.001
29	C	430	VAL	0	-0.026	-0.015	6.535	0.123	0.123	0.000	0.000	0.000	0.000
30	C	431	LEU	0	-0.003	0.017	10.015	-0.206	-0.206	0.000	0.000	0.000	0.000
31	C	432	LEU	0	-0.026	-0.012	12.621	-0.032	-0.032	0.000	0.000	0.000	0.000
32	C	433	PHE	0	0.060	-0.004	16.101	-0.082	-0.082	0.000	0.000	0.000	0.000
33	C	434	GLU	-1	-0.805	-0.885	18.636	0.241	0.241	0.000	0.000	0.000	0.000
34	C	435	ASP	-1	-0.828	-0.909	22.217	0.226	0.226	0.000	0.000	0.000	0.000
35	C	436	GLY	0	0.001	0.002	19.308	0.016	0.016	0.000	0.000	0.000	0.000
36	C	437	ILE	0	-0.018	-0.004	19.678	0.042	0.042	0.000	0.000	0.000	0.000
37	C	438	TYR	0	-0.022	-0.018	21.483	0.002	0.002	0.000	0.000	0.000	0.000
38	C	439	ALA	0	-0.020	-0.013	19.410	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	440	ALA	0	0.020	0.006	19.416	0.037	0.037	0.000	0.000	0.000	0.000
40	C	441	LEU	0	-0.043	0.004	20.606	-0.023	-0.023	0.000	0.000	0.000	0.000
41	C	442	ALA	0	0.049	0.023	24.325	0.021	0.021	0.000	0.000	0.000	0.000
42	C	443	GLY	0	-0.038	-0.024	25.966	-0.022	-0.022	0.000	0.000	0.000	0.000
43	C	444	THR	0	-0.037	-0.007	24.959	-0.006	-0.006	0.000	0.000	0.000	0.000
44	C	445	ARG	1	0.909	0.944	25.191	-0.358	-0.358	0.000	0.000	0.000	0.000
45	C	446	VAL	0	-0.015	-0.016	21.985	0.005	0.005	0.000	0.000	0.000	0.000
46	C	447	GLU	-1	-0.785	-0.881	21.943	0.410	0.410	0.000	0.000	0.000	0.000
47	C	448	SER	0	0.012	0.009	21.744	0.032	0.032	0.000	0.000	0.000	0.000
48	C	449	GLN	0	-0.030	-0.027	19.353	-0.010	-0.010	0.000	0.000	0.000	0.000
49	C	450	VAL	0	-0.013	-0.004	17.347	0.112	0.112	0.000	0.000	0.000	0.000
50	C	451	THR	0	-0.012	-0.022	17.023	0.065	0.065	0.000	0.000	0.000	0.000
51	C	452	GLU	-1	-0.932	-0.972	17.546	0.694	0.694	0.000	0.000	0.000	0.000
52	C	453	ALA	0	-0.077	-0.033	13.608	0.108	0.108	0.000	0.000	0.000	0.000
53	C	454	LEU	0	0.005	-0.010	12.747	0.212	0.212	0.000	0.000	0.000	0.000
54	C	455	GLY	0	-0.026	0.004	13.525	0.012	0.012	0.000	0.000	0.000	0.000
55	C	456	LYS	1	0.829	0.931	9.835	-2.090	-2.090	0.000	0.000	0.000	0.000
56	C	457	LEU	0	-0.043	-0.021	7.524	0.610	0.610	0.000	0.000	0.000	0.000
57	C	458	LYS	1	0.935	0.979	4.593	-2.372	-2.324	-0.001	-0.002	-0.045	0.000
58	C	459	LEU	0	0.000	0.003	9.546	0.118	0.118	0.000	0.000	0.000	0.000
59	C	460	TYR	0	0.035	0.011	8.470	-0.102	-0.102	0.000	0.000	0.000	0.000
60	C	461	VAL	0	-0.011	-0.013	13.640	0.044	0.044	0.000	0.000	0.000	0.000
61	C	462	LEU	0	0.017	0.020	16.947	-0.058	-0.058	0.000	0.000	0.000	0.000
62	C	463	GLY	0	0.049	0.017	18.824	-0.004	-0.004	0.000	0.000	0.000	0.000
63	C	464	PRO	0	-0.038	-0.030	21.110	-0.005	-0.005	0.000	0.000	0.000	0.000
64	C	465	ASP	-1	-0.750	-0.862	21.742	0.175	0.175	0.000	0.000	0.000	0.000
65	C	466	LEU	0	-0.007	0.005	21.515	0.006	0.006	0.000	0.000	0.000	0.000
66	C	467	LYS	1	0.829	0.900	24.758	-0.137	-0.137	0.000	0.000	0.000	0.000
67	C	468	ALA	0	-0.043	-0.016	27.147	-0.008	-0.008	0.000	0.000	0.000	0.000
68	C	469	ARG	1	0.751	0.859	25.068	-0.205	-0.205	0.000	0.000	0.000	0.000
69	C	470	GLY	0	-0.010	0.014	29.185	0.004	0.004	0.000	0.000	0.000	0.000
70	C	471	PHE	0	-0.083	-0.058	26.597	0.005	0.005	0.000	0.000	0.000	0.000
71	C	472	SER	0	-0.034	-0.043	27.229	-0.004	-0.004	0.000	0.000	0.000	0.000
72	C	473	ASP	-1	-0.750	-0.878	23.596	0.168	0.168	0.000	0.000	0.000	0.000
73	C	474	GLU	-1	-0.855	-0.905	24.259	0.175	0.175	0.000	0.000	0.000	0.000
74	C	475	ARG	1	0.855	0.936	26.527	-0.183	-0.183	0.000	0.000	0.000	0.000
75	C	476	VAL	0	-0.009	-0.001	20.094	0.014	0.014	0.000	0.000	0.000	0.000
76	C	477	ILE	0	0.002	0.004	20.471	-0.019	-0.019	0.000	0.000	0.000	0.000
77	C	478	PRO	0	-0.038	-0.035	20.317	0.029	0.029	0.000	0.000	0.000	0.000
78	C	479	GLY	0	0.038	0.025	17.848	0.022	0.022	0.000	0.000	0.000	0.000
79	C	480	ILE	0	-0.049	-0.005	15.562	0.050	0.050	0.000	0.000	0.000	0.000
80	C	481	SER	0	-0.005	0.002	13.841	-0.111	-0.111	0.000	0.000	0.000	0.000
81	C	482	VAL	0	-0.028	-0.016	15.698	0.018	0.018	0.000	0.000	0.000	0.000
82	C	483	VAL	0	0.005	0.014	14.146	-0.038	-0.038	0.000	0.000	0.000	0.000
83	C	484	ASP	-1	-0.815	-0.920	17.501	-0.024	-0.024	0.000	0.000	0.000	0.000
84	C	485	TYR	0	0.025	-0.009	17.629	0.004	0.004	0.000	0.000	0.000	0.000
85	C	486	ALA	0	-0.015	0.001	17.842	-0.033	-0.033	0.000	0.000	0.000	0.000
86	C	487	GLY	0	0.076	0.030	15.187	-0.055	-0.055	0.000	0.000	0.000	0.000
87	C	488	PHE	0	-0.069	-0.035	13.387	0.010	0.010	0.000	0.000	0.000	0.000
88	C	489	VAL	0	0.002	-0.001	12.891	-0.049	-0.049	0.000	0.000	0.000	0.000
89	C	490	ASP	-1	-0.858	-0.908	12.831	-0.521	-0.521	0.000	0.000	0.000	0.000
90	C	491	LEU	0	0.026	0.013	8.843	-0.198	-0.198	0.000	0.000	0.000	0.000
91	C	492	THR	0	-0.162	-0.102	8.106	-0.139	-0.139	0.000	0.000	0.000	0.000
92	C	493	THR	0	-0.090	-0.053	8.974	-0.219	-0.219	0.000	0.000	0.000	0.000
93	C	494	GLU	-1	-0.957	-0.975	6.971	-0.770	-0.770	0.000	0.000	0.000	0.000
94	C	495	CYS	0	-0.097	-0.037	3.555	-0.495	0.075	0.019	-0.137	-0.452	0.000
95	C	496	ASP	-1	-0.820	-0.881	1.674	-33.953	-37.169	17.388	-8.271	-5.900	-0.084
96	C	497	THR	0	-0.082	-0.054	4.250	2.031	2.204	-0.001	-0.024	-0.148	0.000
97	C	498	VAL	0	0.033	0.025	6.381	0.250	0.250	0.000	0.000	0.000	0.000
98	C	499	GLN	0	-0.022	-0.014	9.095	0.327	0.327	0.000	0.000	0.000	0.000
99	C	500	ALA	0	0.022	0.009	10.870	0.149	0.149	0.000	0.000	0.000	0.000
100	C	501	TRP	0	-0.006	-0.013	10.655	-0.184	-0.184	0.000	0.000	0.000	0.000
101	C	502	LEU	0	-0.049	-0.022	15.706	-0.067	-0.067	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:402:SER)