FMO DATABASE

FMODB ID: 3J4YL

Calculation Name: 2HY5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HY5

Chain ID: B

ChEMBL ID:

UniProt ID: O87896

Base Structure: X-ray

Registration Date: 2023-09-23

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	132
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1198962.240206
FMO2-HF: Nuclear repulsion	1145428.871071
FMO2-HF: Total energy	-53533.369135
FMO2-MP2: Total energy	-53688.445447

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(B:205:VAL)

Summations of interaction energy for fragment #1(B:205:VAL)

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.
-12.829	-6.454	2.882	-4.245	-5.011	-0.033

Interaction energy analysis for fragmet #1(B:205:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.039

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	B	207	LYS	1	0.877	0.943	3.774	-0.990	1.707	-0.023	-1.406	-1.268	0.002
4	B	208	PHE	0	-0.053	-0.043	6.708	-0.225	-0.225	0.000	0.000	0.000	0.000
5	B	209	MET	0	0.081	0.045	8.641	0.100	0.100	0.000	0.000	0.000	0.000
6	B	210	TYR	0	-0.042	-0.025	10.612	-0.046	-0.046	0.000	0.000	0.000	0.000
7	B	211	LEU	0	0.003	0.002	14.851	0.024	0.024	0.000	0.000	0.000	0.000
8	B	212	ASN	0	-0.019	-0.004	18.200	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	213	ARG	1	0.898	0.928	21.130	0.050	0.050	0.000	0.000	0.000	0.000
10	B	214	LYS	1	0.877	0.948	24.525	0.053	0.053	0.000	0.000	0.000	0.000
11	B	215	ALA	0	0.101	0.059	26.591	-0.001	-0.001	0.000	0.000	0.000	0.000
12	B	216	PRO	0	0.023	0.007	27.842	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	217	TYR	0	-0.025	-0.029	29.180	0.002	0.002	0.000	0.000	0.000	0.000
14	B	218	GLY	0	-0.030	0.004	31.750	0.000	0.000	0.000	0.000	0.000	0.000
15	B	219	THR	0	-0.055	-0.036	29.110	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	220	ILE	0	0.039	0.019	26.390	0.003	0.003	0.000	0.000	0.000	0.000
17	B	221	TYR	0	-0.018	-0.023	24.205	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	222	ALA	0	0.026	0.030	22.998	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	223	TRP	0	0.014	0.007	22.733	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	224	GLU	-1	-0.884	-0.972	22.446	-0.082	-0.082	0.000	0.000	0.000	0.000
21	B	225	ALA	0	-0.003	0.013	19.240	-0.012	-0.012	0.000	0.000	0.000	0.000
22	B	226	LEU	0	-0.027	-0.019	17.897	-0.011	-0.011	0.000	0.000	0.000	0.000
23	B	227	GLU	-1	-0.917	-0.964	18.113	-0.102	-0.102	0.000	0.000	0.000	0.000
24	B	228	VAL	0	-0.060	-0.026	13.748	-0.018	-0.018	0.000	0.000	0.000	0.000
25	B	229	VAL	0	-0.010	0.003	13.460	-0.034	-0.034	0.000	0.000	0.000	0.000
26	B	230	LEU	0	-0.013	-0.002	13.337	-0.009	-0.009	0.000	0.000	0.000	0.000
27	B	231	ILE	0	-0.056	-0.023	13.513	-0.014	-0.014	0.000	0.000	0.000	0.000
28	B	232	GLY	0	-0.025	-0.029	10.569	-0.044	-0.044	0.000	0.000	0.000	0.000
29	B	233	ALA	0	0.045	0.033	9.107	-0.096	-0.096	0.000	0.000	0.000	0.000
30	B	234	ALA	0	-0.034	-0.016	9.790	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	235	PHE	0	-0.144	-0.063	6.576	0.033	0.033	0.000	0.000	0.000	0.000
32	B	236	ASP	-1	-0.848	-0.902	5.042	-2.469	-2.356	-0.001	-0.007	-0.105	0.000
33	B	237	GLN	0	-0.068	-0.041	2.255	-8.087	-4.785	2.905	-2.799	-3.407	-0.035
34	B	238	ASP	-1	-0.873	-0.925	3.837	0.662	0.949	0.002	-0.032	-0.257	0.000
35	B	239	VAL	0	0.003	-0.011	5.881	-0.620	-0.644	-0.001	-0.001	0.026	0.000
36	B	240	CYM	-1	-0.838	-0.887	8.980	0.051	0.051	0.000	0.000	0.000	0.000
37	B	241	VAL	0	-0.019	-0.003	12.514	-0.052	-0.052	0.000	0.000	0.000	0.000
38	B	242	LEU	0	0.018	0.019	15.586	0.014	0.014	0.000	0.000	0.000	0.000
39	B	243	PHE	0	-0.068	-0.034	18.453	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	244	LEU	0	0.052	0.012	22.004	0.005	0.005	0.000	0.000	0.000	0.000
41	B	245	ASP	-1	-0.817	-0.912	24.271	-0.033	-0.033	0.000	0.000	0.000	0.000
42	B	246	ASP	-1	-0.850	-0.949	27.801	-0.024	-0.024	0.000	0.000	0.000	0.000
43	B	247	GLY	0	-0.054	-0.013	24.600	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	248	VAL	0	0.005	0.002	25.321	0.000	0.000	0.000	0.000	0.000	0.000
45	B	249	TYR	0	-0.008	-0.015	26.712	0.002	0.002	0.000	0.000	0.000	0.000
46	B	250	GLN	0	-0.099	-0.060	23.151	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	251	LEU	0	0.011	0.023	22.633	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	252	THR	0	0.014	0.041	26.703	0.002	0.002	0.000	0.000	0.000	0.000
49	B	253	ARG	1	0.915	0.960	30.318	0.005	0.005	0.000	0.000	0.000	0.000
50	B	254	GLY	0	-0.038	-0.028	32.024	0.000	0.000	0.000	0.000	0.000	0.000
51	B	255	GLN	0	0.009	0.011	29.235	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	256	ASP	-1	-0.900	-0.958	34.222	-0.020	-0.020	0.000	0.000	0.000	0.000
53	B	257	THR	0	-0.009	-0.041	33.586	0.001	0.001	0.000	0.000	0.000	0.000
54	B	258	LYS	1	0.946	0.967	36.866	0.020	0.020	0.000	0.000	0.000	0.000
55	B	259	GLY	0	-0.015	-0.001	39.955	0.000	0.000	0.000	0.000	0.000	0.000
56	B	260	ILE	0	-0.016	-0.010	35.411	0.001	0.001	0.000	0.000	0.000	0.000
57	B	261	GLY	0	-0.027	0.001	39.151	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	262	MET	0	0.022	0.023	32.073	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	263	LYS	1	0.966	1.000	28.357	0.050	0.050	0.000	0.000	0.000	0.000
60	B	264	ASN	0	0.055	0.050	31.202	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	265	PHE	0	-0.017	-0.018	25.260	0.000	0.000	0.000	0.000	0.000	0.000
62	B	266	SER	0	0.018	-0.011	26.335	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	267	PRO	0	-0.064	-0.057	26.271	0.001	0.001	0.000	0.000	0.000	0.000
64	B	268	THR	0	0.060	0.041	21.471	0.003	0.003	0.000	0.000	0.000	0.000
65	B	269	TYR	0	0.030	0.028	21.556	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	270	ARG	1	0.909	0.953	21.611	0.024	0.024	0.000	0.000	0.000	0.000
67	B	271	THR	0	-0.027	-0.018	21.347	0.001	0.001	0.000	0.000	0.000	0.000
68	B	272	LEU	0	0.001	-0.001	16.568	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	273	GLY	0	0.032	0.031	16.469	0.001	0.001	0.000	0.000	0.000	0.000
70	B	274	ASP	-1	-0.904	-0.953	17.021	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	275	TYR	0	-0.158	-0.086	14.516	-0.017	-0.017	0.000	0.000	0.000	0.000
72	B	276	GLU	-1	-0.865	-0.939	9.789	-0.034	-0.034	0.000	0.000	0.000	0.000
73	B	277	VAL	0	-0.070	-0.014	12.103	0.058	0.058	0.000	0.000	0.000	0.000
74	B	278	ARG	1	0.903	0.961	12.887	-0.119	-0.119	0.000	0.000	0.000	0.000
75	B	279	ARG	1	0.873	0.940	12.792	-0.165	-0.165	0.000	0.000	0.000	0.000
76	B	280	ILE	0	0.054	0.032	14.907	-0.018	-0.018	0.000	0.000	0.000	0.000
77	B	281	TYR	0	0.048	0.018	14.783	0.003	0.003	0.000	0.000	0.000	0.000
78	B	282	VAL	0	-0.002	-0.014	19.785	-0.011	-0.011	0.000	0.000	0.000	0.000
79	B	283	ASP	-1	-0.761	-0.872	23.245	-0.007	-0.007	0.000	0.000	0.000	0.000
80	B	284	ARG	1	0.973	0.967	25.131	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	285	ASP	-1	-0.881	-0.933	28.345	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	286	SER	0	-0.069	-0.059	27.637	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	287	LEU	0	-0.015	0.000	28.007	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	288	GLU	-1	-0.913	-0.942	30.949	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	289	ALA	0	-0.059	-0.025	33.173	0.000	0.000	0.000	0.000	0.000	0.000
86	B	290	ARG	1	0.739	0.863	31.023	0.019	0.019	0.000	0.000	0.000	0.000
87	B	291	GLY	0	-0.039	-0.011	35.064	0.000	0.000	0.000	0.000	0.000	0.000
88	B	292	LEU	0	-0.053	-0.020	31.681	0.000	0.000	0.000	0.000	0.000	0.000
89	B	293	THR	0	-0.017	-0.010	32.832	0.002	0.002	0.000	0.000	0.000	0.000
90	B	294	GLN	0	0.015	-0.012	25.670	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	295	ASP	-1	-0.901	-0.945	30.445	0.000	0.000	0.000	0.000	0.000	0.000
92	B	296	ASP	-1	-0.914	-0.960	32.706	-0.009	-0.009	0.000	0.000	0.000	0.000
93	B	297	LEU	0	-0.045	-0.036	26.662	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	298	VAL	0	-0.109	-0.054	25.573	0.001	0.001	0.000	0.000	0.000	0.000
95	B	299	GLU	-1	-0.960	-0.964	26.218	0.003	0.003	0.000	0.000	0.000	0.000
96	B	300	ILE	0	-0.068	-0.056	20.124	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	301	ALA	0	0.059	0.042	22.330	0.006	0.006	0.000	0.000	0.000	0.000
98	B	302	PHE	0	-0.027	-0.033	14.673	0.000	0.000	0.000	0.000	0.000	0.000
99	B	303	GLU	-1	-0.929	-0.952	19.510	0.001	0.001	0.000	0.000	0.000	0.000
100	B	304	ASP	-1	-0.830	-0.898	15.040	0.041	0.041	0.000	0.000	0.000	0.000
101	B	305	MET	0	-0.021	-0.032	18.285	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	306	GLU	-1	-1.033	-1.006	14.934	0.018	0.018	0.000	0.000	0.000	0.000
103	B	307	THR	0	-0.097	-0.073	16.565	0.006	0.006	0.000	0.000	0.000	0.000
104	B	308	GLU	-1	-0.988	-0.972	19.042	0.020	0.020	0.000	0.000	0.000	0.000
105	B	309	GLU	-1	-0.909	-0.938	16.415	0.097	0.097	0.000	0.000	0.000	0.000
106	B	310	GLU	-1	-0.900	-0.968	21.209	0.010	0.010	0.000	0.000	0.000	0.000
107	B	311	PHE	0	-0.096	-0.051	19.942	0.001	0.001	0.000	0.000	0.000	0.000
108	B	312	ASP	-1	-0.865	-0.937	23.687	0.008	0.008	0.000	0.000	0.000	0.000
109	B	313	ASN	0	-0.006	-0.030	24.116	-0.005	-0.005	0.000	0.000	0.000	0.000
110	B	314	ILE	0	0.002	0.010	18.700	0.004	0.004	0.000	0.000	0.000	0.000
111	B	315	VAL	0	-0.074	-0.025	20.371	0.004	0.004	0.000	0.000	0.000	0.000
112	B	316	GLU	-1	-0.888	-0.948	20.139	0.046	0.046	0.000	0.000	0.000	0.000
113	B	317	VAL	0	-0.048	-0.023	22.412	-0.004	-0.004	0.000	0.000	0.000	0.000
114	B	318	ILE	0	-0.008	0.001	20.101	0.003	0.003	0.000	0.000	0.000	0.000
115	B	319	ASP	-1	-0.877	-0.960	24.234	0.007	0.007	0.000	0.000	0.000	0.000
116	B	320	SER	0	0.071	0.026	24.313	0.001	0.001	0.000	0.000	0.000	0.000
117	B	321	ALA	0	-0.019	-0.006	24.101	-0.003	-0.003	0.000	0.000	0.000	0.000
118	B	322	ARG	1	0.963	0.997	16.009	-0.055	-0.055	0.000	0.000	0.000	0.000
119	B	323	VAL	0	0.002	0.002	19.581	0.000	0.000	0.000	0.000	0.000	0.000
120	B	324	SER	0	-0.032	-0.032	19.297	-0.008	-0.008	0.000	0.000	0.000	0.000
121	B	325	GLU	-1	-0.961	-0.977	16.927	0.023	0.023	0.000	0.000	0.000	0.000
122	B	326	LEU	0	0.042	0.021	14.864	-0.005	-0.005	0.000	0.000	0.000	0.000
123	B	327	MET	0	-0.075	-0.043	14.419	-0.017	-0.017	0.000	0.000	0.000	0.000
124	B	328	ASN	0	-0.070	-0.043	15.091	-0.028	-0.028	0.000	0.000	0.000	0.000
125	B	329	GLU	-1	-0.961	-0.963	11.577	0.038	0.038	0.000	0.000	0.000	0.000
126	B	330	SER	0	-0.058	-0.030	10.341	-0.037	-0.037	0.000	0.000	0.000	0.000
127	B	331	ASP	-1	-0.876	-0.922	6.536	-0.810	-0.810	0.000	0.000	0.000	0.000
128	B	332	ALA	0	-0.107	-0.066	9.263	0.039	0.039	0.000	0.000	0.000	0.000
129	B	333	VAL	0	0.024	0.017	11.041	0.013	0.013	0.000	0.000	0.000	0.000
130	B	334	PHE	0	-0.048	-0.004	10.069	0.020	0.020	0.000	0.000	0.000	0.000
131	B	335	SER	0	0.007	-0.008	15.215	0.027	0.027	0.000	0.000	0.000	0.000
132	B	336	PHE	0	0.000	0.000	16.175	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:205:VAL)