FMO DATABASE

FMODB ID: QYGKY

Calculation Name: 2BYG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BYG

Chain ID: A

ChEMBL ID:

UniProt ID: Q15700

Base Structure: X-ray

Registration Date: 2023-09-19

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-665847.262363
FMO2-HF: Nuclear repulsion	629106.41137
FMO2-HF: Total energy	-36740.850993
FMO2-MP2: Total energy	-36849.090473

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:186:PHE)

Summations of interaction energy for fragment #1(A:186:PHE)

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.
-5.004	1.841	2.22	-2.969	-6.095	0.003

Interaction energy analysis for fragmet #1(A:186:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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	188	SER	0	-0.003	0.001	3.835	0.231	1.936	-0.019	-0.790	-0.896	0.001
4	A	189	MET	0	-0.012	0.014	6.152	-0.030	-0.030	0.000	0.000	0.000	0.000
5	A	190	THR	0	-0.024	-0.004	9.961	-0.037	-0.037	0.000	0.000	0.000	0.000
6	A	191	VAL	0	0.003	0.004	12.410	0.021	0.021	0.000	0.000	0.000	0.000
7	A	192	VAL	0	-0.020	-0.011	15.851	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	193	GLU	-1	-0.823	-0.902	18.811	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	194	ILE	0	-0.056	-0.028	20.561	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	195	LYS	1	0.909	0.972	24.573	0.060	0.060	0.000	0.000	0.000	0.000
11	A	196	LEU	0	-0.012	-0.006	26.046	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	197	PHE	0	0.032	0.011	29.768	0.005	0.005	0.000	0.000	0.000	0.000
13	A	198	LYS	1	0.838	0.918	32.889	0.013	0.013	0.000	0.000	0.000	0.000
14	A	199	GLY	0	0.045	0.030	33.854	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	200	PRO	0	0.022	-0.003	35.585	0.002	0.002	0.000	0.000	0.000	0.000
16	A	201	LYS	1	0.893	0.961	31.836	0.046	0.046	0.000	0.000	0.000	0.000
17	A	202	GLY	0	0.006	0.006	33.476	0.001	0.001	0.000	0.000	0.000	0.000
18	A	203	LEU	0	0.040	0.004	28.692	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	204	GLY	0	-0.018	-0.002	28.740	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	205	PHE	0	-0.002	-0.010	24.147	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	206	SER	0	-0.013	0.001	24.418	0.004	0.004	0.000	0.000	0.000	0.000
22	A	207	ILE	0	0.004	-0.007	23.115	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	208	ALA	0	0.015	0.013	21.515	0.000	0.000	0.000	0.000	0.000	0.000
24	A	209	GLY	0	0.035	0.021	21.685	0.000	0.000	0.000	0.000	0.000	0.000
25	A	210	GLY	0	0.048	0.020	22.440	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	211	VAL	0	-0.022	-0.018	24.117	0.011	0.011	0.000	0.000	0.000	0.000
27	A	212	GLY	0	-0.043	-0.025	25.708	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	213	ASN	0	-0.071	-0.039	25.609	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	214	GLN	0	0.015	0.013	20.531	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	215	HIS	0	0.012	0.012	17.110	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	216	ILE	0	-0.020	-0.011	13.427	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	217	PRO	0	0.006	-0.011	16.502	0.012	0.012	0.000	0.000	0.000	0.000
33	A	218	GLY	0	-0.019	-0.009	16.450	0.041	0.041	0.000	0.000	0.000	0.000
34	A	219	ASP	-1	-0.807	-0.845	15.102	0.248	0.248	0.000	0.000	0.000	0.000
35	A	220	ASN	0	-0.001	-0.022	17.862	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	221	SER	0	-0.052	-0.021	17.597	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	222	ILE	0	-0.012	0.007	19.701	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	223	TYR	0	-0.057	-0.085	14.145	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	224	VAL	0	0.009	0.006	18.978	0.001	0.001	0.000	0.000	0.000	0.000
40	A	225	THR	0	0.014	0.003	18.896	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	226	LYS	1	0.944	0.969	20.890	0.039	0.039	0.000	0.000	0.000	0.000
42	A	227	ILE	0	0.031	0.029	20.217	0.006	0.006	0.000	0.000	0.000	0.000
43	A	228	ILE	0	-0.094	-0.048	23.747	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	229	ASP	-1	-0.834	-0.924	27.102	-0.077	-0.077	0.000	0.000	0.000	0.000
45	A	230	GLY	0	0.057	0.024	27.871	0.008	0.008	0.000	0.000	0.000	0.000
46	A	231	GLY	0	-0.106	-0.064	28.952	0.005	0.005	0.000	0.000	0.000	0.000
47	A	232	ALA	0	-0.001	0.006	28.890	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	233	ALA	0	0.034	0.011	24.537	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	234	GLN	0	0.029	0.021	24.295	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	235	LYS	1	0.909	0.942	25.245	0.051	0.051	0.000	0.000	0.000	0.000
51	A	236	ASP	-1	-0.824	-0.892	24.976	-0.099	-0.099	0.000	0.000	0.000	0.000
52	A	237	GLY	0	0.013	0.019	23.142	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	238	ARG	1	0.825	0.901	20.462	0.085	0.085	0.000	0.000	0.000	0.000
54	A	239	LEU	0	-0.001	0.000	19.130	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	240	GLN	0	-0.022	-0.027	15.862	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	241	VAL	0	-0.017	-0.010	16.502	0.019	0.019	0.000	0.000	0.000	0.000
57	A	242	GLY	0	0.003	0.000	14.237	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	243	ASP	-1	-0.794	-0.876	14.296	-0.137	-0.137	0.000	0.000	0.000	0.000
59	A	244	ARG	1	0.957	0.977	12.884	-0.196	-0.196	0.000	0.000	0.000	0.000
60	A	245	LEU	0	-0.038	-0.019	17.308	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	246	LEU	0	0.022	-0.001	16.686	0.017	0.017	0.000	0.000	0.000	0.000
62	A	247	MET	0	-0.003	0.001	21.002	0.006	0.006	0.000	0.000	0.000	0.000
63	A	248	VAL	0	0.011	0.009	24.450	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	249	ASN	0	0.015	0.005	27.597	0.001	0.001	0.000	0.000	0.000	0.000
65	A	250	ASN	0	0.011	-0.011	28.560	0.000	0.000	0.000	0.000	0.000	0.000
66	A	251	TYR	0	-0.003	0.017	29.232	0.005	0.005	0.000	0.000	0.000	0.000
67	A	252	SER	0	-0.004	-0.005	24.738	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	253	LEU	0	-0.014	-0.016	23.434	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	254	GLU	-1	-0.974	-0.987	20.482	0.132	0.132	0.000	0.000	0.000	0.000
70	A	255	GLU	-1	-0.849	-0.920	21.069	0.169	0.169	0.000	0.000	0.000	0.000
71	A	256	VAL	0	0.010	0.033	24.170	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	257	THR	0	0.052	0.033	26.184	0.005	0.005	0.000	0.000	0.000	0.000
73	A	258	HIS	0	-0.028	-0.020	25.762	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	259	GLU	-1	-0.907	-0.972	28.086	0.043	0.043	0.000	0.000	0.000	0.000
75	A	260	GLU	-1	-0.877	-0.935	30.196	0.054	0.054	0.000	0.000	0.000	0.000
76	A	261	ALA	0	0.034	0.015	26.761	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	262	VAL	0	-0.039	-0.017	28.702	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	263	ALA	0	-0.018	-0.005	30.887	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	264	ILE	0	0.025	0.016	29.137	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	265	LEU	0	-0.010	-0.012	26.854	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	266	LYS	1	0.893	0.953	31.169	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	267	ASN	0	-0.040	-0.009	34.729	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	268	THR	0	-0.039	-0.011	31.742	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	269	SER	0	0.011	-0.004	35.173	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	270	GLU	-1	-0.938	-0.977	35.567	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	271	VAL	0	-0.007	0.005	33.146	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	272	VAL	0	-0.030	-0.022	29.006	0.005	0.005	0.000	0.000	0.000	0.000
88	A	273	TYR	0	-0.005	-0.007	27.829	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	274	LEU	0	0.004	-0.004	24.071	0.009	0.009	0.000	0.000	0.000	0.000
90	A	275	LYS	1	0.923	0.974	19.993	0.001	0.001	0.000	0.000	0.000	0.000
91	A	276	VAL	0	-0.010	-0.021	17.599	0.014	0.014	0.000	0.000	0.000	0.000
92	A	277	GLY	0	0.020	-0.013	15.184	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	278	LYS	1	0.815	0.892	13.447	0.193	0.193	0.000	0.000	0.000	0.000
94	A	279	PRO	0	0.006	0.014	8.800	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	280	THR	0	-0.026	-0.016	6.875	-0.091	-0.091	0.000	0.000	0.000	0.000
96	A	281	THR	0	0.017	0.003	2.951	-2.117	-0.862	1.532	-0.624	-2.162	0.005
97	A	282	ILE	0	-0.063	-0.031	2.584	-1.448	0.236	0.505	-0.774	-1.415	0.002
98	A	283	TYR	0	0.018	0.008	3.301	-1.860	0.341	0.202	-0.781	-1.622	-0.005

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Interactive mode: IFIE and PIEDA for fragment #1(A:186:PHE)