FMO DATABASE

FMODB ID: K9LK3

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	OptHSide
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	-666315.336766
FMO2-HF: Nuclear repulsion	629574.306978
FMO2-HF: Total energy	-36741.029788
FMO2-MP2: Total energy	-36849.279288

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.
-7.229	0.053999999999999	3.232	-3.453	-7.064	0.002

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	0.000	-0.001	3.835	-0.003	1.745	-0.020	-0.813	-0.916	0.002
4	A	189	MET	0	-0.005	0.015	6.135	0.001	0.001	0.000	0.000	0.000	0.000
5	A	190	THR	0	-0.016	-0.001	9.945	-0.064	-0.064	0.000	0.000	0.000	0.000
6	A	191	VAL	0	0.003	0.006	12.399	0.026	0.026	0.000	0.000	0.000	0.000
7	A	192	VAL	0	-0.015	-0.011	15.839	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	193	GLU	-1	-0.799	-0.880	18.800	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	194	ILE	0	-0.046	-0.026	20.709	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	195	LYS	1	0.879	0.963	24.561	0.051	0.051	0.000	0.000	0.000	0.000
11	A	196	LEU	0	-0.001	-0.001	26.103	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	197	PHE	0	0.045	0.014	29.942	0.005	0.005	0.000	0.000	0.000	0.000
13	A	198	LYS	1	0.805	0.898	33.050	0.002	0.002	0.000	0.000	0.000	0.000
14	A	199	GLY	0	0.046	0.030	33.973	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	200	PRO	0	0.020	-0.004	35.726	0.003	0.003	0.000	0.000	0.000	0.000
16	A	201	LYS	1	0.883	0.955	31.759	0.037	0.037	0.000	0.000	0.000	0.000
17	A	202	GLY	0	0.009	0.012	33.579	0.002	0.002	0.000	0.000	0.000	0.000
18	A	203	LEU	0	0.040	0.005	28.830	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	204	GLY	0	-0.019	-0.003	28.869	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	205	PHE	0	0.002	-0.008	24.282	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	206	SER	0	-0.022	-0.005	24.447	0.002	0.002	0.000	0.000	0.000	0.000
22	A	207	ILE	0	-0.001	-0.011	23.278	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	208	ALA	0	0.016	0.013	21.672	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	209	GLY	0	0.030	0.021	21.794	0.003	0.003	0.000	0.000	0.000	0.000
25	A	210	GLY	0	0.056	0.024	22.536	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	211	VAL	0	-0.021	-0.020	24.186	0.012	0.012	0.000	0.000	0.000	0.000
27	A	212	GLY	0	-0.042	-0.024	25.773	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	213	ASN	0	-0.064	-0.037	25.657	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	214	GLN	0	0.007	0.008	20.579	0.000	0.000	0.000	0.000	0.000	0.000
30	A	215	HIS	0	0.011	0.010	17.268	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	216	ILE	0	-0.019	-0.012	13.527	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	217	PRO	0	0.012	-0.007	16.382	0.009	0.009	0.000	0.000	0.000	0.000
33	A	218	GLY	0	-0.011	-0.003	16.421	0.047	0.047	0.000	0.000	0.000	0.000
34	A	219	ASP	-1	-0.758	-0.827	15.270	0.326	0.326	0.000	0.000	0.000	0.000
35	A	220	ASN	0	-0.019	-0.025	17.901	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	221	SER	0	-0.059	-0.041	17.705	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	222	ILE	0	-0.016	0.007	19.824	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	223	TYR	0	-0.025	-0.049	14.382	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	224	VAL	0	0.015	0.010	19.179	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	225	THR	0	0.017	0.009	18.938	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	226	LYS	1	0.947	0.966	20.912	0.022	0.022	0.000	0.000	0.000	0.000
42	A	227	ILE	0	0.034	0.032	20.547	0.006	0.006	0.000	0.000	0.000	0.000
43	A	228	ILE	0	-0.100	-0.053	23.837	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	229	ASP	-1	-0.813	-0.912	27.144	-0.072	-0.072	0.000	0.000	0.000	0.000
45	A	230	GLY	0	0.046	0.022	27.976	0.007	0.007	0.000	0.000	0.000	0.000
46	A	231	GLY	0	-0.088	-0.058	29.070	0.004	0.004	0.000	0.000	0.000	0.000
47	A	232	ALA	0	0.006	0.008	29.036	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	233	ALA	0	0.030	0.013	24.705	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	234	GLN	0	0.015	0.006	24.445	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	235	LYS	1	0.914	0.950	25.415	0.045	0.045	0.000	0.000	0.000	0.000
51	A	236	ASP	-1	-0.816	-0.869	25.038	-0.090	-0.090	0.000	0.000	0.000	0.000
52	A	237	GLY	0	0.021	0.021	23.329	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	238	ARG	1	0.797	0.873	20.671	0.075	0.075	0.000	0.000	0.000	0.000
54	A	239	LEU	0	-0.007	-0.001	19.317	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	240	GLN	0	-0.026	-0.033	16.076	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	241	VAL	0	-0.021	-0.011	16.756	0.021	0.021	0.000	0.000	0.000	0.000
57	A	242	GLY	0	0.009	0.003	14.289	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	243	ASP	-1	-0.792	-0.869	14.488	-0.070	-0.070	0.000	0.000	0.000	0.000
59	A	244	ARG	1	0.882	0.933	13.674	-0.286	-0.286	0.000	0.000	0.000	0.000
60	A	245	LEU	0	-0.041	-0.020	17.511	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	246	LEU	0	0.028	0.005	16.698	0.017	0.017	0.000	0.000	0.000	0.000
62	A	247	MET	0	0.000	0.007	20.983	0.002	0.002	0.000	0.000	0.000	0.000
63	A	248	VAL	0	0.010	0.008	24.432	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	249	ASN	0	0.007	0.001	27.580	0.000	0.000	0.000	0.000	0.000	0.000
65	A	250	ASN	0	0.002	-0.019	28.502	0.000	0.000	0.000	0.000	0.000	0.000
66	A	251	TYR	0	0.007	0.025	29.215	0.004	0.004	0.000	0.000	0.000	0.000
67	A	252	SER	0	0.008	-0.003	24.505	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	253	LEU	0	-0.023	-0.021	23.499	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	254	GLU	-1	-0.961	-0.979	20.387	0.160	0.160	0.000	0.000	0.000	0.000
70	A	255	GLU	-1	-0.852	-0.920	21.128	0.202	0.202	0.000	0.000	0.000	0.000
71	A	256	VAL	0	-0.013	0.023	24.149	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	257	THR	0	0.018	-0.017	26.292	0.007	0.007	0.000	0.000	0.000	0.000
73	A	258	HIS	0	-0.067	-0.035	25.866	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	259	GLU	-1	-0.876	-0.960	28.201	0.061	0.061	0.000	0.000	0.000	0.000
75	A	260	GLU	-1	-0.824	-0.872	30.278	0.072	0.072	0.000	0.000	0.000	0.000
76	A	261	ALA	0	0.040	0.015	26.903	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	262	VAL	0	-0.039	-0.018	28.863	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	263	ALA	0	-0.020	-0.004	31.050	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	264	ILE	0	0.031	0.017	29.264	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	265	LEU	0	-0.012	-0.013	26.930	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	266	LYS	1	0.894	0.951	31.371	-0.031	-0.031	0.000	0.000	0.000	0.000
82	A	267	ASN	0	-0.044	-0.008	34.925	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	268	THR	0	-0.040	-0.007	31.933	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	269	SER	0	0.021	0.004	35.365	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	270	GLU	-1	-0.925	-0.970	35.812	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	271	VAL	0	-0.003	0.010	33.223	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	272	VAL	0	-0.022	-0.018	29.255	0.005	0.005	0.000	0.000	0.000	0.000
88	A	273	TYR	0	0.009	-0.005	27.841	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	274	LEU	0	0.009	0.000	24.128	0.010	0.010	0.000	0.000	0.000	0.000
90	A	275	LYS	1	0.864	0.928	20.050	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	276	VAL	0	-0.015	-0.019	17.971	0.017	0.017	0.000	0.000	0.000	0.000
92	A	277	GLY	0	0.037	0.003	15.170	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	278	LYS	1	0.814	0.885	13.697	0.153	0.153	0.000	0.000	0.000	0.000
94	A	279	PRO	0	0.008	0.013	8.968	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	280	THR	0	-0.028	-0.021	7.153	-0.113	-0.113	0.000	0.000	0.000	0.000
96	A	281	THR	0	0.011	-0.003	2.918	-2.320	-1.159	2.240	-0.775	-2.626	0.005
97	A	282	ILE	0	-0.075	-0.039	2.527	-1.759	0.092	0.587	-0.893	-1.545	0.002
98	A	283	TYR	0	0.029	0.013	3.029	-3.354	-0.831	0.425	-0.972	-1.977	-0.007

Top

Graph

Manual

About

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