FMO DATABASE

FMODB ID: 49VQN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-668202.443938
FMO2-HF: Nuclear repulsion	631461.316237
FMO2-HF: Total energy	-36741.127701
FMO2-MP2: Total energy	-36849.398943

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.
-7.755	-0.526	3.006	-3.379	-6.855	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 : 0.039 / 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	188	SER	0	0.003	0.001	3.835	-0.439	1.264	-0.014	-0.849	-0.840	0.002
4	A	189	MET	0	-0.001	0.019	6.388	0.018	0.018	0.000	0.000	0.000	0.000
5	A	190	THR	0	-0.012	-0.004	10.246	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	191	VAL	0	-0.003	0.001	12.649	0.026	0.026	0.000	0.000	0.000	0.000
7	A	192	VAL	0	-0.026	-0.015	15.982	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	193	GLU	-1	-0.793	-0.875	19.017	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	194	ILE	0	-0.052	-0.042	20.516	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	195	LYS	1	0.881	0.958	24.770	0.046	0.046	0.000	0.000	0.000	0.000
11	A	196	LEU	0	0.019	0.016	26.186	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	197	PHE	0	0.037	0.000	29.800	0.004	0.004	0.000	0.000	0.000	0.000
13	A	198	LYS	1	0.806	0.906	32.748	0.001	0.001	0.000	0.000	0.000	0.000
14	A	199	GLY	0	0.042	0.033	33.983	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	200	PRO	0	0.014	-0.008	35.659	0.003	0.003	0.000	0.000	0.000	0.000
16	A	201	LYS	1	0.859	0.932	31.883	0.029	0.029	0.000	0.000	0.000	0.000
17	A	202	GLY	0	0.024	0.017	33.659	0.002	0.002	0.000	0.000	0.000	0.000
18	A	203	LEU	0	0.041	0.001	29.004	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	204	GLY	0	-0.015	0.002	28.789	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	205	PHE	0	-0.013	-0.012	24.355	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	206	SER	0	-0.021	-0.011	24.713	0.001	0.001	0.000	0.000	0.000	0.000
22	A	207	ILE	0	-0.012	-0.012	23.474	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	208	ALA	0	0.015	0.011	22.142	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	209	GLY	0	0.034	0.024	22.025	0.003	0.003	0.000	0.000	0.000	0.000
25	A	210	GLY	0	0.077	0.021	22.816	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	211	VAL	0	-0.038	-0.020	24.761	0.013	0.013	0.000	0.000	0.000	0.000
27	A	212	GLY	0	-0.037	-0.014	26.063	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	213	ASN	0	-0.081	-0.042	26.060	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	214	GLN	0	0.014	0.005	20.859	0.004	0.004	0.000	0.000	0.000	0.000
30	A	215	HIS	0	0.012	0.008	17.261	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	216	ILE	0	-0.011	-0.007	13.665	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	217	PRO	0	-0.008	-0.013	16.953	0.006	0.006	0.000	0.000	0.000	0.000
33	A	218	GLY	0	0.004	0.005	16.932	0.049	0.049	0.000	0.000	0.000	0.000
34	A	219	ASP	-1	-0.786	-0.833	15.915	0.305	0.305	0.000	0.000	0.000	0.000
35	A	220	ASN	0	-0.020	-0.027	18.352	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	221	SER	0	-0.030	-0.025	17.804	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	222	ILE	0	-0.028	-0.001	20.122	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	223	TYR	0	-0.008	-0.034	14.483	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	224	VAL	0	-0.023	-0.011	19.397	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	225	THR	0	0.035	0.021	19.202	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	226	LYS	1	0.909	0.951	21.025	0.013	0.013	0.000	0.000	0.000	0.000
42	A	227	ILE	0	0.056	0.043	21.019	0.004	0.004	0.000	0.000	0.000	0.000
43	A	228	ILE	0	-0.072	-0.043	24.120	0.000	0.000	0.000	0.000	0.000	0.000
44	A	229	ASP	-1	-0.774	-0.882	27.340	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	230	GLY	0	0.042	0.024	28.306	0.006	0.006	0.000	0.000	0.000	0.000
46	A	231	GLY	0	-0.052	-0.032	29.460	0.003	0.003	0.000	0.000	0.000	0.000
47	A	232	ALA	0	0.006	0.009	29.330	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	233	ALA	0	0.035	0.013	24.567	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	234	GLN	0	-0.047	-0.033	24.679	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	235	LYS	1	0.894	0.941	25.625	0.037	0.037	0.000	0.000	0.000	0.000
51	A	236	ASP	-1	-0.809	-0.867	24.759	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	237	GLY	0	0.023	0.022	22.889	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	238	ARG	1	0.790	0.881	20.519	0.066	0.066	0.000	0.000	0.000	0.000
54	A	239	LEU	0	-0.012	-0.003	19.363	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	240	GLN	0	-0.043	-0.049	16.494	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	241	VAL	0	-0.023	-0.012	17.118	0.018	0.018	0.000	0.000	0.000	0.000
57	A	242	GLY	0	0.020	0.014	14.498	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	243	ASP	-1	-0.797	-0.880	14.778	-0.050	-0.050	0.000	0.000	0.000	0.000
59	A	244	ARG	1	0.897	0.940	13.806	-0.266	-0.266	0.000	0.000	0.000	0.000
60	A	245	LEU	0	-0.052	-0.030	17.552	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	246	LEU	0	0.015	0.002	16.916	0.017	0.017	0.000	0.000	0.000	0.000
62	A	247	MET	0	-0.007	0.007	21.041	0.001	0.001	0.000	0.000	0.000	0.000
63	A	248	VAL	0	0.010	0.008	24.622	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	249	ASN	0	-0.034	-0.029	27.803	0.000	0.000	0.000	0.000	0.000	0.000
65	A	250	ASN	0	0.006	-0.012	28.654	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	251	TYR	0	0.019	0.021	29.036	0.004	0.004	0.000	0.000	0.000	0.000
67	A	252	SER	0	0.016	-0.002	24.492	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	253	LEU	0	-0.011	-0.022	23.389	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	254	GLU	-1	-0.948	-0.969	20.311	0.133	0.133	0.000	0.000	0.000	0.000
70	A	255	GLU	-1	-0.862	-0.927	21.208	0.182	0.182	0.000	0.000	0.000	0.000
71	A	256	VAL	0	-0.009	0.026	24.064	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	257	THR	0	-0.003	-0.038	26.404	0.008	0.008	0.000	0.000	0.000	0.000
73	A	258	HIS	0	-0.050	-0.018	25.989	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	259	GLU	-1	-0.849	-0.945	28.326	0.063	0.063	0.000	0.000	0.000	0.000
75	A	260	GLU	-1	-0.814	-0.870	30.418	0.064	0.064	0.000	0.000	0.000	0.000
76	A	261	ALA	0	0.033	0.024	27.085	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	262	VAL	0	-0.036	-0.026	29.107	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	263	ALA	0	-0.035	-0.015	31.222	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	264	ILE	0	0.013	0.004	29.316	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	265	LEU	0	-0.012	-0.012	27.150	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	266	LYS	1	0.891	0.959	31.584	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	267	ASN	0	-0.025	0.006	34.960	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	268	THR	0	-0.048	-0.019	31.973	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	269	SER	0	0.035	0.010	35.296	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	270	GLU	-1	-0.920	-0.969	36.378	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	271	VAL	0	-0.017	-0.002	33.592	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	272	VAL	0	0.006	-0.007	29.328	0.004	0.004	0.000	0.000	0.000	0.000
88	A	273	TYR	0	0.036	0.015	28.049	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	274	LEU	0	0.015	0.016	24.363	0.009	0.009	0.000	0.000	0.000	0.000
90	A	275	LYS	1	0.832	0.907	20.564	0.001	0.001	0.000	0.000	0.000	0.000
91	A	276	VAL	0	-0.012	-0.016	18.118	0.015	0.015	0.000	0.000	0.000	0.000
92	A	277	GLY	0	0.063	0.014	15.378	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	278	LYS	1	0.823	0.896	13.889	0.137	0.137	0.000	0.000	0.000	0.000
94	A	279	PRO	0	0.004	0.014	9.379	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	280	THR	0	-0.029	-0.019	7.662	-0.098	-0.098	0.000	0.000	0.000	0.000
96	A	281	THR	0	-0.005	-0.026	2.927	-2.134	-1.051	2.306	-0.765	-2.624	0.005
97	A	282	ILE	0	-0.076	-0.035	2.548	-1.649	0.066	0.529	-0.808	-1.435	0.002
98	A	283	TYR	0	0.020	0.011	3.194	-3.755	-1.027	0.185	-0.957	-1.956	-0.006

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