FMO DATABASE

FMODB ID: LL589

Calculation Name: 2R39-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R39

Chain ID: A

ChEMBL ID:

UniProt ID: Q87KC5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	112
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-864551.158506
FMO2-HF: Nuclear repulsion	820835.04163
FMO2-HF: Total energy	-43716.116876
FMO2-MP2: Total energy	-43844.972789

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:376:ACE )

Summations of interaction energy for fragment #1(A:376:ACE )

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.
0.605	1.425	-0.004	-0.319	-0.497	0

Interaction energy analysis for fragmet #1(A:376:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.011

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].
3	A	378	ASP	-1	-0.896	-0.924	3.877	-0.118	0.702	-0.004	-0.319	-0.497
4	A	379	PRO	0	0.019	0.012	6.499	-0.045	-0.045	0.000	0.000	0.000
5	A	380	ALA	0	0.040	0.023	9.441	0.071	0.071	0.000	0.000	0.000
6	A	381	GLY	0	-0.030	-0.029	10.617	-0.113	-0.113	0.000	0.000	0.000
7	A	382	MET	0	0.027	0.025	12.940	0.064	0.064	0.000	0.000	0.000
8	A	383	SER	0	-0.066	-0.026	15.562	-0.016	-0.016	0.000	0.000	0.000
9	A	384	VAL	0	0.049	0.020	18.231	0.016	0.016	0.000	0.000	0.000
10	A	385	ILE	0	-0.013	0.002	21.722	-0.002	-0.002	0.000	0.000	0.000
11	A	386	ARG	1	0.908	0.967	24.927	0.070	0.070	0.000	0.000	0.000
12	A	387	ASP	-1	-0.870	-0.899	27.837	-0.086	-0.086	0.000	0.000	0.000
13	A	388	ARG	1	0.963	0.972	30.939	0.070	0.070	0.000	0.000	0.000
14	A	389	ASN	0	-0.053	-0.031	32.978	0.007	0.007	0.000	0.000	0.000
15	A	390	GLN	0	0.012	0.017	31.994	0.003	0.003	0.000	0.000	0.000
16	A	391	LEU	0	0.009	-0.008	36.593	0.003	0.003	0.000	0.000	0.000
17	A	392	PHE	0	-0.040	-0.025	36.914	0.003	0.003	0.000	0.000	0.000
18	A	393	ARG	1	0.940	0.965	39.853	0.044	0.044	0.000	0.000	0.000
19	A	394	VAL	0	0.070	0.055	41.415	0.000	0.000	0.000	0.000	0.000
20	A	395	ASN	0	-0.095	-0.064	43.282	0.000	0.000	0.000	0.000	0.000
21	A	396	SER	0	-0.010	0.008	43.655	0.002	0.002	0.000	0.000	0.000
22	A	397	ALA	0	0.060	0.034	41.094	0.002	0.002	0.000	0.000	0.000
23	A	398	GLY	0	-0.033	-0.007	43.121	0.000	0.000	0.000	0.000	0.000
24	A	399	GLU	-1	-0.764	-0.809	38.581	-0.031	-0.031	0.000	0.000	0.000
25	A	400	VAL	0	-0.046	-0.032	37.726	-0.001	-0.001	0.000	0.000	0.000
26	A	401	GLU	-1	-0.837	-0.911	35.643	-0.047	-0.047	0.000	0.000	0.000
27	A	402	ASN	0	-0.078	-0.041	31.835	-0.002	-0.002	0.000	0.000	0.000
28	A	403	THR	0	-0.014	-0.045	31.843	0.001	0.001	0.000	0.000	0.000
29	A	404	TYR	0	0.005	-0.037	26.413	-0.001	-0.001	0.000	0.000	0.000
30	A	405	THR	0	-0.013	-0.002	25.092	0.004	0.004	0.000	0.000	0.000
31	A	406	LEU	0	-0.001	0.004	21.598	-0.011	-0.011	0.000	0.000	0.000
32	A	407	LYS	1	0.935	0.978	18.927	0.222	0.222	0.000	0.000	0.000
33	A	408	VAL	0	0.027	0.009	17.128	-0.019	-0.019	0.000	0.000	0.000
34	A	409	ILE	0	-0.063	-0.023	13.742	0.000	0.000	0.000	0.000	0.000
35	A	410	ASN	0	0.053	0.063	14.442	-0.072	-0.072	0.000	0.000	0.000
36	A	411	LYS	1	0.854	0.924	9.327	0.932	0.932	0.000	0.000	0.000
37	A	412	THR	0	-0.003	-0.012	10.724	-0.040	-0.040	0.000	0.000	0.000
38	A	413	GLN	0	-0.029	-0.037	12.518	-0.023	-0.023	0.000	0.000	0.000
39	A	414	GLN	0	-0.017	-0.011	15.328	0.037	0.037	0.000	0.000	0.000
40	A	415	VAL	0	0.047	0.033	17.001	-0.025	-0.025	0.000	0.000	0.000
41	A	416	GLN	0	-0.027	-0.004	14.873	0.032	0.032	0.000	0.000	0.000
42	A	417	GLU	-1	-0.958	-0.983	18.523	-0.049	-0.049	0.000	0.000	0.000
43	A	418	TYR	0	-0.036	-0.032	14.637	-0.007	-0.007	0.000	0.000	0.000
44	A	419	ASN	0	0.024	0.018	19.766	0.005	0.005	0.000	0.000	0.000
45	A	420	LEU	0	-0.064	-0.037	20.190	-0.013	-0.013	0.000	0.000	0.000
46	A	421	ASP	-1	-0.886	-0.931	22.211	-0.035	-0.035	0.000	0.000	0.000
47	A	422	VAL	0	0.007	-0.013	23.230	-0.010	-0.010	0.000	0.000	0.000
48	A	423	LYS	1	0.916	0.968	21.545	0.022	0.022	0.000	0.000	0.000
49	A	424	GLY	0	0.028	-0.007	25.780	-0.005	-0.005	0.000	0.000	0.000
50	A	425	LEU	0	-0.022	0.001	28.204	0.001	0.001	0.000	0.000	0.000
51	A	426	ASN	0	-0.022	-0.019	31.493	0.001	0.001	0.000	0.000	0.000
52	A	427	ASP	-1	-0.885	-0.942	34.259	-0.020	-0.020	0.000	0.000	0.000
53	A	428	VAL	0	-0.047	-0.039	30.913	-0.003	-0.003	0.000	0.000	0.000
54	A	429	SER	0	-0.058	-0.065	34.326	0.002	0.002	0.000	0.000	0.000
55	A	430	TRP	0	-0.012	-0.024	24.686	-0.002	-0.002	0.000	0.000	0.000
56	A	431	TYR	0	-0.053	-0.032	31.821	0.003	0.003	0.000	0.000	0.000
57	A	432	GLY	0	0.053	0.009	30.204	-0.005	-0.005	0.000	0.000	0.000
58	A	433	LYS	1	0.910	0.952	26.237	0.078	0.078	0.000	0.000	0.000
59	A	434	GLN	0	0.041	0.041	26.240	-0.001	-0.001	0.000	0.000	0.000
60	A	435	THR	0	0.064	0.025	24.259	-0.002	-0.002	0.000	0.000	0.000
61	A	436	ILE	0	-0.119	-0.061	20.639	0.001	0.001	0.000	0.000	0.000
62	A	437	GLN	0	0.043	0.019	22.457	-0.003	-0.003	0.000	0.000	0.000
63	A	438	VAL	0	-0.046	-0.019	18.761	-0.003	-0.003	0.000	0.000	0.000
64	A	439	GLU	-1	-0.841	-0.946	19.698	-0.115	-0.115	0.000	0.000	0.000
65	A	440	PRO	0	-0.012	0.000	16.921	-0.028	-0.028	0.000	0.000	0.000
66	A	441	GLY	0	-0.006	0.004	16.094	0.009	0.009	0.000	0.000	0.000
67	A	442	GLU	-1	-0.910	-0.933	17.034	-0.146	-0.146	0.000	0.000	0.000
68	A	443	VAL	0	-0.039	-0.035	18.034	-0.025	-0.025	0.000	0.000	0.000
69	A	444	LEU	0	0.007	0.009	20.148	0.025	0.025	0.000	0.000	0.000
70	A	445	ASN	0	-0.029	-0.030	21.993	-0.022	-0.022	0.000	0.000	0.000
71	A	446	LEU	0	-0.022	-0.027	22.881	0.014	0.014	0.000	0.000	0.000
72	A	447	PRO	0	-0.015	0.017	26.063	0.000	0.000	0.000	0.000	0.000
73	A	448	MET	0	-0.042	-0.014	26.767	0.001	0.001	0.000	0.000	0.000
74	A	449	SER	0	-0.062	-0.046	30.017	-0.001	-0.001	0.000	0.000	0.000
75	A	450	LEU	0	-0.016	0.007	28.100	0.001	0.001	0.000	0.000	0.000
76	A	451	GLY	0	0.048	0.018	32.407	0.000	0.000	0.000	0.000	0.000
77	A	452	ALA	0	0.040	0.031	35.044	0.001	0.001	0.000	0.000	0.000
78	A	453	ASP	-1	-0.783	-0.896	36.968	-0.020	-0.020	0.000	0.000	0.000
79	A	454	PRO	0	-0.045	-0.043	39.750	0.000	0.000	0.000	0.000	0.000
80	A	455	ASP	-1	-0.898	-0.943	41.076	-0.016	-0.016	0.000	0.000	0.000
81	A	456	LYS	1	0.853	0.930	39.170	0.016	0.016	0.000	0.000	0.000
82	A	457	LEU	0	-0.076	-0.015	35.382	0.000	0.000	0.000	0.000	0.000
83	A	458	ASN	0	0.008	0.001	34.500	0.002	0.002	0.000	0.000	0.000
84	A	459	SER	0	-0.017	-0.015	35.560	0.001	0.001	0.000	0.000	0.000
85	A	460	ALA	0	0.016	0.014	36.953	-0.002	-0.002	0.000	0.000	0.000
86	A	461	ILE	0	-0.021	-0.006	31.566	-0.004	-0.004	0.000	0.000	0.000
87	A	462	THR	0	0.009	0.013	30.241	0.004	0.004	0.000	0.000	0.000
88	A	463	THR	0	-0.025	-0.016	25.311	-0.007	-0.007	0.000	0.000	0.000
89	A	464	ILE	0	-0.005	0.012	25.607	0.005	0.005	0.000	0.000	0.000
90	A	465	GLN	0	0.015	-0.003	18.959	-0.002	-0.002	0.000	0.000	0.000
91	A	466	PHE	0	0.009	0.002	21.130	0.008	0.008	0.000	0.000	0.000
92	A	467	ILE	0	-0.009	-0.015	17.800	-0.009	-0.009	0.000	0.000	0.000
93	A	468	LEU	0	-0.007	0.005	14.705	0.005	0.005	0.000	0.000	0.000
94	A	469	THR	0	0.026	0.001	16.130	0.004	0.004	0.000	0.000	0.000
95	A	470	ASP	-1	-0.792	-0.881	14.029	-0.134	-0.134	0.000	0.000	0.000
96	A	471	LYS	1	1.021	0.983	15.167	0.021	0.021	0.000	0.000	0.000
97	A	472	SER	0	-0.072	-0.019	16.383	0.020	0.020	0.000	0.000	0.000
98	A	473	ASN	0	-0.064	-0.045	11.345	0.035	0.035	0.000	0.000	0.000
99	A	474	GLU	-1	-1.014	-0.995	11.880	0.115	0.115	0.000	0.000	0.000
100	A	475	PHE	0	-0.006	-0.010	8.099	0.016	0.016	0.000	0.000	0.000
101	A	476	THR	0	-0.042	-0.061	12.285	-0.008	-0.008	0.000	0.000	0.000
102	A	477	ILE	0	-0.004	0.016	11.677	-0.027	-0.027	0.000	0.000	0.000
103	A	478	GLU	-1	-0.861	-0.900	13.726	-0.042	-0.042	0.000	0.000	0.000
104	A	479	VAL	0	-0.044	-0.022	15.817	-0.022	-0.022	0.000	0.000	0.000
105	A	480	GLU	-1	-0.883	-0.921	18.255	-0.043	-0.043	0.000	0.000	0.000
106	A	481	SER	0	0.000	-0.004	21.241	-0.007	-0.007	0.000	0.000	0.000
107	A	482	ARG	1	0.820	0.877	24.518	0.069	0.069	0.000	0.000	0.000
108	A	483	PHE	0	0.027	0.038	28.256	-0.004	-0.004	0.000	0.000	0.000
109	A	484	ILE	0	-0.049	-0.038	31.301	0.003	0.003	0.000	0.000	0.000
110	A	485	LYS	1	0.932	0.982	34.415	0.024	0.024	0.000	0.000	0.000
111	A	486	LYS	1	0.943	0.966	38.092	0.031	0.031	0.000	0.000	0.000
112	A	487	LEU	-1	-0.896	-0.948	40.948	-0.027	-0.027	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:376:ACE )