FMO DATABASE

FMODB ID: J3629

Calculation Name: 3QKB-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKB

Chain ID: A

ChEMBL ID:

UniProt ID: Q03GF5

Base Structure: X-ray

Registration Date: 2021-09-07

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	96
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-613260.48158
FMO2-HF: Nuclear repulsion	576715.041399
FMO2-HF: Total energy	-36545.440181
FMO2-MP2: Total energy	-36651.965064

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:-3:ACE )

Summations of interaction energy for fragment #1(A:-3: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.
-0.227	0.548	-0.005	-0.356	-0.414	0

Interaction energy analysis for fragmet #1(A:-3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014

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	-1	GLN	0	-0.042	-0.032	3.848	1.277	2.052	-0.005	-0.356	-0.414
4	A	0	GLY	0	-0.023	-0.002	7.067	0.249	0.249	0.000	0.000	0.000
5	A	1	MET	0	0.016	0.029	9.111	-0.012	-0.012	0.000	0.000	0.000
6	A	2	PHE	0	-0.026	-0.005	11.248	0.117	0.117	0.000	0.000	0.000
7	A	3	ILE	0	-0.002	-0.009	14.964	-0.010	-0.010	0.000	0.000	0.000
8	A	4	THR	0	-0.032	-0.004	17.964	0.030	0.030	0.000	0.000	0.000
9	A	5	THR	0	0.026	0.015	21.678	0.001	0.001	0.000	0.000	0.000
10	A	6	GLU	-1	-0.925	-0.959	25.153	-0.108	-0.108	0.000	0.000	0.000
11	A	7	GLY	0	0.031	0.004	24.371	-0.016	-0.016	0.000	0.000	0.000
12	A	8	ILE	0	-0.010	-0.009	20.099	-0.001	-0.001	0.000	0.000	0.000
13	A	9	ASN	0	-0.035	-0.016	24.252	0.003	0.003	0.000	0.000	0.000
14	A	10	ALA	0	0.020	-0.002	22.025	0.001	0.001	0.000	0.000	0.000
15	A	11	GLY	0	0.000	0.012	23.253	0.003	0.003	0.000	0.000	0.000
16	A	12	TYR	0	0.006	-0.001	20.177	-0.018	-0.018	0.000	0.000	0.000
17	A	13	THR	0	-0.009	0.005	19.575	0.020	0.020	0.000	0.000	0.000
18	A	14	ILE	0	0.008	-0.018	20.125	-0.026	-0.026	0.000	0.000	0.000
19	A	15	LYS	1	0.887	0.963	15.788	0.332	0.332	0.000	0.000	0.000
20	A	16	ASP	-1	-0.828	-0.914	19.831	-0.153	-0.153	0.000	0.000	0.000
21	A	17	VAL	0	-0.092	-0.037	20.956	-0.021	-0.021	0.000	0.000	0.000
22	A	18	VAL	0	-0.009	0.009	18.351	-0.001	-0.001	0.000	0.000	0.000
23	A	19	GLU	-1	-0.851	-0.955	21.607	-0.144	-0.144	0.000	0.000	0.000
24	A	20	ALA	0	-0.082	-0.045	20.501	-0.006	-0.006	0.000	0.000	0.000
25	A	21	THR	0	-0.003	0.006	22.625	0.009	0.009	0.000	0.000	0.000
26	A	22	SER	0	-0.057	-0.021	23.436	-0.003	-0.003	0.000	0.000	0.000
27	A	23	SER	0	0.004	-0.002	25.470	0.003	0.003	0.000	0.000	0.000
28	A	24	LEU	0	-0.009	0.010	27.959	0.001	0.001	0.000	0.000	0.000
29	A	25	MET	0	-0.022	-0.008	30.444	0.002	0.002	0.000	0.000	0.000
30	A	26	LEU	0	0.010	0.009	33.942	0.001	0.001	0.000	0.000	0.000
31	A	27	ALA	0	0.024	0.009	36.287	0.002	0.002	0.000	0.000	0.000
32	A	28	SER	0	-0.013	-0.030	38.757	-0.002	-0.002	0.000	0.000	0.000
33	A	29	GLU	-1	-0.922	-0.962	40.480	-0.020	-0.020	0.000	0.000	0.000
34	A	30	ASP	-1	-0.918	-0.958	36.927	-0.027	-0.027	0.000	0.000	0.000
35	A	31	ILE	0	-0.021	-0.017	38.399	-0.003	-0.003	0.000	0.000	0.000
36	A	32	ASP	-1	-0.872	-0.939	40.713	-0.030	-0.030	0.000	0.000	0.000
37	A	33	LYS	1	0.872	0.958	35.673	0.026	0.026	0.000	0.000	0.000
38	A	34	TYR	0	0.006	-0.015	35.051	-0.004	-0.004	0.000	0.000	0.000
39	A	35	ASN	0	0.041	0.012	32.536	-0.003	-0.003	0.000	0.000	0.000
40	A	36	MET	0	0.000	0.004	30.549	-0.003	-0.003	0.000	0.000	0.000
41	A	37	PHE	0	-0.020	-0.022	29.372	-0.004	-0.004	0.000	0.000	0.000
42	A	38	ASP	-1	-0.929	-0.946	26.805	-0.079	-0.079	0.000	0.000	0.000
43	A	39	GLN	0	0.003	-0.016	24.504	-0.007	-0.007	0.000	0.000	0.000
44	A	40	LEU	0	0.010	0.022	23.545	-0.012	-0.012	0.000	0.000	0.000
45	A	41	PHE	0	0.051	0.018	23.922	-0.013	-0.013	0.000	0.000	0.000
46	A	42	ASP	-1	-0.926	-0.958	20.370	-0.152	-0.152	0.000	0.000	0.000
47	A	43	GLU	-1	-0.946	-0.985	19.305	-0.127	-0.127	0.000	0.000	0.000
48	A	44	ALA	0	-0.014	-0.011	19.457	-0.020	-0.020	0.000	0.000	0.000
49	A	45	LYS	1	0.968	0.979	18.000	0.156	0.156	0.000	0.000	0.000
50	A	46	GLN	0	0.008	0.008	12.783	-0.056	-0.056	0.000	0.000	0.000
51	A	47	LYS	1	0.871	0.941	14.840	0.085	0.085	0.000	0.000	0.000
52	A	48	LEU	0	-0.043	-0.005	16.386	-0.022	-0.022	0.000	0.000	0.000
53	A	49	LYS	1	0.975	0.984	12.422	0.382	0.382	0.000	0.000	0.000
54	A	50	LYS	1	0.872	0.955	7.894	0.710	0.710	0.000	0.000	0.000
55	A	51	LYS	1	0.927	0.953	12.528	0.172	0.172	0.000	0.000	0.000
56	A	52	ALA	0	0.028	0.014	13.520	0.010	0.010	0.000	0.000	0.000
57	A	53	ASP	-1	-0.900	-0.958	7.424	-1.644	-1.644	0.000	0.000	0.000
58	A	54	LEU	0	-0.054	-0.032	10.418	-0.006	-0.006	0.000	0.000	0.000
59	A	55	LEU	0	-0.027	-0.005	12.391	0.046	0.046	0.000	0.000	0.000
60	A	56	GLU	-1	-0.983	-0.981	10.452	-0.434	-0.434	0.000	0.000	0.000
61	A	57	GLY	0	-0.010	-0.002	11.981	0.067	0.067	0.000	0.000	0.000
62	A	58	ASP	-1	-0.824	-0.919	11.426	-0.721	-0.721	0.000	0.000	0.000
63	A	59	GLY	0	-0.027	-0.036	12.513	-0.047	-0.047	0.000	0.000	0.000
64	A	60	ILE	0	-0.059	-0.015	14.797	0.036	0.036	0.000	0.000	0.000
65	A	61	ILE	0	0.009	-0.005	18.040	0.015	0.015	0.000	0.000	0.000
66	A	62	GLY	0	-0.005	0.005	21.514	0.003	0.003	0.000	0.000	0.000
67	A	63	LEU	0	-0.066	-0.026	21.224	0.006	0.006	0.000	0.000	0.000
68	A	64	LYS	1	0.893	0.948	23.995	0.144	0.144	0.000	0.000	0.000
69	A	65	TYR	0	0.025	-0.008	22.396	-0.010	-0.010	0.000	0.000	0.000
70	A	66	ASN	0	-0.015	0.007	28.016	0.005	0.005	0.000	0.000	0.000
71	A	67	THR	0	-0.015	-0.015	30.014	-0.003	-0.003	0.000	0.000	0.000
72	A	68	GLU	-1	-0.812	-0.878	32.414	-0.072	-0.072	0.000	0.000	0.000
73	A	69	VAL	0	0.007	-0.001	34.387	-0.001	-0.001	0.000	0.000	0.000
74	A	70	VAL	0	-0.004	0.008	35.824	0.002	0.002	0.000	0.000	0.000
75	A	71	GLU	-1	-0.918	-0.961	38.357	-0.036	-0.036	0.000	0.000	0.000
76	A	72	VAL	0	-0.044	-0.037	40.327	0.000	0.000	0.000	0.000	0.000
77	A	73	ASN	0	-0.070	-0.046	43.097	0.001	0.001	0.000	0.000	0.000
78	A	74	GLY	0	0.032	0.021	46.422	0.001	0.001	0.000	0.000	0.000
79	A	75	ALA	0	0.033	0.023	43.962	0.001	0.001	0.000	0.000	0.000
80	A	76	PRO	0	0.030	0.025	39.831	-0.001	-0.001	0.000	0.000	0.000
81	A	77	LYS	1	0.892	0.952	38.073	0.030	0.030	0.000	0.000	0.000
82	A	78	PHE	0	0.006	-0.007	33.698	0.000	0.000	0.000	0.000	0.000
83	A	79	LEU	0	0.005	0.034	32.002	0.000	0.000	0.000	0.000	0.000
84	A	80	VAL	0	0.023	-0.004	30.025	-0.003	-0.003	0.000	0.000	0.000
85	A	81	VAL	0	0.050	0.030	25.923	0.001	0.001	0.000	0.000	0.000
86	A	82	HIS	1	0.764	0.834	26.611	0.087	0.087	0.000	0.000	0.000
87	A	83	GLY	0	0.040	0.017	23.726	0.003	0.003	0.000	0.000	0.000
88	A	84	TYR	0	-0.006	-0.008	23.257	-0.003	-0.003	0.000	0.000	0.000
89	A	85	GLY	0	0.056	0.024	22.200	0.004	0.004	0.000	0.000	0.000
90	A	86	THR	0	0.003	0.001	21.922	0.005	0.005	0.000	0.000	0.000
91	A	87	VAL	0	-0.012	0.010	15.731	-0.017	-0.017	0.000	0.000	0.000
92	A	88	ILE	0	-0.032	-0.013	17.474	0.029	0.029	0.000	0.000	0.000
93	A	89	LEU	0	0.006	-0.002	13.410	-0.057	-0.057	0.000	0.000	0.000
94	A	90	ILE	0	-0.043	-0.026	15.770	0.054	0.054	0.000	0.000	0.000
95	A	91	ASP	-1	-0.918	-0.947	17.281	-0.220	-0.220	0.000	0.000	0.000
96	A	92	NME	0	-0.060	-0.028	18.898	0.019	0.019	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:ACE )