FMO DATABASE

FMODB ID: 1416Z

Calculation Name: 3QKB-A-Xray372

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: 2023-06-20

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608922.986202
FMO2-HF: Nuclear repulsion	572547.922576
FMO2-HF: Total energy	-36375.063626
FMO2-MP2: Total energy	-36481.067399

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:-2:PHE)

Summations of interaction energy for fragment #1(A:-2: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.
-19.568	-14.457	8.492	-5.7	-7.905	0.014

Interaction energy analysis for fragmet #1(A:-2:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.016

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

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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	0	GLY	0	-0.027	-0.006	3.907	-1.254	0.676	-0.016	-0.990	-0.925	0.000
4	A	1	MET	0	0.004	0.026	4.974	0.239	0.239	0.000	0.000	0.000	0.000
5	A	2	PHE	0	-0.019	-0.001	7.134	0.142	0.142	0.000	0.000	0.000	0.000
6	A	3	ILE	0	0.002	-0.010	10.919	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	4	THR	0	-0.025	-0.004	13.407	0.060	0.060	0.000	0.000	0.000	0.000
8	A	5	THR	0	0.006	0.012	17.200	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	6	GLU	-1	-0.845	-0.918	20.402	-0.103	-0.103	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.031	0.009	19.897	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	8	ILE	0	-0.010	-0.009	16.421	0.007	0.007	0.000	0.000	0.000	0.000
12	A	9	ASN	0	-0.032	-0.016	20.575	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.017	-0.001	19.065	0.011	0.011	0.000	0.000	0.000	0.000
14	A	11	GLY	0	0.006	0.014	20.781	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	12	TYR	0	-0.007	-0.010	16.889	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	13	THR	0	0.003	0.012	17.096	0.015	0.015	0.000	0.000	0.000	0.000
17	A	14	ILE	0	-0.005	-0.025	16.577	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.810	0.918	11.443	0.643	0.643	0.000	0.000	0.000	0.000
19	A	16	ASP	-1	-0.820	-0.914	15.498	-0.181	-0.181	0.000	0.000	0.000	0.000
20	A	17	VAL	0	-0.088	-0.033	15.955	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	18	VAL	0	-0.026	-0.004	12.918	0.008	0.008	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.827	-0.942	16.209	-0.141	-0.141	0.000	0.000	0.000	0.000
23	A	20	ALA	0	-0.045	-0.007	14.497	0.010	0.010	0.000	0.000	0.000	0.000
24	A	21	THR	0	0.008	0.014	16.628	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	SER	0	-0.048	-0.014	17.113	0.007	0.007	0.000	0.000	0.000	0.000
26	A	23	SER	0	0.027	0.006	19.059	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	24	LEU	0	-0.030	0.001	21.411	0.005	0.005	0.000	0.000	0.000	0.000
28	A	25	MET	0	-0.006	0.000	23.960	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	26	LEU	0	0.010	0.016	27.459	0.003	0.003	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.030	0.016	29.966	0.000	0.000	0.000	0.000	0.000	0.000
31	A	28	SER	0	-0.007	-0.020	32.492	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.888	-0.952	34.524	0.006	0.006	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.877	-0.931	31.317	0.007	0.007	0.000	0.000	0.000	0.000
34	A	31	ILE	0	-0.017	-0.009	32.458	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	32	ASP	-1	-0.830	-0.899	34.682	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.781	0.888	30.193	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	34	TYR	0	-0.001	-0.026	29.390	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	35	ASN	0	0.027	0.003	27.315	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	36	MET	0	0.006	0.013	25.102	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	37	PHE	0	-0.009	-0.020	23.655	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	38	ASP	-1	-0.924	-0.945	21.928	-0.035	-0.035	0.000	0.000	0.000	0.000
42	A	39	GLN	0	-0.006	-0.021	19.108	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	40	LEU	0	0.010	0.025	17.844	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	41	PHE	0	0.052	0.023	17.938	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.849	-0.922	15.104	-0.135	-0.135	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.868	-0.932	13.508	-0.082	-0.082	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.019	-0.010	13.382	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	45	LYS	1	0.877	0.933	12.503	0.123	0.123	0.000	0.000	0.000	0.000
49	A	46	GLN	0	0.023	0.011	7.483	-0.125	-0.125	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.819	0.897	8.711	0.006	0.006	0.000	0.000	0.000	0.000
51	A	48	LEU	0	-0.036	-0.003	10.420	0.011	0.011	0.000	0.000	0.000	0.000
52	A	49	LYS	1	0.935	0.964	6.846	0.646	0.646	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.846	0.917	2.263	-12.106	-12.122	6.612	-2.526	-4.070	0.037
54	A	51	LYS	1	0.886	0.933	6.731	0.327	0.327	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.023	0.008	8.350	0.009	0.009	0.000	0.000	0.000	0.000
56	A	53	ASP	-1	-0.889	-0.936	2.499	-5.772	-2.575	1.896	-2.184	-2.910	-0.023
57	A	54	LEU	0	-0.032	-0.025	5.588	0.097	0.097	0.000	0.000	0.000	0.000
58	A	55	LEU	0	-0.003	0.012	8.389	-0.043	-0.043	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.950	-0.959	7.332	-0.953	-0.953	0.000	0.000	0.000	0.000
60	A	57	GLY	0	-0.001	-0.002	8.346	0.159	0.159	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.832	-0.910	7.403	-0.890	-0.890	0.000	0.000	0.000	0.000
62	A	59	GLY	0	-0.016	-0.030	8.647	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	60	ILE	0	-0.055	-0.015	10.328	0.042	0.042	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.005	-0.001	13.092	0.037	0.037	0.000	0.000	0.000	0.000
65	A	62	GLY	0	-0.001	0.006	16.766	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.053	-0.017	16.390	0.007	0.007	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.820	0.900	18.795	0.144	0.144	0.000	0.000	0.000	0.000
68	A	65	TYR	0	0.030	-0.003	17.157	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	66	ASN	0	-0.015	0.004	22.352	0.003	0.003	0.000	0.000	0.000	0.000
70	A	67	THR	0	0.008	-0.001	23.985	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.825	-0.892	26.373	-0.053	-0.053	0.000	0.000	0.000	0.000
72	A	69	VAL	0	0.005	0.000	28.287	0.001	0.001	0.000	0.000	0.000	0.000
73	A	70	VAL	0	-0.014	0.000	29.349	0.001	0.001	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.908	-0.954	31.983	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	72	VAL	0	-0.046	-0.042	33.671	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.068	-0.046	36.494	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	GLY	0	0.036	0.024	39.888	0.001	0.001	0.000	0.000	0.000	0.000
78	A	75	ALA	0	0.031	0.027	37.660	0.001	0.001	0.000	0.000	0.000	0.000
79	A	76	PRO	0	0.034	0.023	33.521	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.845	0.917	31.658	0.005	0.005	0.000	0.000	0.000	0.000
81	A	78	PHE	0	0.006	-0.004	26.918	0.002	0.002	0.000	0.000	0.000	0.000
82	A	79	LEU	0	0.005	0.039	25.788	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	80	VAL	0	0.014	-0.013	23.653	0.001	0.001	0.000	0.000	0.000	0.000
84	A	81	VAL	0	0.040	0.027	20.049	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	82	HIS	1	0.762	0.830	20.505	0.067	0.067	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.038	0.018	17.821	0.002	0.002	0.000	0.000	0.000	0.000
87	A	84	TYR	0	-0.019	-0.015	17.707	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	85	GLY	0	0.054	0.024	16.852	0.006	0.006	0.000	0.000	0.000	0.000
89	A	86	THR	0	-0.006	-0.002	16.825	0.007	0.007	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.015	0.010	10.773	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	88	ILE	0	-0.029	-0.018	12.936	0.043	0.043	0.000	0.000	0.000	0.000
92	A	89	LEU	0	0.004	0.000	11.082	-0.106	-0.106	0.000	0.000	0.000	0.000
93	A	90	ILE	0	-0.029	-0.025	13.080	0.069	0.069	0.000	0.000	0.000	0.000
94	A	91	ASP	-1	-0.986	-0.984	15.233	-0.179	-0.179	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PHE)