FMO DATABASE

FMODB ID: VR3K1

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	OptH
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	-608543.15885
FMO2-HF: Nuclear repulsion	572168.637297
FMO2-HF: Total energy	-36374.521554
FMO2-MP2: Total energy	-36480.507832

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.
-19.949	-13.093	6.459	-5.199	-8.116	0.011

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 : 0.046 / q_NPA : 0.012

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	-0.022	-0.002	3.907	-1.165	0.740	-0.016	-0.962	-0.928	0.000
4	A	1	MET	0	0.014	0.030	4.625	0.129	0.321	-0.001	-0.005	-0.186	0.000
5	A	2	PHE	0	-0.028	-0.005	7.121	0.142	0.142	0.000	0.000	0.000	0.000
6	A	3	ILE	0	-0.005	-0.010	10.906	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	4	THR	0	-0.029	-0.003	13.389	0.058	0.058	0.000	0.000	0.000	0.000
8	A	5	THR	0	0.025	0.015	17.178	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	6	GLU	-1	-0.925	-0.959	20.386	-0.087	-0.087	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.031	0.004	19.857	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	8	ILE	0	-0.012	-0.009	16.422	0.007	0.007	0.000	0.000	0.000	0.000
12	A	9	ASN	0	-0.034	-0.016	20.560	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.022	-0.001	19.056	0.011	0.011	0.000	0.000	0.000	0.000
14	A	11	GLY	0	0.001	0.013	20.767	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	12	TYR	0	0.002	-0.003	16.815	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	13	THR	0	-0.027	-0.003	16.823	0.014	0.014	0.000	0.000	0.000	0.000
17	A	14	ILE	0	0.012	-0.016	16.494	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.887	0.963	12.418	0.555	0.555	0.000	0.000	0.000	0.000
19	A	16	ASP	-1	-0.828	-0.914	15.445	-0.181	-0.181	0.000	0.000	0.000	0.000
20	A	17	VAL	0	-0.089	-0.036	15.915	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	18	VAL	0	-0.012	0.009	13.032	0.005	0.005	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.850	-0.955	16.203	-0.135	-0.135	0.000	0.000	0.000	0.000
23	A	20	ALA	0	-0.083	-0.045	14.526	0.012	0.012	0.000	0.000	0.000	0.000
24	A	21	THR	0	-0.002	0.006	16.651	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	22	SER	0	-0.055	-0.020	17.047	0.007	0.007	0.000	0.000	0.000	0.000
26	A	23	SER	0	0.004	-0.003	19.032	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	24	LEU	0	-0.008	0.011	21.407	0.005	0.005	0.000	0.000	0.000	0.000
28	A	25	MET	0	-0.020	-0.007	23.961	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	26	LEU	0	0.005	0.008	27.459	0.003	0.003	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.026	0.010	29.975	0.000	0.000	0.000	0.000	0.000	0.000
31	A	28	SER	0	-0.015	-0.031	32.512	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.921	-0.963	34.593	0.009	0.009	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.918	-0.957	31.074	0.010	0.010	0.000	0.000	0.000	0.000
34	A	31	ILE	0	-0.024	-0.018	32.466	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	32	ASP	-1	-0.872	-0.939	34.685	0.001	0.001	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.873	0.959	30.144	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	34	TYR	0	0.006	-0.014	29.392	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	35	ASN	0	0.042	0.012	27.546	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	36	MET	0	-0.003	0.003	25.082	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	37	PHE	0	-0.016	-0.020	23.666	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	38	ASP	-1	-0.932	-0.948	21.887	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	39	GLN	0	0.004	-0.016	19.136	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	40	LEU	0	0.008	0.022	17.858	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	41	PHE	0	0.053	0.018	17.962	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.926	-0.958	15.015	-0.097	-0.097	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.946	-0.985	13.527	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.017	-0.012	13.385	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	45	LYS	1	0.965	0.978	12.529	0.115	0.115	0.000	0.000	0.000	0.000
49	A	46	GLN	0	0.013	0.011	7.453	-0.106	-0.106	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.874	0.943	8.736	0.005	0.005	0.000	0.000	0.000	0.000
51	A	48	LEU	0	-0.047	-0.007	10.443	0.015	0.015	0.000	0.000	0.000	0.000
52	A	49	LYS	1	0.977	0.985	6.918	0.541	0.541	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.882	0.957	2.536	-11.290	-10.341	4.749	-2.107	-3.590	0.033
54	A	51	LYS	1	0.920	0.951	6.751	0.274	0.274	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.029	0.014	8.121	0.002	0.002	0.000	0.000	0.000	0.000
56	A	53	ASP	-1	-0.908	-0.961	2.836	-6.552	-2.742	1.727	-2.125	-3.412	-0.022
57	A	54	LEU	0	-0.050	-0.032	5.560	0.052	0.052	0.000	0.000	0.000	0.000
58	A	55	LEU	0	-0.026	-0.005	8.375	-0.055	-0.055	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.983	-0.981	7.339	-1.184	-1.184	0.000	0.000	0.000	0.000
60	A	57	GLY	0	-0.010	-0.002	8.257	0.166	0.166	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.822	-0.917	7.318	-0.886	-0.886	0.000	0.000	0.000	0.000
62	A	59	GLY	0	-0.028	-0.038	8.578	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	60	ILE	0	-0.055	-0.013	10.273	0.036	0.036	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.008	-0.006	13.056	0.039	0.039	0.000	0.000	0.000	0.000
65	A	62	GLY	0	-0.007	0.004	16.726	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.065	-0.026	16.143	0.005	0.005	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.892	0.948	18.787	0.134	0.134	0.000	0.000	0.000	0.000
68	A	65	TYR	0	0.027	-0.008	16.908	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	66	ASN	0	-0.014	0.007	22.354	0.004	0.004	0.000	0.000	0.000	0.000
70	A	67	THR	0	-0.013	-0.015	23.999	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.812	-0.878	26.389	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	69	VAL	0	0.007	-0.002	28.275	0.001	0.001	0.000	0.000	0.000	0.000
73	A	70	VAL	0	-0.004	0.008	29.447	0.000	0.000	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.919	-0.962	31.958	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	72	VAL	0	-0.044	-0.037	33.646	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.069	-0.045	36.482	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	GLY	0	0.032	0.020	39.883	0.001	0.001	0.000	0.000	0.000	0.000
78	A	75	ALA	0	0.033	0.023	37.594	0.001	0.001	0.000	0.000	0.000	0.000
79	A	76	PRO	0	0.030	0.024	33.629	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.891	0.951	31.472	0.003	0.003	0.000	0.000	0.000	0.000
81	A	78	PHE	0	0.010	-0.006	27.067	0.002	0.002	0.000	0.000	0.000	0.000
82	A	79	LEU	0	0.003	0.033	25.813	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	80	VAL	0	0.020	-0.005	23.658	0.001	0.001	0.000	0.000	0.000	0.000
84	A	81	VAL	0	0.055	0.032	19.874	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	82	HIS	1	0.759	0.832	20.548	0.060	0.060	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.041	0.018	17.826	0.002	0.002	0.000	0.000	0.000	0.000
87	A	84	TYR	0	-0.011	-0.011	17.699	0.000	0.000	0.000	0.000	0.000	0.000
88	A	85	GLY	0	0.057	0.024	16.839	0.007	0.007	0.000	0.000	0.000	0.000
89	A	86	THR	0	-0.001	0.001	16.788	0.006	0.006	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.007	0.012	10.819	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	88	ILE	0	-0.034	-0.015	12.867	0.039	0.039	0.000	0.000	0.000	0.000
92	A	89	LEU	0	0.004	-0.002	10.745	-0.099	-0.099	0.000	0.000	0.000	0.000
93	A	90	ILE	0	-0.049	-0.029	13.097	0.066	0.066	0.000	0.000	0.000	0.000
94	A	91	ASP	-1	-0.952	-0.966	15.241	-0.188	-0.188	0.000	0.000	0.000	0.000

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