FMO DATABASE

FMODB ID: 76Q6K

Calculation Name: 4XQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XQ3

Chain ID: A

ChEMBL ID:

UniProt ID: D0KRQ0

Base Structure: X-ray

Registration Date: 2023-09-23

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-501666.857652
FMO2-HF: Nuclear repulsion	470824.197311
FMO2-HF: Total energy	-30842.660342
FMO2-MP2: Total energy	-30931.979765

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:7:ASN)

Summations of interaction energy for fragment #1(A:7:ASN)

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.
-17.793	-18.95	16.579	-6.392	-9.029	0.049

Interaction energy analysis for fragmet #1(A:7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.024

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	9	LEU	0	0.035	0.025	2.907	-4.086	-0.754	0.250	-1.575	-2.006	0.009
4	A	10	LYS	1	0.851	0.925	1.993	-12.181	-16.927	16.330	-4.776	-6.808	0.040
5	A	11	SER	0	0.026	0.016	4.331	-1.253	-0.996	-0.001	-0.041	-0.215	0.000
6	A	12	LEU	0	0.023	0.020	6.115	0.166	0.166	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.935	0.960	6.814	-0.538	-0.538	0.000	0.000	0.000	0.000
8	A	14	THR	0	0.013	0.013	9.026	-0.129	-0.129	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.017	0.016	10.639	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.013	0.003	12.707	0.105	0.105	0.000	0.000	0.000	0.000
11	A	17	ASN	0	-0.102	-0.065	15.243	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.962	0.984	16.151	0.175	0.175	0.000	0.000	0.000	0.000
13	A	19	ILE	0	-0.077	-0.038	18.295	0.075	0.075	0.000	0.000	0.000	0.000
14	A	20	VAL	0	0.002	0.021	14.454	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.031	0.010	17.474	0.012	0.012	0.000	0.000	0.000	0.000
16	A	22	VAL	0	-0.032	-0.031	16.051	0.039	0.039	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.989	1.031	18.157	-0.167	-0.167	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.034	0.017	18.939	0.081	0.081	0.000	0.000	0.000	0.000
19	A	25	LYS	1	0.924	0.951	19.468	-0.555	-0.555	0.000	0.000	0.000	0.000
20	A	26	ASP	-1	-0.884	-0.877	22.358	0.249	0.249	0.000	0.000	0.000	0.000
21	A	27	GLY	0	-0.046	-0.035	24.039	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.009	-0.046	25.108	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.896	-0.970	22.363	0.117	0.117	0.000	0.000	0.000	0.000
24	A	30	TYR	0	-0.034	-0.019	21.682	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.022	0.023	20.985	0.011	0.011	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.045	0.006	21.075	0.011	0.011	0.000	0.000	0.000	0.000
27	A	33	LYS	1	0.861	0.943	19.872	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.029	0.028	12.210	0.058	0.058	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.867	-0.931	16.941	0.250	0.250	0.000	0.000	0.000	0.000
30	A	36	GLN	0	-0.005	-0.016	14.437	0.038	0.038	0.000	0.000	0.000	0.000
31	A	37	THR	0	-0.005	-0.006	10.118	0.133	0.133	0.000	0.000	0.000	0.000
32	A	38	ASP	-1	-0.787	-0.909	10.045	1.594	1.594	0.000	0.000	0.000	0.000
33	A	39	GLY	0	-0.011	-0.010	7.469	0.361	0.361	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.016	-0.001	8.515	0.240	0.240	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.040	-0.025	8.268	-0.360	-0.360	0.000	0.000	0.000	0.000
36	A	42	ASN	0	0.006	0.017	11.081	-0.363	-0.363	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.009	0.005	12.245	0.090	0.090	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.017	0.019	15.209	-0.081	-0.081	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.014	0.003	17.161	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	46	ARG	1	0.929	0.967	20.077	-0.162	-0.162	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.965	-0.989	23.226	0.112	0.112	0.000	0.000	0.000	0.000
42	A	48	CYS	0	-0.031	0.009	23.345	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	49	THR	0	-0.024	-0.023	25.008	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.816	-0.948	25.536	0.168	0.168	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.052	-0.003	24.588	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.994	0.992	28.714	-0.073	-0.073	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.890	-0.934	25.833	0.037	0.037	0.000	0.000	0.000	0.000
48	A	54	GLY	0	-0.038	-0.009	26.573	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	55	THR	0	-0.060	-0.029	28.104	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	56	SER	0	-0.012	-0.009	27.476	0.008	0.008	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.933	-0.965	29.183	0.023	0.023	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.098	-0.062	30.553	0.013	0.013	0.000	0.000	0.000	0.000
53	A	59	VAL	0	0.005	0.029	30.917	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.023	0.009	30.584	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.930	0.961	29.520	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	62	TYR	0	0.015	-0.002	26.723	0.006	0.006	0.000	0.000	0.000	0.000
57	A	63	GLY	0	-0.048	-0.006	27.725	0.012	0.012	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.882	0.916	22.970	-0.243	-0.243	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.013	0.016	21.997	0.002	0.002	0.000	0.000	0.000	0.000
60	A	66	LEU	0	0.007	0.004	18.168	0.031	0.031	0.000	0.000	0.000	0.000
61	A	67	ILE	0	0.002	0.002	17.558	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.936	0.964	17.111	-0.570	-0.570	0.000	0.000	0.000	0.000
63	A	69	GLY	0	0.094	0.010	14.235	-0.062	-0.062	0.000	0.000	0.000	0.000
64	A	70	SER	0	-0.041	-0.020	14.972	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.074	-0.048	16.640	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.021	0.026	13.965	-0.087	-0.087	0.000	0.000	0.000	0.000
67	A	73	LEU	0	-0.042	-0.010	15.930	0.050	0.050	0.000	0.000	0.000	0.000
68	A	74	PHE	0	-0.011	-0.018	14.196	0.023	0.023	0.000	0.000	0.000	0.000
69	A	75	ILE	0	0.019	-0.001	11.529	0.045	0.045	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.046	-0.048	13.099	-0.096	-0.096	0.000	0.000	0.000	0.000
71	A	77	VAL	0	-0.031	-0.001	10.168	0.081	0.081	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.868	-0.921	13.117	-0.715	-0.715	0.000	0.000	0.000	0.000
73	A	79	TYR	0	0.053	0.022	15.298	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	80	GLU	-1	-0.863	-0.937	18.279	-0.097	-0.097	0.000	0.000	0.000	0.000
75	A	81	THR	0	-0.041	-0.025	17.952	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	82	VAL	0	-0.013	0.003	19.980	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	83	MET	0	-0.034	-0.018	22.452	0.037	0.037	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.032	-0.005	22.791	0.033	0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ASN)