FMO DATABASE

FMODB ID: 2N9NR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-502416.125512
FMO2-HF: Nuclear repulsion	471572.75586
FMO2-HF: Total energy	-30843.369652
FMO2-MP2: Total energy	-30932.695982

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.
-40.6	-39.614	14.53	-7.709	-7.806	0.08

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 : 0.085 / q_NPA : 0.052

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	0.010	0.013	3.423	-2.382	0.375	0.017	-1.294	-1.480	0.005
4	A	10	LYS	1	0.819	0.899	1.757	-35.523	-37.462	14.514	-6.387	-6.188	0.075
5	A	11	SER	0	0.050	0.020	4.760	-2.036	-1.868	-0.001	-0.028	-0.138	0.000
6	A	12	LEU	0	0.017	0.017	6.258	0.314	0.314	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.933	0.964	7.667	-0.841	-0.841	0.000	0.000	0.000	0.000
8	A	14	THR	0	0.025	0.013	8.672	-0.076	-0.076	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.013	0.016	10.747	0.009	0.009	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.018	-0.001	12.928	0.109	0.109	0.000	0.000	0.000	0.000
11	A	17	ASN	0	-0.080	-0.051	15.482	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.939	0.968	16.389	0.214	0.214	0.000	0.000	0.000	0.000
13	A	19	ILE	0	-0.077	-0.027	18.473	0.073	0.073	0.000	0.000	0.000	0.000
14	A	20	VAL	0	-0.004	0.018	14.878	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.024	0.010	17.539	0.025	0.025	0.000	0.000	0.000	0.000
16	A	22	VAL	0	-0.034	-0.029	16.720	0.017	0.017	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.844	0.933	18.466	-0.065	-0.065	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.030	0.021	19.141	0.073	0.073	0.000	0.000	0.000	0.000
19	A	25	LYS	1	0.897	0.929	18.861	-0.566	-0.566	0.000	0.000	0.000	0.000
20	A	26	ASP	-1	-0.881	-0.898	22.331	0.228	0.228	0.000	0.000	0.000	0.000
21	A	27	GLY	0	-0.008	-0.008	24.073	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.017	-0.023	25.105	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.835	-0.928	22.557	0.048	0.048	0.000	0.000	0.000	0.000
24	A	30	TYR	0	-0.033	-0.033	22.104	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.011	0.018	21.467	0.003	0.003	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.048	0.006	21.544	0.020	0.020	0.000	0.000	0.000	0.000
27	A	33	LYS	1	0.787	0.896	20.279	0.009	0.009	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.031	0.028	12.667	0.069	0.069	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.800	-0.884	17.314	0.261	0.261	0.000	0.000	0.000	0.000
30	A	36	GLN	0	-0.007	-0.013	14.699	0.051	0.051	0.000	0.000	0.000	0.000
31	A	37	THR	0	0.033	0.015	10.390	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	38	ASP	-1	-0.773	-0.888	10.246	1.956	1.956	0.000	0.000	0.000	0.000
33	A	39	GLY	0	-0.010	0.000	7.656	0.334	0.334	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.051	-0.031	8.689	0.158	0.158	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.044	-0.029	8.098	-0.425	-0.425	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.008	-0.012	11.454	-0.466	-0.466	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.020	0.003	12.743	0.118	0.118	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.012	0.009	15.575	-0.077	-0.077	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.021	0.003	17.688	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	46	ARG	1	0.878	0.933	20.459	-0.167	-0.167	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.932	-0.974	23.593	0.109	0.109	0.000	0.000	0.000	0.000
42	A	48	CYS	0	-0.037	0.007	23.415	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	49	THR	0	-0.035	-0.024	25.436	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.766	-0.895	26.006	0.147	0.147	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.042	-0.006	24.546	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.956	0.983	28.939	-0.049	-0.049	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.842	-0.909	25.732	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	54	GLY	0	-0.026	-0.003	26.556	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	55	THR	0	-0.051	-0.021	28.079	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	56	SER	0	-0.012	-0.016	27.549	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.930	-0.961	29.174	0.009	0.009	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.058	-0.046	30.978	0.013	0.013	0.000	0.000	0.000	0.000
53	A	59	VAL	0	0.010	0.015	31.390	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.031	0.016	31.069	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.882	0.941	29.193	-0.087	-0.087	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.022	-0.035	27.059	0.011	0.011	0.000	0.000	0.000	0.000
57	A	63	GLY	0	-0.042	-0.004	28.107	0.015	0.015	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.851	0.889	23.346	-0.276	-0.276	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.015	0.020	22.428	0.005	0.005	0.000	0.000	0.000	0.000
60	A	66	LEU	0	-0.002	0.000	18.573	0.034	0.034	0.000	0.000	0.000	0.000
61	A	67	ILE	0	0.015	0.007	18.034	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.955	0.976	17.479	-0.608	-0.608	0.000	0.000	0.000	0.000
63	A	69	GLY	0	0.078	0.018	14.590	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	70	SER	0	-0.020	-0.019	15.367	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.053	-0.031	16.992	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.022	0.028	14.550	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	73	LEU	0	-0.050	-0.007	15.918	0.049	0.049	0.000	0.000	0.000	0.000
68	A	74	PHE	0	-0.014	-0.016	14.187	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	75	ILE	0	0.019	-0.002	11.790	0.064	0.064	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.033	-0.015	13.099	-0.120	-0.120	0.000	0.000	0.000	0.000
71	A	77	VAL	0	-0.013	-0.022	10.157	0.103	0.103	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.888	-0.932	12.372	-0.918	-0.918	0.000	0.000	0.000	0.000
73	A	79	TYR	0	0.052	0.021	15.232	0.012	0.012	0.000	0.000	0.000	0.000
74	A	80	GLU	-1	-0.778	-0.892	18.374	-0.130	-0.130	0.000	0.000	0.000	0.000
75	A	81	THR	0	-0.042	-0.018	17.545	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	82	VAL	0	0.006	0.015	19.758	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	83	MET	0	-0.038	-0.018	22.274	0.041	0.041	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.040	-0.018	22.785	0.030	0.030	0.000	0.000	0.000	0.000

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