FMO DATABASE

FMODB ID: 1NK2Z

Calculation Name: 3EJ9-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJ9

Chain ID: C

ChEMBL ID:

UniProt ID: Q9EV84

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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-318231.651397
FMO2-HF: Nuclear repulsion	293117.406102
FMO2-HF: Total energy	-25114.245295
FMO2-MP2: Total energy	-25186.25099

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(C:1:PRO)

Summations of interaction energy for fragment #1(C:1:PRO)

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.
-15.531	-7.864	10.728	-6.937	-11.459	-0.044

Interaction energy analysis for fragmet #1(C:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.001

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	C	3	ILE	0	-0.001	0.004	3.335	-0.552	1.412	0.000	-0.807	-1.158	0.003
4	C	4	SER	0	0.003	-0.002	6.138	-0.184	-0.184	0.000	0.000	0.000	0.000
5	C	5	CYS	0	-0.022	-0.015	9.854	0.056	0.056	0.000	0.000	0.000	0.000
6	C	6	ASP	-1	-0.812	-0.865	12.815	0.065	0.065	0.000	0.000	0.000	0.000
7	C	7	MET	0	-0.066	-0.038	16.225	0.003	0.003	0.000	0.000	0.000	0.000
8	C	8	ARG	1	0.911	0.950	19.016	0.004	0.004	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.040	0.026	21.960	-0.011	-0.011	0.000	0.000	0.000	0.000
10	C	10	GLY	0	0.019	0.001	23.792	0.006	0.006	0.000	0.000	0.000	0.000
11	C	11	ARG	1	0.845	0.935	20.150	0.058	0.058	0.000	0.000	0.000	0.000
12	C	12	THR	0	0.038	0.012	22.631	-0.008	-0.008	0.000	0.000	0.000	0.000
13	C	13	ASP	-1	-0.781	-0.889	20.593	-0.205	-0.205	0.000	0.000	0.000	0.000
14	C	14	GLU	-1	-0.908	-0.959	19.595	-0.246	-0.246	0.000	0.000	0.000	0.000
15	C	15	GLN	0	0.010	0.004	19.614	-0.014	-0.014	0.000	0.000	0.000	0.000
16	C	16	LYS	1	0.851	0.922	16.511	0.123	0.123	0.000	0.000	0.000	0.000
17	C	17	ARG	1	0.884	0.928	14.997	0.217	0.217	0.000	0.000	0.000	0.000
18	C	18	ALA	0	0.008	0.011	15.114	-0.048	-0.048	0.000	0.000	0.000	0.000
19	C	19	LEU	0	-0.017	-0.005	12.761	-0.019	-0.019	0.000	0.000	0.000	0.000
20	C	20	SER	0	-0.019	-0.008	10.703	-0.033	-0.033	0.000	0.000	0.000	0.000
21	C	21	ALA	0	0.013	0.008	10.178	-0.109	-0.109	0.000	0.000	0.000	0.000
22	C	22	GLY	0	-0.032	-0.020	11.533	-0.053	-0.053	0.000	0.000	0.000	0.000
23	C	23	LEU	0	0.021	-0.005	7.939	0.007	0.007	0.000	0.000	0.000	0.000
24	C	24	LEU	0	-0.005	-0.003	6.430	0.001	0.001	0.000	0.000	0.000	0.000
25	C	25	ARG	1	0.942	0.986	7.325	0.204	0.204	0.000	0.000	0.000	0.000
26	C	26	VAL	0	-0.013	-0.014	8.742	-0.023	-0.023	0.000	0.000	0.000	0.000
27	C	27	ILE	0	0.020	0.010	2.604	-0.592	0.058	0.618	-0.262	-1.006	0.000
28	C	28	SER	0	-0.053	-0.022	4.686	-0.267	-0.123	-0.001	-0.010	-0.132	0.000
29	C	29	GLU	-1	-0.963	-0.973	6.025	-0.346	-0.346	0.000	0.000	0.000	0.000
30	C	30	ALA	0	-0.069	-0.029	6.449	0.094	0.094	0.000	0.000	0.000	0.000
31	C	31	THR	0	-0.057	-0.060	2.620	-2.087	-0.695	0.531	-0.691	-1.232	-0.005
32	C	32	GLY	0	0.012	0.021	5.136	0.047	0.077	-0.001	-0.002	-0.027	0.000
33	C	33	GLU	-1	-0.871	-0.921	2.281	-2.813	-2.212	1.873	-0.697	-1.777	-0.003
34	C	34	PRO	0	0.021	0.033	4.807	0.076	0.135	-0.001	-0.007	-0.051	0.000
35	C	35	ARG	1	0.971	0.948	5.044	0.175	0.252	-0.001	-0.001	-0.075	0.000
36	C	36	GLU	-1	-0.980	-0.981	6.787	-1.116	-1.116	0.000	0.000	0.000	0.000
37	C	37	ASN	0	-0.063	-0.029	3.457	0.234	0.747	0.016	-0.188	-0.342	0.000
38	C	38	ILE	0	-0.023	-0.002	2.018	-10.097	-8.474	7.689	-4.111	-5.202	-0.039
39	C	39	PHE	0	-0.014	0.002	3.499	1.841	2.455	0.005	-0.161	-0.457	0.000
40	C	40	PHE	0	-0.008	-0.027	5.514	0.113	0.113	0.000	0.000	0.000	0.000
41	C	41	VAL	0	-0.022	-0.004	7.960	0.086	0.086	0.000	0.000	0.000	0.000
42	C	42	ILE	0	0.005	0.001	11.328	0.072	0.072	0.000	0.000	0.000	0.000
43	C	43	ARG	1	0.850	0.905	11.788	-0.148	-0.148	0.000	0.000	0.000	0.000
44	C	44	GLU	-1	-0.815	-0.917	16.882	-0.093	-0.093	0.000	0.000	0.000	0.000
45	C	45	GLY	0	0.024	0.016	20.294	0.010	0.010	0.000	0.000	0.000	0.000
46	C	46	SER	0	0.035	0.005	23.430	-0.009	-0.009	0.000	0.000	0.000	0.000
47	C	47	GLY	0	-0.006	-0.015	25.726	0.007	0.007	0.000	0.000	0.000	0.000
48	C	48	ILE	0	0.029	0.014	27.043	0.006	0.006	0.000	0.000	0.000	0.000
49	C	49	ASN	0	-0.024	-0.006	24.311	0.006	0.006	0.000	0.000	0.000	0.000
50	C	50	PHE	0	-0.053	-0.010	19.329	0.010	0.010	0.000	0.000	0.000	0.000
51	C	51	VAL	0	0.030	0.015	24.072	-0.007	-0.007	0.000	0.000	0.000	0.000
52	C	52	GLN	0	-0.029	-0.016	20.998	0.017	0.017	0.000	0.000	0.000	0.000
53	C	53	HIS	0	0.022	0.001	25.462	-0.001	-0.001	0.000	0.000	0.000	0.000
54	C	54	GLY	0	-0.006	0.007	27.806	-0.003	-0.003	0.000	0.000	0.000	0.000
55	C	55	GLU	-1	-0.942	-0.958	29.281	0.028	0.028	0.000	0.000	0.000	0.000
56	C	56	HIS	0	-0.053	-0.046	28.443	0.004	0.004	0.000	0.000	0.000	0.000
57	C	57	LEU	0	-0.040	-0.013	23.928	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	58	PRO	0	0.041	0.030	28.323	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	59	ASP	-1	-0.811	-0.913	28.477	-0.008	-0.008	0.000	0.000	0.000	0.000
60	C	60	TYR	0	-0.066	-0.044	25.071	-0.004	-0.004	0.000	0.000	0.000	0.000
61	C	61	VAL	0	0.023	0.011	27.608	-0.002	-0.002	0.000	0.000	0.000	0.000
62	C	62	PRO	0	-0.037	-0.014	27.612	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	63	GLY	0	0.014	0.020	27.856	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:PRO)