FMO DATABASE

FMODB ID: 3N2JL

Calculation Name: 3KJL-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KJL

Chain ID: A

ChEMBL ID:

UniProt ID: Q03067

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-533607.904706
FMO2-HF: Nuclear repulsion	498485.798117
FMO2-HF: Total energy	-35122.106589
FMO2-MP2: Total energy	-35224.982664

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:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

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.
-0.082	0.878	-0.006	-0.425	-0.528	-0.001

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.013

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

Sort

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	8	LEU	0	0.046	0.030	3.825	0.616	1.576	-0.006	-0.425	-0.528	-0.001
4	A	9	LYS	1	0.978	0.982	5.061	-0.495	-0.495	0.000	0.000	0.000	0.000
5	A	10	SER	0	0.010	-0.006	6.417	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	11	GLN	0	0.075	0.046	9.159	-0.038	-0.038	0.000	0.000	0.000	0.000
7	A	12	ILE	0	-0.002	-0.002	6.645	0.051	0.051	0.000	0.000	0.000	0.000
8	A	13	GLN	0	-0.040	-0.019	10.904	0.025	0.025	0.000	0.000	0.000	0.000
9	A	14	GLN	0	0.032	0.008	13.351	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	15	TYR	0	0.086	0.041	13.503	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.032	-0.015	15.417	0.008	0.008	0.000	0.000	0.000	0.000
12	A	17	VAL	0	-0.029	-0.003	17.915	0.007	0.007	0.000	0.000	0.000	0.000
13	A	18	GLU	-1	-0.859	-0.931	18.681	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	19	SER	0	-0.015	-0.019	20.326	0.000	0.000	0.000	0.000	0.000	0.000
15	A	20	GLY	0	0.010	0.006	22.035	0.002	0.002	0.000	0.000	0.000	0.000
16	A	21	ASN	0	-0.003	0.000	23.899	0.006	0.006	0.000	0.000	0.000	0.000
17	A	22	TYR	0	-0.001	0.002	25.032	0.000	0.000	0.000	0.000	0.000	0.000
18	A	23	GLU	-1	-0.975	-0.992	25.806	0.023	0.023	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.024	0.013	27.854	0.000	0.000	0.000	0.000	0.000	0.000
20	A	25	ILE	0	-0.046	-0.016	28.633	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	26	SER	0	-0.057	-0.026	30.876	0.001	0.001	0.000	0.000	0.000	0.000
22	A	27	ASN	0	-0.065	-0.044	31.095	0.002	0.002	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.804	-0.893	34.208	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	29	LEU	0	0.011	0.004	35.674	0.000	0.000	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.921	0.953	34.535	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	31	ALA	0	0.001	0.008	38.867	0.001	0.001	0.000	0.000	0.000	0.000
27	A	32	ARG	1	0.901	0.958	38.901	0.004	0.004	0.000	0.000	0.000	0.000
28	A	33	LEU	0	0.051	0.034	40.780	0.000	0.000	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.043	-0.027	43.142	0.000	0.000	0.000	0.000	0.000	0.000
30	A	35	GLN	0	-0.053	-0.029	43.732	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-0.836	-0.912	45.651	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	37	GLY	0	-0.001	0.011	48.177	0.000	0.000	0.000	0.000	0.000	0.000
33	A	38	TRP	0	-0.011	-0.011	43.084	0.000	0.000	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.001	-0.017	43.939	0.000	0.000	0.000	0.000	0.000	0.000
35	A	40	ASP	-1	-0.964	-0.987	46.857	0.001	0.001	0.000	0.000	0.000	0.000
36	A	41	LYS	1	1.027	1.020	50.424	0.005	0.005	0.000	0.000	0.000	0.000
37	A	42	VAL	0	0.011	0.018	46.131	0.000	0.000	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.904	0.948	47.366	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	44	ASP	-1	-0.905	-0.951	50.389	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.052	-0.021	50.115	0.000	0.000	0.000	0.000	0.000	0.000
41	A	46	THR	0	0.004	-0.008	49.301	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	47	LYS	1	0.951	0.962	51.651	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	48	SER	0	0.000	0.008	54.823	0.000	0.000	0.000	0.000	0.000	0.000
44	A	49	GLU	-1	-0.875	-0.957	52.776	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	50	MET	0	-0.114	-0.056	50.902	0.000	0.000	0.000	0.000	0.000	0.000
46	A	51	ASN	0	-0.044	-0.008	55.743	0.000	0.000	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.049	-0.007	58.025	0.000	0.000	0.000	0.000	0.000	0.000
48	A	53	ASN	0	-0.023	-0.014	54.728	0.000	0.000	0.000	0.000	0.000	0.000
49	A	54	GLU	-1	-0.907	-0.941	57.869	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	55	SER	0	-0.088	-0.031	54.041	0.001	0.001	0.000	0.000	0.000	0.000
51	A	56	THR	0	0.059	0.018	53.313	0.000	0.000	0.000	0.000	0.000	0.000
52	A	57	ASN	0	-0.030	-0.026	48.194	0.000	0.000	0.000	0.000	0.000	0.000
53	A	58	PHE	0	0.080	0.025	41.328	0.000	0.000	0.000	0.000	0.000	0.000
54	A	59	THR	0	0.033	0.010	44.836	0.000	0.000	0.000	0.000	0.000	0.000
55	A	60	GLN	0	-0.012	-0.019	46.418	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	61	ILE	0	0.017	0.024	49.290	0.000	0.000	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.016	0.000	42.069	0.000	0.000	0.000	0.000	0.000	0.000
58	A	63	SER	0	-0.039	-0.022	46.516	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.027	-0.002	47.759	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	65	VAL	0	0.015	0.009	47.403	0.000	0.000	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.950	-0.971	41.628	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	67	PRO	0	-0.003	-0.012	45.730	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	68	LYS	1	1.007	1.003	46.984	0.008	0.008	0.000	0.000	0.000	0.000
64	A	69	ALA	0	0.025	0.005	45.658	0.000	0.000	0.000	0.000	0.000	0.000
65	A	70	LEU	0	-0.039	-0.025	41.120	0.000	0.000	0.000	0.000	0.000	0.000
66	A	71	GLU	-1	-0.939	-0.966	44.558	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	72	MET	0	-0.130	-0.057	47.511	0.001	0.001	0.000	0.000	0.000	0.000
68	A	73	VAL	0	-0.089	-0.021	42.357	0.001	0.001	0.000	0.000	0.000	0.000
69	A	74	SER	0	0.020	0.007	45.672	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	75	ASP	-1	-0.840	-0.937	45.222	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	76	SER	0	-0.008	-0.013	44.749	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.071	-0.038	40.964	0.000	0.000	0.000	0.000	0.000	0.000
73	A	78	ARG	1	0.956	0.987	40.482	0.018	0.018	0.000	0.000	0.000	0.000
74	A	79	GLU	-1	-0.821	-0.919	39.483	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	80	THR	0	-0.098	-0.047	38.819	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	81	VAL	0	0.025	0.004	35.108	0.000	0.000	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.006	-0.001	34.860	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	83	LYS	1	0.889	0.931	34.687	0.009	0.009	0.000	0.000	0.000	0.000
79	A	84	GLN	0	-0.008	0.000	31.865	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	85	ILE	0	-0.023	-0.023	30.336	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	86	ARG	1	0.914	0.980	29.890	0.023	0.023	0.000	0.000	0.000	0.000
82	A	87	GLU	-1	-0.892	-0.935	29.737	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	88	PHE	0	-0.025	-0.009	23.639	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	89	LEU	0	-0.034	-0.028	25.187	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	90	GLU	-1	-0.965	-0.990	25.524	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.954	-0.962	21.444	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.062	-0.017	20.156	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	93	NME	0	-0.083	-0.040	21.627	-0.017	-0.017	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )