FMO DATABASE

FMODB ID: JLYY9

Calculation Name: 2J4U-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J4U

Chain ID: S

ChEMBL ID:

UniProt ID: P06996

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-204098.942473
FMO2-HF: Nuclear repulsion	184963.546225
FMO2-HF: Total energy	-19135.396249
FMO2-MP2: Total energy	-19187.542858

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(S:1001:ALA)

Summations of interaction energy for fragment #1(S:1001:ALA)

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.
-0.779	3.033	1.288	-1.946	-3.151	0.001

Interaction energy analysis for fragmet #1(S:1001:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.075 / q_NPA : 0.039

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	S	1003	LYS	1	0.961	0.967	3.891	0.290	2.632	-0.013	-1.307	-1.022	0.003
4	S	1004	LYS	1	0.934	0.967	5.999	1.195	1.281	-0.001	-0.005	-0.080	0.000
5	S	1005	SER	0	0.017	0.009	6.926	0.227	0.227	0.000	0.000	0.000	0.000
6	S	1006	VAL	0	0.040	0.040	6.114	-0.085	-0.085	0.000	0.000	0.000	0.000
7	S	1007	ARG	1	0.918	0.965	2.865	-0.939	-0.290	0.200	-0.164	-0.684	0.000
8	S	1008	TRP	0	-0.002	-0.023	5.579	-0.157	-0.157	0.000	0.000	0.000	0.000
9	S	1045	CYS	0	-0.092	-0.048	6.672	-0.023	-0.023	0.000	0.000	0.000	0.000
10	S	1010	THR	0	0.012	0.015	8.677	-0.067	-0.067	0.000	0.000	0.000	0.000
11	S	1011	THR	0	-0.070	-0.041	11.462	0.029	0.029	0.000	0.000	0.000	0.000
12	S	1012	SER	0	0.051	0.014	13.892	0.026	0.026	0.000	0.000	0.000	0.000
13	S	1013	PRO	0	0.014	0.013	15.755	-0.010	-0.010	0.000	0.000	0.000	0.000
14	S	1014	ALA	0	0.023	-0.005	18.066	0.024	0.024	0.000	0.000	0.000	0.000
15	S	1015	GLU	-1	-0.758	-0.843	15.466	0.353	0.353	0.000	0.000	0.000	0.000
16	S	1016	SER	0	0.040	0.004	12.929	-0.039	-0.039	0.000	0.000	0.000	0.000
17	S	1017	LYS	1	0.956	0.998	15.827	-0.192	-0.192	0.000	0.000	0.000	0.000
18	S	1018	LYS	1	0.901	0.931	16.834	-0.261	-0.261	0.000	0.000	0.000	0.000
19	S	1019	CYS	0	-0.061	-0.013	5.835	0.459	0.459	0.000	0.000	0.000	0.000
20	S	1020	ALA	0	0.054	0.038	12.769	0.005	0.005	0.000	0.000	0.000	0.000
21	S	1021	GLN	0	0.113	0.047	13.821	-0.052	-0.052	0.000	0.000	0.000	0.000
22	S	1022	TRP	0	0.018	0.005	12.201	-0.055	-0.055	0.000	0.000	0.000	0.000
23	S	1023	GLN	0	0.058	0.036	9.192	-0.056	-0.056	0.000	0.000	0.000	0.000
24	S	1024	ARG	1	0.794	0.896	8.889	-0.181	-0.181	0.000	0.000	0.000	0.000
25	S	1025	ARG	1	0.888	0.935	14.153	-0.051	-0.051	0.000	0.000	0.000	0.000
26	S	1026	MET	0	-0.009	0.052	10.491	-0.036	-0.036	0.000	0.000	0.000	0.000
27	S	1027	LYS	1	0.961	0.991	12.019	0.105	0.105	0.000	0.000	0.000	0.000
28	S	1028	LYS	1	0.901	0.929	14.351	0.012	0.012	0.000	0.000	0.000	0.000
29	S	1029	VAL	0	0.134	0.074	17.842	0.007	0.007	0.000	0.000	0.000	0.000
30	S	1030	ARG	1	0.938	0.940	13.473	0.352	0.352	0.000	0.000	0.000	0.000
31	S	1031	GLY	0	0.115	0.082	13.402	-0.014	-0.014	0.000	0.000	0.000	0.000
32	S	1032	PRO	0	0.021	0.001	13.913	-0.055	-0.055	0.000	0.000	0.000	0.000
33	S	1033	SER	0	-0.067	-0.040	9.102	0.009	0.009	0.000	0.000	0.000	0.000
34	S	1034	VAL	0	0.050	0.023	7.784	-0.087	-0.087	0.000	0.000	0.000	0.000
35	S	1035	THR	0	-0.008	-0.031	3.466	-0.028	0.258	0.008	-0.077	-0.217	0.000
36	S	1037	VAL	0	0.018	-0.005	2.405	-0.546	-0.093	1.095	-0.392	-1.155	-0.002
37	S	1038	LYN	0	-0.028	0.006	5.363	-0.177	-0.181	-0.001	-0.001	0.007	0.000
38	S	1039	LYS	1	0.872	0.936	5.928	-1.054	-1.054	0.000	0.000	0.000	0.000
39	S	1040	THR	0	0.072	0.030	10.599	-0.064	-0.064	0.000	0.000	0.000	0.000
40	S	1041	SER	0	0.007	-0.010	13.418	-0.064	-0.064	0.000	0.000	0.000	0.000
41	S	1042	ARG	1	0.938	0.941	13.108	-0.233	-0.233	0.000	0.000	0.000	0.000
42	S	1043	PHE	0	-0.015	0.018	13.963	-0.011	-0.011	0.000	0.000	0.000	0.000
43	S	1044	GLU	-1	-0.759	-0.866	9.790	0.665	0.665	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:1001:ALA)