FMO DATABASE

FMODB ID: N988Q

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	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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-202536.131672
FMO2-HF: Nuclear repulsion	183402.629136
FMO2-HF: Total energy	-19133.502536
FMO2-MP2: Total energy	-19186.025465

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.
-2.937	0.372	2.972	-2.39	-3.89	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 : 0.070 / q_NPA : 0.022

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	1.000	1.017	3.966	0.406	2.464	0.013	-1.121	-0.950	0.001
4	S	1004	LYS	1	0.935	0.955	6.302	0.937	0.937	0.000	0.000	0.000	0.000
5	S	1005	SER	0	0.008	0.009	7.378	0.063	0.063	0.000	0.000	0.000	0.000
6	S	1006	VAL	0	0.025	0.022	6.099	0.049	0.049	0.000	0.000	0.000	0.000
7	S	1007	ARG	1	0.959	0.962	2.331	-2.639	-2.258	1.008	-0.369	-1.021	0.000
8	S	1008	TRP	0	-0.010	0.007	6.003	-0.363	-0.363	0.000	0.000	0.000	0.000
9	S	1045	CYS	0	-0.158	-0.084	6.805	0.097	0.097	0.000	0.000	0.000	0.000
10	S	1010	THR	0	0.001	0.008	8.222	-0.029	-0.029	0.000	0.000	0.000	0.000
11	S	1011	THR	0	-0.020	-0.004	11.023	-0.037	-0.037	0.000	0.000	0.000	0.000
12	S	1012	SER	0	0.015	0.022	13.876	0.015	0.015	0.000	0.000	0.000	0.000
13	S	1013	PRO	0	0.025	0.021	16.208	-0.001	-0.001	0.000	0.000	0.000	0.000
14	S	1014	ALA	0	-0.008	-0.015	18.693	0.024	0.024	0.000	0.000	0.000	0.000
15	S	1015	GLU	-1	-0.803	-0.885	15.242	0.585	0.585	0.000	0.000	0.000	0.000
16	S	1016	SER	0	0.008	0.006	13.619	-0.033	-0.033	0.000	0.000	0.000	0.000
17	S	1017	LYS	1	0.926	0.976	16.514	-0.213	-0.213	0.000	0.000	0.000	0.000
18	S	1018	LYS	1	0.993	0.974	17.466	-0.292	-0.292	0.000	0.000	0.000	0.000
19	S	1019	CYS	0	-0.021	0.007	5.333	-0.345	-0.345	0.000	0.000	0.000	0.000
20	S	1020	ALA	0	0.025	-0.007	12.635	0.043	0.043	0.000	0.000	0.000	0.000
21	S	1021	GLN	0	0.025	-0.028	13.242	-0.012	-0.012	0.000	0.000	0.000	0.000
22	S	1022	TRP	0	0.065	0.035	12.562	-0.067	-0.067	0.000	0.000	0.000	0.000
23	S	1023	GLN	0	0.127	0.066	9.571	-0.046	-0.046	0.000	0.000	0.000	0.000
24	S	1024	ARG	1	0.791	0.899	9.220	-0.076	-0.076	0.000	0.000	0.000	0.000
25	S	1025	ARG	1	0.883	0.950	14.431	-0.054	-0.054	0.000	0.000	0.000	0.000
26	S	1026	MET	0	0.000	0.078	10.570	-0.022	-0.022	0.000	0.000	0.000	0.000
27	S	1027	LYS	1	0.937	0.976	12.086	0.254	0.254	0.000	0.000	0.000	0.000
28	S	1028	LYS	1	0.845	0.939	14.622	0.025	0.025	0.000	0.000	0.000	0.000
29	S	1029	VAL	0	0.158	0.064	18.124	0.009	0.009	0.000	0.000	0.000	0.000
30	S	1030	ARG	1	0.926	0.941	13.572	0.369	0.369	0.000	0.000	0.000	0.000
31	S	1031	GLY	0	0.159	0.106	13.741	0.001	0.001	0.000	0.000	0.000	0.000
32	S	1032	PRO	0	0.011	-0.024	13.824	-0.052	-0.052	0.000	0.000	0.000	0.000
33	S	1033	SER	0	-0.064	-0.049	9.118	0.023	0.023	0.000	0.000	0.000	0.000
34	S	1034	VAL	0	0.052	0.033	8.105	-0.011	-0.011	0.000	0.000	0.000	0.000
35	S	1035	THR	0	-0.021	-0.013	2.817	-0.030	0.450	0.125	-0.194	-0.410	-0.001
36	S	1037	VAL	0	-0.017	-0.012	2.110	-0.266	0.143	1.827	-0.698	-1.538	0.001
37	S	1038	LYN	0	0.068	0.027	5.283	-0.344	-0.363	-0.001	-0.008	0.029	0.000
38	S	1039	LYS	1	0.853	0.932	6.044	-1.445	-1.445	0.000	0.000	0.000	0.000
39	S	1040	THR	0	0.114	0.021	10.839	-0.068	-0.068	0.000	0.000	0.000	0.000
40	S	1041	SER	0	-0.060	-0.037	13.648	-0.072	-0.072	0.000	0.000	0.000	0.000
41	S	1042	ARG	1	1.077	1.027	12.802	-0.358	-0.358	0.000	0.000	0.000	0.000
42	S	1043	PHE	0	-0.049	0.004	12.819	0.065	0.065	0.000	0.000	0.000	0.000
43	S	1044	GLU	-1	-0.810	-0.913	8.974	0.973	0.973	0.000	0.000	0.000	0.000

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