FMO DATABASE

FMODB ID: NN8YQ

Calculation Name: 1W0T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W0T

Chain ID: A

ChEMBL ID:

UniProt ID: P54274

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	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	52
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-315878.378375
FMO2-HF: Nuclear repulsion	293254.007116
FMO2-HF: Total energy	-22624.371259
FMO2-MP2: Total energy	-22690.759715

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:379:LYS)

Summations of interaction energy for fragment #1(A:379:LYS)

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.
83.946	82.89	10.25	-4.456	-4.739	-0.053

Interaction energy analysis for fragmet #1(A:379:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.009 / q_NPA : 0.998

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	381	GLN	0	-0.030	-0.029	1.872	-36.628	-37.926	10.249	-4.386	-4.566	-0.053
4	A	382	ALA	0	0.048	0.031	3.954	9.002	9.244	0.001	-0.070	-0.173	0.000
5	A	383	TRP	0	0.020	-0.003	6.887	-0.730	-0.730	0.000	0.000	0.000	0.000
6	A	384	LEU	0	0.040	0.033	8.284	0.370	0.370	0.000	0.000	0.000	0.000
7	A	385	TRP	0	0.047	0.012	11.740	1.935	1.935	0.000	0.000	0.000	0.000
8	A	386	GLU	-1	-0.811	-0.918	14.089	-20.274	-20.274	0.000	0.000	0.000	0.000
9	A	387	GLU	-1	-0.761	-0.859	10.307	-28.424	-28.424	0.000	0.000	0.000	0.000
10	A	388	ASP	-1	-0.699	-0.827	14.924	-19.359	-19.359	0.000	0.000	0.000	0.000
11	A	389	LYS	1	0.921	0.980	16.839	15.292	15.292	0.000	0.000	0.000	0.000
12	A	390	ASN	0	-0.031	-0.010	17.042	1.836	1.836	0.000	0.000	0.000	0.000
13	A	391	LEU	0	-0.018	-0.002	16.873	0.763	0.763	0.000	0.000	0.000	0.000
14	A	392	ARG	1	0.939	0.950	19.201	16.053	16.053	0.000	0.000	0.000	0.000
15	A	393	SER	0	-0.089	-0.059	22.329	0.944	0.944	0.000	0.000	0.000	0.000
16	A	394	GLY	0	0.038	0.013	22.639	0.548	0.548	0.000	0.000	0.000	0.000
17	A	395	VAL	0	-0.025	-0.021	22.750	0.466	0.466	0.000	0.000	0.000	0.000
18	A	396	ARG	1	0.915	0.960	25.309	12.165	12.165	0.000	0.000	0.000	0.000
19	A	397	LYS	1	0.898	0.976	27.145	11.598	11.598	0.000	0.000	0.000	0.000
20	A	398	TYR	0	-0.004	-0.018	25.188	0.347	0.347	0.000	0.000	0.000	0.000
21	A	399	GLY	0	0.075	0.055	28.124	0.199	0.199	0.000	0.000	0.000	0.000
22	A	400	GLU	-1	-0.808	-0.899	24.877	-12.833	-12.833	0.000	0.000	0.000	0.000
23	A	401	GLY	0	0.046	0.020	24.403	0.390	0.390	0.000	0.000	0.000	0.000
24	A	402	ASN	0	-0.024	-0.002	24.158	-0.272	-0.272	0.000	0.000	0.000	0.000
25	A	403	TRP	0	0.029	0.000	19.202	-0.411	-0.411	0.000	0.000	0.000	0.000
26	A	404	SER	0	0.027	-0.009	19.966	-0.788	-0.788	0.000	0.000	0.000	0.000
27	A	405	LYS	1	0.991	1.007	21.007	11.073	11.073	0.000	0.000	0.000	0.000
28	A	406	ILE	0	-0.019	0.016	19.890	-0.095	-0.095	0.000	0.000	0.000	0.000
29	A	407	LEU	0	-0.016	-0.027	14.739	-0.235	-0.235	0.000	0.000	0.000	0.000
30	A	408	LEU	0	0.001	0.006	18.649	-0.338	-0.338	0.000	0.000	0.000	0.000
31	A	409	HIS	0	-0.048	-0.014	21.278	0.882	0.882	0.000	0.000	0.000	0.000
32	A	410	TYR	0	-0.015	-0.001	19.656	0.426	0.426	0.000	0.000	0.000	0.000
33	A	411	LYS	1	0.926	0.975	12.340	22.514	22.514	0.000	0.000	0.000	0.000
34	A	412	PHE	0	0.058	0.017	13.257	-0.248	-0.248	0.000	0.000	0.000	0.000
35	A	413	ASN	0	-0.043	-0.029	8.359	2.272	2.272	0.000	0.000	0.000	0.000
36	A	414	ASN	0	0.010	0.013	7.424	-1.630	-1.630	0.000	0.000	0.000	0.000
37	A	415	ARG	1	0.813	0.891	7.717	31.148	31.148	0.000	0.000	0.000	0.000
38	A	416	THR	0	0.100	0.036	10.704	1.340	1.340	0.000	0.000	0.000	0.000
39	A	417	SER	0	0.049	0.015	13.280	-0.578	-0.578	0.000	0.000	0.000	0.000
40	A	418	VAL	0	0.035	0.015	14.160	0.382	0.382	0.000	0.000	0.000	0.000
41	A	419	MET	0	0.025	0.027	7.397	-0.371	-0.371	0.000	0.000	0.000	0.000
42	A	420	LEU	0	-0.018	0.007	13.301	-0.127	-0.127	0.000	0.000	0.000	0.000
43	A	421	LYS	1	0.868	0.943	16.298	16.992	16.992	0.000	0.000	0.000	0.000
44	A	422	ASP	-1	-0.789	-0.892	14.855	-17.265	-17.265	0.000	0.000	0.000	0.000
45	A	423	ARG	1	0.790	0.874	13.128	20.837	20.837	0.000	0.000	0.000	0.000
46	A	424	TRP	0	0.030	-0.003	15.646	0.215	0.215	0.000	0.000	0.000	0.000
47	A	425	ARG	1	0.874	0.932	17.376	16.552	16.552	0.000	0.000	0.000	0.000
48	A	426	THR	0	-0.060	-0.034	14.823	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	427	MET	0	-0.037	-0.018	17.401	0.311	0.311	0.000	0.000	0.000	0.000
50	A	428	LYS	1	0.839	0.901	19.485	12.703	12.703	0.000	0.000	0.000	0.000
51	A	429	LYS	1	0.930	0.981	20.325	15.241	15.241	0.000	0.000	0.000	0.000
52	A	430	LEU	0	-0.010	0.007	16.759	-0.143	-0.143	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:379:LYS)