FMO DATABASE

FMODB ID: LZ429

Calculation Name: 1T2K-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T2K

Chain ID: D

ChEMBL ID:

UniProt ID: P15336

Base Structure: X-ray

Registration Date: 2023-09-20

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-260545.889718
FMO2-HF: Nuclear repulsion	236238.815223
FMO2-HF: Total energy	-24307.074494
FMO2-MP2: Total energy	-24379.940799

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(D:336:LYS)

Summations of interaction energy for fragment #1(D:336: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.
174.857	178.198	0.447	-1.039	-2.751	0.001

Interaction energy analysis for fragmet #1(D:336:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.086 / q_NPA : 1.035

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	D	338	ARG	1	1.012	0.996	3.894	23.456	24.888	-0.004	-0.596	-0.833	0.001
4	D	339	LYS	1	0.877	0.925	2.604	42.135	43.735	0.452	-0.397	-1.656	0.000
5	D	340	PHE	0	0.044	0.029	4.111	2.363	2.672	-0.001	-0.046	-0.262	0.000
6	D	341	LEU	0	0.000	-0.004	5.639	3.259	3.259	0.000	0.000	0.000	0.000
7	D	342	GLU	-1	-0.842	-0.907	7.736	-32.609	-32.609	0.000	0.000	0.000	0.000
8	D	343	ARG	1	0.957	0.976	5.741	38.692	38.692	0.000	0.000	0.000	0.000
9	D	344	ASN	0	0.048	0.025	9.418	2.283	2.283	0.000	0.000	0.000	0.000
10	D	345	ARG	1	0.972	1.000	11.362	23.031	23.031	0.000	0.000	0.000	0.000
11	D	346	ALA	0	0.017	0.003	12.605	1.366	1.366	0.000	0.000	0.000	0.000
12	D	347	ALA	0	-0.006	-0.002	13.290	1.226	1.226	0.000	0.000	0.000	0.000
13	D	348	ALA	0	0.033	0.006	15.009	1.223	1.223	0.000	0.000	0.000	0.000
14	D	349	SER	0	-0.013	-0.004	17.050	1.059	1.059	0.000	0.000	0.000	0.000
15	D	350	ARG	1	0.966	0.982	14.257	19.884	19.884	0.000	0.000	0.000	0.000
16	D	351	SER	0	-0.037	-0.014	19.219	0.878	0.878	0.000	0.000	0.000	0.000
17	D	352	ARG	1	0.974	0.984	18.680	14.686	14.686	0.000	0.000	0.000	0.000
18	D	353	GLN	0	0.062	0.037	22.830	0.498	0.498	0.000	0.000	0.000	0.000
19	D	354	LYS	1	0.974	0.988	22.017	13.646	13.646	0.000	0.000	0.000	0.000
20	D	355	ARG	1	0.958	0.974	25.202	11.107	11.107	0.000	0.000	0.000	0.000
21	D	356	LYS	1	0.965	0.991	27.076	10.641	10.641	0.000	0.000	0.000	0.000
22	D	357	VAL	0	0.013	0.008	28.396	0.319	0.319	0.000	0.000	0.000	0.000
23	D	358	TRP	0	-0.001	0.003	29.714	0.235	0.235	0.000	0.000	0.000	0.000
24	D	359	VAL	0	-0.013	-0.005	31.315	0.240	0.240	0.000	0.000	0.000	0.000
25	D	360	GLN	0	0.059	0.023	32.469	-0.047	-0.047	0.000	0.000	0.000	0.000
26	D	361	SER	0	-0.020	-0.006	34.312	0.243	0.243	0.000	0.000	0.000	0.000
27	D	362	LEU	0	-0.048	-0.018	35.734	0.222	0.222	0.000	0.000	0.000	0.000
28	D	363	GLU	-1	-0.887	-0.957	36.496	-8.287	-8.287	0.000	0.000	0.000	0.000
29	D	364	LYS	1	0.889	0.935	38.857	7.516	7.516	0.000	0.000	0.000	0.000
30	D	365	LYS	1	0.830	0.901	40.146	7.584	7.584	0.000	0.000	0.000	0.000
31	D	366	ALA	0	0.026	0.009	41.749	0.189	0.189	0.000	0.000	0.000	0.000
32	D	367	GLU	-1	-0.871	-0.938	43.447	-6.971	-6.971	0.000	0.000	0.000	0.000
33	D	368	ASP	-1	-0.824	-0.875	43.861	-7.029	-7.029	0.000	0.000	0.000	0.000
34	D	369	LEU	0	-0.028	-0.018	44.774	0.160	0.160	0.000	0.000	0.000	0.000
35	D	370	SER	0	-0.033	-0.011	47.779	0.187	0.187	0.000	0.000	0.000	0.000
36	D	371	SER	0	0.013	0.013	49.492	0.149	0.149	0.000	0.000	0.000	0.000
37	D	372	LEU	0	0.007	-0.001	50.152	0.114	0.114	0.000	0.000	0.000	0.000
38	D	373	ASN	0	-0.034	-0.023	51.959	0.185	0.185	0.000	0.000	0.000	0.000
39	D	374	GLY	0	0.042	0.018	53.753	0.121	0.121	0.000	0.000	0.000	0.000
40	D	375	GLN	0	-0.013	-0.007	53.195	0.147	0.147	0.000	0.000	0.000	0.000
41	D	376	LEU	0	0.070	0.053	54.867	0.120	0.120	0.000	0.000	0.000	0.000
42	D	377	GLN	0	-0.032	-0.008	57.215	0.201	0.201	0.000	0.000	0.000	0.000
43	D	378	SER	0	-0.065	-0.029	59.896	0.126	0.126	0.000	0.000	0.000	0.000
44	D	379	GLU	-1	-0.864	-0.950	58.695	-5.344	-5.344	0.000	0.000	0.000	0.000
45	D	380	VAL	0	0.003	-0.005	61.561	0.112	0.112	0.000	0.000	0.000	0.000
46	D	381	THR	0	-0.059	-0.038	63.822	0.113	0.113	0.000	0.000	0.000	0.000
47	D	382	LEU	0	-0.003	-0.004	64.704	0.097	0.097	0.000	0.000	0.000	0.000
48	D	383	LEU	0	0.020	0.009	64.567	0.091	0.091	0.000	0.000	0.000	0.000
49	D	384	ARG	1	0.908	0.955	66.182	4.823	4.823	0.000	0.000	0.000	0.000
50	D	385	ASN	0	-0.017	0.002	69.786	0.087	0.087	0.000	0.000	0.000	0.000
51	D	386	GLU	-1	-0.852	-0.932	71.010	-4.288	-4.288	0.000	0.000	0.000	0.000
52	D	387	VAL	0	-0.002	-0.007	70.924	0.070	0.070	0.000	0.000	0.000	0.000
53	D	388	ALA	0	-0.038	-0.016	73.623	0.069	0.069	0.000	0.000	0.000	0.000
54	D	389	GLN	0	-0.031	-0.019	75.163	0.088	0.088	0.000	0.000	0.000	0.000
55	D	390	LEU	0	0.010	0.013	76.226	0.076	0.076	0.000	0.000	0.000	0.000
56	D	391	LYS	1	0.887	0.940	77.483	4.054	4.054	0.000	0.000	0.000	0.000
57	D	392	GLN	0	-0.035	-0.025	78.321	0.088	0.088	0.000	0.000	0.000	0.000
58	D	393	LEU	0	0.024	0.005	80.838	0.052	0.052	0.000	0.000	0.000	0.000
59	D	394	LEU	0	0.001	0.010	80.248	0.048	0.048	0.000	0.000	0.000	0.000
60	D	395	LEU	0	-0.025	-0.012	80.845	0.004	0.004	0.000	0.000	0.000	0.000
61	D	396	ALA	0	-0.079	-0.017	83.584	0.069	0.069	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:336:LYS)