FMO DATABASE

FMODB ID: JLGZ9

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	OptH
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	-261144.74967
FMO2-HF: Nuclear repulsion	236839.014335
FMO2-HF: Total energy	-24305.735335
FMO2-MP2: Total energy	-24378.826592

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.
210.697	212.621	4.847	-2.121	-4.649	0.003

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 : 1.061 / q_NPA : 1.018

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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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	1.014	0.989	3.806	24.502	26.059	-0.010	-0.639	-0.908	0.002
4	D	339	LYS	1	1.031	1.011	1.767	69.364	69.164	4.858	-1.395	-3.263	0.001
5	D	340	PHE	0	0.021	0.035	3.799	3.178	3.634	0.000	-0.082	-0.374	0.000
6	D	341	LEU	0	-0.005	-0.014	5.063	4.145	4.256	-0.001	-0.005	-0.104	0.000
7	D	342	GLU	-1	-0.924	-0.973	6.989	-33.868	-33.868	0.000	0.000	0.000	0.000
8	D	343	ARG	1	0.968	0.964	5.387	39.375	39.375	0.000	0.000	0.000	0.000
9	D	344	ASN	0	-0.006	0.012	8.871	2.933	2.933	0.000	0.000	0.000	0.000
10	D	345	ARG	1	1.023	1.021	11.054	25.418	25.418	0.000	0.000	0.000	0.000
11	D	346	ALA	0	0.014	0.016	12.191	1.535	1.535	0.000	0.000	0.000	0.000
12	D	347	ALA	0	0.064	-0.078	12.966	1.556	1.556	0.000	0.000	0.000	0.000
13	D	348	ALA	0	0.037	0.017	14.701	1.356	1.356	0.000	0.000	0.000	0.000
14	D	349	SER	0	-0.036	-0.017	16.860	1.333	1.333	0.000	0.000	0.000	0.000
15	D	350	ARG	1	0.913	1.071	13.420	21.095	21.095	0.000	0.000	0.000	0.000
16	D	351	SER	0	-0.054	-0.025	18.604	0.943	0.943	0.000	0.000	0.000	0.000
17	D	352	ARG	1	0.989	0.978	19.151	15.161	15.161	0.000	0.000	0.000	0.000
18	D	353	GLN	0	0.036	0.035	22.160	0.472	0.472	0.000	0.000	0.000	0.000
19	D	354	LYS	1	0.996	0.988	22.525	13.787	13.787	0.000	0.000	0.000	0.000
20	D	355	ARG	1	0.934	0.967	24.692	11.267	11.267	0.000	0.000	0.000	0.000
21	D	356	LYS	1	1.001	0.994	26.643	11.015	11.015	0.000	0.000	0.000	0.000
22	D	357	VAL	0	0.025	0.015	27.500	0.368	0.368	0.000	0.000	0.000	0.000
23	D	358	TRP	0	0.002	0.013	29.229	0.271	0.271	0.000	0.000	0.000	0.000
24	D	359	VAL	0	0.024	0.011	30.937	0.248	0.248	0.000	0.000	0.000	0.000
25	D	360	GLN	0	0.033	0.010	31.880	0.109	0.109	0.000	0.000	0.000	0.000
26	D	361	SER	0	-0.065	-0.029	33.494	0.352	0.352	0.000	0.000	0.000	0.000
27	D	362	LEU	0	-0.010	-0.003	35.032	0.202	0.202	0.000	0.000	0.000	0.000
28	D	363	GLU	-1	-0.918	-0.974	36.951	-8.334	-8.334	0.000	0.000	0.000	0.000
29	D	364	LYS	1	0.853	0.926	38.354	7.618	7.618	0.000	0.000	0.000	0.000
30	D	365	LYS	1	0.927	0.967	39.486	7.716	7.716	0.000	0.000	0.000	0.000
31	D	366	ALA	0	-0.010	-0.026	41.052	0.207	0.207	0.000	0.000	0.000	0.000
32	D	367	GLU	-1	-0.861	-0.928	42.732	-7.175	-7.175	0.000	0.000	0.000	0.000
33	D	368	ASP	-1	-0.826	-0.882	43.421	-7.059	-7.059	0.000	0.000	0.000	0.000
34	D	369	LEU	0	-0.002	0.005	44.918	0.149	0.149	0.000	0.000	0.000	0.000
35	D	370	SER	0	-0.033	-0.013	47.371	0.148	0.148	0.000	0.000	0.000	0.000
36	D	371	SER	0	-0.014	-0.019	48.711	0.206	0.206	0.000	0.000	0.000	0.000
37	D	372	LEU	0	-0.023	-0.010	49.589	0.097	0.097	0.000	0.000	0.000	0.000
38	D	373	ASN	0	-0.113	-0.063	51.184	0.191	0.191	0.000	0.000	0.000	0.000
39	D	374	GLY	0	0.040	0.009	52.971	0.123	0.123	0.000	0.000	0.000	0.000
40	D	375	GLN	0	0.028	0.020	53.644	0.087	0.087	0.000	0.000	0.000	0.000
41	D	376	LEU	0	0.053	0.040	55.063	0.128	0.128	0.000	0.000	0.000	0.000
42	D	377	GLN	0	0.023	0.020	57.510	0.201	0.201	0.000	0.000	0.000	0.000
43	D	378	SER	0	-0.063	-0.026	59.473	0.131	0.131	0.000	0.000	0.000	0.000
44	D	379	GLU	-1	-0.863	-0.953	58.387	-5.398	-5.398	0.000	0.000	0.000	0.000
45	D	380	VAL	0	-0.005	0.010	61.213	0.111	0.111	0.000	0.000	0.000	0.000
46	D	381	THR	0	-0.040	-0.030	63.564	0.121	0.121	0.000	0.000	0.000	0.000
47	D	382	LEU	0	0.006	-0.007	65.162	0.094	0.094	0.000	0.000	0.000	0.000
48	D	383	LEU	0	0.041	0.018	64.926	0.090	0.090	0.000	0.000	0.000	0.000
49	D	384	ARG	1	0.886	0.953	65.993	4.862	4.862	0.000	0.000	0.000	0.000
50	D	385	ASN	0	-0.013	-0.012	69.274	0.083	0.083	0.000	0.000	0.000	0.000
51	D	386	GLU	-1	-0.920	-0.945	70.058	-4.412	-4.412	0.000	0.000	0.000	0.000
52	D	387	VAL	0	0.021	-0.001	71.003	0.066	0.066	0.000	0.000	0.000	0.000
53	D	388	ALA	0	-0.037	-0.019	73.104	0.074	0.074	0.000	0.000	0.000	0.000
54	D	389	GLN	0	-0.011	0.000	75.125	0.039	0.039	0.000	0.000	0.000	0.000
55	D	390	LEU	0	0.014	0.019	75.513	0.076	0.076	0.000	0.000	0.000	0.000
56	D	391	LYS	1	0.884	0.938	76.880	4.101	4.101	0.000	0.000	0.000	0.000
57	D	392	GLN	0	-0.083	-0.073	78.265	0.075	0.075	0.000	0.000	0.000	0.000
58	D	393	LEU	0	-0.005	0.000	80.473	0.051	0.051	0.000	0.000	0.000	0.000
59	D	394	LEU	0	-0.001	0.015	79.651	0.049	0.049	0.000	0.000	0.000	0.000
60	D	395	LEU	0	-0.041	-0.010	80.592	0.025	0.025	0.000	0.000	0.000	0.000
61	D	396	ALA	0	-0.001	0.012	83.233	0.039	0.039	0.000	0.000	0.000	0.000

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