FMO DATABASE

FMODB ID: VQG11

Calculation Name: 3C8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8P

Chain ID: A

ChEMBL ID:

UniProt ID: P83554

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:

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	-201373.564003
FMO2-HF: Nuclear repulsion	182753.487388
FMO2-HF: Total energy	-18620.076616
FMO2-MP2: Total energy	-18669.190265

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:1:LYS)

Summations of interaction energy for fragment #1(A:1: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.
47.066	54.964	24.841	-15.226	-17.514	-0.16

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.939

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	A	3	CYS	0	-0.045	-0.006	2.892	-12.749	-8.342	0.947	-0.974	-4.381	-0.015
4	A	4	CYS	0	-0.117	-0.046	4.993	3.613	3.690	-0.002	-0.004	-0.071	0.000
5	A	5	PRO	0	0.083	0.045	8.474	-1.529	-1.529	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.022	0.008	11.850	0.569	0.569	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.039	0.003	12.229	-1.739	-1.739	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.065	0.038	13.510	-0.332	-0.332	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.058	0.040	12.558	0.286	0.286	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.814	0.870	4.800	35.782	35.842	-0.001	0.000	-0.058	0.000
11	A	11	ASN	0	0.031	0.002	10.758	-1.014	-1.014	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.029	0.036	13.952	0.494	0.494	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.036	-0.023	6.598	-0.205	-0.205	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.018	-0.017	9.651	-1.018	-1.018	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.042	0.015	11.782	0.802	0.802	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.003	0.008	10.669	1.060	1.060	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.861	0.905	8.783	20.282	20.282	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.019	0.001	12.476	0.186	0.186	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.005	0.007	15.582	0.466	0.466	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.017	0.032	15.668	0.589	0.589	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.005	0.009	14.803	0.348	0.348	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.025	0.016	12.120	-1.173	-1.173	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.999	0.979	5.238	23.251	23.251	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.807	-0.890	9.121	-16.652	-16.652	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.056	0.017	10.858	0.260	0.260	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.051	-0.009	8.845	-0.447	-0.447	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.853	0.921	10.804	15.022	15.022	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.020	0.017	14.210	0.206	0.206	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.035	-0.043	11.671	-0.393	-0.393	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.032	0.024	13.277	-0.401	-0.401	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.903	0.960	7.411	24.307	24.307	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.017	-0.018	3.469	-4.551	-3.968	0.034	-0.252	-0.365	0.001
33	A	35	ILE	0	0.013	0.000	2.669	3.216	4.553	0.079	-0.488	-0.928	0.000
34	A	36	SER	0	0.047	0.035	1.875	-13.997	-16.477	9.848	-4.303	-3.066	-0.044
35	A	37	ALA	0	0.017	0.007	3.286	4.616	5.198	0.023	-0.177	-0.428	0.001
36	A	38	SER	0	0.070	0.034	2.670	-13.269	-9.596	1.365	-2.174	-2.864	-0.021
37	A	39	THR	0	-0.023	-0.018	1.866	-39.195	-39.681	12.549	-6.830	-5.233	-0.082
38	A	41	PRO	0	0.069	0.042	4.425	2.573	2.718	-0.001	-0.024	-0.120	0.000
39	A	42	SER	0	0.058	0.008	8.109	-0.855	-0.855	0.000	0.000	0.000	0.000
40	A	43	ASN	0	0.029	0.021	10.415	-0.861	-0.861	0.000	0.000	0.000	0.000
41	A	44	TYR	0	-0.054	-0.038	8.159	1.983	1.983	0.000	0.000	0.000	0.000
42	A	45	PRO	0	0.065	0.042	7.201	-5.195	-5.195	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.960	1.009	6.526	22.730	22.730	0.000	0.000	0.000	0.000

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