FMO DATABASE

FMODB ID: 94QK2

Calculation Name: 3BG4-D-Xray372

Preferred Name: Alpha-chymotrypsin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BG4

Chain ID: D

ChEMBL ID: CHEMBL3314

UniProt ID: P00766

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	41
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-189049.552816
FMO2-HF: Nuclear repulsion	168822.855496
FMO2-HF: Total energy	-20226.69732
FMO2-MP2: Total energy	-20275.297289

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:12:CYS)

Summations of interaction energy for fragment #1(D:12:CYS)

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.
-26.702	-12.074	19.113	-11.302	-22.438	-0.012

Interaction energy analysis for fragmet #1(D:12:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.017

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	14	GLU	-1	-0.998	-0.986	3.641	-4.062	-2.393	-0.004	-0.671	-0.993	0.006
4	D	15	LYS	1	0.921	0.943	3.785	-1.339	-0.843	0.001	-0.086	-0.411	0.000
5	D	16	THR	0	0.020	0.005	2.692	-6.841	-4.747	0.840	-1.458	-1.476	-0.019
6	D	17	CYS	0	-0.168	-0.063	2.524	-3.104	1.249	9.361	-4.229	-9.485	-0.013
7	D	18	SER	0	0.025	-0.025	4.996	-0.803	-0.771	-0.002	-0.012	-0.019	0.000
8	D	19	PRO	0	0.003	-0.020	6.260	-0.703	-0.703	0.000	0.000	0.000	0.000
9	D	20	ALA	0	-0.045	0.003	6.860	-1.028	-1.028	0.000	0.000	0.000	0.000
10	D	21	GLN	0	-0.020	-0.015	3.489	-1.676	1.423	-0.002	-1.585	-1.512	-0.007
13	D	25	ASN	0	-0.013	-0.014	3.785	-0.912	1.513	-0.040	-1.050	-1.336	0.004
14	D	26	ASN	0	-0.014	-0.002	3.117	-1.366	-0.621	1.359	-0.650	-1.453	-0.001
15	D	27	GLU	-1	-0.856	-0.940	3.333	2.903	2.559	2.939	0.016	-2.611	-0.011
16	D	29	ALA	0	0.069	0.030	2.080	-10.425	-11.382	4.380	-1.242	-2.181	0.029
17	D	30	CYS	0	-0.062	-0.025	3.247	-0.358	0.547	0.285	-0.329	-0.861	0.000
18	D	31	THR	0	0.051	0.033	4.850	0.059	0.125	-0.002	-0.007	-0.056	0.000
19	D	32	ALA	0	-0.005	-0.003	5.789	0.642	0.687	-0.002	0.001	-0.044	0.000
20	D	33	ILE	0	-0.021	-0.010	8.296	0.089	0.089	0.000	0.000	0.000	0.000
21	D	34	ARG	1	0.825	0.884	10.073	0.147	0.147	0.000	0.000	0.000	0.000
22	D	35	CYS	0	-0.030	-0.019	11.141	0.117	0.117	0.000	0.000	0.000	0.000
23	D	36	MET	0	0.002	0.018	15.811	0.096	0.096	0.000	0.000	0.000	0.000
24	D	37	ILE	0	-0.036	-0.029	18.015	0.036	0.036	0.000	0.000	0.000	0.000
25	D	38	PHE	0	0.030	0.006	19.983	0.019	0.019	0.000	0.000	0.000	0.000
26	D	39	CYS	0	-0.027	0.010	15.970	0.010	0.010	0.000	0.000	0.000	0.000
27	D	40	PRO	0	-0.005	0.000	21.949	0.033	0.033	0.000	0.000	0.000	0.000
28	D	41	ASN	0	-0.013	-0.006	22.932	0.037	0.037	0.000	0.000	0.000	0.000
29	D	42	GLY	0	0.038	0.023	19.738	0.035	0.035	0.000	0.000	0.000	0.000
30	D	43	PHE	0	-0.014	-0.019	14.405	-0.048	-0.048	0.000	0.000	0.000	0.000
31	D	44	LYS	1	0.922	0.966	15.147	0.219	0.219	0.000	0.000	0.000	0.000
32	D	45	VAL	0	0.031	0.018	13.474	-0.071	-0.071	0.000	0.000	0.000	0.000
33	D	46	ASP	-1	-0.765	-0.874	8.970	0.928	0.928	0.000	0.000	0.000	0.000
34	D	47	GLU	-1	-0.968	-0.987	12.347	0.711	0.711	0.000	0.000	0.000	0.000
35	D	48	ASN	0	-0.038	-0.011	8.434	-0.232	-0.232	0.000	0.000	0.000	0.000
36	D	49	GLY	0	-0.032	-0.010	11.117	0.289	0.289	0.000	0.000	0.000	0.000
37	D	51	GLU	-1	-0.808	-0.892	10.107	-0.094	-0.094	0.000	0.000	0.000	0.000
38	D	52	TYR	0	-0.014	-0.019	9.588	-0.226	-0.226	0.000	0.000	0.000	0.000
39	D	53	PRO	0	-0.010	0.000	8.494	0.186	0.186	0.000	0.000	0.000	0.000
40	D	55	THR	0	0.046	0.030	13.718	0.053	0.053	0.000	0.000	0.000	0.000
41	D	57	ALA	0	0.006	0.008	18.734	-0.023	-0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:12:CYS)