FMO DATABASE

FMODB ID: MVZJZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-188816.03948
FMO2-HF: Nuclear repulsion	168589.124542
FMO2-HF: Total energy	-20226.914938
FMO2-MP2: Total energy	-20275.470991

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.
-26.992	-12.089	19.137	-11.923	-22.118	-0.01

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 : -0.052 / q_NPA : -0.020

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	3.676	-4.136	-2.274	-0.008	-0.867	-0.988	0.007
4	D	15	LYS	1	0.910	0.932	3.796	-1.764	-1.331	-0.001	-0.070	-0.362	0.000
5	D	16	THR	0	0.008	0.004	2.670	-6.801	-4.642	0.686	-1.445	-1.400	-0.018
6	D	17	CYS	0	-0.142	-0.055	2.527	-3.240	0.650	10.387	-4.668	-9.610	-0.012
7	D	18	SER	0	0.022	-0.009	5.038	-0.764	-0.734	-0.002	-0.014	-0.014	0.000
8	D	19	PRO	0	0.002	-0.016	6.260	-0.695	-0.695	0.000	0.000	0.000	0.000
9	D	20	ALA	0	-0.058	-0.005	6.860	-1.055	-1.055	0.000	0.000	0.000	0.000
10	D	21	GLN	0	-0.030	-0.029	3.497	-1.320	1.830	-0.003	-1.605	-1.541	-0.007
13	D	25	ASN	0	-0.045	-0.025	3.785	-1.037	1.390	-0.040	-1.043	-1.344	0.003
14	D	26	ASN	0	-0.023	-0.013	3.140	-1.391	-0.639	1.275	-0.652	-1.376	-0.001
15	D	27	GLU	-1	-0.819	-0.915	3.387	2.554	2.572	2.399	-0.043	-2.374	-0.010
16	D	29	ALA	0	0.071	0.035	2.102	-10.171	-10.991	4.163	-1.188	-2.154	0.028
17	D	30	CYS	0	-0.058	-0.014	3.247	-0.359	0.532	0.285	-0.322	-0.854	0.000
18	D	31	THR	0	0.058	0.037	4.797	0.050	0.116	-0.002	-0.007	-0.057	0.000
19	D	32	ALA	0	-0.002	0.006	5.789	0.637	0.682	-0.002	0.001	-0.044	0.000
20	D	33	ILE	0	-0.024	-0.014	8.230	0.082	0.082	0.000	0.000	0.000	0.000
21	D	34	ARG	1	0.830	0.886	9.613	0.148	0.148	0.000	0.000	0.000	0.000
22	D	35	CYS	0	-0.032	-0.020	11.141	0.120	0.120	0.000	0.000	0.000	0.000
23	D	36	MET	0	0.004	0.016	15.811	0.096	0.096	0.000	0.000	0.000	0.000
24	D	37	ILE	0	-0.040	-0.032	17.918	0.037	0.037	0.000	0.000	0.000	0.000
25	D	38	PHE	0	0.036	0.010	19.983	0.019	0.019	0.000	0.000	0.000	0.000
26	D	39	CYS	0	0.033	0.038	15.970	0.009	0.009	0.000	0.000	0.000	0.000
27	D	40	PRO	0	0.003	0.002	21.949	0.033	0.033	0.000	0.000	0.000	0.000
28	D	41	ASN	0	-0.028	-0.009	22.774	0.035	0.035	0.000	0.000	0.000	0.000
29	D	42	GLY	0	0.041	0.024	19.738	0.035	0.035	0.000	0.000	0.000	0.000
30	D	43	PHE	0	-0.015	-0.022	14.457	-0.053	-0.053	0.000	0.000	0.000	0.000
31	D	44	LYS	1	0.843	0.921	15.063	0.285	0.285	0.000	0.000	0.000	0.000
32	D	45	VAL	0	0.022	0.017	13.468	-0.063	-0.063	0.000	0.000	0.000	0.000
33	D	46	ASP	-1	-0.766	-0.878	8.829	0.805	0.805	0.000	0.000	0.000	0.000
34	D	47	GLU	-1	-0.953	-0.979	12.347	0.731	0.731	0.000	0.000	0.000	0.000
35	D	48	ASN	0	-0.053	-0.033	8.916	0.046	0.046	0.000	0.000	0.000	0.000
36	D	49	GLY	0	-0.009	-0.003	11.117	0.288	0.288	0.000	0.000	0.000	0.000
37	D	51	GLU	-1	-0.799	-0.884	10.107	-0.128	-0.128	0.000	0.000	0.000	0.000
38	D	52	TYR	0	0.009	-0.015	9.588	-0.247	-0.247	0.000	0.000	0.000	0.000
39	D	53	PRO	0	-0.008	0.005	8.545	0.173	0.173	0.000	0.000	0.000	0.000
40	D	55	THR	0	0.016	0.016	13.798	0.076	0.076	0.000	0.000	0.000	0.000
41	D	57	ALA	0	0.026	0.024	18.734	-0.027	-0.027	0.000	0.000	0.000	0.000

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