FMO DATABASE

FMODB ID: 521MZ

Calculation Name: 3P45-D-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: D

ChEMBL ID: CHEMBL3308

UniProt ID: P55212

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-417728.144767
FMO2-HF: Nuclear repulsion	388652.875085
FMO2-HF: Total energy	-29075.269682
FMO2-MP2: Total energy	-29156.536189

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:200:LEU)

Summations of interaction energy for fragment #1(D:200:LEU)

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.
-12.919	-11.001	7.246	-3.892	-5.27	0.016

Interaction energy analysis for fragmet #1(D:200:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.008

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	202	ALA	0	0.039	0.025	3.746	-1.379	0.206	-0.002	-0.784	-0.799	0.002
4	D	203	GLY	0	0.024	0.013	6.356	0.616	0.616	0.000	0.000	0.000	0.000
5	D	204	ALA	0	0.013	-0.008	8.140	-0.019	-0.019	0.000	0.000	0.000	0.000
6	D	205	ASP	-1	-0.787	-0.870	10.555	-0.449	-0.449	0.000	0.000	0.000	0.000
7	D	206	PHE	0	-0.009	0.020	7.329	-0.033	-0.033	0.000	0.000	0.000	0.000
8	D	207	LEU	0	-0.033	-0.029	7.205	0.127	0.127	0.000	0.000	0.000	0.000
9	D	208	MET	0	-0.013	0.014	3.297	-0.584	0.013	0.021	-0.128	-0.490	-0.001
10	D	209	CYS	0	-0.015	-0.017	5.918	0.722	0.722	0.000	0.000	0.000	0.000
11	D	210	TYR	0	0.022	-0.001	1.933	-10.289	-10.995	6.211	-2.568	-2.936	0.014
12	D	211	SER	0	0.059	0.022	8.946	-0.078	-0.078	0.000	0.000	0.000	0.000
13	D	212	VAL	0	-0.006	0.017	9.403	-0.088	-0.088	0.000	0.000	0.000	0.000
14	D	222	THR	0	0.015	-0.009	24.176	-0.012	-0.012	0.000	0.000	0.000	0.000
15	D	223	VAL	0	0.048	0.016	25.764	0.009	0.009	0.000	0.000	0.000	0.000
16	D	224	ASN	0	0.013	0.019	27.484	-0.014	-0.014	0.000	0.000	0.000	0.000
17	D	225	GLY	0	0.018	0.025	23.328	-0.001	-0.001	0.000	0.000	0.000	0.000
18	D	226	SER	0	-0.003	-0.007	18.063	0.003	0.003	0.000	0.000	0.000	0.000
19	D	227	TRP	0	0.012	-0.008	20.174	-0.003	-0.003	0.000	0.000	0.000	0.000
20	D	228	TYR	0	0.079	0.033	12.096	-0.030	-0.030	0.000	0.000	0.000	0.000
21	D	229	ILE	0	0.042	0.028	15.492	-0.011	-0.011	0.000	0.000	0.000	0.000
22	D	230	GLN	0	0.035	0.016	18.690	-0.016	-0.016	0.000	0.000	0.000	0.000
23	D	231	ASP	-1	-0.755	-0.868	19.738	0.289	0.289	0.000	0.000	0.000	0.000
24	D	232	LEU	0	0.002	0.002	14.995	-0.014	-0.014	0.000	0.000	0.000	0.000
25	D	233	CYS	0	-0.029	-0.020	18.738	-0.041	-0.041	0.000	0.000	0.000	0.000
26	D	234	GLU	-1	-0.828	-0.893	21.769	0.171	0.171	0.000	0.000	0.000	0.000
27	D	235	MET	0	-0.033	-0.024	19.947	-0.017	-0.017	0.000	0.000	0.000	0.000
28	D	236	LEU	0	0.008	-0.004	17.900	-0.021	-0.021	0.000	0.000	0.000	0.000
29	D	237	GLY	0	-0.001	-0.001	21.660	-0.021	-0.021	0.000	0.000	0.000	0.000
30	D	238	LYS	1	0.822	0.921	24.733	-0.163	-0.163	0.000	0.000	0.000	0.000
31	D	239	TYR	0	0.014	-0.014	22.633	0.001	0.001	0.000	0.000	0.000	0.000
32	D	240	GLY	0	0.040	0.021	21.318	-0.003	-0.003	0.000	0.000	0.000	0.000
33	D	241	SER	0	-0.025	-0.002	22.296	-0.012	-0.012	0.000	0.000	0.000	0.000
34	D	242	SER	0	-0.025	-0.029	24.128	-0.007	-0.007	0.000	0.000	0.000	0.000
35	D	243	LEU	0	0.013	0.013	20.804	-0.005	-0.005	0.000	0.000	0.000	0.000
36	D	244	GLU	-1	-0.786	-0.848	15.943	0.085	0.085	0.000	0.000	0.000	0.000
37	D	245	PHE	0	0.046	0.003	12.997	0.054	0.054	0.000	0.000	0.000	0.000
38	D	246	THR	0	-0.006	-0.034	11.674	0.076	0.076	0.000	0.000	0.000	0.000
39	D	247	GLU	-1	-0.806	-0.879	13.909	0.199	0.199	0.000	0.000	0.000	0.000
40	D	248	LEU	0	-0.016	0.000	17.222	0.035	0.035	0.000	0.000	0.000	0.000
41	D	249	LEU	0	0.002	-0.010	11.326	0.031	0.031	0.000	0.000	0.000	0.000
42	D	250	THR	0	-0.026	-0.021	14.432	0.102	0.102	0.000	0.000	0.000	0.000
43	D	251	LEU	0	-0.058	-0.028	15.416	0.005	0.005	0.000	0.000	0.000	0.000
44	D	252	VAL	0	-0.013	0.001	15.622	0.000	0.000	0.000	0.000	0.000	0.000
45	D	253	ASN	0	0.034	0.008	11.511	0.043	0.043	0.000	0.000	0.000	0.000
46	D	254	ARG	1	0.938	0.995	15.458	-0.293	-0.293	0.000	0.000	0.000	0.000
47	D	255	LYS	1	0.800	0.886	18.961	-0.261	-0.261	0.000	0.000	0.000	0.000
48	D	256	VAL	0	0.002	-0.002	17.213	-0.020	-0.020	0.000	0.000	0.000	0.000
49	D	257	SER	0	0.015	0.005	17.824	-0.035	-0.035	0.000	0.000	0.000	0.000
50	D	258	GLN	0	-0.041	-0.022	19.719	-0.024	-0.024	0.000	0.000	0.000	0.000
51	D	259	ARG	1	0.785	0.911	22.160	-0.319	-0.319	0.000	0.000	0.000	0.000
52	D	260	ARG	1	0.895	0.937	22.865	-0.313	-0.313	0.000	0.000	0.000	0.000
53	D	274	GLN	0	0.010	-0.008	15.480	-0.076	-0.076	0.000	0.000	0.000	0.000
54	D	275	VAL	0	-0.028	-0.038	13.630	-0.070	-0.070	0.000	0.000	0.000	0.000
55	D	276	PRO	0	-0.046	0.010	12.081	0.103	0.103	0.000	0.000	0.000	0.000
56	D	277	CYS	0	-0.025	-0.017	7.746	0.233	0.233	0.000	0.000	0.000	0.000
57	D	278	PHE	0	0.021	-0.002	6.978	-0.051	-0.051	0.000	0.000	0.000	0.000
58	D	279	ALA	0	0.012	0.018	2.498	-0.275	0.126	1.017	-0.399	-1.019	0.001
59	D	280	SER	0	0.007	-0.010	4.474	-0.935	-0.894	-0.001	-0.013	-0.026	0.000
60	D	281	MET	0	0.010	0.014	5.258	-0.203	-0.203	0.000	0.000	0.000	0.000
61	D	282	LEU	0	-0.029	0.003	7.830	-0.052	-0.052	0.000	0.000	0.000	0.000
62	D	283	THR	0	-0.050	-0.058	11.367	0.081	0.081	0.000	0.000	0.000	0.000
63	D	284	LYS	1	0.835	0.914	14.031	0.346	0.346	0.000	0.000	0.000	0.000
64	D	285	LYS	1	0.854	0.933	15.514	-0.071	-0.071	0.000	0.000	0.000	0.000
65	D	286	LEU	0	-0.009	-0.009	14.617	-0.031	-0.031	0.000	0.000	0.000	0.000
66	D	287	HIS	0	0.013	-0.003	17.857	0.040	0.040	0.000	0.000	0.000	0.000
67	D	288	PHE	0	-0.029	-0.013	16.145	-0.026	-0.026	0.000	0.000	0.000	0.000
68	D	289	PHE	0	-0.011	0.001	22.118	0.008	0.008	0.000	0.000	0.000	0.000
69	D	290	PRO	0	0.013	0.003	25.779	-0.012	-0.012	0.000	0.000	0.000	0.000
70	D	291	LYS	1	0.958	0.996	25.925	0.079	0.079	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:200:LEU)