FMO DATABASE

FMODB ID: 2JV6R

Calculation Name: 3P45-H-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: H

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	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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-401081.298576
FMO2-HF: Nuclear repulsion	372779.722215
FMO2-HF: Total energy	-28301.576361
FMO2-MP2: Total energy	-28380.59237

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(H:200:LEU)

Summations of interaction energy for fragment #1(H: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.
-12.544	-12.442	8.342	-3.872	-4.573	0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	H	202	ALA	0	0.040	0.028	3.823	-1.714	-0.180	-0.009	-0.681	-0.845	0.003
4	H	203	GLY	0	0.024	0.012	6.483	0.481	0.481	0.000	0.000	0.000	0.000
5	H	204	ALA	0	-0.020	-0.009	7.846	0.039	0.039	0.000	0.000	0.000	0.000
6	H	205	ASP	-1	-0.816	-0.898	10.312	-0.469	-0.469	0.000	0.000	0.000	0.000
7	H	206	PHE	0	-0.029	0.005	7.203	-0.026	-0.026	0.000	0.000	0.000	0.000
8	H	207	LEU	0	0.003	-0.003	7.774	0.109	0.109	0.000	0.000	0.000	0.000
9	H	208	MET	0	-0.020	0.005	3.131	-0.665	-0.090	0.034	-0.142	-0.468	-0.001
10	H	209	CYS	0	-0.016	-0.002	6.301	0.554	0.554	0.000	0.000	0.000	0.000
11	H	210	TYR	0	0.029	-0.006	1.837	-9.285	-11.802	8.291	-2.931	-2.843	0.012
12	H	211	SER	0	0.006	0.001	8.830	-0.109	-0.109	0.000	0.000	0.000	0.000
13	H	212	VAL	0	0.051	0.033	11.360	-0.003	-0.003	0.000	0.000	0.000	0.000
14	H	225	GLY	0	0.067	0.034	23.391	-0.011	-0.011	0.000	0.000	0.000	0.000
15	H	226	SER	0	-0.037	-0.026	18.125	0.003	0.003	0.000	0.000	0.000	0.000
16	H	227	TRP	0	0.077	0.018	20.203	-0.006	-0.006	0.000	0.000	0.000	0.000
17	H	228	TYR	0	0.057	0.030	12.202	-0.034	-0.034	0.000	0.000	0.000	0.000
18	H	229	ILE	0	0.050	0.022	15.500	-0.013	-0.013	0.000	0.000	0.000	0.000
19	H	230	GLN	0	0.038	0.025	18.748	-0.022	-0.022	0.000	0.000	0.000	0.000
20	H	231	ASP	-1	-0.750	-0.862	20.267	0.320	0.320	0.000	0.000	0.000	0.000
21	H	232	LEU	0	-0.024	-0.019	15.153	-0.020	-0.020	0.000	0.000	0.000	0.000
22	H	233	CYS	0	-0.037	-0.028	19.067	-0.042	-0.042	0.000	0.000	0.000	0.000
23	H	234	GLU	-1	-0.841	-0.897	21.865	0.200	0.200	0.000	0.000	0.000	0.000
24	H	235	MET	0	-0.022	-0.016	20.861	-0.024	-0.024	0.000	0.000	0.000	0.000
25	H	236	LEU	0	0.005	0.008	18.348	-0.023	-0.023	0.000	0.000	0.000	0.000
26	H	237	GLY	0	-0.013	-0.010	22.399	-0.024	-0.024	0.000	0.000	0.000	0.000
27	H	238	LYS	1	0.888	0.958	25.878	-0.158	-0.158	0.000	0.000	0.000	0.000
28	H	239	TYR	0	0.039	-0.011	23.599	-0.007	-0.007	0.000	0.000	0.000	0.000
29	H	240	GLY	0	0.044	0.041	22.057	-0.006	-0.006	0.000	0.000	0.000	0.000
30	H	241	SER	0	-0.051	-0.015	22.967	-0.012	-0.012	0.000	0.000	0.000	0.000
31	H	242	SER	0	-0.014	-0.025	25.179	-0.011	-0.011	0.000	0.000	0.000	0.000
32	H	243	LEU	0	-0.007	-0.012	21.751	-0.008	-0.008	0.000	0.000	0.000	0.000
33	H	244	GLU	-1	-0.787	-0.846	16.822	0.107	0.107	0.000	0.000	0.000	0.000
34	H	245	PHE	0	0.067	0.007	13.421	0.047	0.047	0.000	0.000	0.000	0.000
35	H	246	THR	0	-0.016	-0.036	12.622	0.071	0.071	0.000	0.000	0.000	0.000
36	H	247	GLU	-1	-0.839	-0.918	14.854	0.207	0.207	0.000	0.000	0.000	0.000
37	H	248	LEU	0	-0.030	-0.004	17.917	0.034	0.034	0.000	0.000	0.000	0.000
38	H	249	LEU	0	0.023	0.000	11.860	0.039	0.039	0.000	0.000	0.000	0.000
39	H	250	THR	0	-0.064	-0.039	15.388	0.085	0.085	0.000	0.000	0.000	0.000
40	H	251	LEU	0	-0.067	-0.033	16.284	0.005	0.005	0.000	0.000	0.000	0.000
41	H	252	VAL	0	-0.001	0.007	16.454	0.003	0.003	0.000	0.000	0.000	0.000
42	H	253	ASN	0	0.040	0.019	12.708	0.047	0.047	0.000	0.000	0.000	0.000
43	H	254	ARG	1	0.955	0.994	16.620	-0.313	-0.313	0.000	0.000	0.000	0.000
44	H	255	LYS	1	0.805	0.899	20.102	-0.279	-0.279	0.000	0.000	0.000	0.000
45	H	256	VAL	0	-0.001	-0.021	17.809	-0.013	-0.013	0.000	0.000	0.000	0.000
46	H	257	SER	0	-0.083	-0.039	18.602	-0.021	-0.021	0.000	0.000	0.000	0.000
47	H	258	GLN	0	-0.045	-0.026	20.387	-0.024	-0.024	0.000	0.000	0.000	0.000
48	H	259	ARG	1	0.775	0.904	22.336	-0.374	-0.374	0.000	0.000	0.000	0.000
49	H	260	ARG	1	0.987	0.983	24.732	-0.215	-0.215	0.000	0.000	0.000	0.000
50	H	261	VAL	0	0.005	0.011	26.802	-0.022	-0.022	0.000	0.000	0.000	0.000
51	H	274	GLN	0	-0.011	-0.018	15.384	-0.092	-0.092	0.000	0.000	0.000	0.000
52	H	275	VAL	0	-0.041	-0.044	14.486	-0.083	-0.083	0.000	0.000	0.000	0.000
53	H	276	PRO	0	-0.038	0.019	12.807	0.108	0.108	0.000	0.000	0.000	0.000
54	H	277	CYS	0	0.003	-0.007	7.388	0.069	0.069	0.000	0.000	0.000	0.000
55	H	278	PHE	0	-0.005	0.004	8.105	0.022	0.022	0.000	0.000	0.000	0.000
56	H	279	ALA	0	0.021	0.000	3.233	-0.120	0.243	0.028	-0.092	-0.299	0.000
57	H	280	SER	0	-0.014	-0.016	5.393	-0.631	-0.628	-0.001	-0.001	-0.001	0.000
58	H	281	MET	0	-0.005	0.002	5.108	-0.488	-0.344	-0.001	-0.025	-0.117	0.000
59	H	282	LEU	0	-0.027	0.001	8.058	-0.067	-0.067	0.000	0.000	0.000	0.000
60	H	283	THR	0	-0.037	-0.043	11.713	0.058	0.058	0.000	0.000	0.000	0.000
61	H	284	LYS	1	0.922	0.960	14.297	0.286	0.286	0.000	0.000	0.000	0.000
62	H	285	LYS	1	0.892	0.964	16.128	-0.058	-0.058	0.000	0.000	0.000	0.000
63	H	286	LEU	0	-0.013	-0.012	15.064	-0.027	-0.027	0.000	0.000	0.000	0.000
64	H	287	HIS	0	-0.003	-0.010	18.467	0.036	0.036	0.000	0.000	0.000	0.000
65	H	288	PHE	0	-0.028	-0.009	17.241	-0.025	-0.025	0.000	0.000	0.000	0.000
66	H	289	PHE	0	0.009	0.013	23.104	0.009	0.009	0.000	0.000	0.000	0.000
67	H	290	PRO	0	0.000	0.004	26.669	-0.010	-0.010	0.000	0.000	0.000	0.000
68	H	291	LYS	1	0.977	0.992	25.811	0.071	0.071	0.000	0.000	0.000	0.000

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