FMO DATABASE

FMODB ID: 6N19Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-401638.510304
FMO2-HF: Nuclear repulsion	373336.676433
FMO2-HF: Total energy	-28301.833871
FMO2-MP2: Total energy	-28380.851331

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.
-13.167	-12.427	8.579	-4.296	-5.021	0.015

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 : 0.044 / q_NPA : 0.015

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	0.038	0.027	3.466	-1.883	-0.072	0.016	-0.888	-0.939	0.001
4	H	203	GLY	0	0.022	0.013	6.085	0.674	0.674	0.000	0.000	0.000	0.000
5	H	204	ALA	0	0.013	-0.006	7.692	-0.010	-0.010	0.000	0.000	0.000	0.000
6	H	205	ASP	-1	-0.786	-0.870	10.111	-0.500	-0.500	0.000	0.000	0.000	0.000
7	H	206	PHE	0	0.000	0.020	7.302	-0.022	-0.022	0.000	0.000	0.000	0.000
8	H	207	LEU	0	-0.027	-0.025	7.545	0.125	0.125	0.000	0.000	0.000	0.000
9	H	208	MET	0	-0.021	0.009	2.787	-0.819	-0.028	0.098	-0.198	-0.691	-0.001
10	H	209	CYS	0	-0.010	-0.012	5.890	0.602	0.602	0.000	0.000	0.000	0.000
11	H	210	TYR	0	0.003	-0.012	1.844	-9.679	-12.181	8.395	-3.051	-2.842	0.015
12	H	211	SER	0	0.049	0.022	8.811	-0.067	-0.067	0.000	0.000	0.000	0.000
13	H	212	VAL	0	0.018	0.024	10.690	0.024	0.024	0.000	0.000	0.000	0.000
14	H	225	GLY	0	0.054	0.023	23.120	-0.012	-0.012	0.000	0.000	0.000	0.000
15	H	226	SER	0	-0.012	-0.016	18.050	0.001	0.001	0.000	0.000	0.000	0.000
16	H	227	TRP	0	0.015	-0.003	20.013	-0.001	-0.001	0.000	0.000	0.000	0.000
17	H	228	TYR	0	0.082	0.034	11.739	-0.050	-0.050	0.000	0.000	0.000	0.000
18	H	229	ILE	0	0.036	0.025	15.280	-0.015	-0.015	0.000	0.000	0.000	0.000
19	H	230	GLN	0	0.037	0.031	18.487	-0.024	-0.024	0.000	0.000	0.000	0.000
20	H	231	ASP	-1	-0.733	-0.854	19.800	0.324	0.324	0.000	0.000	0.000	0.000
21	H	232	LEU	0	0.006	0.004	14.921	-0.019	-0.019	0.000	0.000	0.000	0.000
22	H	233	CYS	0	-0.040	-0.025	18.818	-0.045	-0.045	0.000	0.000	0.000	0.000
23	H	234	GLU	-1	-0.845	-0.906	21.751	0.196	0.196	0.000	0.000	0.000	0.000
24	H	235	MET	0	-0.036	-0.023	20.485	-0.023	-0.023	0.000	0.000	0.000	0.000
25	H	236	LEU	0	-0.003	-0.008	17.893	-0.024	-0.024	0.000	0.000	0.000	0.000
26	H	237	GLY	0	-0.001	0.003	21.972	-0.024	-0.024	0.000	0.000	0.000	0.000
27	H	238	LYS	1	0.880	0.953	25.494	-0.161	-0.161	0.000	0.000	0.000	0.000
28	H	239	TYR	0	0.042	0.000	23.464	-0.004	-0.004	0.000	0.000	0.000	0.000
29	H	240	GLY	0	0.038	0.020	21.940	-0.006	-0.006	0.000	0.000	0.000	0.000
30	H	241	SER	0	-0.039	-0.007	22.880	-0.012	-0.012	0.000	0.000	0.000	0.000
31	H	242	SER	0	-0.028	-0.028	24.633	-0.009	-0.009	0.000	0.000	0.000	0.000
32	H	243	LEU	0	0.022	0.011	21.434	-0.007	-0.007	0.000	0.000	0.000	0.000
33	H	244	GLU	-1	-0.770	-0.840	16.351	0.081	0.081	0.000	0.000	0.000	0.000
34	H	245	PHE	0	0.041	0.000	13.160	0.055	0.055	0.000	0.000	0.000	0.000
35	H	246	THR	0	-0.001	-0.032	12.185	0.079	0.079	0.000	0.000	0.000	0.000
36	H	247	GLU	-1	-0.815	-0.883	14.528	0.205	0.205	0.000	0.000	0.000	0.000
37	H	248	LEU	0	-0.021	-0.004	17.878	0.036	0.036	0.000	0.000	0.000	0.000
38	H	249	LEU	0	0.008	-0.006	11.729	0.033	0.033	0.000	0.000	0.000	0.000
39	H	250	THR	0	-0.024	-0.021	15.237	0.101	0.101	0.000	0.000	0.000	0.000
40	H	251	LEU	0	-0.072	-0.035	16.432	0.004	0.004	0.000	0.000	0.000	0.000
41	H	252	VAL	0	-0.015	-0.002	16.368	0.003	0.003	0.000	0.000	0.000	0.000
42	H	253	ASN	0	0.024	0.000	12.462	0.038	0.038	0.000	0.000	0.000	0.000
43	H	254	ARG	1	0.944	0.988	16.551	-0.314	-0.314	0.000	0.000	0.000	0.000
44	H	255	LYS	1	0.791	0.885	19.997	-0.281	-0.281	0.000	0.000	0.000	0.000
45	H	256	VAL	0	-0.005	-0.010	17.586	-0.019	-0.019	0.000	0.000	0.000	0.000
46	H	257	SER	0	-0.052	-0.026	18.900	-0.021	-0.021	0.000	0.000	0.000	0.000
47	H	258	GLN	0	-0.036	-0.015	20.656	-0.021	-0.021	0.000	0.000	0.000	0.000
48	H	259	ARG	1	0.770	0.894	22.204	-0.367	-0.367	0.000	0.000	0.000	0.000
49	H	260	ARG	1	0.979	0.981	24.531	-0.214	-0.214	0.000	0.000	0.000	0.000
50	H	261	VAL	0	0.015	0.012	26.606	-0.021	-0.021	0.000	0.000	0.000	0.000
51	H	274	GLN	0	0.003	-0.013	15.606	-0.087	-0.087	0.000	0.000	0.000	0.000
52	H	275	VAL	0	-0.016	-0.028	14.664	-0.074	-0.074	0.000	0.000	0.000	0.000
53	H	276	PRO	0	-0.058	0.005	12.926	0.121	0.121	0.000	0.000	0.000	0.000
54	H	277	CYS	0	-0.020	-0.020	7.839	0.064	0.064	0.000	0.000	0.000	0.000
55	H	278	PHE	0	0.021	0.002	7.577	-0.088	-0.088	0.000	0.000	0.000	0.000
56	H	279	ALA	0	0.031	0.021	3.031	-0.211	0.269	0.072	-0.137	-0.414	0.000
57	H	280	SER	0	-0.002	-0.012	5.178	-0.796	-0.789	-0.001	-0.002	-0.004	0.000
58	H	281	MET	0	0.010	0.011	5.242	-0.426	-0.273	-0.001	-0.020	-0.131	0.000
59	H	282	LEU	0	-0.032	0.001	8.113	-0.052	-0.052	0.000	0.000	0.000	0.000
60	H	283	THR	0	-0.049	-0.055	11.671	0.072	0.072	0.000	0.000	0.000	0.000
61	H	284	LYS	1	0.829	0.911	14.376	0.397	0.397	0.000	0.000	0.000	0.000
62	H	285	LYS	1	0.859	0.934	15.827	-0.066	-0.066	0.000	0.000	0.000	0.000
63	H	286	LEU	0	-0.017	-0.008	14.585	-0.032	-0.032	0.000	0.000	0.000	0.000
64	H	287	HIS	0	0.001	-0.009	18.022	0.042	0.042	0.000	0.000	0.000	0.000
65	H	288	PHE	0	-0.033	-0.019	16.587	-0.029	-0.029	0.000	0.000	0.000	0.000
66	H	289	PHE	0	0.006	0.012	22.572	0.009	0.009	0.000	0.000	0.000	0.000
67	H	290	PRO	0	-0.015	-0.001	26.216	-0.011	-0.011	0.000	0.000	0.000	0.000
68	H	291	LYS	1	0.980	0.996	25.524	0.093	0.093	0.000	0.000	0.000	0.000

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