FMO DATABASE

FMODB ID: 721LK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-400251.475961
FMO2-HF: Nuclear repulsion	371950.431997
FMO2-HF: Total energy	-28301.043964
FMO2-MP2: Total energy	-28380.072658

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.
-1.974	-1.152	4.542	-1.824	-3.539	0.005

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 : -0.008 / q_NPA : -0.021

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	0.051	0.018	3.839	-2.269	-1.102	-0.010	-0.453	-0.703	0.003
4	H	203	GLY	0	0.015	0.003	6.421	0.075	0.075	0.000	0.000	0.000	0.000
5	H	204	ALA	0	-0.015	-0.008	7.960	0.115	0.115	0.000	0.000	0.000	0.000
6	H	205	ASP	-1	-0.836	-0.911	10.439	-0.066	-0.066	0.000	0.000	0.000	0.000
7	H	206	PHE	0	-0.031	0.006	7.250	0.102	0.102	0.000	0.000	0.000	0.000
8	H	207	LEU	0	0.002	-0.006	7.798	-0.029	-0.029	0.000	0.000	0.000	0.000
9	H	208	MET	0	-0.011	0.006	3.564	-1.603	-0.964	0.024	-0.219	-0.444	0.001
10	H	209	CYS	0	-0.023	-0.007	6.526	-0.179	-0.179	0.000	0.000	0.000	0.000
11	H	210	TYR	0	0.036	0.005	2.738	3.429	1.964	4.520	-1.040	-2.015	0.001
12	H	211	SER	0	0.002	0.002	9.005	-0.211	-0.211	0.000	0.000	0.000	0.000
13	H	212	VAL	0	0.050	0.037	10.798	-0.042	-0.042	0.000	0.000	0.000	0.000
14	H	225	GLY	0	0.046	0.008	23.858	-0.001	-0.001	0.000	0.000	0.000	0.000
15	H	226	SER	0	-0.010	0.004	18.495	-0.007	-0.007	0.000	0.000	0.000	0.000
16	H	227	TRP	0	0.081	0.024	20.102	0.008	0.008	0.000	0.000	0.000	0.000
17	H	228	TYR	0	0.053	0.030	12.740	0.010	0.010	0.000	0.000	0.000	0.000
18	H	229	ILE	0	0.048	0.022	16.236	0.011	0.011	0.000	0.000	0.000	0.000
19	H	230	GLN	0	0.002	0.003	19.261	-0.018	-0.018	0.000	0.000	0.000	0.000
20	H	231	ASP	-1	-0.790	-0.902	20.424	0.277	0.277	0.000	0.000	0.000	0.000
21	H	232	LEU	0	-0.028	-0.020	15.823	-0.010	-0.010	0.000	0.000	0.000	0.000
22	H	233	CYS	0	-0.043	-0.037	19.314	-0.019	-0.019	0.000	0.000	0.000	0.000
23	H	234	GLU	-1	-0.895	-0.936	22.329	0.201	0.201	0.000	0.000	0.000	0.000
24	H	235	MET	0	-0.032	-0.023	20.890	-0.026	-0.026	0.000	0.000	0.000	0.000
25	H	236	LEU	0	0.005	0.008	18.785	-0.015	-0.015	0.000	0.000	0.000	0.000
26	H	237	GLY	0	-0.011	-0.008	22.501	-0.020	-0.020	0.000	0.000	0.000	0.000
27	H	238	LYS	1	0.906	0.963	25.909	-0.169	-0.169	0.000	0.000	0.000	0.000
28	H	239	TYR	0	0.017	-0.017	23.591	-0.020	-0.020	0.000	0.000	0.000	0.000
29	H	240	GLY	0	0.038	0.043	22.074	-0.001	-0.001	0.000	0.000	0.000	0.000
30	H	241	SER	0	-0.046	-0.017	22.987	-0.002	-0.002	0.000	0.000	0.000	0.000
31	H	242	SER	0	-0.012	-0.024	25.213	-0.014	-0.014	0.000	0.000	0.000	0.000
32	H	243	LEU	0	-0.013	-0.018	21.880	-0.011	-0.011	0.000	0.000	0.000	0.000
33	H	244	GLU	-1	-0.736	-0.779	16.969	0.291	0.291	0.000	0.000	0.000	0.000
34	H	245	PHE	0	0.049	-0.001	13.563	0.025	0.025	0.000	0.000	0.000	0.000
35	H	246	THR	0	-0.054	-0.094	12.624	0.042	0.042	0.000	0.000	0.000	0.000
36	H	247	GLU	-1	-0.876	-0.942	15.167	0.222	0.222	0.000	0.000	0.000	0.000
37	H	248	LEU	0	-0.034	-0.009	18.010	0.008	0.008	0.000	0.000	0.000	0.000
38	H	249	LEU	0	0.022	-0.004	11.831	0.018	0.018	0.000	0.000	0.000	0.000
39	H	250	THR	0	-0.060	-0.041	15.577	0.025	0.025	0.000	0.000	0.000	0.000
40	H	251	LEU	0	-0.079	-0.036	16.408	-0.026	-0.026	0.000	0.000	0.000	0.000
41	H	252	VAL	0	0.004	0.012	16.417	-0.015	-0.015	0.000	0.000	0.000	0.000
42	H	253	ASN	0	0.031	0.014	12.391	0.026	0.026	0.000	0.000	0.000	0.000
43	H	254	ARG	1	0.952	0.992	16.466	-0.255	-0.255	0.000	0.000	0.000	0.000
44	H	255	LYS	1	0.911	0.963	19.952	-0.241	-0.241	0.000	0.000	0.000	0.000
45	H	256	VAL	0	0.015	-0.016	17.667	-0.015	-0.015	0.000	0.000	0.000	0.000
46	H	257	SER	0	-0.075	-0.028	18.251	-0.028	-0.028	0.000	0.000	0.000	0.000
47	H	258	GLN	0	-0.047	-0.021	20.020	-0.023	-0.023	0.000	0.000	0.000	0.000
48	H	259	ARG	1	0.803	0.928	22.155	-0.292	-0.292	0.000	0.000	0.000	0.000
49	H	260	ARG	1	0.992	0.988	24.260	-0.144	-0.144	0.000	0.000	0.000	0.000
50	H	261	VAL	0	0.001	0.008	26.362	-0.008	-0.008	0.000	0.000	0.000	0.000
51	H	274	GLN	0	-0.039	-0.053	14.940	-0.058	-0.058	0.000	0.000	0.000	0.000
52	H	275	VAL	0	-0.015	-0.013	14.198	-0.038	-0.038	0.000	0.000	0.000	0.000
53	H	276	PRO	0	-0.033	0.021	12.577	0.034	0.034	0.000	0.000	0.000	0.000
54	H	277	CYS	0	0.001	-0.006	7.085	0.008	0.008	0.000	0.000	0.000	0.000
55	H	278	PHE	0	0.002	0.004	8.138	0.149	0.149	0.000	0.000	0.000	0.000
56	H	279	ALA	0	0.018	0.001	3.675	-0.360	-0.070	0.008	-0.064	-0.234	0.000
57	H	280	SER	0	-0.019	-0.018	5.758	0.023	0.023	0.000	0.000	0.000	0.000
58	H	281	MET	0	-0.007	0.010	4.817	-0.551	-0.360	0.000	-0.048	-0.143	0.000
59	H	282	LEU	0	-0.019	0.001	7.868	-0.076	-0.076	0.000	0.000	0.000	0.000
60	H	283	THR	0	-0.019	-0.027	11.483	-0.012	-0.012	0.000	0.000	0.000	0.000
61	H	284	LYS	1	0.926	0.956	14.150	0.003	0.003	0.000	0.000	0.000	0.000
62	H	285	LYS	1	0.957	0.990	16.189	-0.081	-0.081	0.000	0.000	0.000	0.000
63	H	286	LEU	0	-0.002	0.003	15.126	-0.023	-0.023	0.000	0.000	0.000	0.000
64	H	287	HIS	0	-0.002	-0.002	18.473	0.017	0.017	0.000	0.000	0.000	0.000
65	H	288	PHE	0	-0.026	-0.008	17.621	-0.009	-0.009	0.000	0.000	0.000	0.000
66	H	289	PHE	0	-0.004	0.008	23.120	-0.002	-0.002	0.000	0.000	0.000	0.000
67	H	290	PRO	0	-0.007	0.006	26.683	0.001	0.001	0.000	0.000	0.000	0.000
68	H	291	LYS	1	0.980	0.987	26.103	-0.105	-0.105	0.000	0.000	0.000	0.000

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