FMO DATABASE

FMODB ID: 391YL

Calculation Name: 3P45-L-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: L

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-386704.104827
FMO2-HF: Nuclear repulsion	358998.202242
FMO2-HF: Total energy	-27705.902585
FMO2-MP2: Total energy	-27782.994486

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(L:202:ALA)

Summations of interaction energy for fragment #1(L:202:ALA)

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.
-3.906	-0.008	4.343	-3.673	-4.567	-0.018

Interaction energy analysis for fragmet #1(L:202:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.026

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

Sort

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	L	204	ALA	0	0.018	-0.010	3.864	-1.080	0.364	-0.019	-0.795	-0.631	0.002
4	L	205	ASP	-1	-0.776	-0.863	6.370	0.125	0.125	0.000	0.000	0.000	0.000
5	L	206	PHE	0	0.027	0.026	2.662	-2.502	-0.489	4.333	-2.757	-3.588	-0.020
6	L	207	LEU	0	-0.004	-0.014	5.535	-0.063	-0.063	0.000	0.000	0.000	0.000
7	L	208	MET	0	0.004	0.028	3.826	-0.065	0.269	0.029	-0.077	-0.286	0.000
8	L	209	CYS	0	-0.025	-0.020	6.569	-0.010	-0.010	0.000	0.000	0.000	0.000
9	L	210	TYR	0	0.021	0.002	6.710	0.040	0.040	0.000	0.000	0.000	0.000
10	L	211	SER	0	0.038	0.006	12.473	0.006	0.006	0.000	0.000	0.000	0.000
11	L	212	VAL	0	-0.038	0.000	14.192	0.010	0.010	0.000	0.000	0.000	0.000
12	L	224	ASN	0	0.028	0.000	29.198	0.003	0.003	0.000	0.000	0.000	0.000
13	L	225	GLY	0	0.045	0.038	25.516	-0.002	-0.002	0.000	0.000	0.000	0.000
14	L	226	SER	0	0.015	0.002	20.744	0.000	0.000	0.000	0.000	0.000	0.000
15	L	227	TRP	0	0.021	-0.008	23.517	0.000	0.000	0.000	0.000	0.000	0.000
16	L	228	TYR	0	0.097	0.046	14.344	0.007	0.007	0.000	0.000	0.000	0.000
17	L	229	ILE	0	0.037	0.024	17.530	-0.001	-0.001	0.000	0.000	0.000	0.000
18	L	230	GLN	0	0.027	0.018	20.853	0.003	0.003	0.000	0.000	0.000	0.000
19	L	231	ASP	-1	-0.772	-0.890	22.407	-0.072	-0.072	0.000	0.000	0.000	0.000
20	L	232	LEU	0	-0.003	-0.001	16.425	0.001	0.001	0.000	0.000	0.000	0.000
21	L	233	CYS	0	-0.022	-0.015	20.459	0.007	0.007	0.000	0.000	0.000	0.000
22	L	234	GLU	-1	-0.801	-0.880	22.922	-0.049	-0.049	0.000	0.000	0.000	0.000
23	L	235	MET	0	-0.038	-0.024	21.701	0.003	0.003	0.000	0.000	0.000	0.000
24	L	236	LEU	0	0.004	-0.009	18.320	0.003	0.003	0.000	0.000	0.000	0.000
25	L	237	GLY	0	0.000	0.003	22.397	0.005	0.005	0.000	0.000	0.000	0.000
26	L	238	LYS	1	0.823	0.921	26.020	0.054	0.054	0.000	0.000	0.000	0.000
27	L	239	TYR	0	0.034	0.004	23.943	0.001	0.001	0.000	0.000	0.000	0.000
28	L	240	GLY	0	0.036	0.021	21.550	-0.003	-0.003	0.000	0.000	0.000	0.000
29	L	241	SER	0	-0.044	-0.015	22.087	0.000	0.000	0.000	0.000	0.000	0.000
30	L	242	SER	0	-0.039	-0.033	24.017	0.004	0.004	0.000	0.000	0.000	0.000
31	L	243	LEU	0	0.009	0.008	21.950	-0.001	-0.001	0.000	0.000	0.000	0.000
32	L	244	GLU	-1	-0.790	-0.854	16.110	-0.151	-0.151	0.000	0.000	0.000	0.000
33	L	245	PHE	0	0.039	0.001	12.483	-0.006	-0.006	0.000	0.000	0.000	0.000
34	L	246	THR	0	0.001	-0.029	13.163	-0.015	-0.015	0.000	0.000	0.000	0.000
35	L	247	GLU	-1	-0.805	-0.878	15.832	-0.096	-0.096	0.000	0.000	0.000	0.000
36	L	248	LEU	0	-0.020	-0.006	18.699	0.002	0.002	0.000	0.000	0.000	0.000
37	L	249	LEU	0	0.006	-0.007	13.078	0.005	0.005	0.000	0.000	0.000	0.000
38	L	250	THR	0	-0.025	-0.022	17.302	-0.008	-0.008	0.000	0.000	0.000	0.000
39	L	251	LEU	0	-0.064	-0.029	19.272	0.007	0.007	0.000	0.000	0.000	0.000
40	L	252	VAL	0	-0.012	-0.001	18.612	0.006	0.006	0.000	0.000	0.000	0.000
41	L	253	ASN	0	0.040	0.012	16.066	0.008	0.008	0.000	0.000	0.000	0.000
42	L	254	ARG	1	0.956	1.007	20.016	0.097	0.097	0.000	0.000	0.000	0.000
43	L	255	LYS	1	0.824	0.915	23.617	0.067	0.067	0.000	0.000	0.000	0.000
44	L	256	VAL	0	0.006	-0.005	20.748	0.006	0.006	0.000	0.000	0.000	0.000
45	L	257	SER	0	-0.014	-0.023	23.085	0.006	0.006	0.000	0.000	0.000	0.000
46	L	258	GLN	0	-0.046	-0.021	24.729	0.002	0.002	0.000	0.000	0.000	0.000
47	L	259	ARG	1	0.781	0.901	25.693	0.075	0.075	0.000	0.000	0.000	0.000
48	L	260	ARG	1	0.923	0.963	28.768	0.077	0.077	0.000	0.000	0.000	0.000
49	L	274	GLN	0	0.010	0.006	21.829	0.000	0.000	0.000	0.000	0.000	0.000
50	L	275	VAL	0	-0.028	-0.032	19.381	0.010	0.010	0.000	0.000	0.000	0.000
51	L	276	PRO	0	-0.025	0.013	16.387	-0.009	-0.009	0.000	0.000	0.000	0.000
52	L	277	CYS	0	-0.021	-0.016	12.940	-0.018	-0.018	0.000	0.000	0.000	0.000
53	L	278	PHE	0	0.009	-0.006	10.484	0.018	0.018	0.000	0.000	0.000	0.000
54	L	279	ALA	0	0.022	0.012	6.923	-0.001	-0.001	0.000	0.000	0.000	0.000
55	L	280	SER	0	-0.004	-0.005	6.840	-0.097	-0.097	0.000	0.000	0.000	0.000
56	L	281	MET	0	-0.014	-0.001	4.901	-0.572	-0.465	0.000	-0.044	-0.062	0.000
57	L	282	LEU	0	-0.040	-0.001	7.807	0.101	0.101	0.000	0.000	0.000	0.000
58	L	283	THR	0	-0.035	-0.036	10.597	0.026	0.026	0.000	0.000	0.000	0.000
59	L	284	LYS	1	0.807	0.887	13.002	0.070	0.070	0.000	0.000	0.000	0.000
60	L	285	LYS	1	0.835	0.920	14.938	0.073	0.073	0.000	0.000	0.000	0.000
61	L	286	LEU	0	-0.007	-0.010	12.971	0.022	0.022	0.000	0.000	0.000	0.000
62	L	287	HIS	0	0.029	0.008	16.645	-0.018	-0.018	0.000	0.000	0.000	0.000
63	L	288	PHE	0	-0.026	-0.014	14.857	0.012	0.012	0.000	0.000	0.000	0.000
64	L	289	PHE	0	-0.008	0.001	20.833	0.003	0.003	0.000	0.000	0.000	0.000
65	L	290	PRO	0	0.007	0.002	24.232	0.007	0.007	0.000	0.000	0.000	0.000
66	L	291	LYS	1	0.964	0.997	22.291	-0.039	-0.039	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:202:ALA)