FMO DATABASE

FMODB ID: 171RZ

Calculation Name: 3P45-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: B

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-438357.156416
FMO2-HF: Nuclear repulsion	408371.993723
FMO2-HF: Total energy	-29985.162693
FMO2-MP2: Total energy	-30069.145905

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(B:198:TYR)

Summations of interaction energy for fragment #1(B:198:TYR)

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.
-11.632	-2.78	6.056	-4.189	-10.718	-0.008

Interaction energy analysis for fragmet #1(B:198:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.029

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	B	200	LEU	0	0.016	0.021	3.255	-0.614	1.776	0.016	-1.057	-1.348	-0.001
4	B	201	PRO	0	-0.030	-0.032	5.154	-0.002	0.063	-0.001	-0.002	-0.061	0.000
5	B	202	ALA	0	0.030	0.021	8.494	0.007	0.007	0.000	0.000	0.000	0.000
6	B	203	GLY	0	0.026	0.015	11.100	0.063	0.063	0.000	0.000	0.000	0.000
7	B	204	ALA	0	0.021	-0.005	13.587	0.006	0.006	0.000	0.000	0.000	0.000
8	B	205	ASP	-1	-0.786	-0.861	16.145	-0.058	-0.058	0.000	0.000	0.000	0.000
9	B	206	PHE	0	-0.002	0.021	10.956	0.006	0.006	0.000	0.000	0.000	0.000
10	B	207	LEU	0	-0.026	-0.026	10.515	0.016	0.016	0.000	0.000	0.000	0.000
11	B	208	MET	0	-0.030	0.007	5.578	0.086	0.086	0.000	0.000	0.000	0.000
12	B	209	CYS	0	-0.008	-0.011	6.958	0.144	0.144	0.000	0.000	0.000	0.000
13	B	210	TYR	0	0.048	0.008	2.549	-5.456	-1.595	3.924	-1.686	-6.098	-0.008
14	B	211	SER	0	0.056	0.024	4.357	-0.314	-0.159	-0.001	-0.013	-0.141	0.000
15	B	212	VAL	0	-0.024	0.007	2.227	-4.455	-2.074	2.118	-1.431	-3.070	0.001
16	B	222	THR	0	0.005	0.002	16.231	-0.017	-0.017	0.000	0.000	0.000	0.000
17	B	223	VAL	0	0.016	-0.009	18.029	0.026	0.026	0.000	0.000	0.000	0.000
18	B	224	ASN	0	0.008	0.015	20.406	-0.007	-0.007	0.000	0.000	0.000	0.000
19	B	225	GLY	0	0.042	0.038	16.588	0.008	0.008	0.000	0.000	0.000	0.000
20	B	226	SER	0	0.006	-0.008	11.352	-0.035	-0.035	0.000	0.000	0.000	0.000
21	B	227	TRP	0	0.017	-0.006	12.325	0.029	0.029	0.000	0.000	0.000	0.000
22	B	228	TYR	0	0.083	0.039	8.386	0.047	0.047	0.000	0.000	0.000	0.000
23	B	229	ILE	0	0.039	0.026	10.242	-0.039	-0.039	0.000	0.000	0.000	0.000
24	B	230	GLN	0	0.023	0.009	13.189	-0.065	-0.065	0.000	0.000	0.000	0.000
25	B	231	ASP	-1	-0.775	-0.896	14.544	0.303	0.303	0.000	0.000	0.000	0.000
26	B	232	LEU	0	-0.006	-0.002	11.596	-0.041	-0.041	0.000	0.000	0.000	0.000
27	B	233	CYS	0	-0.030	-0.020	15.018	-0.055	-0.055	0.000	0.000	0.000	0.000
28	B	234	GLU	-1	-0.795	-0.869	17.972	0.164	0.164	0.000	0.000	0.000	0.000
29	B	235	MET	0	-0.027	-0.020	17.639	-0.038	-0.038	0.000	0.000	0.000	0.000
30	B	236	LEU	0	0.024	0.000	15.945	-0.030	-0.030	0.000	0.000	0.000	0.000
31	B	237	GLY	0	-0.010	-0.005	19.888	-0.023	-0.023	0.000	0.000	0.000	0.000
32	B	238	LYS	1	0.796	0.902	22.675	-0.181	-0.181	0.000	0.000	0.000	0.000
33	B	239	TYR	0	0.022	-0.005	21.592	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	240	GLY	0	0.031	0.016	21.560	-0.007	-0.007	0.000	0.000	0.000	0.000
35	B	241	SER	0	-0.040	-0.010	22.293	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	242	SER	0	-0.021	-0.022	24.954	-0.012	-0.012	0.000	0.000	0.000	0.000
37	B	243	LEU	0	0.010	0.012	22.381	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	244	GLU	-1	-0.795	-0.863	18.780	0.111	0.111	0.000	0.000	0.000	0.000
39	B	245	PHE	0	0.041	0.003	13.442	0.022	0.022	0.000	0.000	0.000	0.000
40	B	246	THR	0	-0.027	-0.038	14.112	0.042	0.042	0.000	0.000	0.000	0.000
41	B	247	GLU	-1	-0.829	-0.903	15.933	0.137	0.137	0.000	0.000	0.000	0.000
42	B	248	LEU	0	-0.008	0.000	16.929	0.017	0.017	0.000	0.000	0.000	0.000
43	B	249	LEU	0	0.010	-0.009	11.525	0.034	0.034	0.000	0.000	0.000	0.000
44	B	250	THR	0	-0.037	-0.025	14.175	0.058	0.058	0.000	0.000	0.000	0.000
45	B	251	LEU	0	-0.067	-0.030	16.204	-0.011	-0.011	0.000	0.000	0.000	0.000
46	B	252	VAL	0	-0.012	0.000	12.526	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	253	ASN	0	0.023	0.000	11.465	0.109	0.109	0.000	0.000	0.000	0.000
48	B	254	ARG	1	0.949	0.987	13.138	-0.195	-0.195	0.000	0.000	0.000	0.000
49	B	255	LYS	1	0.839	0.930	16.173	-0.243	-0.243	0.000	0.000	0.000	0.000
50	B	256	VAL	0	0.001	-0.004	10.526	-0.011	-0.011	0.000	0.000	0.000	0.000
51	B	257	SER	0	-0.061	-0.031	12.989	-0.049	-0.049	0.000	0.000	0.000	0.000
52	B	258	GLN	0	-0.033	-0.012	13.816	-0.036	-0.036	0.000	0.000	0.000	0.000
53	B	259	ARG	1	0.776	0.894	14.919	-0.320	-0.320	0.000	0.000	0.000	0.000
54	B	260	ARG	1	0.984	0.998	15.479	-0.090	-0.090	0.000	0.000	0.000	0.000
55	B	274	GLN	0	0.008	-0.007	7.601	-0.168	-0.168	0.000	0.000	0.000	0.000
56	B	275	VAL	0	-0.022	-0.031	7.757	0.033	0.033	0.000	0.000	0.000	0.000
57	B	276	PRO	0	-0.049	0.006	6.470	-0.023	-0.023	0.000	0.000	0.000	0.000
58	B	277	CYS	0	-0.013	-0.014	5.559	-0.418	-0.418	0.000	0.000	0.000	0.000
59	B	278	PHE	0	0.018	0.002	7.167	0.200	0.200	0.000	0.000	0.000	0.000
60	B	279	ALA	0	0.023	0.018	5.843	-0.084	-0.084	0.000	0.000	0.000	0.000
61	B	280	SER	0	0.001	-0.008	7.677	-0.097	-0.097	0.000	0.000	0.000	0.000
62	B	281	MET	0	0.014	0.013	10.249	-0.015	-0.015	0.000	0.000	0.000	0.000
63	B	282	LEU	0	-0.035	0.001	13.296	0.003	0.003	0.000	0.000	0.000	0.000
64	B	283	THR	0	-0.045	-0.043	15.974	0.012	0.012	0.000	0.000	0.000	0.000
65	B	284	LYS	1	0.823	0.890	19.189	0.040	0.040	0.000	0.000	0.000	0.000
66	B	285	LYS	1	0.891	0.963	19.514	-0.072	-0.072	0.000	0.000	0.000	0.000
67	B	286	LEU	0	-0.013	-0.003	17.030	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	287	HIS	0	0.009	-0.011	20.663	0.014	0.014	0.000	0.000	0.000	0.000
69	B	288	PHE	0	-0.026	-0.016	18.427	-0.009	-0.009	0.000	0.000	0.000	0.000
70	B	289	PHE	0	0.000	0.013	23.678	0.004	0.004	0.000	0.000	0.000	0.000
71	B	290	PRO	0	0.012	0.007	27.438	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	291	LYS	1	0.962	0.989	27.046	-0.048	-0.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:198:TYR)