FMO DATABASE

FMODB ID: YZ532

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

Total energy (hartree)

FMO2-HF: Electronic energy	-436721.038063
FMO2-HF: Nuclear repulsion	406736.720975
FMO2-HF: Total energy	-29984.317088
FMO2-MP2: Total energy	-30068.303909

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.
-10.018	-2.869	6.717	-4.14	-9.726	-0.014

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 : -0.021 / q_NPA : -0.033

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	-0.033	-0.008	3.602	-3.008	1.075	-0.040	-1.948	-2.095	-0.008
4	B	201	PRO	0	-0.059	-0.025	5.574	0.311	0.311	0.000	0.000	0.000	0.000
5	B	202	ALA	0	0.074	0.028	8.903	-0.047	-0.047	0.000	0.000	0.000	0.000
6	B	203	GLY	0	0.013	0.005	11.292	0.039	0.039	0.000	0.000	0.000	0.000
7	B	204	ALA	0	-0.005	-0.008	13.897	-0.010	-0.010	0.000	0.000	0.000	0.000
8	B	205	ASP	-1	-0.858	-0.912	16.198	-0.110	-0.110	0.000	0.000	0.000	0.000
9	B	206	PHE	0	-0.001	0.022	11.149	0.040	0.040	0.000	0.000	0.000	0.000
10	B	207	LEU	0	-0.010	-0.012	10.520	-0.061	-0.061	0.000	0.000	0.000	0.000
11	B	208	MET	0	-0.028	-0.004	6.033	0.129	0.129	0.000	0.000	0.000	0.000
12	B	209	CYS	0	-0.007	-0.019	7.834	-0.029	-0.029	0.000	0.000	0.000	0.000
13	B	210	TYR	0	0.060	0.029	2.538	-3.306	-1.744	5.254	-1.408	-5.409	-0.010
14	B	211	SER	0	0.037	0.017	4.792	-0.223	-0.116	-0.001	-0.009	-0.097	0.000
15	B	212	VAL	0	-0.015	-0.001	2.346	-2.982	-1.585	1.504	-0.775	-2.125	0.004
16	B	222	THR	0	0.026	0.002	16.629	-0.021	-0.021	0.000	0.000	0.000	0.000
17	B	223	VAL	0	0.007	-0.011	17.922	0.041	0.041	0.000	0.000	0.000	0.000
18	B	224	ASN	0	0.003	0.014	20.530	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	225	GLY	0	0.023	0.021	16.823	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	226	SER	0	-0.016	-0.014	11.339	-0.039	-0.039	0.000	0.000	0.000	0.000
21	B	227	TRP	0	0.064	0.013	12.456	0.017	0.017	0.000	0.000	0.000	0.000
22	B	228	TYR	0	0.068	0.041	9.068	0.029	0.029	0.000	0.000	0.000	0.000
23	B	229	ILE	0	0.040	0.020	10.634	-0.048	-0.048	0.000	0.000	0.000	0.000
24	B	230	GLN	0	0.006	0.005	13.454	-0.092	-0.092	0.000	0.000	0.000	0.000
25	B	231	ASP	-1	-0.790	-0.897	15.080	0.244	0.244	0.000	0.000	0.000	0.000
26	B	232	LEU	0	-0.047	-0.028	12.110	-0.042	-0.042	0.000	0.000	0.000	0.000
27	B	233	CYS	0	-0.026	-0.030	15.266	-0.047	-0.047	0.000	0.000	0.000	0.000
28	B	234	GLU	-1	-0.925	-0.958	18.146	0.130	0.130	0.000	0.000	0.000	0.000
29	B	235	MET	0	-0.037	-0.029	18.201	-0.044	-0.044	0.000	0.000	0.000	0.000
30	B	236	LEU	0	0.005	0.002	16.972	-0.029	-0.029	0.000	0.000	0.000	0.000
31	B	237	GLY	0	-0.007	0.007	20.513	-0.021	-0.021	0.000	0.000	0.000	0.000
32	B	238	LYS	1	0.869	0.958	23.265	-0.125	-0.125	0.000	0.000	0.000	0.000
33	B	239	TYR	0	0.010	-0.028	22.508	-0.013	-0.013	0.000	0.000	0.000	0.000
34	B	240	GLY	0	0.026	0.021	21.880	-0.010	-0.010	0.000	0.000	0.000	0.000
35	B	241	SER	0	-0.053	-0.018	22.700	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	242	SER	0	-0.023	-0.024	25.484	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	243	LEU	0	0.011	0.005	22.528	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	244	GLU	-1	-0.696	-0.785	19.363	-0.020	-0.020	0.000	0.000	0.000	0.000
39	B	245	PHE	0	0.012	-0.006	14.181	0.015	0.015	0.000	0.000	0.000	0.000
40	B	246	THR	0	-0.059	-0.092	14.926	0.026	0.026	0.000	0.000	0.000	0.000
41	B	247	GLU	-1	-0.846	-0.933	16.593	0.011	0.011	0.000	0.000	0.000	0.000
42	B	248	LEU	0	-0.023	0.004	16.946	0.017	0.017	0.000	0.000	0.000	0.000
43	B	249	LEU	0	0.002	-0.016	12.189	0.035	0.035	0.000	0.000	0.000	0.000
44	B	250	THR	0	-0.054	-0.024	14.657	0.027	0.027	0.000	0.000	0.000	0.000
45	B	251	LEU	0	-0.063	-0.043	16.536	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	252	VAL	0	-0.009	0.006	12.948	0.009	0.009	0.000	0.000	0.000	0.000
47	B	253	ASN	0	0.024	0.005	12.122	0.111	0.111	0.000	0.000	0.000	0.000
48	B	254	ARG	1	0.912	0.964	14.171	-0.047	-0.047	0.000	0.000	0.000	0.000
49	B	255	LYS	1	0.942	0.973	17.099	-0.137	-0.137	0.000	0.000	0.000	0.000
50	B	256	VAL	0	0.034	0.011	11.387	0.000	0.000	0.000	0.000	0.000	0.000
51	B	257	SER	0	-0.067	-0.017	14.005	-0.035	-0.035	0.000	0.000	0.000	0.000
52	B	258	GLN	0	-0.025	-0.012	14.867	-0.028	-0.028	0.000	0.000	0.000	0.000
53	B	259	ARG	1	0.826	0.929	15.261	-0.267	-0.267	0.000	0.000	0.000	0.000
54	B	260	ARG	1	0.967	0.994	16.277	-0.027	-0.027	0.000	0.000	0.000	0.000
55	B	274	GLN	0	-0.005	-0.021	8.101	-0.223	-0.223	0.000	0.000	0.000	0.000
56	B	275	VAL	0	-0.023	-0.021	8.286	-0.019	-0.019	0.000	0.000	0.000	0.000
57	B	276	PRO	0	-0.051	0.016	7.492	0.135	0.135	0.000	0.000	0.000	0.000
58	B	277	CYS	0	0.013	-0.006	6.115	-0.405	-0.405	0.000	0.000	0.000	0.000
59	B	278	PHE	0	-0.022	-0.019	7.842	0.197	0.197	0.000	0.000	0.000	0.000
60	B	279	ALA	0	0.046	0.031	6.226	-0.165	-0.165	0.000	0.000	0.000	0.000
61	B	280	SER	0	-0.005	-0.007	8.130	0.044	0.044	0.000	0.000	0.000	0.000
62	B	281	MET	0	0.009	0.020	10.401	-0.046	-0.046	0.000	0.000	0.000	0.000
63	B	282	LEU	0	-0.032	-0.009	13.238	0.040	0.040	0.000	0.000	0.000	0.000
64	B	283	THR	0	-0.024	-0.036	16.044	-0.012	-0.012	0.000	0.000	0.000	0.000
65	B	284	LYS	1	0.922	0.951	19.452	0.083	0.083	0.000	0.000	0.000	0.000
66	B	285	LYS	1	0.940	0.983	20.009	0.073	0.073	0.000	0.000	0.000	0.000
67	B	286	LEU	0	-0.008	0.011	17.646	0.004	0.004	0.000	0.000	0.000	0.000
68	B	287	HIS	0	0.009	0.002	21.272	-0.003	-0.003	0.000	0.000	0.000	0.000
69	B	288	PHE	0	-0.026	-0.015	18.972	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	289	PHE	0	0.010	0.020	24.433	0.007	0.007	0.000	0.000	0.000	0.000
71	B	290	PRO	0	0.004	-0.004	28.151	0.003	0.003	0.000	0.000	0.000	0.000
72	B	291	LYS	1	0.978	1.001	27.602	-0.055	-0.055	0.000	0.000	0.000	0.000

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