FMO DATABASE

FMODB ID: 85Y3Y

Calculation Name: 3P45-N-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: N

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-382382.349496
FMO2-HF: Nuclear repulsion	354652.022343
FMO2-HF: Total energy	-27730.327153
FMO2-MP2: Total energy	-27807.431815

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(N:202:ALA)

Summations of interaction energy for fragment #1(N: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.
-4.866	-1.479	5.862	-3.993	-5.259	-0.018

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.002

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	N	204	ALA	0	0.009	-0.009	3.868	-0.254	1.739	-0.014	-1.126	-0.854	0.006
4	N	205	ASP	-1	-0.769	-0.853	6.793	-0.666	-0.666	0.000	0.000	0.000	0.000
5	N	206	PHE	0	0.007	0.019	2.390	-3.365	-1.905	1.821	-1.239	-2.043	-0.015
6	N	207	LEU	0	-0.002	-0.013	5.274	0.449	0.501	-0.001	-0.002	-0.049	0.000
7	N	208	MET	0	0.005	0.028	3.897	-1.236	-0.716	0.041	-0.176	-0.386	0.000
8	N	209	CYS	0	-0.018	-0.019	6.599	-0.340	-0.340	0.000	0.000	0.000	0.000
9	N	210	TYR	0	0.015	0.000	5.822	0.170	0.170	0.000	0.000	0.000	0.000
10	N	211	SER	0	0.034	0.005	12.448	-0.083	-0.083	0.000	0.000	0.000	0.000
11	N	212	VAL	0	-0.027	0.003	14.565	-0.023	-0.023	0.000	0.000	0.000	0.000
12	N	222	THR	0	-0.005	-0.005	27.820	-0.005	-0.005	0.000	0.000	0.000	0.000
13	N	223	VAL	0	0.013	-0.013	28.379	0.008	0.008	0.000	0.000	0.000	0.000
14	N	224	ASN	0	0.011	0.017	29.855	-0.006	-0.006	0.000	0.000	0.000	0.000
15	N	225	GLY	0	0.039	0.032	25.779	0.003	0.003	0.000	0.000	0.000	0.000
16	N	226	SER	0	0.017	0.003	21.292	-0.004	-0.004	0.000	0.000	0.000	0.000
17	N	227	TRP	0	0.021	-0.004	23.466	0.007	0.007	0.000	0.000	0.000	0.000
18	N	228	TYR	0	0.102	0.047	13.646	-0.015	-0.015	0.000	0.000	0.000	0.000
19	N	229	ILE	0	0.032	0.022	17.665	0.004	0.004	0.000	0.000	0.000	0.000
20	N	230	GLN	0	0.032	0.013	20.689	-0.011	-0.011	0.000	0.000	0.000	0.000
21	N	231	ASP	-1	-0.749	-0.866	22.406	0.223	0.223	0.000	0.000	0.000	0.000
22	N	232	LEU	0	0.006	0.007	16.177	-0.010	-0.010	0.000	0.000	0.000	0.000
23	N	233	CYS	0	-0.034	-0.026	20.297	-0.024	-0.024	0.000	0.000	0.000	0.000
24	N	234	GLU	-1	-0.810	-0.878	22.598	0.144	0.144	0.000	0.000	0.000	0.000
25	N	235	MET	0	-0.028	-0.022	21.463	-0.021	-0.021	0.000	0.000	0.000	0.000
26	N	236	LEU	0	0.000	-0.005	17.835	-0.018	-0.018	0.000	0.000	0.000	0.000
27	N	237	GLY	0	-0.008	-0.002	21.964	-0.020	-0.020	0.000	0.000	0.000	0.000
28	N	238	LYS	1	0.807	0.907	25.563	-0.155	-0.155	0.000	0.000	0.000	0.000
29	N	239	TYR	0	0.031	-0.004	23.576	-0.005	-0.005	0.000	0.000	0.000	0.000
30	N	240	GLY	0	0.034	0.018	21.348	-0.003	-0.003	0.000	0.000	0.000	0.000
31	N	241	SER	0	-0.044	-0.012	21.968	-0.007	-0.007	0.000	0.000	0.000	0.000
32	N	242	SER	0	-0.014	-0.023	23.881	-0.013	-0.013	0.000	0.000	0.000	0.000
33	N	243	LEU	0	0.013	0.012	21.397	-0.007	-0.007	0.000	0.000	0.000	0.000
34	N	244	GLU	-1	-0.788	-0.856	15.207	0.191	0.191	0.000	0.000	0.000	0.000
35	N	245	PHE	0	0.035	0.001	13.282	0.020	0.020	0.000	0.000	0.000	0.000
36	N	246	THR	0	-0.018	-0.036	12.235	0.066	0.066	0.000	0.000	0.000	0.000
37	N	247	GLU	-1	-0.804	-0.879	14.971	0.160	0.160	0.000	0.000	0.000	0.000
38	N	248	LEU	0	-0.017	-0.002	18.302	0.012	0.012	0.000	0.000	0.000	0.000
39	N	249	LEU	0	0.026	-0.002	12.717	0.006	0.006	0.000	0.000	0.000	0.000
40	N	250	THR	0	-0.038	-0.025	16.842	0.034	0.034	0.000	0.000	0.000	0.000
41	N	251	LEU	0	-0.062	-0.028	18.534	-0.015	-0.015	0.000	0.000	0.000	0.000
42	N	252	VAL	0	-0.016	-0.001	18.365	-0.012	-0.012	0.000	0.000	0.000	0.000
43	N	253	ASN	0	0.022	0.002	15.474	0.012	0.012	0.000	0.000	0.000	0.000
44	N	254	ARG	1	0.957	0.993	19.572	-0.224	-0.224	0.000	0.000	0.000	0.000
45	N	255	LYS	1	0.819	0.899	23.202	-0.207	-0.207	0.000	0.000	0.000	0.000
46	N	256	VAL	0	0.000	-0.004	20.697	-0.013	-0.013	0.000	0.000	0.000	0.000
47	N	257	SER	0	-0.081	-0.046	22.595	-0.016	-0.016	0.000	0.000	0.000	0.000
48	N	258	GLN	0	-0.031	-0.016	24.251	-0.010	-0.010	0.000	0.000	0.000	0.000
49	N	259	ARG	1	0.803	0.915	25.865	-0.238	-0.238	0.000	0.000	0.000	0.000
50	N	275	VAL	0	-0.023	-0.025	18.634	-0.018	-0.018	0.000	0.000	0.000	0.000
51	N	276	PRO	0	-0.036	0.008	16.437	0.039	0.039	0.000	0.000	0.000	0.000
52	N	277	CYS	0	-0.012	-0.012	12.388	-0.005	-0.005	0.000	0.000	0.000	0.000
53	N	278	PHE	0	0.016	-0.006	10.245	0.045	0.045	0.000	0.000	0.000	0.000
54	N	279	ALA	0	0.018	0.012	5.979	-0.107	-0.107	0.000	0.000	0.000	0.000
55	N	280	SER	0	0.003	-0.004	5.932	0.424	0.424	0.000	0.000	0.000	0.000
56	N	281	MET	0	-0.017	0.003	2.911	0.248	-0.390	4.015	-1.450	-1.927	-0.009
57	N	282	LEU	0	-0.034	0.002	6.160	-0.402	-0.402	0.000	0.000	0.000	0.000
58	N	283	THR	0	-0.050	-0.046	9.314	0.074	0.074	0.000	0.000	0.000	0.000
59	N	284	LYS	1	0.812	0.886	11.977	0.369	0.369	0.000	0.000	0.000	0.000
60	N	285	LYS	1	0.846	0.926	13.730	-0.056	-0.056	0.000	0.000	0.000	0.000
61	N	286	LEU	0	-0.016	-0.009	12.658	-0.043	-0.043	0.000	0.000	0.000	0.000
62	N	287	HIS	0	0.022	0.000	16.013	0.045	0.045	0.000	0.000	0.000	0.000
63	N	288	PHE	0	-0.022	-0.013	14.827	-0.029	-0.029	0.000	0.000	0.000	0.000
64	N	289	PHE	0	0.005	0.012	20.756	0.005	0.005	0.000	0.000	0.000	0.000
65	N	290	PRO	0	-0.009	-0.010	24.285	-0.011	-0.011	0.000	0.000	0.000	0.000
66	N	291	LYS	1	0.931	0.977	22.151	0.072	0.072	0.000	0.000	0.000	0.000
67	N	292	SER	0	0.033	0.025	26.750	0.001	0.001	0.000	0.000	0.000	0.000

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