FMO DATABASE

FMODB ID: G6391

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	OptHSide
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	-380823.195639
FMO2-HF: Nuclear repulsion	353093.120816
FMO2-HF: Total energy	-27730.074823
FMO2-MP2: Total energy	-27807.187454

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.
-2.505	-1.694	9.029	-4.677	-5.163	-0.02

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 : 0.004 / q_NPA : -0.028

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	N	204	ALA	0	-0.014	-0.016	3.043	-0.066	1.036	0.209	-0.228	-1.083	-0.001
4	N	205	ASP	-1	-0.816	-0.893	5.712	-0.598	-0.598	0.000	0.000	0.000	0.000
5	N	206	PHE	0	-0.020	0.008	2.953	-2.171	-0.890	0.244	-0.578	-0.947	-0.005
6	N	207	LEU	0	-0.013	-0.015	4.847	0.924	1.025	-0.001	-0.003	-0.096	0.000
7	N	208	MET	0	-0.002	0.017	3.653	-1.437	-1.105	0.015	-0.095	-0.252	0.000
8	N	209	CYS	0	-0.009	-0.008	6.437	0.038	0.038	0.000	0.000	0.000	0.000
9	N	210	TYR	0	0.022	0.003	5.923	-0.345	-0.345	0.000	0.000	0.000	0.000
10	N	211	SER	0	0.037	0.005	11.916	-0.049	-0.049	0.000	0.000	0.000	0.000
11	N	212	VAL	0	-0.009	0.003	15.258	0.004	0.004	0.000	0.000	0.000	0.000
12	N	222	THR	0	0.040	0.022	28.674	-0.001	-0.001	0.000	0.000	0.000	0.000
13	N	223	VAL	0	-0.016	-0.029	28.797	0.004	0.004	0.000	0.000	0.000	0.000
14	N	224	ASN	0	0.022	0.016	30.136	-0.010	-0.010	0.000	0.000	0.000	0.000
15	N	225	GLY	0	0.016	0.017	25.754	0.001	0.001	0.000	0.000	0.000	0.000
16	N	226	SER	0	0.002	-0.004	21.054	0.005	0.005	0.000	0.000	0.000	0.000
17	N	227	TRP	0	0.050	0.000	23.415	0.001	0.001	0.000	0.000	0.000	0.000
18	N	228	TYR	0	0.077	0.045	13.418	-0.002	-0.002	0.000	0.000	0.000	0.000
19	N	229	ILE	0	0.046	0.024	17.410	0.005	0.005	0.000	0.000	0.000	0.000
20	N	230	GLN	0	0.008	0.009	20.417	-0.001	-0.001	0.000	0.000	0.000	0.000
21	N	231	ASP	-1	-0.738	-0.856	22.076	0.170	0.170	0.000	0.000	0.000	0.000
22	N	232	LEU	0	-0.011	0.001	16.049	-0.001	-0.001	0.000	0.000	0.000	0.000
23	N	233	CYS	0	-0.017	-0.030	19.933	-0.018	-0.018	0.000	0.000	0.000	0.000
24	N	234	GLU	-1	-0.856	-0.899	22.284	0.110	0.110	0.000	0.000	0.000	0.000
25	N	235	MET	0	-0.022	-0.023	21.236	-0.012	-0.012	0.000	0.000	0.000	0.000
26	N	236	LEU	0	0.001	0.003	17.803	-0.010	-0.010	0.000	0.000	0.000	0.000
27	N	237	GLY	0	-0.001	0.005	21.924	-0.014	-0.014	0.000	0.000	0.000	0.000
28	N	238	LYS	1	0.802	0.916	25.523	-0.119	-0.119	0.000	0.000	0.000	0.000
29	N	239	TYR	0	0.050	-0.012	23.355	-0.003	-0.003	0.000	0.000	0.000	0.000
30	N	240	GLY	0	0.010	0.012	21.067	0.003	0.003	0.000	0.000	0.000	0.000
31	N	241	SER	0	-0.049	-0.014	21.609	-0.002	-0.002	0.000	0.000	0.000	0.000
32	N	242	SER	0	-0.024	-0.030	23.996	-0.007	-0.007	0.000	0.000	0.000	0.000
33	N	243	LEU	0	0.020	0.010	21.508	0.000	0.000	0.000	0.000	0.000	0.000
34	N	244	GLU	-1	-0.794	-0.851	15.582	0.256	0.256	0.000	0.000	0.000	0.000
35	N	245	PHE	0	0.035	-0.011	12.780	0.021	0.021	0.000	0.000	0.000	0.000
36	N	246	THR	0	-0.024	-0.042	12.507	0.055	0.055	0.000	0.000	0.000	0.000
37	N	247	GLU	-1	-0.817	-0.904	15.124	0.216	0.216	0.000	0.000	0.000	0.000
38	N	248	LEU	0	-0.017	0.006	17.985	0.003	0.003	0.000	0.000	0.000	0.000
39	N	249	LEU	0	0.010	-0.004	12.436	-0.006	-0.006	0.000	0.000	0.000	0.000
40	N	250	THR	0	-0.037	-0.029	16.584	0.037	0.037	0.000	0.000	0.000	0.000
41	N	251	LEU	0	-0.067	-0.036	18.414	-0.016	-0.016	0.000	0.000	0.000	0.000
42	N	252	VAL	0	-0.033	-0.005	17.844	-0.011	-0.011	0.000	0.000	0.000	0.000
43	N	253	ASN	0	0.048	0.013	15.854	-0.003	-0.003	0.000	0.000	0.000	0.000
44	N	254	ARG	1	0.953	0.992	19.524	-0.233	-0.233	0.000	0.000	0.000	0.000
45	N	255	LYS	1	0.836	0.900	23.175	-0.169	-0.169	0.000	0.000	0.000	0.000
46	N	256	VAL	0	0.008	-0.006	20.262	-0.013	-0.013	0.000	0.000	0.000	0.000
47	N	257	SER	0	-0.089	-0.037	22.749	-0.011	-0.011	0.000	0.000	0.000	0.000
48	N	258	GLN	0	-0.042	-0.029	24.293	-0.008	-0.008	0.000	0.000	0.000	0.000
49	N	259	ARG	1	0.833	0.940	25.463	-0.178	-0.178	0.000	0.000	0.000	0.000
50	N	275	VAL	0	-0.042	-0.039	18.866	-0.021	-0.021	0.000	0.000	0.000	0.000
51	N	276	PRO	0	-0.034	0.024	15.699	0.021	0.021	0.000	0.000	0.000	0.000
52	N	277	CYS	0	-0.021	-0.025	12.237	0.060	0.060	0.000	0.000	0.000	0.000
53	N	278	PHE	0	0.011	-0.001	10.177	-0.020	-0.020	0.000	0.000	0.000	0.000
54	N	279	ALA	0	0.022	0.024	6.292	-0.038	-0.038	0.000	0.000	0.000	0.000
55	N	280	SER	0	-0.002	-0.015	6.488	0.357	0.357	0.000	0.000	0.000	0.000
56	N	281	MET	0	0.001	0.015	2.640	1.156	-0.849	8.562	-3.773	-2.785	-0.014
57	N	282	LEU	0	-0.007	0.013	5.744	-0.551	-0.551	0.000	0.000	0.000	0.000
58	N	283	THR	0	-0.020	-0.034	8.767	0.083	0.083	0.000	0.000	0.000	0.000
59	N	284	LYS	1	0.847	0.911	11.338	0.188	0.188	0.000	0.000	0.000	0.000
60	N	285	LYS	1	0.891	0.966	13.621	-0.134	-0.134	0.000	0.000	0.000	0.000
61	N	286	LEU	0	-0.016	-0.011	12.612	-0.046	-0.046	0.000	0.000	0.000	0.000
62	N	287	HIS	0	0.005	0.002	16.226	0.044	0.044	0.000	0.000	0.000	0.000
63	N	288	PHE	0	-0.017	-0.007	14.726	-0.032	-0.032	0.000	0.000	0.000	0.000
64	N	289	PHE	0	0.011	0.015	20.647	0.006	0.006	0.000	0.000	0.000	0.000
65	N	290	PRO	0	0.003	-0.009	24.150	-0.013	-0.013	0.000	0.000	0.000	0.000
66	N	291	LYS	1	0.935	0.977	22.129	0.095	0.095	0.000	0.000	0.000	0.000
67	N	292	SER	0	0.035	0.026	26.587	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)