FMO DATABASE

FMODB ID: K94N3

Calculation Name: 3P45-D-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: D

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-415668.872797
FMO2-HF: Nuclear repulsion	386594.371175
FMO2-HF: Total energy	-29074.501622
FMO2-MP2: Total energy	-29155.716915

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(D:200:LEU)

Summations of interaction energy for fragment #1(D:200:LEU)

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.
-7.308	-5.912	5.329	-2.318	-4.409	0.011

Interaction energy analysis for fragmet #1(D:200:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.025

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	D	202	ALA	0	0.046	0.014	3.837	-1.646	-0.605	-0.007	-0.435	-0.600	0.002
4	D	203	GLY	0	0.004	-0.006	6.467	0.202	0.202	0.000	0.000	0.000	0.000
5	D	204	ALA	0	-0.019	-0.024	8.326	0.037	0.037	0.000	0.000	0.000	0.000
6	D	205	ASP	-1	-0.849	-0.909	10.730	-0.154	-0.154	0.000	0.000	0.000	0.000
7	D	206	PHE	0	-0.021	0.019	7.049	0.078	0.078	0.000	0.000	0.000	0.000
8	D	207	LEU	0	-0.009	-0.019	7.398	-0.030	-0.030	0.000	0.000	0.000	0.000
9	D	208	MET	0	-0.022	0.011	3.520	-1.073	-0.616	0.012	-0.117	-0.352	0.000
10	D	209	CYS	0	-0.005	-0.008	6.376	0.000	0.000	0.000	0.000	0.000	0.000
11	D	210	TYR	0	0.032	0.003	2.431	-2.840	-3.442	4.755	-1.495	-2.659	0.008
12	D	211	SER	0	0.028	0.001	9.272	-0.216	-0.216	0.000	0.000	0.000	0.000
13	D	212	VAL	0	-0.001	0.033	9.493	-0.108	-0.108	0.000	0.000	0.000	0.000
14	D	222	THR	0	0.004	-0.048	25.332	0.000	0.000	0.000	0.000	0.000	0.000
15	D	223	VAL	0	0.027	0.035	26.646	0.018	0.018	0.000	0.000	0.000	0.000
16	D	224	ASN	0	0.006	0.013	28.309	-0.006	-0.006	0.000	0.000	0.000	0.000
17	D	225	GLY	0	0.008	0.011	24.090	0.003	0.003	0.000	0.000	0.000	0.000
18	D	226	SER	0	0.005	0.013	18.797	-0.008	-0.008	0.000	0.000	0.000	0.000
19	D	227	TRP	0	0.073	0.008	20.008	0.001	0.001	0.000	0.000	0.000	0.000
20	D	228	TYR	0	0.032	0.018	12.556	0.009	0.009	0.000	0.000	0.000	0.000
21	D	229	ILE	0	0.042	0.018	16.141	0.003	0.003	0.000	0.000	0.000	0.000
22	D	230	GLN	0	0.013	0.014	19.196	-0.018	-0.018	0.000	0.000	0.000	0.000
23	D	231	ASP	-1	-0.726	-0.854	19.923	0.276	0.276	0.000	0.000	0.000	0.000
24	D	232	LEU	0	-0.013	-0.009	15.217	-0.014	-0.014	0.000	0.000	0.000	0.000
25	D	233	CYS	0	-0.013	-0.024	18.807	-0.026	-0.026	0.000	0.000	0.000	0.000
26	D	234	GLU	-1	-0.938	-0.957	21.769	0.184	0.184	0.000	0.000	0.000	0.000
27	D	235	MET	0	-0.067	-0.039	20.293	-0.028	-0.028	0.000	0.000	0.000	0.000
28	D	236	LEU	0	0.007	-0.010	18.296	-0.019	-0.019	0.000	0.000	0.000	0.000
29	D	237	GLY	0	-0.010	0.007	21.943	-0.020	-0.020	0.000	0.000	0.000	0.000
30	D	238	LYS	1	0.900	0.971	25.302	-0.177	-0.177	0.000	0.000	0.000	0.000
31	D	239	TYR	0	0.018	-0.017	23.048	-0.013	-0.013	0.000	0.000	0.000	0.000
32	D	240	GLY	0	0.031	0.019	21.753	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	241	SER	0	-0.047	-0.015	22.622	-0.002	-0.002	0.000	0.000	0.000	0.000
34	D	242	SER	0	-0.009	-0.019	24.708	-0.013	-0.013	0.000	0.000	0.000	0.000
35	D	243	LEU	0	-0.009	0.001	20.961	-0.010	-0.010	0.000	0.000	0.000	0.000
36	D	244	GLU	-1	-0.747	-0.804	16.168	0.196	0.196	0.000	0.000	0.000	0.000
37	D	245	PHE	0	0.039	0.001	13.085	0.024	0.024	0.000	0.000	0.000	0.000
38	D	246	THR	0	-0.031	-0.077	11.971	0.049	0.049	0.000	0.000	0.000	0.000
39	D	247	GLU	-1	-0.896	-0.931	14.099	0.179	0.179	0.000	0.000	0.000	0.000
40	D	248	LEU	0	-0.016	-0.004	17.204	0.011	0.011	0.000	0.000	0.000	0.000
41	D	249	LEU	0	0.018	-0.006	11.476	0.022	0.022	0.000	0.000	0.000	0.000
42	D	250	THR	0	-0.040	-0.032	14.534	0.041	0.041	0.000	0.000	0.000	0.000
43	D	251	LEU	0	-0.066	-0.032	15.340	-0.014	-0.014	0.000	0.000	0.000	0.000
44	D	252	VAL	0	-0.003	0.002	15.814	-0.013	-0.013	0.000	0.000	0.000	0.000
45	D	253	ASN	0	0.043	0.022	11.653	0.052	0.052	0.000	0.000	0.000	0.000
46	D	254	ARG	1	0.944	0.988	15.696	-0.222	-0.222	0.000	0.000	0.000	0.000
47	D	255	LYS	1	0.863	0.925	19.168	-0.261	-0.261	0.000	0.000	0.000	0.000
48	D	256	VAL	0	-0.004	-0.011	17.124	-0.014	-0.014	0.000	0.000	0.000	0.000
49	D	257	SER	0	0.050	0.027	18.187	-0.024	-0.024	0.000	0.000	0.000	0.000
50	D	258	GLN	0	-0.104	-0.043	19.860	-0.025	-0.025	0.000	0.000	0.000	0.000
51	D	259	ARG	1	0.832	0.937	21.894	-0.288	-0.288	0.000	0.000	0.000	0.000
52	D	260	ARG	1	0.903	0.948	22.778	-0.189	-0.189	0.000	0.000	0.000	0.000
53	D	274	GLN	0	-0.029	-0.049	14.882	-0.057	-0.057	0.000	0.000	0.000	0.000
54	D	275	VAL	0	-0.010	-0.017	13.628	-0.045	-0.045	0.000	0.000	0.000	0.000
55	D	276	PRO	0	-0.033	0.019	11.847	0.052	0.052	0.000	0.000	0.000	0.000
56	D	277	CYS	0	0.009	-0.011	6.911	0.044	0.044	0.000	0.000	0.000	0.000
57	D	278	PHE	0	-0.037	-0.018	7.220	0.212	0.212	0.000	0.000	0.000	0.000
58	D	279	ALA	0	0.053	0.040	2.565	-0.717	-0.245	0.570	-0.263	-0.779	0.001
59	D	280	SER	0	-0.006	-0.013	4.595	-0.208	-0.180	-0.001	-0.008	-0.019	0.000
60	D	281	MET	0	0.022	0.027	5.151	-0.375	-0.375	0.000	0.000	0.000	0.000
61	D	282	LEU	0	-0.023	0.006	7.551	-0.045	-0.045	0.000	0.000	0.000	0.000
62	D	283	THR	0	-0.012	-0.035	11.137	0.004	0.004	0.000	0.000	0.000	0.000
63	D	284	LYS	1	0.910	0.952	13.677	0.053	0.053	0.000	0.000	0.000	0.000
64	D	285	LYS	1	0.962	0.986	15.568	-0.054	-0.054	0.000	0.000	0.000	0.000
65	D	286	LEU	0	-0.025	-0.002	14.962	-0.018	-0.018	0.000	0.000	0.000	0.000
66	D	287	HIS	0	0.004	0.000	18.198	0.016	0.016	0.000	0.000	0.000	0.000
67	D	288	PHE	0	-0.019	-0.014	17.062	-0.011	-0.011	0.000	0.000	0.000	0.000
68	D	289	PHE	0	0.002	0.011	22.695	0.002	0.002	0.000	0.000	0.000	0.000
69	D	290	PRO	0	0.005	0.000	26.277	0.000	0.000	0.000	0.000	0.000	0.000
70	D	291	LYS	1	0.975	0.998	26.239	-0.074	-0.074	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:200:LEU)