FMO DATABASE

FMODB ID: 4917N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-416330.929013
FMO2-HF: Nuclear repulsion	387255.850729
FMO2-HF: Total energy	-29075.078284
FMO2-MP2: Total energy	-29156.285061

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.
-11.039	-8.086	4.688	-3.118	-4.52	0.009

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 : 0.017 / q_NPA : -0.006

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	D	202	ALA	0	0.044	0.025	3.843	-1.501	0.003	-0.010	-0.703	-0.790	0.004
4	D	203	GLY	0	0.013	0.010	6.560	0.482	0.482	0.000	0.000	0.000	0.000
5	D	204	ALA	0	-0.022	-0.026	8.406	0.003	0.003	0.000	0.000	0.000	0.000
6	D	205	ASP	-1	-0.828	-0.897	10.788	-0.408	-0.408	0.000	0.000	0.000	0.000
7	D	206	PHE	0	-0.023	0.018	7.200	-0.073	-0.073	0.000	0.000	0.000	0.000
8	D	207	LEU	0	-0.008	-0.015	7.419	0.142	0.142	0.000	0.000	0.000	0.000
9	D	208	MET	0	-0.016	0.011	3.628	-0.442	-0.053	0.008	-0.078	-0.319	0.000
10	D	209	CYS	0	-0.004	-0.005	6.366	0.653	0.653	0.000	0.000	0.000	0.000
11	D	210	TYR	0	0.031	0.001	1.976	-8.362	-7.832	4.200	-2.074	-2.655	0.004
12	D	211	SER	0	0.034	0.005	8.923	-0.052	-0.052	0.000	0.000	0.000	0.000
13	D	212	VAL	0	-0.007	0.015	9.584	-0.037	-0.037	0.000	0.000	0.000	0.000
14	D	222	THR	0	0.007	-0.013	24.750	0.000	0.000	0.000	0.000	0.000	0.000
15	D	223	VAL	0	0.029	0.005	26.016	0.007	0.007	0.000	0.000	0.000	0.000
16	D	224	ASN	0	0.027	0.023	27.635	-0.015	-0.015	0.000	0.000	0.000	0.000
17	D	225	GLY	0	0.012	0.018	23.391	-0.003	-0.003	0.000	0.000	0.000	0.000
18	D	226	SER	0	0.002	0.004	18.006	0.010	0.010	0.000	0.000	0.000	0.000
19	D	227	TRP	0	0.049	-0.002	20.054	-0.007	-0.007	0.000	0.000	0.000	0.000
20	D	228	TYR	0	0.055	0.029	12.444	-0.018	-0.018	0.000	0.000	0.000	0.000
21	D	229	ILE	0	0.052	0.025	15.382	-0.008	-0.008	0.000	0.000	0.000	0.000
22	D	230	GLN	0	0.020	0.020	18.705	-0.010	-0.010	0.000	0.000	0.000	0.000
23	D	231	ASP	-1	-0.758	-0.867	19.772	0.262	0.262	0.000	0.000	0.000	0.000
24	D	232	LEU	0	-0.005	-0.006	14.996	-0.010	-0.010	0.000	0.000	0.000	0.000
25	D	233	CYS	0	-0.019	-0.027	18.789	-0.035	-0.035	0.000	0.000	0.000	0.000
26	D	234	GLU	-1	-0.833	-0.893	21.699	0.155	0.155	0.000	0.000	0.000	0.000
27	D	235	MET	0	-0.051	-0.027	20.314	-0.016	-0.016	0.000	0.000	0.000	0.000
28	D	236	LEU	0	0.012	-0.005	18.326	-0.017	-0.017	0.000	0.000	0.000	0.000
29	D	237	GLY	0	-0.008	0.006	21.934	-0.018	-0.018	0.000	0.000	0.000	0.000
30	D	238	LYS	1	0.824	0.925	25.275	-0.150	-0.150	0.000	0.000	0.000	0.000
31	D	239	TYR	0	0.024	-0.013	22.973	-0.003	-0.003	0.000	0.000	0.000	0.000
32	D	240	GLY	0	0.033	0.015	21.785	0.000	0.000	0.000	0.000	0.000	0.000
33	D	241	SER	0	-0.013	-0.001	22.624	-0.011	-0.011	0.000	0.000	0.000	0.000
34	D	242	SER	0	-0.039	-0.031	24.811	-0.007	-0.007	0.000	0.000	0.000	0.000
35	D	243	LEU	0	-0.006	0.002	21.086	-0.002	-0.002	0.000	0.000	0.000	0.000
36	D	244	GLU	-1	-0.776	-0.838	16.380	0.104	0.104	0.000	0.000	0.000	0.000
37	D	245	PHE	0	0.054	0.010	13.152	0.044	0.044	0.000	0.000	0.000	0.000
38	D	246	THR	0	0.002	-0.032	11.993	0.063	0.063	0.000	0.000	0.000	0.000
39	D	247	GLU	-1	-0.859	-0.926	14.158	0.207	0.207	0.000	0.000	0.000	0.000
40	D	248	LEU	0	-0.026	-0.007	17.307	0.031	0.031	0.000	0.000	0.000	0.000
41	D	249	LEU	0	0.019	-0.001	11.361	0.025	0.025	0.000	0.000	0.000	0.000
42	D	250	THR	0	-0.035	-0.023	14.527	0.092	0.092	0.000	0.000	0.000	0.000
43	D	251	LEU	0	-0.062	-0.033	15.326	0.010	0.010	0.000	0.000	0.000	0.000
44	D	252	VAL	0	-0.018	-0.003	15.783	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	253	ASN	0	0.044	0.021	11.837	0.046	0.046	0.000	0.000	0.000	0.000
46	D	254	ARG	1	0.932	0.977	15.621	-0.286	-0.286	0.000	0.000	0.000	0.000
47	D	255	LYS	1	0.823	0.900	19.096	-0.240	-0.240	0.000	0.000	0.000	0.000
48	D	256	VAL	0	0.002	-0.007	17.108	-0.016	-0.016	0.000	0.000	0.000	0.000
49	D	257	SER	0	0.018	0.016	18.295	-0.021	-0.021	0.000	0.000	0.000	0.000
50	D	258	GLN	0	-0.066	-0.030	19.891	-0.021	-0.021	0.000	0.000	0.000	0.000
51	D	259	ARG	1	0.815	0.927	21.858	-0.293	-0.293	0.000	0.000	0.000	0.000
52	D	260	ARG	1	0.904	0.946	22.806	-0.295	-0.295	0.000	0.000	0.000	0.000
53	D	274	GLN	0	0.017	-0.004	15.060	-0.070	-0.070	0.000	0.000	0.000	0.000
54	D	275	VAL	0	-0.059	-0.052	13.672	-0.070	-0.070	0.000	0.000	0.000	0.000
55	D	276	PRO	0	-0.023	0.023	11.895	0.107	0.107	0.000	0.000	0.000	0.000
56	D	277	CYS	0	-0.019	-0.011	7.579	0.232	0.232	0.000	0.000	0.000	0.000
57	D	278	PHE	0	-0.004	-0.014	7.165	0.023	0.023	0.000	0.000	0.000	0.000
58	D	279	ALA	0	0.034	0.031	2.624	-0.350	0.162	0.491	-0.256	-0.747	0.001
59	D	280	SER	0	0.009	-0.008	4.647	-0.831	-0.813	-0.001	-0.007	-0.009	0.000
60	D	281	MET	0	0.009	0.006	5.117	-0.232	-0.232	0.000	0.000	0.000	0.000
61	D	282	LEU	0	-0.035	0.001	7.664	-0.081	-0.081	0.000	0.000	0.000	0.000
62	D	283	THR	0	-0.032	-0.040	11.226	0.075	0.075	0.000	0.000	0.000	0.000
63	D	284	LYS	1	0.909	0.952	13.790	0.229	0.229	0.000	0.000	0.000	0.000
64	D	285	LYS	1	0.905	0.960	15.632	-0.081	-0.081	0.000	0.000	0.000	0.000
65	D	286	LEU	0	-0.028	-0.012	14.948	-0.029	-0.029	0.000	0.000	0.000	0.000
66	D	287	HIS	0	-0.004	-0.007	18.317	0.035	0.035	0.000	0.000	0.000	0.000
67	D	288	PHE	0	-0.014	-0.008	16.772	-0.026	-0.026	0.000	0.000	0.000	0.000
68	D	289	PHE	0	0.001	0.008	22.703	0.007	0.007	0.000	0.000	0.000	0.000
69	D	290	PRO	0	0.012	0.005	26.286	-0.011	-0.011	0.000	0.000	0.000	0.000
70	D	291	LYS	1	0.972	0.997	26.233	0.078	0.078	0.000	0.000	0.000	0.000

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