FMO DATABASE

FMODB ID: JL5J9

Calculation Name: 3P45-L-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: L

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-385331.025755
FMO2-HF: Nuclear repulsion	357625.352844
FMO2-HF: Total energy	-27705.672911
FMO2-MP2: Total energy	-27782.760971

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(L:202:ALA)

Summations of interaction energy for fragment #1(L: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.
-5.116	-0.857	1.692	-2.497	-3.455	-0.016

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.024

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	L	204	ALA	0	0.001	-0.019	3.820	-2.571	-0.843	-0.029	-0.932	-0.767	0.001
4	L	205	ASP	-1	-0.763	-0.859	6.479	0.075	0.075	0.000	0.000	0.000	0.000
5	L	206	PHE	0	0.003	0.019	2.840	-2.569	-0.324	1.715	-1.477	-2.483	-0.017
6	L	207	LEU	0	-0.014	-0.015	5.764	0.039	0.039	0.000	0.000	0.000	0.000
7	L	208	MET	0	-0.010	0.015	4.559	-0.190	0.029	0.007	-0.049	-0.178	0.000
8	L	209	CYS	0	-0.014	-0.008	7.231	0.102	0.102	0.000	0.000	0.000	0.000
9	L	210	TYR	0	0.014	-0.011	6.679	0.014	0.014	0.000	0.000	0.000	0.000
10	L	211	SER	0	0.028	-0.003	12.476	0.026	0.026	0.000	0.000	0.000	0.000
11	L	212	VAL	0	-0.002	0.011	14.753	0.028	0.028	0.000	0.000	0.000	0.000
12	L	224	ASN	0	0.024	-0.005	29.226	0.005	0.005	0.000	0.000	0.000	0.000
13	L	225	GLY	0	0.039	0.026	25.879	-0.004	-0.004	0.000	0.000	0.000	0.000
14	L	226	SER	0	0.017	0.003	20.716	0.004	0.004	0.000	0.000	0.000	0.000
15	L	227	TRP	0	0.049	0.005	23.564	-0.003	-0.003	0.000	0.000	0.000	0.000
16	L	228	TYR	0	0.077	0.051	14.729	0.004	0.004	0.000	0.000	0.000	0.000
17	L	229	ILE	0	0.040	0.016	17.057	-0.005	-0.005	0.000	0.000	0.000	0.000
18	L	230	GLN	0	0.009	0.013	20.632	0.009	0.009	0.000	0.000	0.000	0.000
19	L	231	ASP	-1	-0.779	-0.886	22.584	-0.138	-0.138	0.000	0.000	0.000	0.000
20	L	232	LEU	0	0.015	0.004	16.501	0.005	0.005	0.000	0.000	0.000	0.000
21	L	233	CYS	0	-0.026	-0.012	20.475	0.010	0.010	0.000	0.000	0.000	0.000
22	L	234	GLU	-1	-0.778	-0.866	22.632	-0.098	-0.098	0.000	0.000	0.000	0.000
23	L	235	MET	0	-0.046	-0.022	22.152	0.012	0.012	0.000	0.000	0.000	0.000
24	L	236	LEU	0	-0.007	-0.018	18.271	0.006	0.006	0.000	0.000	0.000	0.000
25	L	237	GLY	0	0.000	0.008	22.410	0.009	0.009	0.000	0.000	0.000	0.000
26	L	238	LYS	1	0.848	0.924	26.005	0.105	0.105	0.000	0.000	0.000	0.000
27	L	239	TYR	0	0.014	-0.020	24.242	0.006	0.006	0.000	0.000	0.000	0.000
28	L	240	GLY	0	0.013	0.027	21.825	-0.001	-0.001	0.000	0.000	0.000	0.000
29	L	241	SER	0	-0.032	-0.012	22.403	0.001	0.001	0.000	0.000	0.000	0.000
30	L	242	SER	0	-0.036	-0.028	24.931	0.007	0.007	0.000	0.000	0.000	0.000
31	L	243	LEU	0	-0.024	-0.020	22.688	0.002	0.002	0.000	0.000	0.000	0.000
32	L	244	GLU	-1	-0.782	-0.847	17.208	-0.201	-0.201	0.000	0.000	0.000	0.000
33	L	245	PHE	0	0.040	-0.013	12.884	-0.010	-0.010	0.000	0.000	0.000	0.000
34	L	246	THR	0	-0.023	-0.038	14.004	-0.028	-0.028	0.000	0.000	0.000	0.000
35	L	247	GLU	-1	-0.839	-0.927	16.552	-0.126	-0.126	0.000	0.000	0.000	0.000
36	L	248	LEU	0	-0.046	-0.019	18.958	-0.001	-0.001	0.000	0.000	0.000	0.000
37	L	249	LEU	0	0.026	0.007	13.528	0.005	0.005	0.000	0.000	0.000	0.000
38	L	250	THR	0	-0.019	-0.006	17.724	-0.010	-0.010	0.000	0.000	0.000	0.000
39	L	251	LEU	0	-0.063	-0.029	19.755	0.011	0.011	0.000	0.000	0.000	0.000
40	L	252	VAL	0	-0.007	0.007	18.790	0.009	0.009	0.000	0.000	0.000	0.000
41	L	253	ASN	0	0.039	0.008	17.063	-0.001	-0.001	0.000	0.000	0.000	0.000
42	L	254	ARG	1	0.944	0.999	20.709	0.141	0.141	0.000	0.000	0.000	0.000
43	L	255	LYS	1	0.834	0.920	24.165	0.123	0.123	0.000	0.000	0.000	0.000
44	L	256	VAL	0	0.023	-0.001	21.004	0.008	0.008	0.000	0.000	0.000	0.000
45	L	257	SER	0	-0.052	-0.032	23.654	0.009	0.009	0.000	0.000	0.000	0.000
46	L	258	GLN	0	-0.030	-0.010	25.318	0.006	0.006	0.000	0.000	0.000	0.000
47	L	259	ARG	1	0.817	0.912	25.915	0.143	0.143	0.000	0.000	0.000	0.000
48	L	260	ARG	1	0.919	0.963	28.950	0.115	0.115	0.000	0.000	0.000	0.000
49	L	274	GLN	0	0.006	0.003	22.152	-0.005	-0.005	0.000	0.000	0.000	0.000
50	L	275	VAL	0	-0.040	-0.037	20.024	0.013	0.013	0.000	0.000	0.000	0.000
51	L	276	PRO	0	-0.045	0.012	16.656	-0.014	-0.014	0.000	0.000	0.000	0.000
52	L	277	CYS	0	-0.001	-0.014	13.265	-0.014	-0.014	0.000	0.000	0.000	0.000
53	L	278	PHE	0	0.008	0.002	11.258	-0.007	-0.007	0.000	0.000	0.000	0.000
54	L	279	ALA	0	0.024	0.023	7.844	0.035	0.035	0.000	0.000	0.000	0.000
55	L	280	SER	0	-0.005	-0.014	8.104	-0.129	-0.129	0.000	0.000	0.000	0.000
56	L	281	MET	0	-0.018	0.004	5.762	-0.398	-0.331	-0.001	-0.039	-0.027	0.000
57	L	282	LEU	0	-0.027	0.003	8.504	0.177	0.177	0.000	0.000	0.000	0.000
58	L	283	THR	0	-0.043	-0.055	11.047	0.041	0.041	0.000	0.000	0.000	0.000
59	L	284	LYS	1	0.844	0.919	13.363	-0.015	-0.015	0.000	0.000	0.000	0.000
60	L	285	LYS	1	0.881	0.954	15.642	0.089	0.089	0.000	0.000	0.000	0.000
61	L	286	LEU	0	-0.002	-0.002	13.327	0.022	0.022	0.000	0.000	0.000	0.000
62	L	287	HIS	0	-0.008	0.002	17.201	-0.017	-0.017	0.000	0.000	0.000	0.000
63	L	288	PHE	0	-0.024	-0.013	15.188	0.009	0.009	0.000	0.000	0.000	0.000
64	L	289	PHE	0	0.026	0.017	21.267	0.001	0.001	0.000	0.000	0.000	0.000
65	L	290	PRO	0	-0.017	-0.010	24.615	0.004	0.004	0.000	0.000	0.000	0.000
66	L	291	LYS	1	0.986	1.007	22.442	0.009	0.009	0.000	0.000	0.000	0.000

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