FMO DATABASE

FMODB ID: 171ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-379926.775177
FMO2-HF: Nuclear repulsion	352197.210169
FMO2-HF: Total energy	-27729.565007
FMO2-MP2: Total energy	-27806.652406

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.
0.506	-5.574	25.834	-12.58	-7.174	-0.038

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 : -0.043

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	-0.006	-0.011	2.973	-0.426	1.060	0.275	-0.552	-1.209	-0.004
4	N	205	ASP	-1	-0.875	-0.934	5.664	-0.784	-0.784	0.000	0.000	0.000	0.000
5	N	206	PHE	0	-0.019	0.004	2.967	-1.997	-0.853	0.174	-0.481	-0.837	-0.004
6	N	207	LEU	0	-0.021	-0.020	4.844	1.097	1.187	-0.001	-0.003	-0.086	0.000
7	N	208	MET	0	-0.008	0.015	3.774	-1.644	-1.215	0.047	-0.135	-0.341	0.000
8	N	209	CYS	0	-0.015	-0.012	6.429	0.080	0.080	0.000	0.000	0.000	0.000
9	N	210	TYR	0	0.021	0.003	5.805	-0.389	-0.389	0.000	0.000	0.000	0.000
10	N	211	SER	0	0.047	0.011	11.908	-0.044	-0.044	0.000	0.000	0.000	0.000
11	N	212	VAL	0	-0.015	0.000	15.246	0.009	0.009	0.000	0.000	0.000	0.000
12	N	222	THR	0	0.005	-0.010	28.631	-0.001	-0.001	0.000	0.000	0.000	0.000
13	N	223	VAL	0	0.016	0.001	28.792	0.004	0.004	0.000	0.000	0.000	0.000
14	N	224	ASN	0	0.023	0.020	30.130	-0.011	-0.011	0.000	0.000	0.000	0.000
15	N	225	GLY	0	0.017	0.019	25.749	0.000	0.000	0.000	0.000	0.000	0.000
16	N	226	SER	0	0.003	-0.003	20.903	0.006	0.006	0.000	0.000	0.000	0.000
17	N	227	TRP	0	0.060	0.007	23.303	0.001	0.001	0.000	0.000	0.000	0.000
18	N	228	TYR	0	0.075	0.042	13.784	0.010	0.010	0.000	0.000	0.000	0.000
19	N	229	ILE	0	0.035	0.017	17.213	0.005	0.005	0.000	0.000	0.000	0.000
20	N	230	GLN	0	-0.022	-0.014	20.410	-0.002	-0.002	0.000	0.000	0.000	0.000
21	N	231	ASP	-1	-0.789	-0.898	22.033	0.171	0.171	0.000	0.000	0.000	0.000
22	N	232	LEU	0	-0.025	-0.007	15.947	0.001	0.001	0.000	0.000	0.000	0.000
23	N	233	CYS	0	-0.010	-0.027	19.925	-0.019	-0.019	0.000	0.000	0.000	0.000
24	N	234	GLU	-1	-0.982	-0.973	22.277	0.099	0.099	0.000	0.000	0.000	0.000
25	N	235	MET	0	-0.035	-0.031	21.213	-0.011	-0.011	0.000	0.000	0.000	0.000
26	N	236	LEU	0	-0.008	-0.005	17.833	-0.010	-0.010	0.000	0.000	0.000	0.000
27	N	237	GLY	0	0.005	0.009	21.917	-0.014	-0.014	0.000	0.000	0.000	0.000
28	N	238	LYS	1	0.888	0.961	25.516	-0.116	-0.116	0.000	0.000	0.000	0.000
29	N	239	TYR	0	0.033	-0.015	23.360	-0.003	-0.003	0.000	0.000	0.000	0.000
30	N	240	GLY	0	0.007	0.016	21.061	0.004	0.004	0.000	0.000	0.000	0.000
31	N	241	SER	0	-0.050	-0.017	21.603	-0.002	-0.002	0.000	0.000	0.000	0.000
32	N	242	SER	0	-0.028	-0.029	23.974	-0.006	-0.006	0.000	0.000	0.000	0.000
33	N	243	LEU	0	0.018	0.008	21.534	0.000	0.000	0.000	0.000	0.000	0.000
34	N	244	GLU	-1	-0.762	-0.806	15.718	0.264	0.264	0.000	0.000	0.000	0.000
35	N	245	PHE	0	0.043	-0.007	12.442	0.024	0.024	0.000	0.000	0.000	0.000
36	N	246	THR	0	-0.020	-0.061	12.486	0.049	0.049	0.000	0.000	0.000	0.000
37	N	247	GLU	-1	-0.877	-0.918	15.115	0.223	0.223	0.000	0.000	0.000	0.000
38	N	248	LEU	0	-0.013	0.007	17.663	0.002	0.002	0.000	0.000	0.000	0.000
39	N	249	LEU	0	0.004	-0.011	12.434	-0.006	-0.006	0.000	0.000	0.000	0.000
40	N	250	THR	0	-0.029	-0.036	16.575	0.039	0.039	0.000	0.000	0.000	0.000
41	N	251	LEU	0	-0.072	-0.038	18.404	-0.016	-0.016	0.000	0.000	0.000	0.000
42	N	252	VAL	0	-0.029	-0.008	17.871	-0.012	-0.012	0.000	0.000	0.000	0.000
43	N	253	ASN	0	0.054	0.022	15.837	-0.014	-0.014	0.000	0.000	0.000	0.000
44	N	254	ARG	1	0.938	0.985	19.514	-0.240	-0.240	0.000	0.000	0.000	0.000
45	N	255	LYS	1	0.960	0.974	23.232	-0.170	-0.170	0.000	0.000	0.000	0.000
46	N	256	VAL	0	0.030	0.009	20.268	-0.012	-0.012	0.000	0.000	0.000	0.000
47	N	257	SER	0	-0.093	-0.038	22.693	-0.012	-0.012	0.000	0.000	0.000	0.000
48	N	258	GLN	0	-0.041	-0.026	24.283	-0.011	-0.011	0.000	0.000	0.000	0.000
49	N	259	ARG	1	0.857	0.960	25.609	-0.172	-0.172	0.000	0.000	0.000	0.000
50	N	275	VAL	0	-0.011	-0.024	18.870	-0.024	-0.024	0.000	0.000	0.000	0.000
51	N	276	PRO	0	-0.063	0.009	15.677	0.022	0.022	0.000	0.000	0.000	0.000
52	N	277	CYS	0	-0.026	-0.022	12.152	0.060	0.060	0.000	0.000	0.000	0.000
53	N	278	PHE	0	0.002	-0.011	10.170	-0.029	-0.029	0.000	0.000	0.000	0.000
54	N	279	ALA	0	0.033	0.031	6.272	-0.039	-0.039	0.000	0.000	0.000	0.000
55	N	280	SER	0	-0.016	-0.019	6.478	0.331	0.331	0.000	0.000	0.000	0.000
56	N	281	MET	0	0.000	0.039	2.295	4.711	-4.518	25.339	-11.409	-4.701	-0.030
57	N	282	LEU	0	0.007	0.012	5.788	-0.600	-0.600	0.000	0.000	0.000	0.000
58	N	283	THR	0	-0.001	-0.008	8.763	0.118	0.118	0.000	0.000	0.000	0.000
59	N	284	LYS	1	0.900	0.938	11.342	0.088	0.088	0.000	0.000	0.000	0.000
60	N	285	LYS	1	0.949	0.989	13.612	-0.142	-0.142	0.000	0.000	0.000	0.000
61	N	286	LEU	0	-0.017	-0.019	12.615	-0.046	-0.046	0.000	0.000	0.000	0.000
62	N	287	HIS	0	-0.003	0.002	16.220	0.045	0.045	0.000	0.000	0.000	0.000
63	N	288	PHE	0	-0.019	-0.010	14.849	-0.033	-0.033	0.000	0.000	0.000	0.000
64	N	289	PHE	0	0.002	0.013	20.642	0.006	0.006	0.000	0.000	0.000	0.000
65	N	290	PRO	0	0.000	-0.010	24.146	-0.014	-0.014	0.000	0.000	0.000	0.000
66	N	291	LYS	1	0.942	0.979	22.038	0.106	0.106	0.000	0.000	0.000	0.000
67	N	292	SER	0	0.030	0.023	26.585	0.002	0.002	0.000	0.000	0.000	0.000

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