FMO DATABASE

FMODB ID: N9Y5Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-384273.349551
FMO2-HF: Nuclear repulsion	356568.262069
FMO2-HF: Total energy	-27705.087482
FMO2-MP2: Total energy	-27782.168652

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.
-5.088	-0.75	1.219	-2.477	-3.08	-0.015

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 : -0.025 / q_NPA : -0.019

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	-0.002	-0.019	3.820	-2.620	-0.859	-0.030	-0.956	-0.774	0.001
4	L	205	ASP	-1	-0.836	-0.918	6.468	0.117	0.117	0.000	0.000	0.000	0.000
5	L	206	PHE	0	-0.009	0.009	3.042	-2.611	-0.297	1.229	-1.451	-2.093	-0.016
6	L	207	LEU	0	-0.007	-0.015	5.644	0.054	0.054	0.000	0.000	0.000	0.000
7	L	208	MET	0	-0.020	0.007	4.323	-0.300	-0.037	0.020	-0.070	-0.213	0.000
8	L	209	CYS	0	-0.007	-0.008	7.176	0.111	0.111	0.000	0.000	0.000	0.000
9	L	210	TYR	0	0.015	-0.004	6.555	0.038	0.038	0.000	0.000	0.000	0.000
10	L	211	SER	0	0.041	-0.014	12.464	0.032	0.032	0.000	0.000	0.000	0.000
11	L	212	VAL	0	-0.015	0.022	14.611	0.027	0.027	0.000	0.000	0.000	0.000
12	L	224	ASN	0	0.011	-0.013	28.876	0.006	0.006	0.000	0.000	0.000	0.000
13	L	225	GLY	0	0.042	0.028	25.890	-0.004	-0.004	0.000	0.000	0.000	0.000
14	L	226	SER	0	0.025	0.011	20.676	0.003	0.003	0.000	0.000	0.000	0.000
15	L	227	TRP	0	0.055	0.010	23.555	-0.003	-0.003	0.000	0.000	0.000	0.000
16	L	228	TYR	0	0.067	0.040	14.812	0.002	0.002	0.000	0.000	0.000	0.000
17	L	229	ILE	0	0.023	0.006	16.994	-0.006	-0.006	0.000	0.000	0.000	0.000
18	L	230	GLN	0	-0.022	-0.011	20.613	0.013	0.013	0.000	0.000	0.000	0.000
19	L	231	ASP	-1	-0.781	-0.886	22.556	-0.148	-0.148	0.000	0.000	0.000	0.000
20	L	232	LEU	0	-0.008	-0.008	16.338	0.004	0.004	0.000	0.000	0.000	0.000
21	L	233	CYS	0	-0.028	-0.015	20.427	0.011	0.011	0.000	0.000	0.000	0.000
22	L	234	GLU	-1	-0.891	-0.944	22.588	-0.104	-0.104	0.000	0.000	0.000	0.000
23	L	235	MET	0	-0.060	-0.031	22.136	0.012	0.012	0.000	0.000	0.000	0.000
24	L	236	LEU	0	-0.010	-0.016	18.268	0.006	0.006	0.000	0.000	0.000	0.000
25	L	237	GLY	0	0.002	0.010	22.343	0.009	0.009	0.000	0.000	0.000	0.000
26	L	238	LYS	1	0.864	0.941	25.941	0.111	0.111	0.000	0.000	0.000	0.000
27	L	239	TYR	0	0.012	-0.016	24.240	0.006	0.006	0.000	0.000	0.000	0.000
28	L	240	GLY	0	0.014	0.030	21.739	-0.001	-0.001	0.000	0.000	0.000	0.000
29	L	241	SER	0	-0.027	-0.012	22.312	0.000	0.000	0.000	0.000	0.000	0.000
30	L	242	SER	0	-0.005	-0.022	24.842	0.009	0.009	0.000	0.000	0.000	0.000
31	L	243	LEU	0	-0.061	-0.034	22.659	0.002	0.002	0.000	0.000	0.000	0.000
32	L	244	GLU	-1	-0.770	-0.813	17.231	-0.224	-0.224	0.000	0.000	0.000	0.000
33	L	245	PHE	0	0.056	-0.009	13.141	-0.009	-0.009	0.000	0.000	0.000	0.000
34	L	246	THR	0	-0.050	-0.070	13.871	-0.029	-0.029	0.000	0.000	0.000	0.000
35	L	247	GLU	-1	-0.903	-0.958	16.446	-0.135	-0.135	0.000	0.000	0.000	0.000
36	L	248	LEU	0	-0.031	-0.011	18.527	0.000	0.000	0.000	0.000	0.000	0.000
37	L	249	LEU	0	0.031	0.002	13.392	0.005	0.005	0.000	0.000	0.000	0.000
38	L	250	THR	0	-0.007	0.006	17.643	-0.010	-0.010	0.000	0.000	0.000	0.000
39	L	251	LEU	0	-0.068	-0.034	19.671	0.013	0.013	0.000	0.000	0.000	0.000
40	L	252	VAL	0	-0.005	0.012	18.623	0.010	0.010	0.000	0.000	0.000	0.000
41	L	253	ASN	0	0.032	0.006	16.903	0.004	0.004	0.000	0.000	0.000	0.000
42	L	254	ARG	1	0.936	0.975	20.650	0.153	0.153	0.000	0.000	0.000	0.000
43	L	255	LYS	1	0.968	0.983	24.214	0.132	0.132	0.000	0.000	0.000	0.000
44	L	256	VAL	0	0.034	0.010	20.807	0.009	0.009	0.000	0.000	0.000	0.000
45	L	257	SER	0	-0.063	-0.015	23.614	0.011	0.011	0.000	0.000	0.000	0.000
46	L	258	GLN	0	-0.010	-0.003	25.278	0.007	0.007	0.000	0.000	0.000	0.000
47	L	259	ARG	1	0.855	0.944	26.034	0.149	0.149	0.000	0.000	0.000	0.000
48	L	260	ARG	1	0.908	0.956	28.926	0.120	0.120	0.000	0.000	0.000	0.000
49	L	274	GLN	0	-0.024	-0.028	22.121	-0.004	-0.004	0.000	0.000	0.000	0.000
50	L	275	VAL	0	-0.013	-0.004	19.837	0.014	0.014	0.000	0.000	0.000	0.000
51	L	276	PRO	0	-0.045	0.009	16.637	-0.015	-0.015	0.000	0.000	0.000	0.000
52	L	277	CYS	0	0.004	-0.010	13.368	-0.011	-0.011	0.000	0.000	0.000	0.000
53	L	278	PHE	0	0.007	-0.001	11.202	-0.007	-0.007	0.000	0.000	0.000	0.000
54	L	279	ALA	0	0.024	0.022	7.750	0.038	0.038	0.000	0.000	0.000	0.000
55	L	280	SER	0	-0.020	-0.016	8.009	-0.141	-0.141	0.000	0.000	0.000	0.000
56	L	281	MET	0	-0.026	0.029	5.473	-0.306	-0.306	0.000	0.000	0.000	0.000
57	L	282	LEU	0	-0.027	0.001	8.381	0.190	0.190	0.000	0.000	0.000	0.000
58	L	283	THR	0	-0.017	-0.015	10.919	0.028	0.028	0.000	0.000	0.000	0.000
59	L	284	LYS	1	0.912	0.952	13.840	0.012	0.012	0.000	0.000	0.000	0.000
60	L	285	LYS	1	0.954	0.985	15.516	0.097	0.097	0.000	0.000	0.000	0.000
61	L	286	LEU	0	0.014	0.003	13.278	0.025	0.025	0.000	0.000	0.000	0.000
62	L	287	HIS	0	-0.010	0.003	17.086	-0.017	-0.017	0.000	0.000	0.000	0.000
63	L	288	PHE	0	-0.026	-0.014	15.330	0.010	0.010	0.000	0.000	0.000	0.000
64	L	289	PHE	0	0.017	0.014	21.173	0.002	0.002	0.000	0.000	0.000	0.000
65	L	290	PRO	0	-0.021	-0.011	24.524	0.004	0.004	0.000	0.000	0.000	0.000
66	L	291	LYS	1	0.986	1.005	22.075	0.011	0.011	0.000	0.000	0.000	0.000

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