FMO DATABASE

FMODB ID: V5371

Calculation Name: 3P45-P-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: P

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	OptAll
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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-399570.435868
FMO2-HF: Nuclear repulsion	371221.072584
FMO2-HF: Total energy	-28349.363284
FMO2-MP2: Total energy	-28428.351127

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(P:201:PRO)

Summations of interaction energy for fragment #1(P:201:PRO)

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.
-14.213	-4.788	9.447	-6.076	-12.798	-0.011

Interaction energy analysis for fragmet #1(P:201:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.016

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	P	203	GLY	0	0.026	0.013	3.241	-1.730	1.289	-0.007	-1.542	-1.470	0.000
4	P	204	ALA	0	0.019	-0.005	3.958	-0.363	-0.086	0.001	-0.075	-0.202	0.000
5	P	205	ASP	-1	-0.785	-0.868	6.610	-0.316	-0.316	0.000	0.000	0.000	0.000
6	P	206	PHE	0	0.008	0.019	2.304	-0.416	0.139	1.384	-0.572	-1.367	-0.001
7	P	207	LEU	0	-0.020	-0.021	3.832	-0.972	-0.520	0.014	-0.094	-0.372	0.000
8	P	208	MET	0	-0.014	0.019	2.284	-3.446	-1.632	3.398	-1.422	-3.791	0.006
9	P	209	CYS	0	-0.024	-0.021	4.154	-1.163	-1.069	-0.001	-0.002	-0.091	0.000
10	P	210	TYR	0	0.031	0.003	3.743	-0.469	-0.105	0.001	-0.085	-0.280	0.001
11	P	211	SER	0	0.044	0.012	9.510	-0.175	-0.175	0.000	0.000	0.000	0.000
12	P	212	VAL	0	-0.028	-0.002	11.859	-0.063	-0.063	0.000	0.000	0.000	0.000
13	P	224	ASN	0	0.053	0.020	27.962	-0.012	-0.012	0.000	0.000	0.000	0.000
14	P	225	GLY	0	0.009	0.013	23.801	0.005	0.005	0.000	0.000	0.000	0.000
15	P	226	SER	0	0.016	0.004	19.052	-0.020	-0.020	0.000	0.000	0.000	0.000
16	P	227	TRP	0	0.017	-0.008	20.671	0.010	0.010	0.000	0.000	0.000	0.000
17	P	228	TYR	0	0.103	0.047	11.105	0.009	0.009	0.000	0.000	0.000	0.000
18	P	229	ILE	0	0.033	0.025	16.065	0.008	0.008	0.000	0.000	0.000	0.000
19	P	230	GLN	0	0.032	0.015	18.593	-0.024	-0.024	0.000	0.000	0.000	0.000
20	P	231	ASP	-1	-0.785	-0.900	19.211	0.254	0.254	0.000	0.000	0.000	0.000
21	P	232	LEU	0	-0.001	0.001	14.121	-0.023	-0.023	0.000	0.000	0.000	0.000
22	P	233	CYS	0	-0.027	-0.019	17.675	-0.022	-0.022	0.000	0.000	0.000	0.000
23	P	234	GLU	-1	-0.793	-0.873	20.680	0.154	0.154	0.000	0.000	0.000	0.000
24	P	235	MET	0	-0.033	-0.020	18.478	-0.031	-0.031	0.000	0.000	0.000	0.000
25	P	236	LEU	0	0.007	-0.002	16.184	-0.022	-0.022	0.000	0.000	0.000	0.000
26	P	237	GLY	0	-0.004	0.001	19.930	-0.022	-0.022	0.000	0.000	0.000	0.000
27	P	238	LYS	1	0.819	0.903	23.408	-0.169	-0.169	0.000	0.000	0.000	0.000
28	P	239	TYR	0	0.019	-0.008	20.740	-0.014	-0.014	0.000	0.000	0.000	0.000
29	P	240	GLY	0	0.026	0.015	19.017	-0.008	-0.008	0.000	0.000	0.000	0.000
30	P	241	SER	0	-0.033	-0.008	19.817	-0.007	-0.007	0.000	0.000	0.000	0.000
31	P	242	SER	0	-0.005	-0.017	21.653	-0.017	-0.017	0.000	0.000	0.000	0.000
32	P	243	LEU	0	0.013	0.011	18.874	-0.016	-0.016	0.000	0.000	0.000	0.000
33	P	244	GLU	-1	-0.785	-0.848	13.234	0.034	0.034	0.000	0.000	0.000	0.000
34	P	245	PHE	0	0.040	-0.001	10.185	0.026	0.026	0.000	0.000	0.000	0.000
35	P	246	THR	0	-0.008	-0.033	9.593	0.051	0.051	0.000	0.000	0.000	0.000
36	P	247	GLU	-1	-0.813	-0.885	12.138	0.048	0.048	0.000	0.000	0.000	0.000
37	P	248	LEU	0	-0.020	-0.001	15.541	0.020	0.020	0.000	0.000	0.000	0.000
38	P	249	LEU	0	0.015	-0.003	9.555	0.024	0.024	0.000	0.000	0.000	0.000
39	P	250	THR	0	-0.030	-0.023	13.521	0.021	0.021	0.000	0.000	0.000	0.000
40	P	251	LEU	0	-0.062	-0.031	14.974	-0.012	-0.012	0.000	0.000	0.000	0.000
41	P	252	VAL	0	-0.016	-0.001	14.871	-0.005	-0.005	0.000	0.000	0.000	0.000
42	P	253	ASN	0	0.025	0.003	11.569	0.058	0.058	0.000	0.000	0.000	0.000
43	P	254	ARG	1	0.945	0.987	15.705	-0.148	-0.148	0.000	0.000	0.000	0.000
44	P	255	LYS	1	0.845	0.933	19.282	-0.207	-0.207	0.000	0.000	0.000	0.000
45	P	256	VAL	0	0.009	0.000	17.297	-0.010	-0.010	0.000	0.000	0.000	0.000
46	P	257	SER	0	-0.040	-0.013	18.763	-0.023	-0.023	0.000	0.000	0.000	0.000
47	P	258	GLN	0	-0.019	-0.008	20.498	-0.020	-0.020	0.000	0.000	0.000	0.000
48	P	259	ARG	1	0.806	0.914	22.333	-0.267	-0.267	0.000	0.000	0.000	0.000
49	P	260	ARG	1	0.875	0.930	23.644	-0.171	-0.171	0.000	0.000	0.000	0.000
50	P	274	GLN	0	-0.013	-0.022	17.837	0.001	0.001	0.000	0.000	0.000	0.000
51	P	275	VAL	0	0.020	0.001	14.947	-0.032	-0.032	0.000	0.000	0.000	0.000
52	P	276	PRO	0	-0.048	0.010	12.788	0.035	0.035	0.000	0.000	0.000	0.000
53	P	277	CYS	0	-0.015	-0.014	9.174	-0.013	-0.013	0.000	0.000	0.000	0.000
54	P	278	PHE	0	0.026	0.001	6.428	0.190	0.190	0.000	0.000	0.000	0.000
55	P	279	ALA	0	0.007	0.013	2.523	-0.895	-0.431	0.876	-0.349	-0.992	0.001
56	P	280	SER	0	0.010	-0.004	2.658	-1.226	-0.015	1.178	-0.865	-1.524	-0.011
57	P	281	MET	0	-0.003	0.006	2.421	-3.139	-1.990	2.604	-1.063	-2.690	-0.007
58	P	282	LEU	0	-0.036	-0.001	4.847	0.161	0.187	-0.001	-0.007	-0.019	0.000
59	P	283	THR	0	-0.051	-0.058	8.052	-0.003	-0.003	0.000	0.000	0.000	0.000
60	P	284	LYS	1	0.834	0.914	10.930	0.388	0.388	0.000	0.000	0.000	0.000
61	P	285	LYS	1	0.861	0.936	12.321	0.032	0.032	0.000	0.000	0.000	0.000
62	P	286	LEU	0	-0.011	-0.007	10.631	-0.003	-0.003	0.000	0.000	0.000	0.000
63	P	287	HIS	0	0.008	-0.006	14.090	0.013	0.013	0.000	0.000	0.000	0.000
64	P	288	PHE	0	-0.030	-0.016	12.938	-0.009	-0.009	0.000	0.000	0.000	0.000
65	P	289	PHE	0	0.004	0.013	18.674	0.006	0.006	0.000	0.000	0.000	0.000
66	P	290	PRO	0	-0.014	-0.011	22.291	0.005	0.005	0.000	0.000	0.000	0.000
67	P	291	LYS	1	0.940	0.973	20.869	-0.067	-0.067	0.000	0.000	0.000	0.000
68	P	292	SER	0	0.037	0.031	25.780	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:201:PRO)