FMO DATABASE

FMODB ID: YZ5L2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-398199.265115
FMO2-HF: Nuclear repulsion	369850.153316
FMO2-HF: Total energy	-28349.111799
FMO2-MP2: Total energy	-28428.052349

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.
-11.516	-4.967	7.606	-4.257	-9.895	-0.013

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 : 0.008 / q_NPA : -0.018

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	0.047	0.017	3.840	-1.157	0.781	-0.011	-0.923	-1.004	0.001
4	P	204	ALA	0	0.001	-0.012	4.182	-0.490	-0.307	-0.001	-0.031	-0.151	0.000
5	P	205	ASP	-1	-0.844	-0.902	6.742	-0.605	-0.605	0.000	0.000	0.000	0.000
6	P	206	PHE	0	0.006	0.022	2.544	-0.248	0.439	0.566	-0.290	-0.963	-0.001
7	P	207	LEU	0	-0.030	-0.024	4.038	-0.817	-0.473	0.005	-0.073	-0.275	0.000
8	P	208	MET	0	-0.018	0.003	2.115	-2.190	-1.072	2.981	-1.013	-3.086	0.000
9	P	209	CYS	0	-0.026	-0.005	4.440	-0.718	-0.637	-0.001	-0.009	-0.071	0.000
10	P	210	TYR	0	0.028	-0.006	3.764	-0.880	-0.452	0.002	-0.102	-0.327	0.001
11	P	211	SER	0	0.030	0.005	9.065	-0.191	-0.191	0.000	0.000	0.000	0.000
12	P	212	VAL	0	-0.006	0.003	12.313	-0.092	-0.092	0.000	0.000	0.000	0.000
13	P	224	ASN	0	0.047	0.015	28.080	-0.013	-0.013	0.000	0.000	0.000	0.000
14	P	225	GLY	0	-0.003	-0.002	24.046	0.002	0.002	0.000	0.000	0.000	0.000
15	P	226	SER	0	0.020	0.008	18.855	-0.017	-0.017	0.000	0.000	0.000	0.000
16	P	227	TRP	0	0.039	0.000	20.655	0.002	0.002	0.000	0.000	0.000	0.000
17	P	228	TYR	0	0.094	0.053	11.121	-0.004	-0.004	0.000	0.000	0.000	0.000
18	P	229	ILE	0	0.044	0.029	16.000	-0.007	-0.007	0.000	0.000	0.000	0.000
19	P	230	GLN	0	0.001	0.004	18.600	-0.028	-0.028	0.000	0.000	0.000	0.000
20	P	231	ASP	-1	-0.777	-0.889	19.282	0.241	0.241	0.000	0.000	0.000	0.000
21	P	232	LEU	0	0.011	0.002	14.171	-0.021	-0.021	0.000	0.000	0.000	0.000
22	P	233	CYS	0	-0.019	-0.029	17.683	-0.031	-0.031	0.000	0.000	0.000	0.000
23	P	234	GLU	-1	-0.779	-0.858	20.662	0.141	0.141	0.000	0.000	0.000	0.000
24	P	235	MET	0	-0.022	-0.014	19.034	-0.033	-0.033	0.000	0.000	0.000	0.000
25	P	236	LEU	0	-0.019	0.000	16.284	-0.022	-0.022	0.000	0.000	0.000	0.000
26	P	237	GLY	0	-0.016	-0.011	20.276	-0.024	-0.024	0.000	0.000	0.000	0.000
27	P	238	LYS	1	0.819	0.908	23.885	-0.155	-0.155	0.000	0.000	0.000	0.000
28	P	239	TYR	0	0.014	-0.020	21.347	-0.013	-0.013	0.000	0.000	0.000	0.000
29	P	240	GLY	0	0.040	0.023	19.603	-0.009	-0.009	0.000	0.000	0.000	0.000
30	P	241	SER	0	-0.054	-0.017	20.265	-0.011	-0.011	0.000	0.000	0.000	0.000
31	P	242	SER	0	0.012	-0.010	22.465	-0.013	-0.013	0.000	0.000	0.000	0.000
32	P	243	LEU	0	-0.020	-0.012	19.661	-0.016	-0.016	0.000	0.000	0.000	0.000
33	P	244	GLU	-1	-0.775	-0.839	14.033	-0.064	-0.064	0.000	0.000	0.000	0.000
34	P	245	PHE	0	0.043	-0.005	10.678	0.028	0.028	0.000	0.000	0.000	0.000
35	P	246	THR	0	-0.020	-0.044	10.305	0.050	0.050	0.000	0.000	0.000	0.000
36	P	247	GLU	-1	-0.853	-0.933	12.799	0.014	0.014	0.000	0.000	0.000	0.000
37	P	248	LEU	0	-0.030	-0.005	16.148	0.023	0.023	0.000	0.000	0.000	0.000
38	P	249	LEU	0	-0.001	-0.008	9.923	0.038	0.038	0.000	0.000	0.000	0.000
39	P	250	THR	0	-0.024	-0.016	13.821	0.032	0.032	0.000	0.000	0.000	0.000
40	P	251	LEU	0	-0.055	-0.030	15.340	0.000	0.000	0.000	0.000	0.000	0.000
41	P	252	VAL	0	0.009	0.010	15.249	-0.003	-0.003	0.000	0.000	0.000	0.000
42	P	253	ASN	0	0.044	0.022	12.255	0.073	0.073	0.000	0.000	0.000	0.000
43	P	254	ARG	1	0.944	0.980	16.178	-0.126	-0.126	0.000	0.000	0.000	0.000
44	P	255	LYS	1	0.814	0.914	19.631	-0.195	-0.195	0.000	0.000	0.000	0.000
45	P	256	VAL	0	-0.005	-0.011	17.387	-0.007	-0.007	0.000	0.000	0.000	0.000
46	P	257	SER	0	-0.040	0.001	18.887	-0.018	-0.018	0.000	0.000	0.000	0.000
47	P	258	GLN	0	-0.026	-0.026	20.492	-0.015	-0.015	0.000	0.000	0.000	0.000
48	P	259	ARG	1	0.823	0.932	22.292	-0.273	-0.273	0.000	0.000	0.000	0.000
49	P	260	ARG	1	0.902	0.946	23.859	-0.179	-0.179	0.000	0.000	0.000	0.000
50	P	274	GLN	0	-0.027	-0.030	17.513	0.012	0.012	0.000	0.000	0.000	0.000
51	P	275	VAL	0	0.001	-0.006	14.960	-0.032	-0.032	0.000	0.000	0.000	0.000
52	P	276	PRO	0	-0.016	0.021	12.622	0.046	0.046	0.000	0.000	0.000	0.000
53	P	277	CYS	0	-0.024	-0.013	8.929	-0.004	-0.004	0.000	0.000	0.000	0.000
54	P	278	PHE	0	0.028	0.012	6.779	0.216	0.216	0.000	0.000	0.000	0.000
55	P	279	ALA	0	0.007	0.007	2.527	-0.646	-0.305	0.696	-0.236	-0.801	0.000
56	P	280	SER	0	-0.008	-0.022	3.611	-0.447	0.191	0.047	-0.237	-0.448	-0.001
57	P	281	MET	0	0.018	0.020	2.733	-3.346	-2.574	3.323	-1.339	-2.755	-0.013
58	P	282	LEU	0	-0.030	-0.001	4.953	0.183	0.202	-0.001	-0.004	-0.014	0.000
59	P	283	THR	0	-0.046	-0.046	8.016	0.009	0.009	0.000	0.000	0.000	0.000
60	P	284	LYS	1	0.917	0.960	10.924	0.433	0.433	0.000	0.000	0.000	0.000
61	P	285	LYS	1	0.905	0.966	12.815	0.097	0.097	0.000	0.000	0.000	0.000
62	P	286	LEU	0	-0.027	-0.013	11.256	-0.002	-0.002	0.000	0.000	0.000	0.000
63	P	287	HIS	0	0.007	0.004	14.777	0.013	0.013	0.000	0.000	0.000	0.000
64	P	288	PHE	0	-0.016	-0.008	13.633	-0.007	-0.007	0.000	0.000	0.000	0.000
65	P	289	PHE	0	0.010	0.020	19.327	0.010	0.010	0.000	0.000	0.000	0.000
66	P	290	PRO	0	-0.011	-0.012	22.971	0.001	0.001	0.000	0.000	0.000	0.000
67	P	291	LYS	1	0.937	0.975	21.382	-0.016	-0.016	0.000	0.000	0.000	0.000
68	P	292	SER	0	0.043	0.027	25.963	0.005	0.005	0.000	0.000	0.000	0.000

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