FMO DATABASE

FMODB ID: QY2QY

Calculation Name: 3P45-F-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: F

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	-398375.443448
FMO2-HF: Nuclear repulsion	370024.901051
FMO2-HF: Total energy	-28350.542397
FMO2-MP2: Total energy	-28429.521918

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(F:202:ALA)

Summations of interaction energy for fragment #1(F: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.
-5.987	-4.063	9.978	-5.024	-6.876	-0.021

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.003

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	F	204	ALA	0	0.023	-0.001	3.878	-1.163	1.143	-0.017	-1.443	-0.845	0.005
4	F	205	ASP	-1	-0.778	-0.861	6.539	-0.709	-0.709	0.000	0.000	0.000	0.000
5	F	206	PHE	0	0.005	0.017	2.818	-1.196	-0.395	3.434	-1.243	-2.991	-0.011
6	F	207	LEU	0	-0.007	-0.014	4.571	0.032	0.072	-0.001	-0.009	-0.030	0.000
7	F	208	MET	0	0.007	0.029	3.860	-0.534	-0.122	0.036	-0.089	-0.358	0.000
8	F	209	CYS	0	-0.024	-0.020	6.550	-0.262	-0.262	0.000	0.000	0.000	0.000
9	F	210	TYR	0	0.021	0.004	6.574	0.075	0.075	0.000	0.000	0.000	0.000
10	F	211	SER	0	0.035	0.015	12.293	-0.065	-0.065	0.000	0.000	0.000	0.000
11	F	212	VAL	0	0.015	0.018	15.126	-0.031	-0.031	0.000	0.000	0.000	0.000
12	F	223	VAL	0	0.037	0.006	28.990	0.002	0.002	0.000	0.000	0.000	0.000
13	F	224	ASN	0	-0.006	-0.006	29.730	0.002	0.002	0.000	0.000	0.000	0.000
14	F	225	GLY	0	0.058	0.048	25.650	-0.001	-0.001	0.000	0.000	0.000	0.000
15	F	226	SER	0	0.002	-0.009	20.629	-0.006	-0.006	0.000	0.000	0.000	0.000
16	F	227	TRP	0	0.033	0.000	23.129	0.003	0.003	0.000	0.000	0.000	0.000
17	F	228	TYR	0	0.086	0.039	14.467	-0.006	-0.006	0.000	0.000	0.000	0.000
18	F	229	ILE	0	0.036	0.024	17.300	-0.001	-0.001	0.000	0.000	0.000	0.000
19	F	230	GLN	0	0.026	0.015	20.628	-0.016	-0.016	0.000	0.000	0.000	0.000
20	F	231	ASP	-1	-0.746	-0.857	22.359	0.167	0.167	0.000	0.000	0.000	0.000
21	F	232	LEU	0	0.002	0.000	16.178	-0.014	-0.014	0.000	0.000	0.000	0.000
22	F	233	CYS	0	-0.032	-0.021	20.233	-0.021	-0.021	0.000	0.000	0.000	0.000
23	F	234	GLU	-1	-0.807	-0.876	22.612	0.099	0.099	0.000	0.000	0.000	0.000
24	F	235	MET	0	-0.032	-0.022	21.328	-0.019	-0.019	0.000	0.000	0.000	0.000
25	F	236	LEU	0	0.011	-0.005	17.643	-0.018	-0.018	0.000	0.000	0.000	0.000
26	F	237	GLY	0	-0.004	-0.003	21.761	-0.017	-0.017	0.000	0.000	0.000	0.000
27	F	238	LYS	1	0.800	0.903	25.140	-0.100	-0.100	0.000	0.000	0.000	0.000
28	F	239	TYR	0	0.028	-0.003	23.269	-0.004	-0.004	0.000	0.000	0.000	0.000
29	F	240	GLY	0	0.029	0.014	20.864	-0.008	-0.008	0.000	0.000	0.000	0.000
30	F	241	SER	0	-0.039	-0.008	21.410	-0.010	-0.010	0.000	0.000	0.000	0.000
31	F	242	SER	0	-0.006	-0.018	23.323	-0.010	-0.010	0.000	0.000	0.000	0.000
32	F	243	LEU	0	0.011	0.013	21.378	-0.010	-0.010	0.000	0.000	0.000	0.000
33	F	244	GLU	-1	-0.785	-0.851	15.269	-0.025	-0.025	0.000	0.000	0.000	0.000
34	F	245	PHE	0	0.044	0.003	11.846	0.034	0.034	0.000	0.000	0.000	0.000
35	F	246	THR	0	-0.001	-0.032	12.481	0.050	0.050	0.000	0.000	0.000	0.000
36	F	247	GLU	-1	-0.798	-0.875	15.199	0.039	0.039	0.000	0.000	0.000	0.000
37	F	248	LEU	0	-0.018	-0.003	18.148	0.019	0.019	0.000	0.000	0.000	0.000
38	F	249	LEU	0	0.006	-0.007	12.743	0.018	0.018	0.000	0.000	0.000	0.000
39	F	250	THR	0	-0.023	-0.021	16.958	0.033	0.033	0.000	0.000	0.000	0.000
40	F	251	LEU	0	-0.070	-0.032	18.940	-0.003	-0.003	0.000	0.000	0.000	0.000
41	F	252	VAL	0	-0.018	0.000	18.453	0.000	0.000	0.000	0.000	0.000	0.000
42	F	253	ASN	0	0.031	0.007	15.606	0.018	0.018	0.000	0.000	0.000	0.000
43	F	254	ARG	1	0.955	0.988	19.895	-0.129	-0.129	0.000	0.000	0.000	0.000
44	F	255	LYS	1	0.827	0.907	23.404	-0.146	-0.146	0.000	0.000	0.000	0.000
45	F	256	VAL	0	0.007	-0.002	20.919	-0.006	-0.006	0.000	0.000	0.000	0.000
46	F	257	SER	0	-0.034	-0.018	23.135	-0.012	-0.012	0.000	0.000	0.000	0.000
47	F	258	GLN	0	-0.027	-0.014	24.882	-0.009	-0.009	0.000	0.000	0.000	0.000
48	F	259	ARG	1	0.810	0.915	25.691	-0.188	-0.188	0.000	0.000	0.000	0.000
49	F	260	ARG	1	0.884	0.939	28.181	-0.150	-0.150	0.000	0.000	0.000	0.000
50	F	274	GLN	0	-0.034	-0.037	19.728	-0.026	-0.026	0.000	0.000	0.000	0.000
51	F	275	VAL	0	-0.001	-0.008	18.968	-0.030	-0.030	0.000	0.000	0.000	0.000
52	F	276	PRO	0	-0.055	-0.006	16.791	0.040	0.040	0.000	0.000	0.000	0.000
53	F	277	CYS	0	-0.021	-0.007	12.812	-0.016	-0.016	0.000	0.000	0.000	0.000
54	F	278	PHE	0	0.010	-0.008	10.550	0.025	0.025	0.000	0.000	0.000	0.000
55	F	279	ALA	0	0.021	0.011	6.178	-0.054	-0.054	0.000	0.000	0.000	0.000
56	F	280	SER	0	0.007	-0.002	6.138	0.128	0.128	0.000	0.000	0.000	0.000
57	F	281	MET	0	-0.012	0.004	2.453	-2.359	-3.994	6.526	-2.240	-2.652	-0.015
58	F	282	LEU	0	-0.035	0.001	6.304	-0.213	-0.213	0.000	0.000	0.000	0.000
59	F	283	THR	0	-0.038	-0.039	9.666	0.075	0.075	0.000	0.000	0.000	0.000
60	F	284	LYS	1	0.806	0.885	12.113	0.615	0.615	0.000	0.000	0.000	0.000
61	F	285	LYS	1	0.839	0.921	13.966	0.054	0.054	0.000	0.000	0.000	0.000
62	F	286	LEU	0	-0.015	-0.012	11.921	-0.021	-0.021	0.000	0.000	0.000	0.000
63	F	287	HIS	0	0.019	0.003	15.672	0.029	0.029	0.000	0.000	0.000	0.000
64	F	288	PHE	0	-0.036	-0.019	14.082	-0.019	-0.019	0.000	0.000	0.000	0.000
65	F	289	PHE	0	0.005	0.010	20.026	0.010	0.010	0.000	0.000	0.000	0.000
66	F	290	PRO	0	-0.009	-0.010	23.548	-0.005	-0.005	0.000	0.000	0.000	0.000
67	F	291	LYS	1	0.930	0.976	21.133	0.074	0.074	0.000	0.000	0.000	0.000
68	F	292	SER	0	0.038	0.029	26.060	0.004	0.004	0.000	0.000	0.000	0.000

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