FMO DATABASE

FMODB ID: 521KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-397124.194846
FMO2-HF: Nuclear repulsion	368775.629968
FMO2-HF: Total energy	-28348.564878
FMO2-MP2: Total energy	-28427.487375

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.
-8.707	-4.908	11.821	-5.376	-10.243	-0.019

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 : 0.022 / q_NPA : -0.010

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	0.039	-0.003	3.718	-1.266	0.806	-0.011	-1.007	-1.054	0.002
4	P	204	ALA	0	0.005	-0.010	4.041	-0.611	-0.375	0.000	-0.060	-0.176	0.000
5	P	205	ASP	-1	-0.883	-0.941	6.587	-0.580	-0.580	0.000	0.000	0.000	0.000
6	P	206	PHE	0	0.004	0.019	2.827	-0.196	0.516	0.298	-0.217	-0.793	0.000
7	P	207	LEU	0	-0.025	-0.023	4.155	-0.678	-0.380	0.003	-0.061	-0.240	0.000
8	P	208	MET	0	-0.015	0.007	1.965	-2.022	-1.306	3.753	-1.430	-3.039	-0.001
9	P	209	CYS	0	-0.024	-0.007	4.620	-0.731	-0.673	-0.001	-0.009	-0.048	0.000
10	P	210	TYR	0	0.017	-0.006	4.363	0.886	1.074	-0.001	-0.005	-0.182	0.000
11	P	211	SER	0	0.051	-0.007	9.697	-0.195	-0.195	0.000	0.000	0.000	0.000
12	P	212	VAL	0	-0.031	0.016	12.327	-0.084	-0.084	0.000	0.000	0.000	0.000
13	P	224	ASN	0	0.028	0.006	28.625	-0.014	-0.014	0.000	0.000	0.000	0.000
14	P	225	GLY	0	-0.008	-0.005	24.615	0.003	0.003	0.000	0.000	0.000	0.000
15	P	226	SER	0	0.024	0.011	19.727	-0.017	-0.017	0.000	0.000	0.000	0.000
16	P	227	TRP	0	0.036	0.001	21.220	0.005	0.005	0.000	0.000	0.000	0.000
17	P	228	TYR	0	0.091	0.050	12.273	-0.015	-0.015	0.000	0.000	0.000	0.000
18	P	229	ILE	0	0.030	0.020	16.471	-0.001	-0.001	0.000	0.000	0.000	0.000
19	P	230	GLN	0	0.004	-0.008	19.160	-0.021	-0.021	0.000	0.000	0.000	0.000
20	P	231	ASP	-1	-0.790	-0.894	19.688	0.240	0.240	0.000	0.000	0.000	0.000
21	P	232	LEU	0	0.002	-0.003	14.395	-0.017	-0.017	0.000	0.000	0.000	0.000
22	P	233	CYS	0	-0.016	-0.024	18.121	-0.029	-0.029	0.000	0.000	0.000	0.000
23	P	234	GLU	-1	-0.922	-0.940	20.852	0.151	0.151	0.000	0.000	0.000	0.000
24	P	235	MET	0	-0.047	-0.033	19.319	-0.035	-0.035	0.000	0.000	0.000	0.000
25	P	236	LEU	0	-0.022	-0.004	16.326	-0.020	-0.020	0.000	0.000	0.000	0.000
26	P	237	GLY	0	-0.007	-0.006	20.254	-0.023	-0.023	0.000	0.000	0.000	0.000
27	P	238	LYS	1	0.905	0.953	24.000	-0.151	-0.151	0.000	0.000	0.000	0.000
28	P	239	TYR	0	-0.002	-0.022	21.538	-0.013	-0.013	0.000	0.000	0.000	0.000
29	P	240	GLY	0	0.034	0.025	19.607	-0.007	-0.007	0.000	0.000	0.000	0.000
30	P	241	SER	0	-0.051	-0.020	20.300	-0.009	-0.009	0.000	0.000	0.000	0.000
31	P	242	SER	0	0.011	-0.017	22.450	-0.013	-0.013	0.000	0.000	0.000	0.000
32	P	243	LEU	0	-0.010	-0.002	19.617	-0.014	-0.014	0.000	0.000	0.000	0.000
33	P	244	GLU	-1	-0.768	-0.848	14.108	-0.007	-0.007	0.000	0.000	0.000	0.000
34	P	245	PHE	0	0.038	-0.003	10.935	0.025	0.025	0.000	0.000	0.000	0.000
35	P	246	THR	0	-0.018	-0.034	10.312	0.048	0.048	0.000	0.000	0.000	0.000
36	P	247	GLU	-1	-0.891	-0.950	12.714	0.056	0.056	0.000	0.000	0.000	0.000
37	P	248	LEU	0	-0.033	-0.006	15.930	0.017	0.017	0.000	0.000	0.000	0.000
38	P	249	LEU	0	0.001	-0.013	10.024	0.030	0.030	0.000	0.000	0.000	0.000
39	P	250	THR	0	-0.013	-0.003	13.922	0.027	0.027	0.000	0.000	0.000	0.000
40	P	251	LEU	0	-0.055	-0.033	15.284	-0.004	-0.004	0.000	0.000	0.000	0.000
41	P	252	VAL	0	0.016	0.013	15.478	-0.008	-0.008	0.000	0.000	0.000	0.000
42	P	253	ASN	0	0.049	0.028	12.327	0.061	0.061	0.000	0.000	0.000	0.000
43	P	254	ARG	1	0.920	0.968	16.323	-0.134	-0.134	0.000	0.000	0.000	0.000
44	P	255	LYS	1	0.926	0.965	19.796	-0.178	-0.178	0.000	0.000	0.000	0.000
45	P	256	VAL	0	0.009	0.001	17.408	-0.009	-0.009	0.000	0.000	0.000	0.000
46	P	257	SER	0	-0.050	-0.004	19.050	-0.018	-0.018	0.000	0.000	0.000	0.000
47	P	258	GLN	0	-0.020	-0.023	20.698	-0.012	-0.012	0.000	0.000	0.000	0.000
48	P	259	ARG	1	0.848	0.956	22.822	-0.256	-0.256	0.000	0.000	0.000	0.000
49	P	260	ARG	1	0.893	0.943	24.121	-0.170	-0.170	0.000	0.000	0.000	0.000
50	P	274	GLN	0	-0.017	-0.025	17.412	0.033	0.033	0.000	0.000	0.000	0.000
51	P	275	VAL	0	0.001	-0.011	15.209	-0.029	-0.029	0.000	0.000	0.000	0.000
52	P	276	PRO	0	-0.015	0.027	13.036	0.038	0.038	0.000	0.000	0.000	0.000
53	P	277	CYS	0	-0.025	-0.030	8.793	-0.011	-0.011	0.000	0.000	0.000	0.000
54	P	278	PHE	0	0.019	0.022	7.059	0.208	0.208	0.000	0.000	0.000	0.000
55	P	279	ALA	0	0.020	0.014	2.589	-0.788	-0.381	0.612	-0.279	-0.739	0.001
56	P	280	SER	0	-0.012	-0.022	3.464	-0.480	0.140	0.040	-0.255	-0.404	-0.002
57	P	281	MET	0	0.012	0.039	2.615	-2.192	-3.719	7.129	-2.049	-3.554	-0.019
58	P	282	LEU	0	-0.031	-0.003	4.948	0.094	0.113	-0.001	-0.004	-0.014	0.000
59	P	283	THR	0	-0.007	-0.010	7.932	0.018	0.018	0.000	0.000	0.000	0.000
60	P	284	LYS	1	0.917	0.960	10.862	0.329	0.329	0.000	0.000	0.000	0.000
61	P	285	LYS	1	0.948	0.980	12.775	0.108	0.108	0.000	0.000	0.000	0.000
62	P	286	LEU	0	-0.011	-0.006	11.363	-0.008	-0.008	0.000	0.000	0.000	0.000
63	P	287	HIS	0	-0.008	0.004	14.857	0.012	0.012	0.000	0.000	0.000	0.000
64	P	288	PHE	0	-0.018	-0.008	13.910	-0.007	-0.007	0.000	0.000	0.000	0.000
65	P	289	PHE	0	0.001	0.020	19.427	0.007	0.007	0.000	0.000	0.000	0.000
66	P	290	PRO	0	0.000	-0.004	23.074	0.002	0.002	0.000	0.000	0.000	0.000
67	P	291	LYS	1	0.935	0.968	22.202	-0.036	-0.036	0.000	0.000	0.000	0.000
68	P	292	SER	0	0.036	0.024	26.134	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)