FMO DATABASE

FMODB ID: ZY3LN

Calculation Name: 3V3K-B-Xray372

Preferred Name: Caspase-9

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 3V3K

Chain ID: B

ChEMBL ID: CHEMBL2273

UniProt ID: P55211

Base Structure: X-ray

Registration Date: 2023-06-20

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	165
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1660418.098326
FMO2-HF: Nuclear repulsion	1592614.838323
FMO2-HF: Total energy	-67803.260002
FMO2-MP2: Total energy	-67995.503435

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(B:25:THR)

Summations of interaction energy for fragment #1(B:25:THR)

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.
-4.176	0.206	1.144	-2.083	-3.443	-0.012

Interaction energy analysis for fragmet #1(B:25:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.009

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

Sort

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	B	27	GLU	-1	-0.822	-0.866	2.639	-4.045	-2.161	0.158	-0.686	-1.356	0.000
4	B	28	SER	0	0.013	-0.029	2.995	0.297	0.835	0.016	-0.140	-0.414	0.000
5	B	29	VAL	0	-0.058	-0.034	2.609	-3.798	-2.339	0.969	-1.170	-1.258	-0.012
6	B	30	SER	0	-0.007	-0.023	4.826	0.242	0.315	-0.001	-0.004	-0.068	0.000
7	B	31	GLU	-1	-0.853	-0.902	7.023	0.238	0.238	0.000	0.000	0.000	0.000
8	B	32	LEU	0	-0.006	-0.010	8.306	-0.184	-0.184	0.000	0.000	0.000	0.000
9	B	33	ASN	0	-0.050	-0.028	7.368	0.132	0.132	0.000	0.000	0.000	0.000
10	B	34	HIS	0	0.046	0.010	11.141	0.007	0.007	0.000	0.000	0.000	0.000
11	B	35	ASN	0	-0.069	-0.046	9.809	0.135	0.135	0.000	0.000	0.000	0.000
12	B	36	HIS	0	-0.023	-0.022	8.309	0.136	0.136	0.000	0.000	0.000	0.000
13	B	37	PHE	0	0.012	0.020	13.891	0.026	0.026	0.000	0.000	0.000	0.000
14	B	38	LEU	0	-0.023	-0.003	17.424	-0.018	-0.018	0.000	0.000	0.000	0.000
15	B	39	SER	0	-0.011	-0.024	20.426	0.008	0.008	0.000	0.000	0.000	0.000
16	B	40	PRO	0	0.015	-0.008	21.901	0.008	0.008	0.000	0.000	0.000	0.000
17	B	41	GLU	-1	-0.831	-0.899	24.677	-0.193	-0.193	0.000	0.000	0.000	0.000
18	B	42	LEU	0	-0.024	-0.005	20.728	0.007	0.007	0.000	0.000	0.000	0.000
19	B	43	GLN	0	-0.031	-0.034	24.739	-0.007	-0.007	0.000	0.000	0.000	0.000
20	B	44	ASP	-1	-0.937	-0.963	26.170	-0.115	-0.115	0.000	0.000	0.000	0.000
21	B	45	LYS	1	0.833	0.892	26.789	0.172	0.172	0.000	0.000	0.000	0.000
22	B	46	LEU	0	-0.012	0.003	24.739	0.007	0.007	0.000	0.000	0.000	0.000
23	B	47	ASP	-1	-0.791	-0.885	28.265	-0.125	-0.125	0.000	0.000	0.000	0.000
24	B	48	VAL	0	-0.001	0.017	31.189	0.010	0.010	0.000	0.000	0.000	0.000
25	B	49	MET	0	-0.023	0.003	29.590	0.004	0.004	0.000	0.000	0.000	0.000
26	B	50	VAL	0	0.029	0.009	29.721	0.006	0.006	0.000	0.000	0.000	0.000
27	B	51	SER	0	-0.046	-0.020	32.754	0.009	0.009	0.000	0.000	0.000	0.000
28	B	52	ILE	0	0.010	0.001	36.049	0.006	0.006	0.000	0.000	0.000	0.000
29	B	53	TYR	0	-0.056	-0.112	34.324	0.005	0.005	0.000	0.000	0.000	0.000
30	B	54	SER	0	-0.026	-0.028	36.254	0.006	0.006	0.000	0.000	0.000	0.000
31	B	55	CYS	0	-0.037	-0.009	37.812	0.007	0.007	0.000	0.000	0.000	0.000
32	B	56	ALA	0	-0.030	0.004	39.903	0.005	0.005	0.000	0.000	0.000	0.000
33	B	57	ARG	1	0.746	0.843	41.745	0.066	0.066	0.000	0.000	0.000	0.000
34	B	58	ASN	0	-0.025	-0.013	44.010	0.001	0.001	0.000	0.000	0.000	0.000
35	B	59	ASN	0	0.045	0.004	40.490	0.000	0.000	0.000	0.000	0.000	0.000
36	B	60	ASN	0	-0.026	-0.022	41.256	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	61	GLU	-1	-0.777	-0.863	42.222	-0.067	-0.067	0.000	0.000	0.000	0.000
38	B	62	LEU	0	0.021	0.023	36.806	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	63	GLU	-1	-0.833	-0.903	37.047	-0.094	-0.094	0.000	0.000	0.000	0.000
40	B	64	GLU	-1	-0.924	-0.959	37.167	-0.093	-0.093	0.000	0.000	0.000	0.000
41	B	65	ILE	0	0.042	0.013	32.829	-0.007	-0.007	0.000	0.000	0.000	0.000
42	B	66	PHE	0	-0.006	-0.005	32.567	-0.009	-0.009	0.000	0.000	0.000	0.000
43	B	67	GLN	0	-0.019	-0.001	32.737	-0.009	-0.009	0.000	0.000	0.000	0.000
44	B	68	GLU	-1	-0.785	-0.866	31.011	-0.156	-0.156	0.000	0.000	0.000	0.000
45	B	69	LEU	0	0.034	0.010	26.685	-0.013	-0.013	0.000	0.000	0.000	0.000
46	B	70	SER	0	-0.053	-0.031	27.613	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	71	ALA	0	0.006	0.019	28.245	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	72	PHE	0	-0.015	-0.003	21.431	-0.008	-0.008	0.000	0.000	0.000	0.000
49	B	73	VAL	0	0.008	-0.008	23.457	-0.022	-0.022	0.000	0.000	0.000	0.000
50	B	74	SER	0	-0.048	-0.034	23.147	-0.016	-0.016	0.000	0.000	0.000	0.000
51	B	75	GLY	0	0.059	0.029	23.670	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	76	LEU	0	-0.016	-0.001	17.687	-0.021	-0.021	0.000	0.000	0.000	0.000
53	B	77	MET	0	0.007	-0.006	18.879	-0.033	-0.033	0.000	0.000	0.000	0.000
54	B	78	ASP	-1	-0.875	-0.933	19.438	-0.230	-0.230	0.000	0.000	0.000	0.000
55	B	79	LYS	1	0.792	0.906	16.319	0.429	0.429	0.000	0.000	0.000	0.000
56	B	80	ARG	1	0.776	0.875	13.076	0.457	0.457	0.000	0.000	0.000	0.000
57	B	81	ASN	0	-0.023	-0.023	14.979	-0.020	-0.020	0.000	0.000	0.000	0.000
58	B	82	SER	0	-0.060	-0.031	17.443	0.013	0.013	0.000	0.000	0.000	0.000
59	B	83	VAL	0	-0.003	-0.007	11.781	0.015	0.015	0.000	0.000	0.000	0.000
60	B	84	PHE	0	-0.027	-0.011	8.468	-0.077	-0.077	0.000	0.000	0.000	0.000
61	B	85	GLU	-1	-0.851	-0.924	11.064	-0.071	-0.071	0.000	0.000	0.000	0.000
62	B	86	VAL	0	0.021	0.015	10.798	-0.084	-0.084	0.000	0.000	0.000	0.000
63	B	87	ARG	1	0.821	0.895	10.840	0.097	0.097	0.000	0.000	0.000	0.000
64	B	88	ASN	0	-0.023	-0.023	13.561	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	89	GLU	-1	-0.810	-0.892	15.934	-0.212	-0.212	0.000	0.000	0.000	0.000
66	B	90	ASN	0	-0.086	-0.048	17.319	0.017	0.017	0.000	0.000	0.000	0.000
67	B	91	THR	0	-0.068	-0.035	17.181	0.021	0.021	0.000	0.000	0.000	0.000
68	B	92	ASP	-1	-0.783	-0.862	17.120	-0.047	-0.047	0.000	0.000	0.000	0.000
69	B	93	GLU	-1	-0.958	-0.979	14.475	0.009	0.009	0.000	0.000	0.000	0.000
70	B	94	VAL	0	-0.031	-0.005	12.351	0.015	0.015	0.000	0.000	0.000	0.000
71	B	95	VAL	0	-0.033	-0.018	7.611	0.017	0.017	0.000	0.000	0.000	0.000
72	B	96	GLY	0	0.041	0.030	7.514	0.013	0.013	0.000	0.000	0.000	0.000
73	B	97	ALA	0	-0.064	-0.044	6.969	0.203	0.203	0.000	0.000	0.000	0.000
74	B	98	LEU	0	0.012	0.007	7.290	-0.150	-0.150	0.000	0.000	0.000	0.000
75	B	99	ARG	1	0.845	0.931	9.578	0.440	0.440	0.000	0.000	0.000	0.000
76	B	100	ALA	0	-0.036	-0.029	13.282	-0.005	-0.005	0.000	0.000	0.000	0.000
77	B	101	GLY	0	-0.024	-0.012	14.651	0.011	0.011	0.000	0.000	0.000	0.000
78	B	102	MET	0	-0.047	0.005	12.387	0.017	0.017	0.000	0.000	0.000	0.000
79	B	103	THR	0	-0.048	-0.049	11.271	-0.021	-0.021	0.000	0.000	0.000	0.000
80	B	104	ILE	0	0.014	-0.015	5.378	-0.108	-0.108	0.000	0.000	0.000	0.000
81	B	105	GLU	-1	-0.925	-0.953	8.849	-0.488	-0.488	0.000	0.000	0.000	0.000
82	B	106	ASP	-1	-0.816	-0.882	12.153	-0.470	-0.470	0.000	0.000	0.000	0.000
83	B	107	ARG	1	0.848	0.908	3.809	3.414	3.584	-0.001	-0.041	-0.128	0.000
84	B	108	ASP	-1	-0.785	-0.871	8.541	-1.376	-1.376	0.000	0.000	0.000	0.000
85	B	109	SER	0	-0.033	-0.023	11.217	0.137	0.137	0.000	0.000	0.000	0.000
86	B	110	TYR	0	-0.038	-0.037	12.576	0.083	0.083	0.000	0.000	0.000	0.000
87	B	111	ILE	0	0.008	0.000	8.415	0.053	0.053	0.000	0.000	0.000	0.000
88	B	112	ARG	1	0.902	0.969	13.081	0.502	0.502	0.000	0.000	0.000	0.000
89	B	113	ASP	-1	-0.837	-0.912	16.145	-0.321	-0.321	0.000	0.000	0.000	0.000
90	B	114	LEU	0	-0.029	-0.014	13.930	0.050	0.050	0.000	0.000	0.000	0.000
91	B	115	PHE	0	0.040	0.010	16.070	0.049	0.049	0.000	0.000	0.000	0.000
92	B	116	PHE	0	-0.027	0.007	18.012	0.044	0.044	0.000	0.000	0.000	0.000
93	B	117	LEU	0	0.005	-0.003	20.089	0.028	0.028	0.000	0.000	0.000	0.000
94	B	118	HIS	0	-0.022	-0.005	19.062	0.008	0.008	0.000	0.000	0.000	0.000
95	B	119	SER	0	-0.025	-0.042	21.137	0.031	0.031	0.000	0.000	0.000	0.000
96	B	120	LEU	0	0.014	0.005	23.146	0.022	0.022	0.000	0.000	0.000	0.000
97	B	121	LYS	1	0.856	0.917	24.314	0.185	0.185	0.000	0.000	0.000	0.000
98	B	122	VAL	0	0.011	0.015	23.740	0.015	0.015	0.000	0.000	0.000	0.000
99	B	123	LYS	1	0.919	0.958	26.581	0.145	0.145	0.000	0.000	0.000	0.000
100	B	124	ILE	0	-0.041	-0.006	29.103	0.012	0.012	0.000	0.000	0.000	0.000
101	B	125	GLU	-1	-0.867	-0.923	27.345	-0.128	-0.128	0.000	0.000	0.000	0.000
102	B	126	GLU	-1	-0.911	-0.958	29.278	-0.103	-0.103	0.000	0.000	0.000	0.000
103	B	127	SER	0	-0.073	-0.056	32.584	0.009	0.009	0.000	0.000	0.000	0.000
104	B	128	ARG	1	0.776	0.886	32.942	0.100	0.100	0.000	0.000	0.000	0.000
105	B	129	GLN	0	0.009	0.008	34.581	0.000	0.000	0.000	0.000	0.000	0.000
106	B	130	GLY	0	-0.033	0.002	36.815	0.004	0.004	0.000	0.000	0.000	0.000
107	B	131	LYS	1	0.838	0.902	39.181	0.066	0.066	0.000	0.000	0.000	0.000
108	B	132	GLU	-1	-0.839	-0.911	35.711	-0.072	-0.072	0.000	0.000	0.000	0.000
109	B	133	ASP	-1	-0.812	-0.892	36.360	-0.068	-0.068	0.000	0.000	0.000	0.000
110	B	134	SER	0	-0.064	-0.037	39.017	0.000	0.000	0.000	0.000	0.000	0.000
111	B	135	LYS	1	0.805	0.888	34.658	0.092	0.092	0.000	0.000	0.000	0.000
112	B	136	CYM	-1	-0.806	-0.749	35.057	-0.106	-0.106	0.000	0.000	0.000	0.000
113	B	137	LYS	1	0.825	0.889	34.598	0.083	0.083	0.000	0.000	0.000	0.000
114	B	138	VAL	0	0.058	0.001	30.934	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	139	TYR	0	0.016	-0.068	29.058	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	140	ASN	0	-0.043	-0.023	29.665	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	141	LEU	0	-0.029	0.002	28.362	-0.005	-0.005	0.000	0.000	0.000	0.000
118	B	142	LEU	0	0.016	0.028	24.817	-0.015	-0.015	0.000	0.000	0.000	0.000
119	B	143	CYS	0	-0.078	-0.027	25.504	-0.006	-0.006	0.000	0.000	0.000	0.000
120	B	144	PRO	0	0.017	0.025	22.753	0.013	0.013	0.000	0.000	0.000	0.000
121	B	145	HIS	0	0.060	0.035	24.966	-0.009	-0.009	0.000	0.000	0.000	0.000
122	B	146	HIS	0	0.058	0.024	23.058	-0.008	-0.008	0.000	0.000	0.000	0.000
123	B	147	SER	0	-0.022	-0.013	22.086	-0.010	-0.010	0.000	0.000	0.000	0.000
124	B	148	SER	0	-0.039	-0.030	21.254	-0.015	-0.015	0.000	0.000	0.000	0.000
125	B	149	GLU	-1	-0.759	-0.892	15.840	-0.367	-0.367	0.000	0.000	0.000	0.000
126	B	150	LEU	0	0.023	0.015	16.783	-0.031	-0.031	0.000	0.000	0.000	0.000
127	B	151	TYR	0	0.009	0.012	18.745	-0.006	-0.006	0.000	0.000	0.000	0.000
128	B	152	GLY	0	0.038	0.017	15.951	0.007	0.007	0.000	0.000	0.000	0.000
129	B	153	ASP	-1	-0.776	-0.866	13.245	-0.635	-0.635	0.000	0.000	0.000	0.000
130	B	154	LEU	0	-0.001	-0.009	15.088	-0.006	-0.006	0.000	0.000	0.000	0.000
131	B	155	ARG	1	0.898	0.952	15.925	0.247	0.247	0.000	0.000	0.000	0.000
132	B	156	ALA	0	0.014	0.014	12.264	0.031	0.031	0.000	0.000	0.000	0.000
133	B	157	MET	0	0.015	-0.001	14.180	-0.009	-0.009	0.000	0.000	0.000	0.000
134	B	158	LYS	1	0.828	0.905	15.311	0.190	0.190	0.000	0.000	0.000	0.000
135	B	159	CYS	0	-0.054	-0.026	15.020	0.031	0.031	0.000	0.000	0.000	0.000
136	B	160	LEU	0	-0.057	-0.022	10.488	0.025	0.025	0.000	0.000	0.000	0.000
137	B	161	VAL	0	-0.060	-0.025	14.790	0.015	0.015	0.000	0.000	0.000	0.000
138	B	162	GLU	-1	-0.816	-0.906	17.588	-0.137	-0.137	0.000	0.000	0.000	0.000
139	B	163	GLY	0	-0.020	0.009	18.272	0.020	0.020	0.000	0.000	0.000	0.000
140	B	164	CYS	0	-0.032	0.002	17.243	0.015	0.015	0.000	0.000	0.000	0.000
141	B	165	SER	0	-0.054	-0.054	18.279	-0.019	-0.019	0.000	0.000	0.000	0.000
142	B	166	ASP	-1	-0.868	-0.947	20.211	-0.027	-0.027	0.000	0.000	0.000	0.000
143	B	167	ASP	-1	-0.858	-0.900	20.285	-0.141	-0.141	0.000	0.000	0.000	0.000
144	B	168	PHE	0	-0.067	-0.059	17.464	0.003	0.003	0.000	0.000	0.000	0.000
145	B	169	ASN	0	-0.099	-0.042	18.757	0.022	0.022	0.000	0.000	0.000	0.000
146	B	170	PRO	0	0.025	0.042	15.761	0.016	0.016	0.000	0.000	0.000	0.000
147	B	171	PHE	0	-0.011	-0.022	13.824	0.003	0.003	0.000	0.000	0.000	0.000
148	B	172	ASP	-1	-0.933	-0.962	12.071	0.082	0.082	0.000	0.000	0.000	0.000
149	B	173	ILE	0	-0.020	-0.010	7.679	-0.018	-0.018	0.000	0.000	0.000	0.000
150	B	174	ILE	0	0.054	0.026	8.691	-0.166	-0.166	0.000	0.000	0.000	0.000
151	B	175	ARG	1	0.829	0.909	3.412	1.374	1.632	0.003	-0.042	-0.219	0.000
152	B	176	VAL	0	0.026	0.003	7.776	0.084	0.084	0.000	0.000	0.000	0.000
153	B	177	PRO	0	-0.039	0.005	7.633	0.097	0.097	0.000	0.000	0.000	0.000
154	B	178	ASP	-1	-0.794	-0.914	8.777	-0.684	-0.684	0.000	0.000	0.000	0.000
155	B	179	LEU	0	-0.047	-0.030	7.298	0.149	0.149	0.000	0.000	0.000	0.000
156	B	180	THR	0	-0.010	-0.017	9.709	0.076	0.076	0.000	0.000	0.000	0.000
157	B	181	TYR	0	-0.083	-0.032	11.989	0.090	0.090	0.000	0.000	0.000	0.000
158	B	182	ASN	0	-0.023	-0.019	14.936	0.031	0.031	0.000	0.000	0.000	0.000
159	B	183	LYS	1	0.876	0.939	15.388	0.303	0.303	0.000	0.000	0.000	0.000
160	B	184	GLY	0	0.053	0.030	16.805	0.006	0.006	0.000	0.000	0.000	0.000
161	B	185	SER	0	-0.027	-0.041	17.864	-0.003	-0.003	0.000	0.000	0.000	0.000
162	B	186	LEU	0	-0.078	-0.028	20.717	0.011	0.011	0.000	0.000	0.000	0.000
163	B	187	GLN	0	-0.025	-0.010	20.438	-0.009	-0.009	0.000	0.000	0.000	0.000
164	B	188	CYS	0	-0.072	-0.033	22.247	0.013	0.013	0.000	0.000	0.000	0.000
165	B	189	GLY	0	-0.016	-0.003	24.874	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:25:THR)