FMO DATABASE

FMODB ID: M367Z

Calculation Name: 3V3K-B-Xray320

Preferred Name: Caspase-9

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V3K

Chain ID: B

ChEMBL ID: CHEMBL2273

UniProt ID: P55211

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1648410.050528
FMO2-HF: Nuclear repulsion	1580609.273365
FMO2-HF: Total energy	-67800.777163
FMO2-MP2: Total energy	-67992.826539

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.
-3.515	0.821	0.393	-1.789	-2.941	-0.007

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 : 0.020 / q_NPA : 0.000

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	-0.870	-0.934	2.905	-3.529	-1.217	0.136	-0.919	-1.529	-0.001
4	B	28	SER	0	-0.007	-0.008	3.132	0.190	0.661	0.009	-0.110	-0.371	0.000
5	B	29	VAL	0	-0.045	-0.027	2.962	-2.921	-1.926	0.244	-0.609	-0.630	-0.006
6	B	30	SER	0	0.017	0.008	5.194	0.334	0.395	0.000	-0.003	-0.059	0.000
7	B	31	GLU	-1	-0.910	-0.950	7.148	0.174	0.174	0.000	0.000	0.000	0.000
8	B	32	LEU	0	-0.016	-0.007	8.370	-0.161	-0.161	0.000	0.000	0.000	0.000
9	B	33	ASN	0	-0.001	0.007	6.794	0.227	0.227	0.000	0.000	0.000	0.000
10	B	34	HIS	0	0.034	-0.005	11.082	0.026	0.026	0.000	0.000	0.000	0.000
11	B	35	ASN	0	-0.045	-0.024	10.160	0.115	0.115	0.000	0.000	0.000	0.000
12	B	36	HIS	0	0.006	0.002	8.511	0.134	0.134	0.000	0.000	0.000	0.000
13	B	37	PHE	0	-0.001	0.018	13.747	0.032	0.032	0.000	0.000	0.000	0.000
14	B	38	LEU	0	-0.011	0.008	17.305	-0.020	-0.020	0.000	0.000	0.000	0.000
15	B	39	SER	0	0.024	0.008	20.303	0.010	0.010	0.000	0.000	0.000	0.000
16	B	40	PRO	0	0.030	-0.014	21.726	0.009	0.009	0.000	0.000	0.000	0.000
17	B	41	GLU	-1	-0.931	-0.953	24.935	-0.161	-0.161	0.000	0.000	0.000	0.000
18	B	42	LEU	0	-0.016	-0.008	20.639	0.008	0.008	0.000	0.000	0.000	0.000
19	B	43	GLN	0	-0.047	-0.028	24.700	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	44	ASP	-1	-0.902	-0.949	26.096	-0.104	-0.104	0.000	0.000	0.000	0.000
21	B	45	LYS	1	0.942	0.976	27.019	0.165	0.165	0.000	0.000	0.000	0.000
22	B	46	LEU	0	-0.031	-0.014	24.840	0.007	0.007	0.000	0.000	0.000	0.000
23	B	47	ASP	-1	-0.875	-0.949	28.280	-0.111	-0.111	0.000	0.000	0.000	0.000
24	B	48	VAL	0	0.012	0.015	31.300	0.010	0.010	0.000	0.000	0.000	0.000
25	B	49	MET	0	-0.005	-0.001	28.628	0.005	0.005	0.000	0.000	0.000	0.000
26	B	50	VAL	0	-0.012	0.004	30.018	0.006	0.006	0.000	0.000	0.000	0.000
27	B	51	SER	0	-0.061	-0.037	32.908	0.008	0.008	0.000	0.000	0.000	0.000
28	B	52	ILE	0	-0.003	-0.006	36.088	0.006	0.006	0.000	0.000	0.000	0.000
29	B	53	TYR	0	-0.061	-0.087	34.513	0.004	0.004	0.000	0.000	0.000	0.000
30	B	54	SER	0	-0.026	-0.005	36.562	0.006	0.006	0.000	0.000	0.000	0.000
31	B	55	CYS	0	-0.041	-0.021	38.254	0.006	0.006	0.000	0.000	0.000	0.000
32	B	56	ALA	0	-0.035	0.003	40.122	0.004	0.004	0.000	0.000	0.000	0.000
33	B	57	ARG	1	0.887	0.945	41.938	0.051	0.051	0.000	0.000	0.000	0.000
34	B	58	ASN	0	-0.030	-0.022	43.699	0.001	0.001	0.000	0.000	0.000	0.000
35	B	59	ASN	0	0.030	-0.011	41.213	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	60	ASN	0	-0.032	-0.022	41.765	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	61	GLU	-1	-0.844	-0.917	42.634	-0.056	-0.056	0.000	0.000	0.000	0.000
38	B	62	LEU	0	0.024	0.021	37.177	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	63	GLU	-1	-0.966	-0.984	37.410	-0.077	-0.077	0.000	0.000	0.000	0.000
40	B	64	GLU	-1	-0.946	-0.966	37.883	-0.077	-0.077	0.000	0.000	0.000	0.000
41	B	65	ILE	0	0.046	0.022	32.997	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	66	PHE	0	-0.042	-0.033	32.947	-0.008	-0.008	0.000	0.000	0.000	0.000
43	B	67	GLN	0	-0.004	-0.004	32.837	-0.009	-0.009	0.000	0.000	0.000	0.000
44	B	68	GLU	-1	-0.878	-0.923	30.800	-0.123	-0.123	0.000	0.000	0.000	0.000
45	B	69	LEU	0	0.035	0.012	26.834	-0.011	-0.011	0.000	0.000	0.000	0.000
46	B	70	SER	0	-0.037	-0.017	27.697	-0.011	-0.011	0.000	0.000	0.000	0.000
47	B	71	ALA	0	0.014	0.014	28.751	-0.004	-0.004	0.000	0.000	0.000	0.000
48	B	72	PHE	0	-0.036	-0.020	21.877	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	73	VAL	0	0.007	-0.010	23.539	-0.019	-0.019	0.000	0.000	0.000	0.000
50	B	74	SER	0	-0.058	-0.029	23.352	-0.014	-0.014	0.000	0.000	0.000	0.000
51	B	75	GLY	0	0.076	0.046	24.179	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	76	LEU	0	-0.041	-0.020	18.117	-0.020	-0.020	0.000	0.000	0.000	0.000
53	B	77	MET	0	-0.016	-0.026	19.050	-0.027	-0.027	0.000	0.000	0.000	0.000
54	B	78	ASP	-1	-0.897	-0.943	19.639	-0.182	-0.182	0.000	0.000	0.000	0.000
55	B	79	LYS	1	0.878	0.942	16.824	0.367	0.367	0.000	0.000	0.000	0.000
56	B	80	ARG	1	0.897	0.965	14.161	0.318	0.318	0.000	0.000	0.000	0.000
57	B	81	ASN	0	0.025	0.008	15.044	-0.027	-0.027	0.000	0.000	0.000	0.000
58	B	82	SER	0	-0.059	-0.019	17.432	0.010	0.010	0.000	0.000	0.000	0.000
59	B	83	VAL	0	0.006	0.008	11.556	0.008	0.008	0.000	0.000	0.000	0.000
60	B	84	PHE	0	-0.040	-0.028	8.507	-0.028	-0.028	0.000	0.000	0.000	0.000
61	B	85	GLU	-1	-0.936	-0.982	11.112	-0.028	-0.028	0.000	0.000	0.000	0.000
62	B	86	VAL	0	0.014	0.005	11.079	-0.029	-0.029	0.000	0.000	0.000	0.000
63	B	87	ARG	1	0.925	0.966	10.943	-0.102	-0.102	0.000	0.000	0.000	0.000
64	B	88	ASN	0	-0.032	-0.021	13.843	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	89	GLU	-1	-0.861	-0.930	16.297	-0.103	-0.103	0.000	0.000	0.000	0.000
66	B	90	ASN	0	-0.040	-0.029	17.914	0.008	0.008	0.000	0.000	0.000	0.000
67	B	91	THR	0	-0.061	-0.027	17.710	0.014	0.014	0.000	0.000	0.000	0.000
68	B	92	ASP	-1	-0.784	-0.897	17.537	0.020	0.020	0.000	0.000	0.000	0.000
69	B	93	GLU	-1	-1.022	-1.000	14.560	0.078	0.078	0.000	0.000	0.000	0.000
70	B	94	VAL	0	-0.025	0.007	12.360	0.004	0.004	0.000	0.000	0.000	0.000
71	B	95	VAL	0	-0.047	-0.031	7.428	0.020	0.020	0.000	0.000	0.000	0.000
72	B	96	GLY	0	0.019	0.014	7.841	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	97	ALA	0	-0.050	-0.042	6.950	0.187	0.187	0.000	0.000	0.000	0.000
74	B	98	LEU	0	-0.013	-0.003	7.278	-0.138	-0.138	0.000	0.000	0.000	0.000
75	B	99	ARG	1	0.874	0.964	9.594	0.338	0.338	0.000	0.000	0.000	0.000
76	B	100	ALA	0	-0.041	-0.035	13.151	-0.011	-0.011	0.000	0.000	0.000	0.000
77	B	101	GLY	0	-0.056	-0.022	14.952	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	102	MET	0	0.023	0.021	12.458	0.009	0.009	0.000	0.000	0.000	0.000
79	B	103	THR	0	-0.033	-0.008	11.048	-0.058	-0.058	0.000	0.000	0.000	0.000
80	B	104	ILE	0	0.021	-0.016	4.964	-0.086	-0.086	0.000	0.000	0.000	0.000
81	B	105	GLU	-1	-0.935	-0.963	8.627	-0.501	-0.501	0.000	0.000	0.000	0.000
82	B	106	ASP	-1	-0.826	-0.929	11.867	-0.411	-0.411	0.000	0.000	0.000	0.000
83	B	107	ARG	1	0.803	0.918	3.763	3.469	3.685	0.001	-0.071	-0.145	0.000
84	B	108	ASP	-1	-0.804	-0.920	8.773	-1.278	-1.278	0.000	0.000	0.000	0.000
85	B	109	SER	0	-0.056	-0.026	11.474	0.136	0.136	0.000	0.000	0.000	0.000
86	B	110	TYR	0	-0.051	-0.032	12.772	0.087	0.087	0.000	0.000	0.000	0.000
87	B	111	ILE	0	0.024	0.013	9.015	0.041	0.041	0.000	0.000	0.000	0.000
88	B	112	ARG	1	0.943	0.988	13.594	0.465	0.465	0.000	0.000	0.000	0.000
89	B	113	ASP	-1	-0.899	-0.953	16.609	-0.266	-0.266	0.000	0.000	0.000	0.000
90	B	114	LEU	0	-0.038	-0.022	14.001	0.041	0.041	0.000	0.000	0.000	0.000
91	B	115	PHE	0	0.042	-0.001	16.289	0.045	0.045	0.000	0.000	0.000	0.000
92	B	116	PHE	0	-0.029	0.004	18.100	0.040	0.040	0.000	0.000	0.000	0.000
93	B	117	LEU	0	0.009	0.003	20.265	0.027	0.027	0.000	0.000	0.000	0.000
94	B	118	HIS	0	0.027	0.022	19.478	0.014	0.014	0.000	0.000	0.000	0.000
95	B	119	SER	0	-0.007	-0.036	21.468	0.025	0.025	0.000	0.000	0.000	0.000
96	B	120	LEU	0	-0.020	-0.006	23.375	0.018	0.018	0.000	0.000	0.000	0.000
97	B	121	LYS	1	0.890	0.934	24.229	0.149	0.149	0.000	0.000	0.000	0.000
98	B	122	VAL	0	0.018	0.020	23.774	0.011	0.011	0.000	0.000	0.000	0.000
99	B	123	LYS	1	0.994	0.999	26.764	0.129	0.129	0.000	0.000	0.000	0.000
100	B	124	ILE	0	-0.046	-0.018	29.412	0.009	0.009	0.000	0.000	0.000	0.000
101	B	125	GLU	-1	-0.889	-0.955	27.823	-0.092	-0.092	0.000	0.000	0.000	0.000
102	B	126	GLU	-1	-0.948	-0.961	29.729	-0.080	-0.080	0.000	0.000	0.000	0.000
103	B	127	SER	0	-0.064	-0.038	33.023	0.006	0.006	0.000	0.000	0.000	0.000
104	B	128	ARG	1	0.809	0.928	34.311	0.076	0.076	0.000	0.000	0.000	0.000
105	B	129	GLN	0	0.070	0.039	35.070	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	130	GLY	0	-0.039	-0.012	37.379	0.003	0.003	0.000	0.000	0.000	0.000
107	B	131	LYS	1	0.939	0.955	40.932	0.048	0.048	0.000	0.000	0.000	0.000
108	B	132	GLU	-1	-0.893	-0.932	36.488	-0.051	-0.051	0.000	0.000	0.000	0.000
109	B	133	ASP	-1	-0.943	-0.981	37.290	-0.046	-0.046	0.000	0.000	0.000	0.000
110	B	134	SER	0	-0.052	-0.035	38.730	0.001	0.001	0.000	0.000	0.000	0.000
111	B	135	LYS	1	0.893	0.957	36.163	0.062	0.062	0.000	0.000	0.000	0.000
112	B	136	CYM	-1	-0.820	-0.830	35.395	-0.079	-0.079	0.000	0.000	0.000	0.000
113	B	137	LYS	1	0.948	0.953	34.974	0.062	0.062	0.000	0.000	0.000	0.000
114	B	138	VAL	0	0.069	0.019	31.635	-0.005	-0.005	0.000	0.000	0.000	0.000
115	B	139	TYR	0	-0.013	-0.032	29.184	-0.005	-0.005	0.000	0.000	0.000	0.000
116	B	140	ASN	0	-0.040	-0.036	29.747	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	141	LEU	0	-0.038	0.003	28.163	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	142	LEU	0	0.015	0.024	24.954	-0.011	-0.011	0.000	0.000	0.000	0.000
119	B	143	CYS	0	-0.088	-0.030	25.310	-0.005	-0.005	0.000	0.000	0.000	0.000
120	B	144	PRO	0	0.028	0.028	22.702	0.011	0.011	0.000	0.000	0.000	0.000
121	B	145	HIS	0	0.055	0.036	25.513	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	146	HIS	0	0.058	0.030	23.315	-0.010	-0.010	0.000	0.000	0.000	0.000
123	B	147	SER	0	-0.016	-0.008	22.311	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	148	SER	0	-0.053	-0.045	21.303	-0.012	-0.012	0.000	0.000	0.000	0.000
125	B	149	GLU	-1	-0.807	-0.922	17.187	-0.231	-0.231	0.000	0.000	0.000	0.000
126	B	150	LEU	0	0.026	0.011	17.160	-0.024	-0.024	0.000	0.000	0.000	0.000
127	B	151	TYR	0	-0.001	0.005	18.923	-0.008	-0.008	0.000	0.000	0.000	0.000
128	B	152	GLY	0	0.040	0.016	16.369	0.006	0.006	0.000	0.000	0.000	0.000
129	B	153	ASP	-1	-0.798	-0.896	13.983	-0.476	-0.476	0.000	0.000	0.000	0.000
130	B	154	LEU	0	-0.004	-0.008	15.333	-0.009	-0.009	0.000	0.000	0.000	0.000
131	B	155	ARG	1	0.942	0.985	16.900	0.146	0.146	0.000	0.000	0.000	0.000
132	B	156	ALA	0	0.025	0.020	12.682	0.024	0.024	0.000	0.000	0.000	0.000
133	B	157	MET	0	-0.026	-0.031	14.244	-0.015	-0.015	0.000	0.000	0.000	0.000
134	B	158	LYS	1	0.946	0.982	15.369	0.125	0.125	0.000	0.000	0.000	0.000
135	B	159	CYS	0	-0.032	0.001	15.233	0.026	0.026	0.000	0.000	0.000	0.000
136	B	160	LEU	0	-0.045	-0.023	10.412	0.018	0.018	0.000	0.000	0.000	0.000
137	B	161	VAL	0	-0.073	-0.030	14.759	0.017	0.017	0.000	0.000	0.000	0.000
138	B	162	GLU	-1	-0.962	-0.994	17.694	-0.089	-0.089	0.000	0.000	0.000	0.000
139	B	163	GLY	0	-0.010	0.017	18.223	0.017	0.017	0.000	0.000	0.000	0.000
140	B	164	CYS	0	-0.050	-0.012	17.317	0.017	0.017	0.000	0.000	0.000	0.000
141	B	165	SER	0	-0.045	-0.049	18.320	-0.017	-0.017	0.000	0.000	0.000	0.000
142	B	166	ASP	-1	-0.941	-0.966	20.582	0.003	0.003	0.000	0.000	0.000	0.000
143	B	167	ASP	-1	-0.916	-0.943	21.279	-0.067	-0.067	0.000	0.000	0.000	0.000
144	B	168	PHE	0	-0.056	-0.055	17.284	0.003	0.003	0.000	0.000	0.000	0.000
145	B	169	ASN	0	-0.010	0.000	19.092	0.015	0.015	0.000	0.000	0.000	0.000
146	B	170	PRO	0	0.001	0.016	16.603	0.010	0.010	0.000	0.000	0.000	0.000
147	B	171	PHE	0	-0.015	-0.025	14.198	0.000	0.000	0.000	0.000	0.000	0.000
148	B	172	ASP	-1	-0.942	-0.951	12.666	0.194	0.194	0.000	0.000	0.000	0.000
149	B	173	ILE	0	-0.031	-0.023	7.865	0.015	0.015	0.000	0.000	0.000	0.000
150	B	174	ILE	0	0.040	0.022	10.503	-0.077	-0.077	0.000	0.000	0.000	0.000
151	B	175	ARG	1	0.890	0.939	3.548	0.044	0.325	0.003	-0.077	-0.207	0.000
152	B	176	VAL	0	0.061	0.015	7.952	0.041	0.041	0.000	0.000	0.000	0.000
153	B	177	PRO	0	-0.054	-0.005	7.914	0.052	0.052	0.000	0.000	0.000	0.000
154	B	178	ASP	-1	-0.851	-0.940	9.293	-0.427	-0.427	0.000	0.000	0.000	0.000
155	B	179	LEU	0	-0.049	-0.034	7.945	0.114	0.114	0.000	0.000	0.000	0.000
156	B	180	THR	0	-0.010	-0.005	9.621	0.073	0.073	0.000	0.000	0.000	0.000
157	B	181	TYR	0	-0.047	-0.019	12.393	0.057	0.057	0.000	0.000	0.000	0.000
158	B	182	ASN	0	0.011	0.004	15.216	0.016	0.016	0.000	0.000	0.000	0.000
159	B	183	LYS	1	0.871	0.944	15.346	0.205	0.205	0.000	0.000	0.000	0.000
160	B	184	GLY	0	0.064	0.025	16.628	0.004	0.004	0.000	0.000	0.000	0.000
161	B	185	SER	0	-0.056	-0.014	18.535	-0.001	-0.001	0.000	0.000	0.000	0.000
162	B	186	LEU	0	-0.045	-0.025	21.079	0.002	0.002	0.000	0.000	0.000	0.000
163	B	187	GLN	0	-0.022	-0.014	20.962	-0.009	-0.009	0.000	0.000	0.000	0.000
164	B	188	CYS	0	-0.103	-0.058	22.675	0.006	0.006	0.000	0.000	0.000	0.000
165	B	189	GLY	-1	-0.950	-0.961	25.432	-0.044	-0.044	0.000	0.000	0.000	0.000

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