FMO DATABASE

FMODB ID: MNZKZ

Calculation Name: 1DK7-A-Xray372

Preferred Name: 60 kDa chaperonin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1DK7

Chain ID: A

ChEMBL ID: CHEMBL4296299

UniProt ID: P0A6F5

Base Structure: X-ray

Registration Date: 2023-09-23

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1319673.811229
FMO2-HF: Nuclear repulsion	1264571.608041
FMO2-HF: Total energy	-55102.203188
FMO2-MP2: Total energy	-55262.597748

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(A:191:GLU)

Summations of interaction energy for fragment #1(A:191:GLU)

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.
45.903	48.317	0.055	-1.324	-1.144	0.002

Interaction energy analysis for fragmet #1(A:191:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.968 / q_NPA : -0.983

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	A	193	MET	0	-0.013	0.012	3.300	-2.084	0.203	0.056	-1.284	-1.058	0.002
4	A	194	GLN	0	0.010	0.004	5.384	-3.057	-3.057	0.000	0.000	0.000	0.000
5	A	195	PHE	0	0.018	0.003	7.405	-0.798	-0.798	0.000	0.000	0.000	0.000
6	A	196	ASP	-1	-0.868	-0.933	10.948	19.636	19.636	0.000	0.000	0.000	0.000
7	A	197	ARG	1	0.773	0.876	13.870	-15.526	-15.526	0.000	0.000	0.000	0.000
8	A	198	GLY	0	0.054	0.061	14.762	0.998	0.998	0.000	0.000	0.000	0.000
9	A	199	TYR	0	-0.038	-0.016	16.507	-0.712	-0.712	0.000	0.000	0.000	0.000
10	A	200	LEU	0	-0.037	-0.021	18.769	-0.449	-0.449	0.000	0.000	0.000	0.000
11	A	201	SER	0	0.000	-0.013	21.806	-0.651	-0.651	0.000	0.000	0.000	0.000
12	A	202	PRO	0	0.038	0.015	21.457	0.404	0.404	0.000	0.000	0.000	0.000
13	A	203	TYR	0	-0.034	-0.020	22.421	0.201	0.201	0.000	0.000	0.000	0.000
14	A	204	PHE	0	0.018	0.010	20.478	-0.206	-0.206	0.000	0.000	0.000	0.000
15	A	205	ILE	0	-0.092	-0.025	18.860	0.484	0.484	0.000	0.000	0.000	0.000
16	A	206	ASN	0	0.007	-0.008	17.982	-0.128	-0.128	0.000	0.000	0.000	0.000
17	A	207	LYS	1	0.835	0.913	15.125	-18.545	-18.545	0.000	0.000	0.000	0.000
18	A	208	PRO	0	0.038	0.008	18.598	0.340	0.340	0.000	0.000	0.000	0.000
19	A	209	GLU	-1	-0.912	-0.962	18.638	13.495	13.495	0.000	0.000	0.000	0.000
20	A	210	THR	0	-0.072	-0.034	13.405	0.820	0.820	0.000	0.000	0.000	0.000
21	A	211	GLY	0	-0.023	0.005	16.224	0.351	0.351	0.000	0.000	0.000	0.000
22	A	212	ALA	0	-0.016	-0.014	14.090	-0.045	-0.045	0.000	0.000	0.000	0.000
23	A	213	VAL	0	-0.005	-0.010	15.528	-0.694	-0.694	0.000	0.000	0.000	0.000
24	A	214	GLU	-1	-0.794	-0.863	11.520	24.403	24.403	0.000	0.000	0.000	0.000
25	A	215	LEU	0	-0.045	-0.008	13.762	-1.395	-1.395	0.000	0.000	0.000	0.000
26	A	216	GLU	-1	-0.821	-0.934	12.771	23.446	23.446	0.000	0.000	0.000	0.000
27	A	217	SER	0	-0.060	-0.042	14.046	-1.391	-1.391	0.000	0.000	0.000	0.000
28	A	218	PRO	0	-0.051	-0.012	13.919	-1.136	-1.136	0.000	0.000	0.000	0.000
29	A	219	PHE	0	0.071	0.029	16.291	0.397	0.397	0.000	0.000	0.000	0.000
30	A	220	ILE	0	-0.028	-0.029	13.610	0.367	0.367	0.000	0.000	0.000	0.000
31	A	221	LEU	0	0.026	0.022	18.112	-0.323	-0.323	0.000	0.000	0.000	0.000
32	A	222	LEU	0	-0.013	0.001	16.653	0.506	0.506	0.000	0.000	0.000	0.000
33	A	223	ALA	0	0.013	0.003	20.661	-0.465	-0.465	0.000	0.000	0.000	0.000
34	A	224	ASP	-1	-0.832	-0.913	23.678	11.534	11.534	0.000	0.000	0.000	0.000
35	A	225	LYS	1	0.772	0.863	24.816	-10.094	-10.094	0.000	0.000	0.000	0.000
36	A	226	LYS	1	0.780	0.878	26.190	-9.836	-9.836	0.000	0.000	0.000	0.000
37	A	227	ILE	0	0.044	0.027	25.261	-0.192	-0.192	0.000	0.000	0.000	0.000
38	A	228	SER	0	0.026	0.004	29.021	0.112	0.112	0.000	0.000	0.000	0.000
39	A	229	ASN	0	-0.009	-0.014	31.929	-0.197	-0.197	0.000	0.000	0.000	0.000
40	A	230	ILE	0	0.024	-0.001	30.417	0.193	0.193	0.000	0.000	0.000	0.000
41	A	231	ARG	1	0.906	0.953	32.740	-7.715	-7.715	0.000	0.000	0.000	0.000
42	A	232	GLU	-1	-0.817	-0.912	31.357	9.435	9.435	0.000	0.000	0.000	0.000
43	A	233	MET	0	0.037	0.019	25.391	0.235	0.235	0.000	0.000	0.000	0.000
44	A	234	LEU	0	-0.042	-0.009	29.490	0.216	0.216	0.000	0.000	0.000	0.000
45	A	235	PRO	0	0.037	0.018	31.131	0.102	0.102	0.000	0.000	0.000	0.000
46	A	236	VAL	0	0.074	0.040	24.851	0.155	0.155	0.000	0.000	0.000	0.000
47	A	237	LEU	0	-0.054	-0.026	26.305	0.340	0.340	0.000	0.000	0.000	0.000
48	A	238	GLU	-1	-0.904	-0.963	28.206	9.282	9.282	0.000	0.000	0.000	0.000
49	A	239	ALA	0	-0.026	0.000	27.390	0.037	0.037	0.000	0.000	0.000	0.000
50	A	240	VAL	0	0.015	0.000	22.943	0.142	0.142	0.000	0.000	0.000	0.000
51	A	241	ALA	0	0.007	0.012	25.405	0.191	0.191	0.000	0.000	0.000	0.000
52	A	242	LYS	1	0.878	0.935	27.931	-10.107	-10.107	0.000	0.000	0.000	0.000
53	A	243	ALA	0	0.016	0.019	24.456	-0.131	-0.131	0.000	0.000	0.000	0.000
54	A	244	GLY	0	-0.031	-0.003	24.576	0.374	0.374	0.000	0.000	0.000	0.000
55	A	245	LYS	1	0.822	0.908	19.429	-13.019	-13.019	0.000	0.000	0.000	0.000
56	A	246	PRO	0	0.000	0.006	17.809	-0.575	-0.575	0.000	0.000	0.000	0.000
57	A	247	LEU	0	-0.014	-0.001	19.681	0.211	0.211	0.000	0.000	0.000	0.000
58	A	248	LEU	0	0.002	0.003	13.918	-0.112	-0.112	0.000	0.000	0.000	0.000
59	A	249	ILE	0	-0.003	-0.012	17.993	-0.370	-0.370	0.000	0.000	0.000	0.000
60	A	250	ILE	0	0.002	0.008	14.859	0.207	0.207	0.000	0.000	0.000	0.000
61	A	251	ALA	0	0.055	0.037	19.115	-0.247	-0.247	0.000	0.000	0.000	0.000
62	A	252	GLU	-1	-0.832	-0.887	21.818	10.763	10.763	0.000	0.000	0.000	0.000
63	A	253	ASP	-1	-0.818	-0.902	24.017	11.063	11.063	0.000	0.000	0.000	0.000
64	A	254	VAL	0	0.021	0.028	23.647	-0.101	-0.101	0.000	0.000	0.000	0.000
65	A	255	GLU	-1	-0.875	-0.958	26.201	9.670	9.670	0.000	0.000	0.000	0.000
66	A	256	GLY	0	0.010	-0.006	29.277	-0.119	-0.119	0.000	0.000	0.000	0.000
67	A	257	GLU	-1	-0.784	-0.870	32.235	8.861	8.861	0.000	0.000	0.000	0.000
68	A	258	ALA	0	0.024	0.030	29.535	0.081	0.081	0.000	0.000	0.000	0.000
69	A	259	LEU	0	-0.013	0.004	25.456	0.186	0.186	0.000	0.000	0.000	0.000
70	A	260	ALA	0	0.004	0.003	28.639	0.163	0.163	0.000	0.000	0.000	0.000
71	A	261	THR	0	-0.025	-0.047	31.132	0.021	0.021	0.000	0.000	0.000	0.000
72	A	262	LEU	0	0.036	0.019	25.948	0.017	0.017	0.000	0.000	0.000	0.000
73	A	263	VAL	0	-0.004	0.018	25.793	0.222	0.222	0.000	0.000	0.000	0.000
74	A	264	VAL	0	0.003	-0.003	27.728	0.039	0.039	0.000	0.000	0.000	0.000
75	A	265	ASN	0	-0.034	-0.041	30.490	-0.293	-0.293	0.000	0.000	0.000	0.000
76	A	266	THR	0	0.014	0.002	23.608	0.129	0.129	0.000	0.000	0.000	0.000
77	A	267	MET	0	-0.036	-0.010	27.025	0.069	0.069	0.000	0.000	0.000	0.000
78	A	268	ARG	1	0.870	0.947	28.570	-8.762	-8.762	0.000	0.000	0.000	0.000
79	A	269	GLY	0	0.019	0.020	27.676	-0.156	-0.156	0.000	0.000	0.000	0.000
80	A	270	ILE	0	-0.053	-0.021	28.758	0.069	0.069	0.000	0.000	0.000	0.000
81	A	271	VAL	0	-0.008	0.003	26.818	0.008	0.008	0.000	0.000	0.000	0.000
82	A	272	LYS	1	0.856	0.911	22.642	-11.260	-11.260	0.000	0.000	0.000	0.000
83	A	273	VAL	0	0.033	0.023	21.503	0.391	0.391	0.000	0.000	0.000	0.000
84	A	274	ALA	0	0.015	0.013	18.287	-0.106	-0.106	0.000	0.000	0.000	0.000
85	A	275	ALA	0	0.012	0.010	20.053	0.114	0.114	0.000	0.000	0.000	0.000
86	A	276	VAL	0	0.019	0.005	16.035	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	277	LYS	1	0.856	0.908	19.234	-11.738	-11.738	0.000	0.000	0.000	0.000
88	A	278	ALA	0	0.073	0.032	17.828	0.817	0.817	0.000	0.000	0.000	0.000
89	A	279	PRO	0	0.002	0.014	14.110	-0.610	-0.610	0.000	0.000	0.000	0.000
90	A	280	GLY	0	0.040	0.018	16.884	-0.376	-0.376	0.000	0.000	0.000	0.000
91	A	281	PHE	0	0.004	-0.020	19.088	-0.327	-0.327	0.000	0.000	0.000	0.000
92	A	282	GLY	0	0.026	0.006	22.896	0.092	0.092	0.000	0.000	0.000	0.000
93	A	283	ASP	-1	-0.809	-0.909	23.828	10.888	10.888	0.000	0.000	0.000	0.000
94	A	284	ARG	1	0.936	0.970	19.457	-11.943	-11.943	0.000	0.000	0.000	0.000
95	A	285	ARG	1	0.800	0.896	19.125	-10.867	-10.867	0.000	0.000	0.000	0.000
96	A	286	LYS	1	0.896	0.947	19.757	-10.176	-10.176	0.000	0.000	0.000	0.000
97	A	287	ALA	0	-0.018	-0.001	19.025	0.204	0.204	0.000	0.000	0.000	0.000
98	A	288	MET	0	0.051	0.019	13.176	0.171	0.171	0.000	0.000	0.000	0.000
99	A	289	LEU	0	-0.024	-0.006	15.529	0.812	0.812	0.000	0.000	0.000	0.000
100	A	290	GLN	0	0.047	0.022	17.702	-0.124	-0.124	0.000	0.000	0.000	0.000
101	A	291	ASP	-1	-0.912	-0.943	13.515	17.489	17.489	0.000	0.000	0.000	0.000
102	A	292	ILE	0	-0.019	-0.022	12.324	1.110	1.110	0.000	0.000	0.000	0.000
103	A	293	ALA	0	-0.006	0.013	14.040	0.519	0.519	0.000	0.000	0.000	0.000
104	A	294	THR	0	-0.044	-0.037	15.575	-0.400	-0.400	0.000	0.000	0.000	0.000
105	A	295	LEU	0	-0.047	-0.017	8.560	0.510	0.510	0.000	0.000	0.000	0.000
106	A	296	THR	0	-0.083	-0.064	12.447	0.692	0.692	0.000	0.000	0.000	0.000
107	A	297	GLY	0	0.021	0.034	14.540	-0.380	-0.380	0.000	0.000	0.000	0.000
108	A	298	GLY	0	0.008	0.004	17.986	-0.486	-0.486	0.000	0.000	0.000	0.000
109	A	299	THR	0	-0.047	-0.049	20.163	0.150	0.150	0.000	0.000	0.000	0.000
110	A	300	VAL	0	-0.053	-0.025	20.643	0.161	0.161	0.000	0.000	0.000	0.000
111	A	301	ILE	0	0.023	0.021	23.123	-0.454	-0.454	0.000	0.000	0.000	0.000
112	A	302	SER	0	-0.053	-0.044	25.699	0.157	0.157	0.000	0.000	0.000	0.000
113	A	303	GLU	-1	-0.820	-0.912	28.382	9.270	9.270	0.000	0.000	0.000	0.000
114	A	304	GLU	-1	-0.953	-0.956	30.803	8.726	8.726	0.000	0.000	0.000	0.000
115	A	305	ILE	0	-0.035	-0.024	32.860	0.039	0.039	0.000	0.000	0.000	0.000
116	A	306	GLY	0	-0.047	-0.028	33.996	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	307	MET	0	-0.039	-0.003	27.181	0.162	0.162	0.000	0.000	0.000	0.000
118	A	308	GLU	-1	-0.725	-0.856	29.476	8.934	8.934	0.000	0.000	0.000	0.000
119	A	309	LEU	0	0.000	-0.017	26.975	0.118	0.118	0.000	0.000	0.000	0.000
120	A	310	GLU	-1	-0.977	-0.995	30.051	8.388	8.388	0.000	0.000	0.000	0.000
121	A	311	LYS	1	0.779	0.885	32.318	-8.615	-8.615	0.000	0.000	0.000	0.000
122	A	312	ALA	0	-0.010	0.020	27.176	0.054	0.054	0.000	0.000	0.000	0.000
123	A	313	THR	0	-0.060	-0.058	28.574	-0.105	-0.105	0.000	0.000	0.000	0.000
124	A	314	LEU	0	-0.053	-0.040	24.361	0.308	0.308	0.000	0.000	0.000	0.000
125	A	315	GLU	-1	-0.900	-0.937	23.929	11.347	11.347	0.000	0.000	0.000	0.000
126	A	316	ASP	-1	-0.790	-0.863	23.971	11.395	11.395	0.000	0.000	0.000	0.000
127	A	317	LEU	0	-0.097	-0.032	21.171	0.482	0.482	0.000	0.000	0.000	0.000
128	A	318	GLY	0	0.094	0.056	17.532	0.156	0.156	0.000	0.000	0.000	0.000
129	A	319	GLN	0	-0.072	-0.055	16.013	-0.097	-0.097	0.000	0.000	0.000	0.000
130	A	320	ALA	0	0.024	0.005	10.703	0.984	0.984	0.000	0.000	0.000	0.000
131	A	321	LYS	1	0.856	0.941	7.511	-33.952	-33.952	0.000	0.000	0.000	0.000
132	A	322	ARG	1	0.842	0.909	6.940	-31.362	-31.362	0.000	0.000	0.000	0.000
133	A	323	VAL	0	0.006	0.015	9.730	1.538	1.538	0.000	0.000	0.000	0.000
134	A	324	VAL	0	-0.015	-0.008	8.622	-0.902	-0.902	0.000	0.000	0.000	0.000
135	A	325	ILE	0	-0.014	-0.005	10.711	0.473	0.473	0.000	0.000	0.000	0.000
136	A	326	ASN	0	0.019	0.006	11.237	-1.749	-1.749	0.000	0.000	0.000	0.000
137	A	327	LYS	1	0.867	0.904	14.626	-14.641	-14.641	0.000	0.000	0.000	0.000
138	A	328	ASP	-1	-0.861	-0.911	14.953	14.593	14.593	0.000	0.000	0.000	0.000
139	A	329	THR	0	-0.033	-0.018	9.769	-0.298	-0.298	0.000	0.000	0.000	0.000
140	A	330	THR	0	0.030	-0.005	11.632	-0.583	-0.583	0.000	0.000	0.000	0.000
141	A	331	THR	0	-0.030	-0.017	5.356	1.253	1.253	0.000	0.000	0.000	0.000
142	A	332	ILE	0	0.006	0.000	7.657	-1.541	-1.541	0.000	0.000	0.000	0.000
143	A	333	ILE	0	0.001	-0.008	4.357	2.569	2.696	-0.001	-0.040	-0.086	0.000
144	A	334	ASP	-1	-0.839	-0.936	5.677	36.517	36.517	0.000	0.000	0.000	0.000
145	A	335	GLY	0	0.009	0.018	7.818	-2.406	-2.406	0.000	0.000	0.000	0.000
146	A	336	VAL	0	-0.052	-0.029	10.924	-0.440	-0.440	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:191:GLU)