FMO DATABASE

FMODB ID: 98Q52

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	OptHSide
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	-1322678.932522
FMO2-HF: Nuclear repulsion	1267577.09676
FMO2-HF: Total energy	-55101.835761
FMO2-MP2: Total energy	-55262.312363

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.
46.047	48.202	-0.015	-1.174	-0.965	0.005

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 : -0.969 / q_NPA : -0.988

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	-0.005	0.008	3.732	-2.881	-0.784	-0.014	-1.154	-0.929	0.005
4	A	194	GLN	0	0.034	0.018	5.517	-3.586	-3.586	0.000	0.000	0.000	0.000
5	A	195	PHE	0	0.009	0.003	7.775	-0.676	-0.676	0.000	0.000	0.000	0.000
6	A	196	ASP	-1	-0.883	-0.951	11.287	19.874	19.874	0.000	0.000	0.000	0.000
7	A	197	ARG	1	0.818	0.912	14.011	-15.467	-15.467	0.000	0.000	0.000	0.000
8	A	198	GLY	0	0.051	0.056	14.903	0.956	0.956	0.000	0.000	0.000	0.000
9	A	199	TYR	0	-0.041	-0.013	16.620	-0.752	-0.752	0.000	0.000	0.000	0.000
10	A	200	LEU	0	-0.021	-0.012	18.961	-0.376	-0.376	0.000	0.000	0.000	0.000
11	A	201	SER	0	-0.004	-0.018	21.955	-0.643	-0.643	0.000	0.000	0.000	0.000
12	A	202	PRO	0	0.054	0.017	21.804	0.414	0.414	0.000	0.000	0.000	0.000
13	A	203	TYR	0	-0.035	-0.021	22.843	0.197	0.197	0.000	0.000	0.000	0.000
14	A	204	PHE	0	0.019	0.019	20.870	-0.169	-0.169	0.000	0.000	0.000	0.000
15	A	205	ILE	0	-0.086	-0.028	19.098	0.515	0.515	0.000	0.000	0.000	0.000
16	A	206	ASN	0	0.006	-0.004	18.223	-0.163	-0.163	0.000	0.000	0.000	0.000
17	A	207	LYS	1	0.845	0.913	15.883	-17.720	-17.720	0.000	0.000	0.000	0.000
18	A	208	PRO	0	0.027	0.013	19.110	0.420	0.420	0.000	0.000	0.000	0.000
19	A	209	GLU	-1	-0.922	-0.964	19.268	13.310	13.310	0.000	0.000	0.000	0.000
20	A	210	THR	0	-0.055	-0.018	14.009	0.319	0.319	0.000	0.000	0.000	0.000
21	A	211	GLY	0	-0.019	-0.002	17.258	0.038	0.038	0.000	0.000	0.000	0.000
22	A	212	ALA	0	-0.039	-0.037	14.489	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	213	VAL	0	-0.011	-0.022	15.871	-0.525	-0.525	0.000	0.000	0.000	0.000
24	A	214	GLU	-1	-0.785	-0.859	12.218	23.089	23.089	0.000	0.000	0.000	0.000
25	A	215	LEU	0	-0.060	-0.017	14.157	-1.274	-1.274	0.000	0.000	0.000	0.000
26	A	216	GLU	-1	-0.847	-0.945	13.124	23.243	23.243	0.000	0.000	0.000	0.000
27	A	217	SER	0	-0.057	-0.044	13.982	-1.317	-1.317	0.000	0.000	0.000	0.000
28	A	218	PRO	0	-0.060	-0.024	13.907	-1.180	-1.180	0.000	0.000	0.000	0.000
29	A	219	PHE	0	0.082	0.039	16.361	0.403	0.403	0.000	0.000	0.000	0.000
30	A	220	ILE	0	-0.037	-0.040	13.679	0.245	0.245	0.000	0.000	0.000	0.000
31	A	221	LEU	0	0.039	0.029	18.262	-0.290	-0.290	0.000	0.000	0.000	0.000
32	A	222	LEU	0	-0.004	0.015	16.623	0.321	0.321	0.000	0.000	0.000	0.000
33	A	223	ALA	0	0.019	0.008	20.649	-0.473	-0.473	0.000	0.000	0.000	0.000
34	A	224	ASP	-1	-0.824	-0.905	23.583	11.760	11.760	0.000	0.000	0.000	0.000
35	A	225	LYS	1	0.797	0.872	24.549	-10.023	-10.023	0.000	0.000	0.000	0.000
36	A	226	LYS	1	0.805	0.901	26.305	-9.967	-9.967	0.000	0.000	0.000	0.000
37	A	227	ILE	0	0.020	0.014	25.470	-0.296	-0.296	0.000	0.000	0.000	0.000
38	A	228	SER	0	0.040	0.005	29.182	0.079	0.079	0.000	0.000	0.000	0.000
39	A	229	ASN	0	-0.009	-0.012	32.086	-0.152	-0.152	0.000	0.000	0.000	0.000
40	A	230	ILE	0	0.053	0.016	30.293	0.174	0.174	0.000	0.000	0.000	0.000
41	A	231	ARG	1	0.911	0.962	32.737	-7.711	-7.711	0.000	0.000	0.000	0.000
42	A	232	GLU	-1	-0.827	-0.921	31.777	9.400	9.400	0.000	0.000	0.000	0.000
43	A	233	MET	0	0.015	0.012	25.509	0.245	0.245	0.000	0.000	0.000	0.000
44	A	234	LEU	0	-0.045	-0.008	29.642	0.233	0.233	0.000	0.000	0.000	0.000
45	A	235	PRO	0	0.053	0.039	31.323	0.099	0.099	0.000	0.000	0.000	0.000
46	A	236	VAL	0	0.084	0.041	25.028	0.142	0.142	0.000	0.000	0.000	0.000
47	A	237	LEU	0	-0.048	-0.028	26.400	0.301	0.301	0.000	0.000	0.000	0.000
48	A	238	GLU	-1	-0.925	-0.972	28.326	9.196	9.196	0.000	0.000	0.000	0.000
49	A	239	ALA	0	-0.030	-0.006	27.364	0.056	0.056	0.000	0.000	0.000	0.000
50	A	240	VAL	0	0.008	-0.008	23.000	0.125	0.125	0.000	0.000	0.000	0.000
51	A	241	ALA	0	0.005	0.009	25.284	0.220	0.220	0.000	0.000	0.000	0.000
52	A	242	LYS	1	0.921	0.965	27.620	-10.022	-10.022	0.000	0.000	0.000	0.000
53	A	243	ALA	0	-0.038	-0.007	24.302	-0.072	-0.072	0.000	0.000	0.000	0.000
54	A	244	GLY	0	-0.004	0.006	24.618	0.353	0.353	0.000	0.000	0.000	0.000
55	A	245	LYS	1	0.804	0.901	19.385	-13.000	-13.000	0.000	0.000	0.000	0.000
56	A	246	PRO	0	-0.015	-0.004	18.221	-0.534	-0.534	0.000	0.000	0.000	0.000
57	A	247	LEU	0	-0.001	-0.006	20.143	0.225	0.225	0.000	0.000	0.000	0.000
58	A	248	LEU	0	0.001	0.007	14.267	-0.107	-0.107	0.000	0.000	0.000	0.000
59	A	249	ILE	0	-0.009	-0.017	18.383	-0.189	-0.189	0.000	0.000	0.000	0.000
60	A	250	ILE	0	0.012	0.012	14.796	0.290	0.290	0.000	0.000	0.000	0.000
61	A	251	ALA	0	0.049	0.023	19.252	-0.241	-0.241	0.000	0.000	0.000	0.000
62	A	252	GLU	-1	-0.885	-0.915	22.093	10.717	10.717	0.000	0.000	0.000	0.000
63	A	253	ASP	-1	-0.802	-0.905	24.033	11.163	11.163	0.000	0.000	0.000	0.000
64	A	254	VAL	0	-0.002	0.033	23.893	-0.168	-0.168	0.000	0.000	0.000	0.000
65	A	255	GLU	-1	-0.903	-0.975	26.477	9.691	9.691	0.000	0.000	0.000	0.000
66	A	256	GLY	0	0.023	-0.002	29.508	-0.135	-0.135	0.000	0.000	0.000	0.000
67	A	257	GLU	-1	-0.780	-0.877	32.258	8.917	8.917	0.000	0.000	0.000	0.000
68	A	258	ALA	0	0.035	0.041	29.801	0.092	0.092	0.000	0.000	0.000	0.000
69	A	259	LEU	0	-0.009	0.003	25.396	0.205	0.205	0.000	0.000	0.000	0.000
70	A	260	ALA	0	-0.013	-0.006	28.827	0.156	0.156	0.000	0.000	0.000	0.000
71	A	261	THR	0	-0.023	-0.050	31.213	0.035	0.035	0.000	0.000	0.000	0.000
72	A	262	LEU	0	0.038	0.030	26.046	0.013	0.013	0.000	0.000	0.000	0.000
73	A	263	VAL	0	0.006	0.021	25.974	0.207	0.207	0.000	0.000	0.000	0.000
74	A	264	VAL	0	0.002	0.000	28.072	0.025	0.025	0.000	0.000	0.000	0.000
75	A	265	ASN	0	-0.043	-0.043	30.517	-0.225	-0.225	0.000	0.000	0.000	0.000
76	A	266	THR	0	0.006	0.002	24.012	0.167	0.167	0.000	0.000	0.000	0.000
77	A	267	MET	0	-0.065	-0.022	27.406	0.061	0.061	0.000	0.000	0.000	0.000
78	A	268	ARG	1	0.888	0.945	28.908	-8.619	-8.619	0.000	0.000	0.000	0.000
79	A	269	GLY	0	-0.005	0.008	28.224	-0.160	-0.160	0.000	0.000	0.000	0.000
80	A	270	ILE	0	-0.072	-0.035	29.310	-0.044	-0.044	0.000	0.000	0.000	0.000
81	A	271	VAL	0	-0.001	0.005	26.907	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	272	LYS	1	0.907	0.949	22.701	-11.493	-11.493	0.000	0.000	0.000	0.000
83	A	273	VAL	0	0.030	0.019	21.739	0.290	0.290	0.000	0.000	0.000	0.000
84	A	274	ALA	0	0.030	0.023	18.313	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	275	ALA	0	0.011	0.019	20.137	0.093	0.093	0.000	0.000	0.000	0.000
86	A	276	VAL	0	0.009	0.002	16.006	-0.089	-0.089	0.000	0.000	0.000	0.000
87	A	277	LYS	1	0.846	0.900	19.260	-11.749	-11.749	0.000	0.000	0.000	0.000
88	A	278	ALA	0	0.053	0.019	17.933	0.794	0.794	0.000	0.000	0.000	0.000
89	A	279	PRO	0	-0.002	0.005	14.303	-0.546	-0.546	0.000	0.000	0.000	0.000
90	A	280	GLY	0	0.029	0.011	17.262	-0.304	-0.304	0.000	0.000	0.000	0.000
91	A	281	PHE	0	0.006	-0.015	19.386	-0.363	-0.363	0.000	0.000	0.000	0.000
92	A	282	GLY	0	0.031	0.007	23.080	0.120	0.120	0.000	0.000	0.000	0.000
93	A	283	ASP	-1	-0.807	-0.912	24.071	10.884	10.884	0.000	0.000	0.000	0.000
94	A	284	ARG	1	0.930	0.966	19.521	-12.175	-12.175	0.000	0.000	0.000	0.000
95	A	285	ARG	1	0.804	0.913	19.151	-10.857	-10.857	0.000	0.000	0.000	0.000
96	A	286	LYS	1	0.948	0.962	19.662	-10.113	-10.113	0.000	0.000	0.000	0.000
97	A	287	ALA	0	-0.018	-0.004	19.186	0.259	0.259	0.000	0.000	0.000	0.000
98	A	288	MET	0	0.039	0.015	13.414	0.269	0.269	0.000	0.000	0.000	0.000
99	A	289	LEU	0	-0.013	-0.003	15.534	0.825	0.825	0.000	0.000	0.000	0.000
100	A	290	GLN	0	0.046	0.024	17.517	-0.063	-0.063	0.000	0.000	0.000	0.000
101	A	291	ASP	-1	-0.907	-0.939	13.404	17.729	17.729	0.000	0.000	0.000	0.000
102	A	292	ILE	0	-0.033	-0.025	12.371	1.122	1.122	0.000	0.000	0.000	0.000
103	A	293	ALA	0	-0.011	0.002	14.039	0.513	0.513	0.000	0.000	0.000	0.000
104	A	294	THR	0	-0.025	-0.024	15.453	-0.291	-0.291	0.000	0.000	0.000	0.000
105	A	295	LEU	0	-0.061	-0.019	8.720	0.507	0.507	0.000	0.000	0.000	0.000
106	A	296	THR	0	-0.081	-0.068	12.659	0.519	0.519	0.000	0.000	0.000	0.000
107	A	297	GLY	0	0.025	0.033	14.428	-0.474	-0.474	0.000	0.000	0.000	0.000
108	A	298	GLY	0	0.000	0.006	17.717	-0.612	-0.612	0.000	0.000	0.000	0.000
109	A	299	THR	0	-0.042	-0.029	19.691	0.124	0.124	0.000	0.000	0.000	0.000
110	A	300	VAL	0	-0.063	-0.037	20.473	0.049	0.049	0.000	0.000	0.000	0.000
111	A	301	ILE	0	0.001	0.017	23.039	-0.418	-0.418	0.000	0.000	0.000	0.000
112	A	302	SER	0	-0.043	-0.045	25.736	0.147	0.147	0.000	0.000	0.000	0.000
113	A	303	GLU	-1	-0.811	-0.911	28.320	9.234	9.234	0.000	0.000	0.000	0.000
114	A	304	GLU	-1	-0.969	-0.966	30.767	8.710	8.710	0.000	0.000	0.000	0.000
115	A	305	ILE	0	-0.010	-0.017	32.875	0.029	0.029	0.000	0.000	0.000	0.000
116	A	306	GLY	0	-0.054	-0.027	33.994	0.050	0.050	0.000	0.000	0.000	0.000
117	A	307	MET	0	-0.043	-0.003	27.103	0.219	0.219	0.000	0.000	0.000	0.000
118	A	308	GLU	-1	-0.734	-0.864	29.637	8.903	8.903	0.000	0.000	0.000	0.000
119	A	309	LEU	0	0.020	-0.006	27.035	0.197	0.197	0.000	0.000	0.000	0.000
120	A	310	GLU	-1	-0.984	-0.995	30.039	8.414	8.414	0.000	0.000	0.000	0.000
121	A	311	LYS	1	0.788	0.891	32.409	-8.555	-8.555	0.000	0.000	0.000	0.000
122	A	312	ALA	0	-0.011	0.018	27.283	0.082	0.082	0.000	0.000	0.000	0.000
123	A	313	THR	0	-0.060	-0.061	28.214	-0.182	-0.182	0.000	0.000	0.000	0.000
124	A	314	LEU	0	-0.051	-0.035	24.083	0.314	0.314	0.000	0.000	0.000	0.000
125	A	315	GLU	-1	-0.907	-0.940	23.772	11.397	11.397	0.000	0.000	0.000	0.000
126	A	316	ASP	-1	-0.814	-0.894	23.734	11.423	11.423	0.000	0.000	0.000	0.000
127	A	317	LEU	0	-0.094	-0.035	21.103	0.440	0.440	0.000	0.000	0.000	0.000
128	A	318	GLY	0	0.068	0.039	17.374	0.110	0.110	0.000	0.000	0.000	0.000
129	A	319	GLN	0	-0.073	-0.049	16.011	-0.150	-0.150	0.000	0.000	0.000	0.000
130	A	320	ALA	0	0.023	0.005	10.876	1.010	1.010	0.000	0.000	0.000	0.000
131	A	321	LYS	1	0.870	0.953	7.588	-33.172	-33.172	0.000	0.000	0.000	0.000
132	A	322	ARG	1	0.855	0.927	7.507	-29.998	-29.998	0.000	0.000	0.000	0.000
133	A	323	VAL	0	0.005	0.012	9.861	1.602	1.602	0.000	0.000	0.000	0.000
134	A	324	VAL	0	-0.028	-0.009	9.256	-1.215	-1.215	0.000	0.000	0.000	0.000
135	A	325	ILE	0	0.000	0.002	10.951	0.517	0.517	0.000	0.000	0.000	0.000
136	A	326	ASN	0	0.003	0.011	11.428	-1.825	-1.825	0.000	0.000	0.000	0.000
137	A	327	LYS	1	0.870	0.908	14.883	-14.285	-14.285	0.000	0.000	0.000	0.000
138	A	328	ASP	-1	-0.847	-0.922	14.791	14.799	14.799	0.000	0.000	0.000	0.000
139	A	329	THR	0	-0.037	-0.007	9.833	-0.234	-0.234	0.000	0.000	0.000	0.000
140	A	330	THR	0	0.047	0.008	11.667	-0.755	-0.755	0.000	0.000	0.000	0.000
141	A	331	THR	0	-0.038	-0.020	5.322	1.220	1.220	0.000	0.000	0.000	0.000
142	A	332	ILE	0	0.000	-0.004	8.077	-1.082	-1.082	0.000	0.000	0.000	0.000
143	A	333	ILE	0	-0.005	-0.018	4.668	2.875	2.933	-0.001	-0.020	-0.036	0.000
144	A	334	ASP	-1	-0.842	-0.937	5.804	35.570	35.570	0.000	0.000	0.000	0.000
145	A	335	GLY	0	0.015	0.020	7.870	-2.376	-2.376	0.000	0.000	0.000	0.000
146	A	336	VAL	0	-0.043	-0.028	10.990	-0.397	-0.397	0.000	0.000	0.000	0.000

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