FMO DATABASE

FMODB ID: LNR59

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1322277.848823
FMO2-HF: Nuclear repulsion	1267176.754773
FMO2-HF: Total energy	-55101.09405
FMO2-MP2: Total energy	-55261.593786

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.
49.334	51.335	-0.011	-1.078	-0.911	0.004

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 : -0.970 / q_NPA : -0.985

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	0.000	0.013	3.705	-2.943	-1.001	-0.010	-1.059	-0.872	0.004
4	A	194	GLN	0	0.016	-0.003	6.079	-2.833	-2.833	0.000	0.000	0.000	0.000
5	A	195	PHE	0	-0.013	-0.002	7.797	-0.863	-0.863	0.000	0.000	0.000	0.000
6	A	196	ASP	-1	-0.871	-0.947	11.314	19.817	19.817	0.000	0.000	0.000	0.000
7	A	197	ARG	1	0.854	0.929	14.078	-15.409	-15.409	0.000	0.000	0.000	0.000
8	A	198	GLY	0	0.059	0.065	14.914	0.941	0.941	0.000	0.000	0.000	0.000
9	A	199	TYR	0	-0.039	-0.015	16.639	-0.753	-0.753	0.000	0.000	0.000	0.000
10	A	200	LEU	0	-0.020	-0.010	18.992	-0.360	-0.360	0.000	0.000	0.000	0.000
11	A	201	SER	0	-0.009	-0.021	21.991	-0.628	-0.628	0.000	0.000	0.000	0.000
12	A	202	PRO	0	0.044	0.017	21.851	0.418	0.418	0.000	0.000	0.000	0.000
13	A	203	TYR	0	-0.019	-0.016	22.896	0.184	0.184	0.000	0.000	0.000	0.000
14	A	204	PHE	0	0.026	0.021	20.868	-0.163	-0.163	0.000	0.000	0.000	0.000
15	A	205	ILE	0	-0.087	-0.033	19.208	0.530	0.530	0.000	0.000	0.000	0.000
16	A	206	ASN	0	0.010	0.001	18.115	-0.224	-0.224	0.000	0.000	0.000	0.000
17	A	207	LYS	1	0.923	0.972	16.427	-16.329	-16.329	0.000	0.000	0.000	0.000
18	A	208	PRO	0	0.033	0.011	19.181	0.412	0.412	0.000	0.000	0.000	0.000
19	A	209	GLU	-1	-0.927	-0.966	19.394	13.380	13.380	0.000	0.000	0.000	0.000
20	A	210	THR	0	-0.068	-0.021	14.174	0.724	0.724	0.000	0.000	0.000	0.000
21	A	211	GLY	0	-0.021	-0.005	17.329	0.040	0.040	0.000	0.000	0.000	0.000
22	A	212	ALA	0	-0.037	-0.035	14.587	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	213	VAL	0	-0.013	-0.022	15.914	-0.542	-0.542	0.000	0.000	0.000	0.000
24	A	214	GLU	-1	-0.926	-0.967	12.696	22.509	22.509	0.000	0.000	0.000	0.000
25	A	215	LEU	0	-0.065	-0.020	14.149	-1.331	-1.331	0.000	0.000	0.000	0.000
26	A	216	GLU	-1	-0.855	-0.948	12.573	23.637	23.637	0.000	0.000	0.000	0.000
27	A	217	SER	0	-0.066	-0.048	14.050	-1.385	-1.385	0.000	0.000	0.000	0.000
28	A	218	PRO	0	-0.058	-0.028	13.939	-1.228	-1.228	0.000	0.000	0.000	0.000
29	A	219	PHE	0	0.082	0.046	16.419	0.404	0.404	0.000	0.000	0.000	0.000
30	A	220	ILE	0	-0.038	-0.041	13.827	0.239	0.239	0.000	0.000	0.000	0.000
31	A	221	LEU	0	0.043	0.030	18.262	-0.293	-0.293	0.000	0.000	0.000	0.000
32	A	222	LEU	0	-0.003	0.015	16.532	0.321	0.321	0.000	0.000	0.000	0.000
33	A	223	ALA	0	0.022	0.009	20.558	-0.471	-0.471	0.000	0.000	0.000	0.000
34	A	224	ASP	-1	-0.829	-0.914	23.512	11.668	11.668	0.000	0.000	0.000	0.000
35	A	225	LYS	1	0.865	0.932	24.475	-10.152	-10.152	0.000	0.000	0.000	0.000
36	A	226	LYS	1	0.889	0.949	26.258	-9.921	-9.921	0.000	0.000	0.000	0.000
37	A	227	ILE	0	0.013	0.011	25.552	-0.323	-0.323	0.000	0.000	0.000	0.000
38	A	228	SER	0	0.038	0.009	29.145	0.104	0.104	0.000	0.000	0.000	0.000
39	A	229	ASN	0	0.009	-0.005	32.086	-0.145	-0.145	0.000	0.000	0.000	0.000
40	A	230	ILE	0	0.059	0.023	29.925	0.174	0.174	0.000	0.000	0.000	0.000
41	A	231	ARG	1	0.909	0.961	32.737	-7.724	-7.724	0.000	0.000	0.000	0.000
42	A	232	GLU	-1	-0.834	-0.931	31.322	9.368	9.368	0.000	0.000	0.000	0.000
43	A	233	MET	0	0.014	0.008	25.413	0.233	0.233	0.000	0.000	0.000	0.000
44	A	234	LEU	0	-0.053	-0.005	29.642	0.232	0.232	0.000	0.000	0.000	0.000
45	A	235	PRO	0	0.056	0.036	31.365	0.123	0.123	0.000	0.000	0.000	0.000
46	A	236	VAL	0	0.100	0.051	24.961	0.138	0.138	0.000	0.000	0.000	0.000
47	A	237	LEU	0	-0.053	-0.032	26.415	0.301	0.301	0.000	0.000	0.000	0.000
48	A	238	GLU	-1	-0.922	-0.973	28.326	9.235	9.235	0.000	0.000	0.000	0.000
49	A	239	ALA	0	-0.033	-0.006	27.274	0.052	0.052	0.000	0.000	0.000	0.000
50	A	240	VAL	0	-0.001	-0.009	23.030	0.125	0.125	0.000	0.000	0.000	0.000
51	A	241	ALA	0	0.004	0.007	25.343	0.219	0.219	0.000	0.000	0.000	0.000
52	A	242	LYS	1	0.913	0.962	27.681	-9.944	-9.944	0.000	0.000	0.000	0.000
53	A	243	ALA	0	-0.046	-0.016	24.319	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	244	GLY	0	-0.032	-0.010	24.677	0.327	0.327	0.000	0.000	0.000	0.000
55	A	245	LYS	1	0.854	0.934	19.419	-13.476	-13.476	0.000	0.000	0.000	0.000
56	A	246	PRO	0	-0.030	-0.013	18.374	-0.531	-0.531	0.000	0.000	0.000	0.000
57	A	247	LEU	0	0.015	-0.002	20.153	0.237	0.237	0.000	0.000	0.000	0.000
58	A	248	LEU	0	0.000	0.006	14.349	-0.115	-0.115	0.000	0.000	0.000	0.000
59	A	249	ILE	0	-0.017	-0.016	18.383	-0.193	-0.193	0.000	0.000	0.000	0.000
60	A	250	ILE	0	0.020	0.015	14.807	0.291	0.291	0.000	0.000	0.000	0.000
61	A	251	ALA	0	0.043	0.019	19.208	-0.228	-0.228	0.000	0.000	0.000	0.000
62	A	252	GLU	-1	-0.971	-0.979	22.068	10.813	10.813	0.000	0.000	0.000	0.000
63	A	253	ASP	-1	-0.928	-0.996	24.002	11.140	11.140	0.000	0.000	0.000	0.000
64	A	254	VAL	0	-0.013	0.030	23.798	-0.166	-0.166	0.000	0.000	0.000	0.000
65	A	255	GLU	-1	-0.890	-0.964	26.477	9.654	9.654	0.000	0.000	0.000	0.000
66	A	256	GLY	0	0.009	-0.009	29.525	-0.137	-0.137	0.000	0.000	0.000	0.000
67	A	257	GLU	-1	-0.799	-0.884	32.286	8.890	8.890	0.000	0.000	0.000	0.000
68	A	258	ALA	0	0.034	0.038	29.788	0.096	0.096	0.000	0.000	0.000	0.000
69	A	259	LEU	0	0.003	0.009	25.441	0.206	0.206	0.000	0.000	0.000	0.000
70	A	260	ALA	0	-0.015	-0.007	28.857	0.158	0.158	0.000	0.000	0.000	0.000
71	A	261	THR	0	-0.021	-0.053	31.255	0.034	0.034	0.000	0.000	0.000	0.000
72	A	262	LEU	0	0.040	0.032	25.949	0.012	0.012	0.000	0.000	0.000	0.000
73	A	263	VAL	0	0.017	0.023	26.104	0.209	0.209	0.000	0.000	0.000	0.000
74	A	264	VAL	0	-0.007	-0.003	28.119	0.030	0.030	0.000	0.000	0.000	0.000
75	A	265	ASN	0	-0.054	-0.061	30.369	-0.219	-0.219	0.000	0.000	0.000	0.000
76	A	266	THR	0	0.008	0.011	24.091	0.175	0.175	0.000	0.000	0.000	0.000
77	A	267	MET	0	-0.066	-0.026	27.424	0.052	0.052	0.000	0.000	0.000	0.000
78	A	268	ARG	1	0.879	0.940	28.969	-8.606	-8.606	0.000	0.000	0.000	0.000
79	A	269	GLY	0	-0.004	0.009	28.224	-0.168	-0.168	0.000	0.000	0.000	0.000
80	A	270	ILE	0	-0.069	-0.030	29.310	-0.054	-0.054	0.000	0.000	0.000	0.000
81	A	271	VAL	0	-0.007	0.007	27.004	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	272	LYS	1	0.917	0.952	22.614	-12.023	-12.023	0.000	0.000	0.000	0.000
83	A	273	VAL	0	0.036	0.024	21.753	0.307	0.307	0.000	0.000	0.000	0.000
84	A	274	ALA	0	0.018	0.020	18.303	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	275	ALA	0	0.024	0.021	20.137	0.097	0.097	0.000	0.000	0.000	0.000
86	A	276	VAL	0	-0.005	-0.002	16.138	-0.091	-0.091	0.000	0.000	0.000	0.000
87	A	277	LYS	1	0.927	0.964	19.278	-11.989	-11.989	0.000	0.000	0.000	0.000
88	A	278	ALA	0	0.050	0.013	17.904	0.777	0.777	0.000	0.000	0.000	0.000
89	A	279	PRO	0	-0.031	-0.010	14.258	-0.531	-0.531	0.000	0.000	0.000	0.000
90	A	280	GLY	0	0.031	0.011	17.254	-0.301	-0.301	0.000	0.000	0.000	0.000
91	A	281	PHE	0	-0.010	-0.019	19.377	-0.390	-0.390	0.000	0.000	0.000	0.000
92	A	282	GLY	0	0.022	0.001	23.051	0.119	0.119	0.000	0.000	0.000	0.000
93	A	283	ASP	-1	-0.859	-0.941	24.021	10.922	10.922	0.000	0.000	0.000	0.000
94	A	284	ARG	1	0.923	0.958	19.616	-12.304	-12.304	0.000	0.000	0.000	0.000
95	A	285	ARG	1	0.872	0.956	19.092	-10.940	-10.940	0.000	0.000	0.000	0.000
96	A	286	LYS	1	0.983	0.986	19.593	-10.090	-10.090	0.000	0.000	0.000	0.000
97	A	287	ALA	0	-0.009	0.003	19.035	0.251	0.251	0.000	0.000	0.000	0.000
98	A	288	MET	0	0.031	0.012	13.546	0.282	0.282	0.000	0.000	0.000	0.000
99	A	289	LEU	0	0.001	0.003	15.438	0.831	0.831	0.000	0.000	0.000	0.000
100	A	290	GLN	0	0.037	0.026	17.404	-0.078	-0.078	0.000	0.000	0.000	0.000
101	A	291	ASP	-1	-0.904	-0.946	13.288	17.682	17.682	0.000	0.000	0.000	0.000
102	A	292	ILE	0	-0.035	-0.024	12.420	1.134	1.134	0.000	0.000	0.000	0.000
103	A	293	ALA	0	-0.005	-0.007	13.916	0.513	0.513	0.000	0.000	0.000	0.000
104	A	294	THR	0	-0.023	-0.016	15.238	-0.293	-0.293	0.000	0.000	0.000	0.000
105	A	295	LEU	0	-0.082	-0.040	8.411	0.476	0.476	0.000	0.000	0.000	0.000
106	A	296	THR	0	-0.073	-0.057	12.497	0.424	0.424	0.000	0.000	0.000	0.000
107	A	297	GLY	0	0.017	0.027	14.275	-0.487	-0.487	0.000	0.000	0.000	0.000
108	A	298	GLY	0	0.004	0.009	17.561	-0.623	-0.623	0.000	0.000	0.000	0.000
109	A	299	THR	0	-0.030	-0.026	19.548	0.095	0.095	0.000	0.000	0.000	0.000
110	A	300	VAL	0	-0.058	-0.035	20.403	0.056	0.056	0.000	0.000	0.000	0.000
111	A	301	ILE	0	0.008	0.020	22.921	-0.404	-0.404	0.000	0.000	0.000	0.000
112	A	302	SER	0	-0.073	-0.052	25.640	0.165	0.165	0.000	0.000	0.000	0.000
113	A	303	GLU	-1	-0.849	-0.943	28.225	9.212	9.212	0.000	0.000	0.000	0.000
114	A	304	GLU	-1	-1.002	-0.989	30.764	8.668	8.668	0.000	0.000	0.000	0.000
115	A	305	ILE	0	0.004	-0.008	32.767	0.027	0.027	0.000	0.000	0.000	0.000
116	A	306	GLY	0	-0.099	-0.049	33.866	0.043	0.043	0.000	0.000	0.000	0.000
117	A	307	MET	0	-0.044	-0.005	27.014	0.226	0.226	0.000	0.000	0.000	0.000
118	A	308	GLU	-1	-0.728	-0.873	29.529	9.045	9.045	0.000	0.000	0.000	0.000
119	A	309	LEU	0	0.022	-0.008	27.012	0.182	0.182	0.000	0.000	0.000	0.000
120	A	310	GLU	-1	-1.001	-1.001	29.946	8.431	8.431	0.000	0.000	0.000	0.000
121	A	311	LYS	1	0.860	0.935	32.298	-8.566	-8.566	0.000	0.000	0.000	0.000
122	A	312	ALA	0	-0.012	0.017	27.202	0.078	0.078	0.000	0.000	0.000	0.000
123	A	313	THR	0	-0.053	-0.043	28.091	-0.150	-0.150	0.000	0.000	0.000	0.000
124	A	314	LEU	0	-0.049	-0.040	24.086	0.314	0.314	0.000	0.000	0.000	0.000
125	A	315	GLU	-1	-0.921	-0.965	23.823	11.433	11.433	0.000	0.000	0.000	0.000
126	A	316	ASP	-1	-0.829	-0.891	23.578	11.424	11.424	0.000	0.000	0.000	0.000
127	A	317	LEU	0	-0.089	-0.034	21.108	0.437	0.437	0.000	0.000	0.000	0.000
128	A	318	GLY	0	0.073	0.042	17.243	0.105	0.105	0.000	0.000	0.000	0.000
129	A	319	GLN	0	-0.078	-0.051	16.062	-0.092	-0.092	0.000	0.000	0.000	0.000
130	A	320	ALA	0	0.025	0.007	10.915	1.013	1.013	0.000	0.000	0.000	0.000
131	A	321	LYS	1	0.890	0.975	7.702	-33.277	-33.277	0.000	0.000	0.000	0.000
132	A	322	ARG	1	0.954	0.993	8.159	-29.790	-29.790	0.000	0.000	0.000	0.000
133	A	323	VAL	0	0.003	0.012	9.923	1.619	1.619	0.000	0.000	0.000	0.000
134	A	324	VAL	0	-0.039	-0.013	9.243	-1.195	-1.195	0.000	0.000	0.000	0.000
135	A	325	ILE	0	0.013	0.011	10.996	0.489	0.489	0.000	0.000	0.000	0.000
136	A	326	ASN	0	0.041	0.044	11.943	-1.550	-1.550	0.000	0.000	0.000	0.000
137	A	327	LYS	1	0.943	0.957	14.925	-13.600	-13.600	0.000	0.000	0.000	0.000
138	A	328	ASP	-1	-0.908	-0.969	14.426	15.472	15.472	0.000	0.000	0.000	0.000
139	A	329	THR	0	-0.061	-0.015	10.701	0.687	0.687	0.000	0.000	0.000	0.000
140	A	330	THR	0	0.033	-0.009	11.674	-0.797	-0.797	0.000	0.000	0.000	0.000
141	A	331	THR	0	-0.024	-0.011	5.337	1.229	1.229	0.000	0.000	0.000	0.000
142	A	332	ILE	0	0.004	-0.003	8.069	-1.104	-1.104	0.000	0.000	0.000	0.000
143	A	333	ILE	0	-0.010	-0.019	4.704	2.916	2.975	-0.001	-0.019	-0.039	0.000
144	A	334	ASP	-1	-0.852	-0.951	6.100	35.441	35.441	0.000	0.000	0.000	0.000
145	A	335	GLY	0	-0.004	0.009	7.915	-2.446	-2.446	0.000	0.000	0.000	0.000
146	A	336	VAL	0	-0.008	-0.002	10.979	-0.012	-0.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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