FMO DATABASE

FMODB ID: R57N8

Calculation Name: 3ME0-B-Xray372

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ME0

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

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:

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-958534.625733
FMO2-HF: Nuclear repulsion	909566.640391
FMO2-HF: Total energy	-48967.985342
FMO2-MP2: Total energy	-49109.633079

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:189:HIS)

Summations of interaction energy for fragment #1(B:189:HIS)

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.
-5.19	2.339	1.042	-4.045	-4.527	-0.008

Interaction energy analysis for fragmet #1(B:189:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.019

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

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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	191	HIS	0	-0.005	-0.036	3.703	-2.384	2.449	0.018	-2.515	-2.337	0.004
4	B	192	HIS	0	-0.001	-0.001	2.826	-3.038	-0.504	1.024	-1.504	-2.054	-0.012
5	B	193	HIS	0	0.009	0.048	4.276	0.482	0.644	0.000	-0.026	-0.136	0.000
6	B	194	HIS	0	-0.016	-0.033	7.103	0.132	0.132	0.000	0.000	0.000	0.000
7	B	195	GLY	0	0.006	0.024	8.661	-0.025	-0.025	0.000	0.000	0.000	0.000
8	B	196	GLY	0	0.025	0.005	10.885	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	197	CYS	0	-0.078	-0.010	12.411	0.012	0.012	0.000	0.000	0.000	0.000
10	B	198	ARG	1	0.981	0.971	9.609	0.093	0.093	0.000	0.000	0.000	0.000
11	B	199	PRO	0	0.007	0.000	15.569	0.031	0.031	0.000	0.000	0.000	0.000
12	B	200	SER	0	-0.053	-0.030	18.013	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	201	ALA	0	-0.010	-0.002	18.499	-0.011	-0.011	0.000	0.000	0.000	0.000
14	B	202	GLN	0	0.008	0.012	20.395	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	203	SER	0	0.050	0.033	24.127	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	204	LEU	0	0.004	-0.008	25.550	0.006	0.006	0.000	0.000	0.000	0.000
17	B	205	GLU	-1	-0.911	-0.963	28.611	0.027	0.027	0.000	0.000	0.000	0.000
18	B	206	ILE	0	-0.025	-0.017	32.113	0.004	0.004	0.000	0.000	0.000	0.000
19	B	207	LYS	1	0.920	0.967	32.133	-0.047	-0.047	0.000	0.000	0.000	0.000
20	B	208	HIS	1	0.811	0.867	37.444	-0.029	-0.029	0.000	0.000	0.000	0.000
21	B	209	GLY	0	0.018	0.020	40.589	0.000	0.000	0.000	0.000	0.000	0.000
22	B	210	ASP	-1	-0.876	-0.932	42.393	0.029	0.029	0.000	0.000	0.000	0.000
23	B	211	LEU	0	-0.028	-0.008	45.059	0.001	0.001	0.000	0.000	0.000	0.000
24	B	212	SER	0	0.007	-0.013	48.021	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	213	ILE	0	0.026	0.017	49.775	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	214	ASN	0	-0.036	-0.032	47.494	0.000	0.000	0.000	0.000	0.000	0.000
27	B	215	SER	0	-0.004	0.012	50.110	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	216	ALA	0	-0.008	0.010	48.166	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	217	ASN	0	0.072	0.009	48.520	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	218	ASN	0	-0.029	-0.019	47.424	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	219	HIS	0	0.066	0.054	42.509	0.001	0.001	0.000	0.000	0.000	0.000
32	B	220	TYR	0	0.022	0.000	36.516	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	221	ALA	0	-0.005	0.008	37.726	0.001	0.001	0.000	0.000	0.000	0.000
34	B	222	ALA	0	-0.030	-0.033	34.073	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	223	GLN	0	0.005	0.023	28.126	0.007	0.007	0.000	0.000	0.000	0.000
36	B	224	THR	0	-0.039	-0.006	26.685	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	225	LEU	0	0.031	0.030	22.876	0.002	0.002	0.000	0.000	0.000	0.000
38	B	226	SER	0	0.036	0.012	20.467	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	227	VAL	0	0.000	0.004	18.499	-0.016	-0.016	0.000	0.000	0.000	0.000
40	B	228	SER	0	0.009	-0.010	14.598	0.036	0.036	0.000	0.000	0.000	0.000
41	B	230	ASP	-1	-0.832	-0.926	8.888	0.050	0.050	0.000	0.000	0.000	0.000
42	B	231	VAL	0	-0.054	-0.027	11.455	0.081	0.081	0.000	0.000	0.000	0.000
43	B	232	PRO	0	-0.034	-0.017	13.988	0.007	0.007	0.000	0.000	0.000	0.000
44	B	233	ALA	0	0.007	-0.002	17.307	-0.032	-0.032	0.000	0.000	0.000	0.000
45	B	234	ASN	0	0.006	0.005	19.531	0.021	0.021	0.000	0.000	0.000	0.000
46	B	235	ILE	0	0.037	0.007	19.533	-0.012	-0.012	0.000	0.000	0.000	0.000
47	B	236	ARG	1	0.847	0.929	23.619	0.010	0.010	0.000	0.000	0.000	0.000
48	B	237	PHE	0	0.003	-0.024	23.151	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	238	MET	0	0.021	0.006	27.957	0.001	0.001	0.000	0.000	0.000	0.000
50	B	239	LEU	0	-0.014	-0.001	30.365	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	240	LEU	0	-0.005	0.000	30.375	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	241	ARG	1	0.905	0.945	33.849	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	242	ASN	0	-0.005	0.013	32.869	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	243	THR	0	0.029	-0.001	37.178	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	244	THR	0	0.018	-0.013	40.389	0.001	0.001	0.000	0.000	0.000	0.000
56	B	245	PRO	0	-0.088	-0.022	42.794	0.001	0.001	0.000	0.000	0.000	0.000
57	B	246	THR	0	0.035	0.016	45.094	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	247	TYR	0	-0.076	-0.062	48.143	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	248	SER	0	-0.012	-0.006	47.672	0.000	0.000	0.000	0.000	0.000	0.000
60	B	249	HIS	1	0.819	0.882	45.039	-0.014	-0.014	0.000	0.000	0.000	0.000
61	B	250	GLY	0	0.021	0.015	46.276	0.001	0.001	0.000	0.000	0.000	0.000
62	B	251	LYS	1	0.989	0.987	43.409	-0.018	-0.018	0.000	0.000	0.000	0.000
63	B	252	LYS	1	0.782	0.875	41.851	-0.024	-0.024	0.000	0.000	0.000	0.000
64	B	253	PHE	0	0.040	0.016	36.185	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	254	SER	0	-0.015	-0.035	39.991	0.002	0.002	0.000	0.000	0.000	0.000
66	B	255	VAL	0	-0.027	-0.004	37.117	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	256	GLY	0	0.017	0.028	40.540	0.002	0.002	0.000	0.000	0.000	0.000
68	B	257	LEU	0	-0.038	-0.034	39.933	0.000	0.000	0.000	0.000	0.000	0.000
69	B	258	GLY	0	0.074	0.046	43.096	0.000	0.000	0.000	0.000	0.000	0.000
70	B	259	HIS	0	-0.004	0.007	46.111	0.001	0.001	0.000	0.000	0.000	0.000
71	B	260	GLY	0	0.043	0.031	49.757	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	261	TRP	0	0.011	0.060	46.401	0.001	0.001	0.000	0.000	0.000	0.000
73	B	262	ASP	-1	-0.688	-0.813	44.352	0.012	0.012	0.000	0.000	0.000	0.000
74	B	263	SER	0	0.042	0.055	39.532	0.003	0.003	0.000	0.000	0.000	0.000
75	B	264	ILE	0	-0.045	-0.028	40.699	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	265	VAL	0	-0.064	-0.021	34.655	0.002	0.002	0.000	0.000	0.000	0.000
77	B	266	SER	0	0.004	0.001	36.217	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	267	VAL	0	0.006	-0.005	30.901	0.001	0.001	0.000	0.000	0.000	0.000
79	B	268	ASN	0	0.008	-0.019	27.939	0.002	0.002	0.000	0.000	0.000	0.000
80	B	269	GLY	0	0.004	0.011	32.213	0.001	0.001	0.000	0.000	0.000	0.000
81	B	270	VAL	0	0.016	0.025	34.967	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	271	ASP	-1	-0.784	-0.887	36.401	0.030	0.030	0.000	0.000	0.000	0.000
83	B	272	THR	0	-0.039	-0.031	37.514	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	273	GLY	0	0.028	0.024	35.794	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	274	GLU	-1	-0.839	-0.901	32.186	0.006	0.006	0.000	0.000	0.000	0.000
86	B	275	THR	0	-0.014	0.000	29.105	0.004	0.004	0.000	0.000	0.000	0.000
87	B	276	THR	0	0.014	0.005	26.786	-0.007	-0.007	0.000	0.000	0.000	0.000
88	B	277	MET	0	-0.037	0.026	23.874	0.008	0.008	0.000	0.000	0.000	0.000
89	B	278	ARG	1	0.990	0.983	23.486	-0.070	-0.070	0.000	0.000	0.000	0.000
90	B	279	TRP	0	-0.013	0.015	18.286	0.001	0.001	0.000	0.000	0.000	0.000
91	B	280	TYR	0	0.008	-0.021	20.494	-0.017	-0.017	0.000	0.000	0.000	0.000
92	B	281	LYS	1	0.979	0.988	15.548	-0.395	-0.395	0.000	0.000	0.000	0.000
93	B	282	ALA	0	0.009	0.030	12.829	-0.026	-0.026	0.000	0.000	0.000	0.000
94	B	283	GLY	0	0.030	-0.004	14.885	0.038	0.038	0.000	0.000	0.000	0.000
95	B	284	THR	0	-0.083	-0.032	16.074	-0.042	-0.042	0.000	0.000	0.000	0.000
96	B	285	GLN	0	-0.001	-0.002	18.578	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	286	ASN	0	0.017	-0.004	22.324	-0.004	-0.004	0.000	0.000	0.000	0.000
98	B	287	LEU	0	-0.004	-0.007	24.956	-0.004	-0.004	0.000	0.000	0.000	0.000
99	B	288	THR	0	-0.007	-0.011	26.847	0.001	0.001	0.000	0.000	0.000	0.000
100	B	289	ILE	0	0.010	0.016	28.368	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	290	GLY	0	0.021	0.015	32.123	0.002	0.002	0.000	0.000	0.000	0.000
102	B	291	SER	0	-0.035	-0.042	35.754	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	292	ARG	1	0.959	0.962	38.439	-0.026	-0.026	0.000	0.000	0.000	0.000
104	B	293	LEU	0	-0.040	-0.012	42.167	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	294	TYR	0	-0.049	-0.047	44.659	0.001	0.001	0.000	0.000	0.000	0.000
106	B	295	GLY	0	0.051	-0.010	47.535	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	296	GLU	-1	-0.886	-0.920	50.572	0.014	0.014	0.000	0.000	0.000	0.000
108	B	297	SER	0	0.015	-0.043	54.102	0.001	0.001	0.000	0.000	0.000	0.000
109	B	298	SER	0	0.017	0.005	56.704	0.000	0.000	0.000	0.000	0.000	0.000
110	B	299	LYS	1	0.918	0.952	53.589	-0.010	-0.010	0.000	0.000	0.000	0.000
111	B	300	ILE	0	-0.072	0.038	52.051	0.000	0.000	0.000	0.000	0.000	0.000
112	B	301	GLN	0	0.060	0.001	52.784	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	302	PRO	0	-0.008	-0.002	51.980	0.001	0.001	0.000	0.000	0.000	0.000
114	B	303	GLY	0	0.000	0.011	50.199	0.001	0.001	0.000	0.000	0.000	0.000
115	B	304	VAL	0	0.033	0.011	43.972	0.001	0.001	0.000	0.000	0.000	0.000
116	B	305	LEU	0	-0.016	0.000	43.536	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	306	SER	0	-0.018	-0.021	39.694	0.002	0.002	0.000	0.000	0.000	0.000
118	B	307	GLY	0	0.034	0.017	38.736	-0.002	-0.002	0.000	0.000	0.000	0.000
119	B	308	SER	0	-0.054	-0.011	34.148	0.000	0.000	0.000	0.000	0.000	0.000
120	B	309	ALA	0	0.024	-0.004	33.458	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	310	THR	0	0.034	0.032	28.373	0.000	0.000	0.000	0.000	0.000	0.000
122	B	311	LEU	0	-0.006	0.003	26.394	0.001	0.001	0.000	0.000	0.000	0.000
123	B	312	LEU	0	-0.007	-0.003	25.664	-0.003	-0.003	0.000	0.000	0.000	0.000
124	B	313	MET	0	-0.013	-0.003	20.604	0.009	0.009	0.000	0.000	0.000	0.000
125	B	314	ILE	0	-0.013	-0.010	23.462	-0.009	-0.009	0.000	0.000	0.000	0.000
126	B	315	LEU	0	0.017	-0.002	18.147	0.009	0.009	0.000	0.000	0.000	0.000
127	B	316	PRO	0	0.004	0.015	20.571	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:189:HIS)