FMO DATABASE

FMODB ID: M363Z

Calculation Name: 3ME0-B-Xray317

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 3ME0

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

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:

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	127
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-958349.581689
FMO2-HF: Nuclear repulsion	909382.111577
FMO2-HF: Total energy	-48967.470112
FMO2-MP2: Total energy	-49109.110384

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.
-5.025	2.409	1.047	-3.988	-4.491	-0.01

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 : 0.070 / q_NPA : 0.017

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	191	HIS	0	-0.006	-0.036	3.703	-2.241	2.469	0.026	-2.439	-2.296	0.003
4	B	192	HIS	0	0.000	-0.001	2.826	-3.076	-0.517	1.020	-1.522	-2.056	-0.013
5	B	193	HIS	0	0.005	0.046	4.260	0.549	0.714	0.001	-0.027	-0.139	0.000
6	B	194	HIS	0	-0.010	-0.029	7.056	0.159	0.159	0.000	0.000	0.000	0.000
7	B	195	GLY	0	0.002	0.023	8.661	-0.028	-0.028	0.000	0.000	0.000	0.000
8	B	196	GLY	0	0.035	0.011	10.884	-0.006	-0.006	0.000	0.000	0.000	0.000
9	B	229	CYS	0	-0.070	-0.004	12.432	0.016	0.016	0.000	0.000	0.000	0.000
10	B	198	ARG	1	0.981	0.969	9.668	0.115	0.115	0.000	0.000	0.000	0.000
11	B	199	PRO	0	0.010	0.002	15.616	0.034	0.034	0.000	0.000	0.000	0.000
12	B	200	SER	0	-0.058	-0.032	18.069	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	201	ALA	0	-0.010	-0.002	18.534	-0.011	-0.011	0.000	0.000	0.000	0.000
14	B	202	GLN	0	0.005	0.010	20.457	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	203	SER	0	0.049	0.031	24.166	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	204	LEU	0	0.008	-0.005	25.600	0.006	0.006	0.000	0.000	0.000	0.000
17	B	205	GLU	-1	-0.912	-0.964	28.667	0.025	0.025	0.000	0.000	0.000	0.000
18	B	206	ILE	0	-0.027	-0.017	32.170	0.004	0.004	0.000	0.000	0.000	0.000
19	B	207	LYS	1	0.922	0.967	32.129	-0.045	-0.045	0.000	0.000	0.000	0.000
20	B	208	HIS	1	0.813	0.867	37.505	-0.027	-0.027	0.000	0.000	0.000	0.000
21	B	209	GLY	0	0.015	0.019	40.652	0.000	0.000	0.000	0.000	0.000	0.000
22	B	210	ASP	-1	-0.875	-0.933	42.430	0.028	0.028	0.000	0.000	0.000	0.000
23	B	211	LEU	0	-0.028	-0.007	45.119	0.001	0.001	0.000	0.000	0.000	0.000
24	B	212	SER	0	0.007	-0.012	48.082	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	213	ILE	0	0.024	0.016	49.749	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	214	ASN	0	-0.034	-0.032	47.525	0.000	0.000	0.000	0.000	0.000	0.000
27	B	215	SER	0	-0.006	0.012	50.170	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	216	ALA	0	-0.008	0.010	48.226	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	217	ASN	0	0.072	0.008	48.577	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	218	ASN	0	-0.026	-0.017	47.478	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	219	HIS	0	0.062	0.053	42.572	0.001	0.001	0.000	0.000	0.000	0.000
32	B	220	TYR	0	0.025	0.001	36.510	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	221	ALA	0	-0.008	0.006	37.788	0.002	0.002	0.000	0.000	0.000	0.000
34	B	222	ALA	0	-0.030	-0.033	34.074	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	223	GLN	0	0.004	0.021	28.189	0.008	0.008	0.000	0.000	0.000	0.000
36	B	224	THR	0	-0.038	-0.005	26.685	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	225	LEU	0	0.028	0.028	22.929	0.002	0.002	0.000	0.000	0.000	0.000
38	B	226	SER	0	0.033	0.011	20.503	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	227	VAL	0	0.009	0.008	18.500	-0.016	-0.016	0.000	0.000	0.000	0.000
40	B	228	SER	0	0.000	-0.013	14.599	0.039	0.039	0.000	0.000	0.000	0.000
41	B	230	ASP	-1	-0.837	-0.930	8.888	0.008	0.008	0.000	0.000	0.000	0.000
42	B	231	VAL	0	-0.050	-0.027	11.454	0.083	0.083	0.000	0.000	0.000	0.000
43	B	232	PRO	0	-0.047	-0.022	13.987	0.011	0.011	0.000	0.000	0.000	0.000
44	B	233	ALA	0	0.022	0.005	17.306	-0.033	-0.033	0.000	0.000	0.000	0.000
45	B	234	ASN	0	0.014	0.009	19.531	0.025	0.025	0.000	0.000	0.000	0.000
46	B	235	ILE	0	0.044	0.013	19.533	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	236	ARG	1	0.855	0.932	23.618	0.020	0.020	0.000	0.000	0.000	0.000
48	B	237	PHE	0	0.000	-0.025	23.151	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	238	MET	0	0.022	0.005	27.988	0.002	0.002	0.000	0.000	0.000	0.000
50	B	239	LEU	0	-0.019	-0.004	30.394	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	240	LEU	0	-0.002	0.001	30.398	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	241	ARG	1	0.900	0.942	33.877	0.000	0.000	0.000	0.000	0.000	0.000
53	B	242	ASN	0	-0.004	0.014	32.900	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	243	THR	0	0.024	-0.003	37.208	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	244	THR	0	0.021	-0.012	40.423	0.001	0.001	0.000	0.000	0.000	0.000
56	B	245	PRO	0	-0.087	-0.021	42.827	0.001	0.001	0.000	0.000	0.000	0.000
57	B	246	THR	0	0.035	0.015	45.130	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	247	TYR	0	-0.079	-0.064	48.182	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	248	SER	0	-0.011	-0.006	47.707	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	249	HIS	1	0.820	0.882	45.076	-0.011	-0.011	0.000	0.000	0.000	0.000
61	B	250	GLY	0	0.019	0.015	46.312	0.001	0.001	0.000	0.000	0.000	0.000
62	B	251	LYS	1	0.989	0.987	43.438	-0.015	-0.015	0.000	0.000	0.000	0.000
63	B	252	LYS	1	0.782	0.875	41.888	-0.021	-0.021	0.000	0.000	0.000	0.000
64	B	253	PHE	0	0.042	0.018	36.218	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	254	SER	0	-0.019	-0.037	40.027	0.002	0.002	0.000	0.000	0.000	0.000
66	B	255	VAL	0	-0.022	-0.002	37.155	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	256	GLY	0	0.014	0.026	40.579	0.002	0.002	0.000	0.000	0.000	0.000
68	B	257	LEU	0	-0.039	-0.034	39.981	0.000	0.000	0.000	0.000	0.000	0.000
69	B	258	GLY	0	0.076	0.047	43.141	0.000	0.000	0.000	0.000	0.000	0.000
70	B	259	HIS	0	-0.002	0.007	46.155	0.001	0.001	0.000	0.000	0.000	0.000
71	B	260	GLY	0	0.039	0.030	49.802	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	261	TRP	0	0.012	0.060	46.450	0.001	0.001	0.000	0.000	0.000	0.000
73	B	262	ASP	-1	-0.687	-0.814	44.396	0.009	0.009	0.000	0.000	0.000	0.000
74	B	263	SER	0	0.042	0.056	39.592	0.003	0.003	0.000	0.000	0.000	0.000
75	B	264	ILE	0	-0.054	-0.032	40.745	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	265	VAL	0	-0.054	-0.017	34.700	0.003	0.003	0.000	0.000	0.000	0.000
77	B	266	SER	0	0.002	0.000	36.241	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	267	VAL	0	0.009	-0.004	30.901	0.001	0.001	0.000	0.000	0.000	0.000
79	B	268	ASN	0	0.004	-0.019	27.939	0.002	0.002	0.000	0.000	0.000	0.000
80	B	269	GLY	0	0.005	0.012	32.214	0.001	0.001	0.000	0.000	0.000	0.000
81	B	270	VAL	0	0.019	0.025	34.967	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	271	ASP	-1	-0.785	-0.888	36.401	0.026	0.026	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	0.022	0.021	35.829	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	274	GLU	-1	-0.840	-0.900	32.191	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	275	THR	0	-0.017	-0.003	29.105	0.004	0.004	0.000	0.000	0.000	0.000
87	B	276	THR	0	0.020	0.009	26.787	-0.007	-0.007	0.000	0.000	0.000	0.000
88	B	277	MET	0	-0.048	0.021	23.874	0.009	0.009	0.000	0.000	0.000	0.000
89	B	278	ARG	1	0.995	0.987	23.485	-0.060	-0.060	0.000	0.000	0.000	0.000
90	B	279	TRP	0	-0.016	0.012	18.285	0.004	0.004	0.000	0.000	0.000	0.000
91	B	280	TYR	0	0.005	-0.021	20.494	-0.017	-0.017	0.000	0.000	0.000	0.000
92	B	281	LYS	1	0.975	0.986	15.548	-0.385	-0.385	0.000	0.000	0.000	0.000
93	B	282	ALA	0	0.010	0.032	12.829	-0.024	-0.024	0.000	0.000	0.000	0.000
94	B	283	GLY	0	0.026	-0.006	14.885	0.041	0.041	0.000	0.000	0.000	0.000
95	B	284	THR	0	-0.079	-0.031	16.073	-0.043	-0.043	0.000	0.000	0.000	0.000
96	B	285	GLN	0	-0.005	-0.004	18.578	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	286	ASN	0	0.013	-0.007	22.325	-0.005	-0.005	0.000	0.000	0.000	0.000
98	B	287	LEU	0	-0.001	-0.004	24.956	-0.004	-0.004	0.000	0.000	0.000	0.000
99	B	288	THR	0	-0.010	-0.013	26.847	0.001	0.001	0.000	0.000	0.000	0.000
100	B	289	ILE	0	0.013	0.018	28.417	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	290	GLY	0	0.021	0.015	32.174	0.003	0.003	0.000	0.000	0.000	0.000
102	B	291	SER	0	-0.038	-0.043	35.788	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	292	ARG	1	0.965	0.963	38.492	-0.023	-0.023	0.000	0.000	0.000	0.000
104	B	293	LEU	0	-0.043	-0.013	42.220	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	294	TYR	0	-0.050	-0.046	44.712	0.001	0.001	0.000	0.000	0.000	0.000
106	B	295	GLY	0	0.051	-0.010	47.584	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	296	GLU	-1	-0.891	-0.922	50.621	0.012	0.012	0.000	0.000	0.000	0.000
108	B	297	SER	0	0.012	-0.045	54.149	0.001	0.001	0.000	0.000	0.000	0.000
109	B	298	SER	0	0.020	0.006	56.753	0.000	0.000	0.000	0.000	0.000	0.000
110	B	299	LYS	1	0.917	0.952	53.631	-0.008	-0.008	0.000	0.000	0.000	0.000
111	B	300	ILE	0	-0.071	0.039	52.099	0.000	0.000	0.000	0.000	0.000	0.000
112	B	301	GLN	0	0.061	0.001	52.831	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	302	PRO	0	-0.009	-0.003	52.030	0.001	0.001	0.000	0.000	0.000	0.000
114	B	303	GLY	0	-0.001	0.011	50.249	0.001	0.001	0.000	0.000	0.000	0.000
115	B	304	VAL	0	0.032	0.011	44.025	0.001	0.001	0.000	0.000	0.000	0.000
116	B	305	LEU	0	-0.019	0.000	43.587	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	306	SER	0	-0.016	-0.021	39.741	0.001	0.001	0.000	0.000	0.000	0.000
118	B	307	GLY	0	0.033	0.016	38.784	-0.002	-0.002	0.000	0.000	0.000	0.000
119	B	308	SER	0	-0.055	-0.012	34.189	0.000	0.000	0.000	0.000	0.000	0.000
120	B	309	ALA	0	0.025	-0.004	33.498	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	310	THR	0	0.031	0.030	28.404	0.000	0.000	0.000	0.000	0.000	0.000
122	B	311	LEU	0	-0.004	0.003	26.443	0.002	0.002	0.000	0.000	0.000	0.000
123	B	312	LEU	0	-0.012	-0.006	25.684	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	313	MET	0	-0.017	-0.006	20.640	0.009	0.009	0.000	0.000	0.000	0.000
125	B	314	ILE	0	-0.026	-0.021	23.480	-0.010	-0.010	0.000	0.000	0.000	0.000
126	B	315	LEU	0	-0.016	-0.019	18.163	0.011	0.011	0.000	0.000	0.000	0.000
127	B	316	PRO	-1	-0.921	-0.945	21.116	-0.087	-0.087	0.000	0.000	0.000	0.000

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