FMO DATABASE

FMODB ID: Q127Y

Calculation Name: 3ME0-B-Xray372

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: 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:

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-958381.422802
FMO2-HF: Nuclear repulsion	909412.66408
FMO2-HF: Total energy	-48968.758722
FMO2-MP2: Total energy	-49110.335459

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.
-4.588	1.356	0.961	-3.05	-3.852	-0.009

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 : 0.047 / q_NPA : 0.004

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	0.030	-0.022	3.754	-1.881	1.485	0.013	-1.703	-1.675	0.000
4	B	192	HIS	0	-0.007	0.001	2.843	-2.956	-0.547	0.948	-1.321	-2.035	-0.009
5	B	193	HIS	0	0.010	0.046	4.258	0.552	0.721	0.000	-0.026	-0.142	0.000
6	B	194	HIS	0	-0.030	-0.035	7.007	0.177	0.177	0.000	0.000	0.000	0.000
7	B	195	GLY	0	-0.005	0.014	8.680	-0.007	-0.007	0.000	0.000	0.000	0.000
8	B	196	GLY	0	0.021	0.000	10.892	-0.033	-0.033	0.000	0.000	0.000	0.000
9	B	197	CYS	0	-0.077	-0.008	12.476	0.025	0.025	0.000	0.000	0.000	0.000
10	B	198	ARG	1	0.964	0.972	9.836	-0.007	-0.007	0.000	0.000	0.000	0.000
11	B	199	PRO	0	0.026	-0.001	15.691	0.040	0.040	0.000	0.000	0.000	0.000
12	B	200	SER	0	-0.049	-0.037	18.153	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	201	ALA	0	0.001	0.005	18.444	-0.016	-0.016	0.000	0.000	0.000	0.000
14	B	202	GLN	0	-0.017	0.001	20.425	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	203	SER	0	0.045	0.029	24.091	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	204	LEU	0	-0.001	-0.004	25.680	0.007	0.007	0.000	0.000	0.000	0.000
17	B	205	GLU	-1	-0.837	-0.907	28.749	0.048	0.048	0.000	0.000	0.000	0.000
18	B	206	ILE	0	-0.014	-0.011	32.252	0.005	0.005	0.000	0.000	0.000	0.000
19	B	207	LYS	1	0.843	0.913	32.593	-0.070	-0.070	0.000	0.000	0.000	0.000
20	B	208	HIS	1	0.819	0.868	37.500	-0.046	-0.046	0.000	0.000	0.000	0.000
21	B	209	GLY	0	0.011	0.018	40.593	0.000	0.000	0.000	0.000	0.000	0.000
22	B	210	ASP	-1	-0.885	-0.933	42.355	0.042	0.042	0.000	0.000	0.000	0.000
23	B	211	LEU	0	-0.028	-0.017	45.236	0.001	0.001	0.000	0.000	0.000	0.000
24	B	212	SER	0	0.016	-0.007	48.064	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	213	ILE	0	0.032	0.017	48.850	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	214	ASN	0	-0.035	-0.027	47.301	0.000	0.000	0.000	0.000	0.000	0.000
27	B	215	SER	0	-0.002	0.018	50.204	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	216	ALA	0	-0.012	0.002	48.299	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	217	ASN	0	0.068	0.020	48.661	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	218	ASN	0	-0.036	-0.022	46.892	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	219	HIS	0	0.074	0.054	42.377	0.003	0.003	0.000	0.000	0.000	0.000
32	B	220	TYR	0	0.022	0.001	37.159	0.000	0.000	0.000	0.000	0.000	0.000
33	B	221	ALA	0	-0.003	0.008	37.909	0.002	0.002	0.000	0.000	0.000	0.000
34	B	222	ALA	0	-0.023	-0.026	34.025	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	223	GLN	0	0.029	0.021	27.656	0.007	0.007	0.000	0.000	0.000	0.000
36	B	224	THR	0	-0.050	-0.023	26.341	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	225	LEU	0	0.025	0.030	23.113	0.002	0.002	0.000	0.000	0.000	0.000
38	B	226	SER	0	0.045	0.025	19.844	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	227	VAL	0	-0.006	-0.002	18.475	-0.018	-0.018	0.000	0.000	0.000	0.000
40	B	228	SER	0	0.015	-0.004	14.305	0.042	0.042	0.000	0.000	0.000	0.000
41	B	230	ASP	-1	-0.825	-0.924	9.391	0.258	0.258	0.000	0.000	0.000	0.000
42	B	231	VAL	0	-0.046	-0.023	11.458	0.097	0.097	0.000	0.000	0.000	0.000
43	B	232	PRO	0	-0.034	-0.012	13.997	0.005	0.005	0.000	0.000	0.000	0.000
44	B	233	ALA	0	0.013	-0.001	17.315	-0.037	-0.037	0.000	0.000	0.000	0.000
45	B	234	ASN	0	-0.006	-0.001	19.537	0.026	0.026	0.000	0.000	0.000	0.000
46	B	235	ILE	0	0.026	0.004	19.432	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	236	ARG	1	0.830	0.896	23.619	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	237	PHE	0	0.012	-0.018	22.931	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	238	MET	0	0.016	0.004	28.043	0.000	0.000	0.000	0.000	0.000	0.000
50	B	239	LEU	0	-0.020	-0.002	30.446	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	240	LEU	0	0.005	0.000	30.698	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	241	ARG	1	0.888	0.928	33.927	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	242	ASN	0	0.009	0.020	33.003	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	243	THR	0	0.037	0.001	37.260	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	244	THR	0	0.000	-0.016	40.479	0.002	0.002	0.000	0.000	0.000	0.000
56	B	245	PRO	0	-0.094	-0.033	42.800	0.001	0.001	0.000	0.000	0.000	0.000
57	B	246	THR	0	0.032	0.007	45.190	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	247	TYR	0	-0.087	-0.072	48.253	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	248	SER	0	0.005	0.008	47.767	0.000	0.000	0.000	0.000	0.000	0.000
60	B	249	HIS	1	0.807	0.880	45.144	-0.025	-0.025	0.000	0.000	0.000	0.000
61	B	250	GLY	0	0.014	0.012	46.373	0.002	0.002	0.000	0.000	0.000	0.000
62	B	251	LYS	1	0.990	0.985	43.472	-0.030	-0.030	0.000	0.000	0.000	0.000
63	B	252	LYS	1	0.803	0.899	41.939	-0.039	-0.039	0.000	0.000	0.000	0.000
64	B	253	PHE	0	0.036	0.015	36.136	-0.003	-0.003	0.000	0.000	0.000	0.000
65	B	254	SER	0	0.008	-0.020	40.088	0.002	0.002	0.000	0.000	0.000	0.000
66	B	255	VAL	0	-0.027	0.001	37.225	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	256	GLY	0	0.032	0.037	40.643	0.002	0.002	0.000	0.000	0.000	0.000
68	B	257	LEU	0	-0.046	-0.036	40.192	0.000	0.000	0.000	0.000	0.000	0.000
69	B	258	GLY	0	0.077	0.048	43.211	0.000	0.000	0.000	0.000	0.000	0.000
70	B	259	HIS	0	0.005	0.004	46.221	0.001	0.001	0.000	0.000	0.000	0.000
71	B	260	GLY	0	0.035	0.029	49.870	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	261	TRP	0	0.016	0.047	46.492	0.001	0.001	0.000	0.000	0.000	0.000
73	B	262	ASP	-1	-0.695	-0.816	44.470	0.022	0.022	0.000	0.000	0.000	0.000
74	B	263	SER	0	0.031	0.035	39.417	0.004	0.004	0.000	0.000	0.000	0.000
75	B	264	ILE	0	-0.064	-0.035	40.884	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	265	VAL	0	-0.049	-0.016	34.778	0.003	0.003	0.000	0.000	0.000	0.000
77	B	266	SER	0	0.003	-0.006	36.233	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	267	VAL	0	-0.006	-0.007	30.917	0.002	0.002	0.000	0.000	0.000	0.000
79	B	268	ASN	0	0.015	-0.004	27.932	0.000	0.000	0.000	0.000	0.000	0.000
80	B	269	GLY	0	0.001	0.014	32.208	0.000	0.000	0.000	0.000	0.000	0.000
81	B	270	VAL	0	0.017	0.023	34.940	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	271	ASP	-1	-0.739	-0.874	36.395	0.046	0.046	0.000	0.000	0.000	0.000
83	B	272	THR	0	-0.042	-0.026	38.219	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	273	GLY	0	0.042	0.031	35.890	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	274	GLU	-1	-0.820	-0.868	32.178	0.022	0.022	0.000	0.000	0.000	0.000
86	B	275	THR	0	-0.026	-0.005	29.278	0.004	0.004	0.000	0.000	0.000	0.000
87	B	276	THR	0	0.021	0.012	26.864	-0.007	-0.007	0.000	0.000	0.000	0.000
88	B	277	MET	0	-0.055	0.009	23.579	0.007	0.007	0.000	0.000	0.000	0.000
89	B	278	ARG	1	0.989	0.980	23.502	-0.103	-0.103	0.000	0.000	0.000	0.000
90	B	279	TRP	0	-0.008	0.020	18.139	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	280	TYR	0	0.013	-0.009	20.502	-0.019	-0.019	0.000	0.000	0.000	0.000
92	B	281	LYS	1	0.960	0.977	15.667	-0.525	-0.525	0.000	0.000	0.000	0.000
93	B	282	ALA	0	0.037	0.035	12.568	-0.032	-0.032	0.000	0.000	0.000	0.000
94	B	283	GLY	0	0.021	-0.003	14.648	0.039	0.039	0.000	0.000	0.000	0.000
95	B	284	THR	0	-0.073	-0.031	15.685	-0.050	-0.050	0.000	0.000	0.000	0.000
96	B	285	GLN	0	-0.025	-0.014	18.219	-0.009	-0.009	0.000	0.000	0.000	0.000
97	B	286	ASN	0	0.028	-0.001	21.963	0.001	0.001	0.000	0.000	0.000	0.000
98	B	287	LEU	0	0.009	-0.004	24.635	-0.006	-0.006	0.000	0.000	0.000	0.000
99	B	288	THR	0	0.005	0.000	26.839	0.002	0.002	0.000	0.000	0.000	0.000
100	B	289	ILE	0	0.015	0.020	28.415	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	290	GLY	0	0.005	0.010	32.162	0.003	0.003	0.000	0.000	0.000	0.000
102	B	291	SER	0	-0.012	-0.010	35.776	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	292	ARG	1	0.887	0.918	38.573	-0.043	-0.043	0.000	0.000	0.000	0.000
104	B	293	LEU	0	-0.040	-0.012	42.295	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	294	TYR	0	-0.023	-0.027	44.791	0.001	0.001	0.000	0.000	0.000	0.000
106	B	295	GLY	0	0.034	-0.006	47.660	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	296	GLU	-1	-0.866	-0.932	50.696	0.023	0.023	0.000	0.000	0.000	0.000
108	B	297	SER	0	0.016	-0.019	54.223	0.000	0.000	0.000	0.000	0.000	0.000
109	B	298	SER	0	0.006	0.003	56.828	0.000	0.000	0.000	0.000	0.000	0.000
110	B	299	LYS	1	0.909	0.950	53.636	-0.018	-0.018	0.000	0.000	0.000	0.000
111	B	300	ILE	0	-0.078	0.004	51.741	0.000	0.000	0.000	0.000	0.000	0.000
112	B	301	GLN	0	0.089	0.018	52.965	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	302	PRO	0	-0.029	-0.010	52.106	0.001	0.001	0.000	0.000	0.000	0.000
114	B	303	GLY	0	-0.002	0.015	50.310	0.001	0.001	0.000	0.000	0.000	0.000
115	B	304	VAL	0	0.018	0.011	43.930	0.001	0.001	0.000	0.000	0.000	0.000
116	B	305	LEU	0	-0.009	0.000	43.709	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	306	SER	0	-0.015	-0.018	39.842	0.002	0.002	0.000	0.000	0.000	0.000
118	B	307	GLY	0	0.043	0.019	38.858	-0.002	-0.002	0.000	0.000	0.000	0.000
119	B	308	SER	0	-0.043	-0.007	34.200	0.001	0.001	0.000	0.000	0.000	0.000
120	B	309	ALA	0	0.006	-0.009	33.557	-0.002	-0.002	0.000	0.000	0.000	0.000
121	B	310	THR	0	0.013	0.014	28.647	0.001	0.001	0.000	0.000	0.000	0.000
122	B	311	LEU	0	-0.004	0.008	26.217	0.001	0.001	0.000	0.000	0.000	0.000
123	B	312	LEU	0	-0.008	-0.001	25.826	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	313	MET	0	-0.008	0.000	21.457	0.011	0.011	0.000	0.000	0.000	0.000
125	B	314	ILE	0	-0.011	-0.009	23.518	-0.011	-0.011	0.000	0.000	0.000	0.000
126	B	315	LEU	0	0.019	-0.001	18.155	0.012	0.012	0.000	0.000	0.000	0.000
127	B	316	PRO	0	0.001	0.013	20.498	-0.014	-0.014	0.000	0.000	0.000	0.000

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