FMO DATABASE

FMODB ID: QY3RY

Calculation Name: 3Q91-B-Xray372

Preferred Name: Uridine diphosphate glucose pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q91

Chain ID: B

ChEMBL ID: CHEMBL4105943

UniProt ID: O95848

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1140482.703012
FMO2-HF: Nuclear repulsion	1088913.137184
FMO2-HF: Total energy	-51569.565827
FMO2-MP2: Total energy	-51720.104207

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:40:HIS)

Summations of interaction energy for fragment #1(B:40: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.
-24.745	-18.495	0.686	-2.542	-4.394	-0.009

Interaction energy analysis for fragmet #1(B:40:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.022

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	42	SER	0	0.011	0.000	3.253	-4.117	-2.141	0.038	-1.012	-1.002	0.000
4	B	43	VAL	0	-0.044	-0.010	5.992	0.816	0.816	0.000	0.000	0.000	0.000
5	B	44	THR	0	0.025	0.018	9.618	-0.086	-0.086	0.000	0.000	0.000	0.000
6	B	45	VAL	0	0.000	-0.007	12.751	0.101	0.101	0.000	0.000	0.000	0.000
7	B	46	LEU	0	-0.018	0.007	16.132	0.009	0.009	0.000	0.000	0.000	0.000
8	B	47	LEU	0	0.052	0.014	19.360	0.017	0.017	0.000	0.000	0.000	0.000
9	B	48	PHE	0	-0.001	-0.007	22.420	0.026	0.026	0.000	0.000	0.000	0.000
10	B	49	ASN	0	0.008	0.000	26.156	0.015	0.015	0.000	0.000	0.000	0.000
11	B	50	SER	0	0.045	-0.002	28.464	0.013	0.013	0.000	0.000	0.000	0.000
12	B	51	SER	0	-0.031	-0.004	31.753	0.010	0.010	0.000	0.000	0.000	0.000
13	B	52	ARG	1	0.861	0.935	30.606	0.246	0.246	0.000	0.000	0.000	0.000
14	B	53	ARG	1	0.944	0.982	32.123	0.138	0.138	0.000	0.000	0.000	0.000
15	B	54	SER	0	-0.053	-0.022	28.948	0.010	0.010	0.000	0.000	0.000	0.000
16	B	55	LEU	0	0.006	0.009	24.477	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	56	VAL	0	-0.037	-0.003	21.815	0.009	0.009	0.000	0.000	0.000	0.000
18	B	57	LEU	0	-0.034	-0.023	20.576	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	58	VAL	0	0.080	0.034	17.523	0.002	0.002	0.000	0.000	0.000	0.000
20	B	59	LYS	1	0.944	0.990	20.183	0.304	0.304	0.000	0.000	0.000	0.000
21	B	60	GLN	0	0.052	0.034	14.424	-0.100	-0.100	0.000	0.000	0.000	0.000
22	B	97	ALA	0	0.001	-0.015	28.166	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	98	GLY	0	-0.005	0.001	23.984	0.020	0.020	0.000	0.000	0.000	0.000
24	B	99	VAL	0	-0.045	-0.014	22.362	-0.023	-0.023	0.000	0.000	0.000	0.000
25	B	100	THR	0	0.045	0.010	18.848	0.028	0.028	0.000	0.000	0.000	0.000
26	B	101	VAL	0	-0.052	-0.023	20.316	-0.050	-0.050	0.000	0.000	0.000	0.000
27	B	102	GLU	-1	-0.939	-0.987	15.228	-0.505	-0.505	0.000	0.000	0.000	0.000
28	B	103	LEU	0	-0.056	-0.040	15.879	0.019	0.019	0.000	0.000	0.000	0.000
29	B	104	CYS	0	-0.057	-0.010	15.249	-0.041	-0.041	0.000	0.000	0.000	0.000
30	B	105	ALA	0	-0.038	-0.049	10.686	0.078	0.078	0.000	0.000	0.000	0.000
31	B	106	GLY	0	0.112	0.078	8.771	0.018	0.018	0.000	0.000	0.000	0.000
32	B	107	LEU	0	-0.020	-0.025	2.638	-0.605	0.206	0.410	-0.256	-0.965	0.000
33	B	108	VAL	0	-0.030	-0.015	4.204	0.249	0.462	-0.001	-0.030	-0.182	0.000
34	B	109	ASP	-1	-0.970	-0.975	2.693	-13.542	-11.696	0.220	-0.804	-1.262	-0.007
35	B	110	GLN	0	-0.001	0.002	3.775	-2.262	-2.008	0.000	-0.076	-0.177	-0.001
36	B	111	PRO	0	-0.035	-0.033	6.017	0.666	0.666	0.000	0.000	0.000	0.000
37	B	112	GLY	0	-0.039	-0.014	7.857	0.203	0.203	0.000	0.000	0.000	0.000
38	B	113	LEU	0	0.046	0.024	9.202	0.098	0.098	0.000	0.000	0.000	0.000
39	B	114	SER	0	-0.021	0.008	10.186	0.037	0.037	0.000	0.000	0.000	0.000
40	B	115	LEU	0	0.034	0.008	8.460	-0.182	-0.182	0.000	0.000	0.000	0.000
41	B	116	GLU	-1	-0.841	-0.944	11.433	-0.593	-0.593	0.000	0.000	0.000	0.000
42	B	117	GLU	-1	-0.899	-0.954	13.454	-0.897	-0.897	0.000	0.000	0.000	0.000
43	B	118	VAL	0	-0.018	-0.011	8.174	-0.062	-0.062	0.000	0.000	0.000	0.000
44	B	119	ALA	0	-0.012	0.002	11.216	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	120	CYS	0	-0.054	-0.028	13.510	0.079	0.079	0.000	0.000	0.000	0.000
46	B	121	LYS	1	0.886	0.952	9.690	2.361	2.361	0.000	0.000	0.000	0.000
47	B	122	GLU	-1	-0.819	-0.915	10.894	-1.861	-1.861	0.000	0.000	0.000	0.000
48	B	123	ALA	0	0.031	0.004	14.154	0.129	0.129	0.000	0.000	0.000	0.000
49	B	124	TRP	0	-0.066	-0.029	17.392	0.136	0.136	0.000	0.000	0.000	0.000
50	B	125	GLU	-1	-0.982	-1.005	13.681	-1.456	-1.456	0.000	0.000	0.000	0.000
51	B	126	GLU	-1	-0.786	-0.870	13.912	-0.998	-0.998	0.000	0.000	0.000	0.000
52	B	127	CYS	0	-0.067	-0.050	17.592	0.117	0.117	0.000	0.000	0.000	0.000
53	B	128	GLY	0	-0.015	0.019	20.496	0.072	0.072	0.000	0.000	0.000	0.000
54	B	129	TYR	0	-0.044	-0.044	21.319	0.093	0.093	0.000	0.000	0.000	0.000
55	B	130	HIS	0	-0.020	-0.010	21.117	-0.085	-0.085	0.000	0.000	0.000	0.000
56	B	131	LEU	0	-0.003	-0.015	18.603	0.055	0.055	0.000	0.000	0.000	0.000
57	B	132	ALA	0	0.021	0.011	20.716	-0.057	-0.057	0.000	0.000	0.000	0.000
58	B	133	PRO	0	0.048	-0.001	17.845	0.033	0.033	0.000	0.000	0.000	0.000
59	B	134	SER	0	-0.058	-0.026	19.660	0.027	0.027	0.000	0.000	0.000	0.000
60	B	135	ASP	-1	-0.880	-0.930	22.406	-0.328	-0.328	0.000	0.000	0.000	0.000
61	B	136	LEU	0	-0.085	-0.014	16.343	0.025	0.025	0.000	0.000	0.000	0.000
62	B	137	ARG	1	0.976	0.992	20.294	0.125	0.125	0.000	0.000	0.000	0.000
63	B	138	ARG	1	0.969	0.980	15.509	-0.119	-0.119	0.000	0.000	0.000	0.000
64	B	139	VAL	0	-0.032	-0.011	18.126	0.052	0.052	0.000	0.000	0.000	0.000
65	B	140	ALA	0	-0.015	-0.015	17.332	0.067	0.067	0.000	0.000	0.000	0.000
66	B	141	THR	0	-0.080	-0.028	11.696	0.001	0.001	0.000	0.000	0.000	0.000
67	B	142	TYR	0	-0.031	-0.021	11.967	0.083	0.083	0.000	0.000	0.000	0.000
68	B	143	TRP	0	0.000	-0.004	5.930	-0.236	-0.236	0.000	0.000	0.000	0.000
69	B	144	SER	0	0.027	0.009	8.432	-0.137	-0.137	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.013	0.004	7.766	0.353	0.353	0.000	0.000	0.000	0.000
71	B	146	VAL	0	-0.072	-0.042	8.846	0.043	0.043	0.000	0.000	0.000	0.000
72	B	147	GLY	0	0.076	0.031	8.881	-0.279	-0.279	0.000	0.000	0.000	0.000
73	B	148	LEU	0	-0.065	-0.036	8.293	0.311	0.311	0.000	0.000	0.000	0.000
74	B	149	THR	0	0.026	0.017	3.410	-0.814	-0.396	0.008	-0.124	-0.302	0.000
75	B	150	GLY	0	-0.038	-0.011	5.452	0.469	0.469	0.000	0.000	0.000	0.000
76	B	151	SER	0	0.051	0.023	3.503	-0.563	0.045	0.012	-0.231	-0.390	-0.001
77	B	152	ARG	1	0.952	1.006	4.564	-1.811	-1.687	-0.001	-0.009	-0.114	0.000
78	B	153	GLN	0	0.038	0.009	6.538	-0.582	-0.582	0.000	0.000	0.000	0.000
79	B	154	THR	0	-0.033	-0.024	9.168	0.399	0.399	0.000	0.000	0.000	0.000
80	B	155	MET	0	-0.007	0.032	12.062	-0.159	-0.159	0.000	0.000	0.000	0.000
81	B	156	PHE	0	0.018	-0.023	12.365	0.115	0.115	0.000	0.000	0.000	0.000
82	B	157	TYR	0	0.017	-0.009	16.956	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	158	THR	0	0.039	0.015	20.459	0.013	0.013	0.000	0.000	0.000	0.000
84	B	159	GLU	-1	-0.927	-0.948	22.958	-0.198	-0.198	0.000	0.000	0.000	0.000
85	B	160	VAL	0	0.010	0.010	23.934	-0.023	-0.023	0.000	0.000	0.000	0.000
86	B	161	THR	0	0.030	0.004	27.008	0.026	0.026	0.000	0.000	0.000	0.000
87	B	162	ASP	-1	-0.839	-0.946	29.019	-0.277	-0.277	0.000	0.000	0.000	0.000
88	B	163	ALA	0	-0.041	-0.019	30.681	-0.013	-0.013	0.000	0.000	0.000	0.000
89	B	164	GLN	0	-0.055	-0.024	25.414	0.019	0.019	0.000	0.000	0.000	0.000
90	B	165	ARG	1	0.938	0.997	25.698	0.297	0.297	0.000	0.000	0.000	0.000
91	B	166	SER	0	0.011	0.012	24.950	0.032	0.032	0.000	0.000	0.000	0.000
92	B	167	GLY	0	-0.036	-0.019	26.919	0.029	0.029	0.000	0.000	0.000	0.000
93	B	178	LEU	0	-0.052	-0.038	18.575	-0.029	-0.029	0.000	0.000	0.000	0.000
94	B	179	ILE	0	0.034	0.038	16.617	0.062	0.062	0.000	0.000	0.000	0.000
95	B	180	GLU	-1	-0.964	-0.990	20.089	-0.364	-0.364	0.000	0.000	0.000	0.000
96	B	181	VAL	0	-0.014	0.006	21.621	0.025	0.025	0.000	0.000	0.000	0.000
97	B	182	VAL	0	-0.037	-0.023	23.350	0.045	0.045	0.000	0.000	0.000	0.000
98	B	183	HIS	0	-0.013	-0.008	24.842	-0.017	-0.017	0.000	0.000	0.000	0.000
99	B	184	LEU	0	-0.005	0.004	26.482	0.018	0.018	0.000	0.000	0.000	0.000
100	B	185	PRO	0	0.008	-0.004	28.552	0.003	0.003	0.000	0.000	0.000	0.000
101	B	186	LEU	0	0.045	0.008	29.465	0.009	0.009	0.000	0.000	0.000	0.000
102	B	187	GLU	-1	-0.979	-0.976	32.011	-0.081	-0.081	0.000	0.000	0.000	0.000
103	B	188	GLY	0	0.009	0.010	33.756	0.011	0.011	0.000	0.000	0.000	0.000
104	B	189	ALA	0	-0.018	-0.010	28.776	0.000	0.000	0.000	0.000	0.000	0.000
105	B	190	GLN	0	-0.003	-0.022	29.338	-0.003	-0.003	0.000	0.000	0.000	0.000
106	B	191	ALA	0	0.027	0.016	30.868	0.007	0.007	0.000	0.000	0.000	0.000
107	B	192	PHE	0	0.007	-0.005	25.175	0.000	0.000	0.000	0.000	0.000	0.000
108	B	193	ALA	0	-0.052	-0.030	26.857	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	194	ASP	-1	-0.907	-0.960	27.839	-0.010	-0.010	0.000	0.000	0.000	0.000
110	B	195	ASP	-1	-0.896	-0.930	30.229	-0.043	-0.043	0.000	0.000	0.000	0.000
111	B	196	PRO	0	-0.056	-0.036	28.481	-0.008	-0.008	0.000	0.000	0.000	0.000
112	B	197	ASP	-1	-0.959	-0.968	28.597	-0.021	-0.021	0.000	0.000	0.000	0.000
113	B	198	ILE	0	-0.011	-0.009	26.076	-0.022	-0.022	0.000	0.000	0.000	0.000
114	B	199	PRO	0	-0.027	-0.017	23.264	0.008	0.008	0.000	0.000	0.000	0.000
115	B	200	LYS	1	0.881	0.972	22.019	0.033	0.033	0.000	0.000	0.000	0.000
116	B	201	THR	0	0.068	0.034	16.403	0.033	0.033	0.000	0.000	0.000	0.000
117	B	202	LEU	0	0.029	-0.001	17.323	0.005	0.005	0.000	0.000	0.000	0.000
118	B	203	GLY	0	0.053	0.030	16.912	0.008	0.008	0.000	0.000	0.000	0.000
119	B	204	VAL	0	0.035	0.028	17.749	0.004	0.004	0.000	0.000	0.000	0.000
120	B	205	ILE	0	0.008	0.008	20.707	0.012	0.012	0.000	0.000	0.000	0.000
121	B	206	PHE	0	-0.039	-0.023	19.026	0.023	0.023	0.000	0.000	0.000	0.000
122	B	207	GLY	0	0.040	0.011	20.912	0.008	0.008	0.000	0.000	0.000	0.000
123	B	208	VAL	0	-0.001	-0.005	21.861	0.002	0.002	0.000	0.000	0.000	0.000
124	B	209	SER	0	0.023	0.021	25.086	0.009	0.009	0.000	0.000	0.000	0.000
125	B	210	TRP	0	-0.023	-0.019	23.306	0.001	0.001	0.000	0.000	0.000	0.000
126	B	211	PHE	0	0.026	-0.009	25.052	0.005	0.005	0.000	0.000	0.000	0.000
127	B	212	LEU	0	-0.022	-0.028	26.435	0.002	0.002	0.000	0.000	0.000	0.000
128	B	213	SER	0	-0.037	-0.002	28.221	0.011	0.011	0.000	0.000	0.000	0.000
129	B	214	GLN	0	-0.082	-0.041	26.405	0.015	0.015	0.000	0.000	0.000	0.000
130	B	215	VAL	0	-0.030	-0.014	26.312	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	216	ALA	0	-0.020	-0.005	29.564	0.000	0.000	0.000	0.000	0.000	0.000
132	B	217	PRO	0	-0.010	0.003	31.822	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	218	ASN	0	-0.111	-0.045	32.079	0.009	0.009	0.000	0.000	0.000	0.000
134	B	219	LEU	0	-0.005	0.006	31.339	-0.008	-0.008	0.000	0.000	0.000	0.000
135	B	220	ASP	-1	-0.972	-0.973	34.865	-0.091	-0.091	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:40:HIS)