FMO DATABASE

FMODB ID: K96Y3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1140339.905904
FMO2-HF: Nuclear repulsion	1088769.605278
FMO2-HF: Total energy	-51570.300626
FMO2-MP2: Total energy	-51720.810436

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.
-31.021	-22.228	1.145	-4.009	-5.931	-0.02

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 : 0.005 / q_NPA : -0.002

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	0.001	0.007	3.109	-5.058	-2.741	0.084	-1.230	-1.171	-0.001
4	B	43	VAL	0	-0.013	-0.007	5.832	0.882	0.882	0.000	0.000	0.000	0.000
5	B	44	THR	0	0.021	0.018	9.478	-0.122	-0.122	0.000	0.000	0.000	0.000
6	B	45	VAL	0	-0.002	-0.011	12.568	0.116	0.116	0.000	0.000	0.000	0.000
7	B	46	LEU	0	-0.019	0.009	15.980	0.005	0.005	0.000	0.000	0.000	0.000
8	B	47	LEU	0	0.034	0.010	19.070	0.018	0.018	0.000	0.000	0.000	0.000
9	B	48	PHE	0	-0.002	-0.006	22.274	0.026	0.026	0.000	0.000	0.000	0.000
10	B	49	ASN	0	0.009	-0.009	26.005	0.020	0.020	0.000	0.000	0.000	0.000
11	B	50	SER	0	0.034	-0.038	28.327	0.024	0.024	0.000	0.000	0.000	0.000
12	B	51	SER	0	-0.067	-0.029	31.622	0.009	0.009	0.000	0.000	0.000	0.000
13	B	52	ARG	1	0.808	0.882	30.903	0.276	0.276	0.000	0.000	0.000	0.000
14	B	53	ARG	1	0.843	0.919	31.877	0.159	0.159	0.000	0.000	0.000	0.000
15	B	54	SER	0	-0.037	-0.013	28.686	0.012	0.012	0.000	0.000	0.000	0.000
16	B	55	LEU	0	0.009	0.010	24.307	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	56	VAL	0	-0.050	-0.014	21.769	0.008	0.008	0.000	0.000	0.000	0.000
18	B	57	LEU	0	-0.023	-0.015	20.381	-0.007	-0.007	0.000	0.000	0.000	0.000
19	B	58	VAL	0	0.066	0.028	17.125	0.001	0.001	0.000	0.000	0.000	0.000
20	B	59	LYS	1	0.951	0.995	19.972	0.354	0.354	0.000	0.000	0.000	0.000
21	B	60	GLN	0	0.004	-0.007	13.848	-0.055	-0.055	0.000	0.000	0.000	0.000
22	B	97	ALA	0	-0.006	-0.022	28.212	-0.009	-0.009	0.000	0.000	0.000	0.000
23	B	98	GLY	0	-0.006	0.002	24.022	0.022	0.022	0.000	0.000	0.000	0.000
24	B	99	VAL	0	-0.048	-0.018	22.410	-0.025	-0.025	0.000	0.000	0.000	0.000
25	B	100	THR	0	0.009	-0.010	18.289	0.044	0.044	0.000	0.000	0.000	0.000
26	B	101	VAL	0	-0.046	-0.028	20.133	-0.053	-0.053	0.000	0.000	0.000	0.000
27	B	102	GLU	-1	-0.860	-0.919	15.188	-0.524	-0.524	0.000	0.000	0.000	0.000
28	B	103	LEU	0	-0.042	-0.032	15.435	0.018	0.018	0.000	0.000	0.000	0.000
29	B	104	CYS	0	-0.048	-0.019	15.024	-0.056	-0.056	0.000	0.000	0.000	0.000
30	B	105	ALA	0	-0.016	-0.031	10.528	0.088	0.088	0.000	0.000	0.000	0.000
31	B	106	GLY	0	0.063	0.050	8.631	0.030	0.030	0.000	0.000	0.000	0.000
32	B	107	LEU	0	-0.020	-0.020	2.931	-0.759	0.464	0.195	-0.345	-1.073	0.001
33	B	108	VAL	0	-0.025	-0.016	4.220	0.067	0.335	-0.001	-0.043	-0.225	0.000
34	B	109	ASP	-1	-0.960	-0.971	2.482	-18.120	-15.204	0.841	-1.586	-2.171	-0.015
35	B	110	GLN	0	0.001	0.006	3.359	-3.061	-2.387	0.013	-0.288	-0.399	-0.004
36	B	111	PRO	0	-0.033	-0.033	5.910	0.839	0.839	0.000	0.000	0.000	0.000
37	B	112	GLY	0	-0.041	-0.018	7.638	0.162	0.162	0.000	0.000	0.000	0.000
38	B	113	LEU	0	0.037	0.026	8.870	0.072	0.072	0.000	0.000	0.000	0.000
39	B	114	SER	0	-0.059	-0.032	9.959	0.043	0.043	0.000	0.000	0.000	0.000
40	B	115	LEU	0	0.020	0.002	8.676	-0.204	-0.204	0.000	0.000	0.000	0.000
41	B	116	GLU	-1	-0.803	-0.907	11.436	-0.664	-0.664	0.000	0.000	0.000	0.000
42	B	117	GLU	-1	-0.870	-0.940	13.073	-0.998	-0.998	0.000	0.000	0.000	0.000
43	B	118	VAL	0	-0.009	-0.008	7.538	-0.066	-0.066	0.000	0.000	0.000	0.000
44	B	119	ALA	0	-0.010	0.000	10.745	-0.022	-0.022	0.000	0.000	0.000	0.000
45	B	120	CYS	0	-0.051	-0.024	13.272	0.086	0.086	0.000	0.000	0.000	0.000
46	B	121	LYS	1	0.798	0.897	9.463	2.491	2.491	0.000	0.000	0.000	0.000
47	B	122	GLU	-1	-0.786	-0.880	9.536	-2.435	-2.435	0.000	0.000	0.000	0.000
48	B	123	ALA	0	0.014	-0.009	13.616	0.151	0.151	0.000	0.000	0.000	0.000
49	B	124	TRP	0	-0.060	-0.026	16.869	0.155	0.155	0.000	0.000	0.000	0.000
50	B	125	GLU	-1	-0.917	-0.972	13.300	-1.715	-1.715	0.000	0.000	0.000	0.000
51	B	126	GLU	-1	-0.787	-0.879	14.098	-1.094	-1.094	0.000	0.000	0.000	0.000
52	B	127	CYS	0	-0.080	-0.044	17.066	0.134	0.134	0.000	0.000	0.000	0.000
53	B	128	GLY	0	-0.007	0.021	19.968	0.081	0.081	0.000	0.000	0.000	0.000
54	B	129	TYR	0	-0.047	-0.044	20.784	0.103	0.103	0.000	0.000	0.000	0.000
55	B	130	HIS	0	-0.023	-0.009	20.595	-0.095	-0.095	0.000	0.000	0.000	0.000
56	B	131	LEU	0	-0.008	-0.018	18.461	0.062	0.062	0.000	0.000	0.000	0.000
57	B	132	ALA	0	-0.003	0.000	20.245	-0.062	-0.062	0.000	0.000	0.000	0.000
58	B	133	PRO	0	0.060	0.004	17.365	0.038	0.038	0.000	0.000	0.000	0.000
59	B	134	SER	0	-0.068	-0.026	19.308	0.031	0.031	0.000	0.000	0.000	0.000
60	B	135	ASP	-1	-0.864	-0.934	22.275	-0.370	-0.370	0.000	0.000	0.000	0.000
61	B	136	LEU	0	-0.082	-0.015	16.408	0.030	0.030	0.000	0.000	0.000	0.000
62	B	137	ARG	1	0.967	0.990	20.249	0.145	0.145	0.000	0.000	0.000	0.000
63	B	138	ARG	1	0.972	0.983	15.461	-0.137	-0.137	0.000	0.000	0.000	0.000
64	B	139	VAL	0	-0.043	-0.017	18.060	0.054	0.054	0.000	0.000	0.000	0.000
65	B	140	ALA	0	-0.004	-0.010	17.202	0.070	0.070	0.000	0.000	0.000	0.000
66	B	141	THR	0	-0.084	-0.032	11.683	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	142	TYR	0	-0.050	-0.045	12.123	0.082	0.082	0.000	0.000	0.000	0.000
68	B	143	TRP	0	0.000	-0.002	5.730	-0.213	-0.213	0.000	0.000	0.000	0.000
69	B	144	SER	0	0.016	0.005	8.483	-0.160	-0.160	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.025	0.008	7.784	0.374	0.374	0.000	0.000	0.000	0.000
71	B	146	VAL	0	-0.071	-0.043	8.865	0.034	0.034	0.000	0.000	0.000	0.000
72	B	147	GLY	0	0.081	0.035	8.910	-0.275	-0.275	0.000	0.000	0.000	0.000
73	B	148	LEU	0	-0.055	-0.037	8.503	0.335	0.335	0.000	0.000	0.000	0.000
74	B	149	THR	0	0.014	0.013	3.435	-0.716	-0.380	0.005	-0.094	-0.247	0.000
75	B	150	GLY	0	-0.058	-0.021	5.154	0.969	1.004	-0.001	-0.005	-0.029	0.000
76	B	151	SER	0	0.015	-0.001	3.546	0.195	1.096	0.010	-0.409	-0.502	-0.001
77	B	152	ARG	1	0.969	1.011	4.609	-2.118	-1.995	-0.001	-0.009	-0.114	0.000
78	B	153	GLN	0	0.016	0.017	6.538	-0.559	-0.559	0.000	0.000	0.000	0.000
79	B	154	THR	0	-0.032	-0.022	9.168	0.390	0.390	0.000	0.000	0.000	0.000
80	B	155	MET	0	0.006	0.028	11.927	-0.174	-0.174	0.000	0.000	0.000	0.000
81	B	156	PHE	0	0.012	-0.018	12.336	0.119	0.119	0.000	0.000	0.000	0.000
82	B	157	TYR	0	0.033	0.004	16.836	-0.016	-0.016	0.000	0.000	0.000	0.000
83	B	158	THR	0	0.035	0.009	20.331	0.015	0.015	0.000	0.000	0.000	0.000
84	B	159	GLU	-1	-0.878	-0.894	22.858	-0.219	-0.219	0.000	0.000	0.000	0.000
85	B	160	VAL	0	-0.002	0.004	23.785	-0.023	-0.023	0.000	0.000	0.000	0.000
86	B	161	THR	0	0.005	-0.008	26.918	0.032	0.032	0.000	0.000	0.000	0.000
87	B	162	ASP	-1	-0.741	-0.864	28.667	-0.327	-0.327	0.000	0.000	0.000	0.000
88	B	163	ALA	0	-0.037	-0.011	30.145	-0.014	-0.014	0.000	0.000	0.000	0.000
89	B	164	GLN	0	-0.019	-0.006	25.182	0.020	0.020	0.000	0.000	0.000	0.000
90	B	165	ARG	1	0.910	0.978	25.170	0.329	0.329	0.000	0.000	0.000	0.000
91	B	166	SER	0	0.013	0.012	24.357	0.038	0.038	0.000	0.000	0.000	0.000
92	B	167	GLY	0	-0.033	-0.014	26.422	0.032	0.032	0.000	0.000	0.000	0.000
93	B	178	LEU	0	-0.025	-0.009	17.761	-0.011	-0.011	0.000	0.000	0.000	0.000
94	B	179	ILE	0	-0.019	0.003	15.950	0.061	0.061	0.000	0.000	0.000	0.000
95	B	180	GLU	-1	-0.959	-0.984	19.753	-0.402	-0.402	0.000	0.000	0.000	0.000
96	B	181	VAL	0	-0.010	-0.003	21.357	0.030	0.030	0.000	0.000	0.000	0.000
97	B	182	VAL	0	-0.021	-0.016	23.176	0.051	0.051	0.000	0.000	0.000	0.000
98	B	183	HIS	0	-0.042	-0.022	24.647	-0.010	-0.010	0.000	0.000	0.000	0.000
99	B	184	LEU	0	0.009	0.014	26.291	0.021	0.021	0.000	0.000	0.000	0.000
100	B	185	PRO	0	0.013	0.002	28.333	0.002	0.002	0.000	0.000	0.000	0.000
101	B	186	LEU	0	0.041	0.004	29.079	0.010	0.010	0.000	0.000	0.000	0.000
102	B	187	GLU	-1	-0.982	-0.977	31.795	-0.096	-0.096	0.000	0.000	0.000	0.000
103	B	188	GLY	0	0.015	0.012	33.528	0.013	0.013	0.000	0.000	0.000	0.000
104	B	189	ALA	0	-0.022	-0.012	28.531	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	190	GLN	0	-0.022	-0.029	29.093	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	191	ALA	0	0.028	0.017	30.595	0.007	0.007	0.000	0.000	0.000	0.000
107	B	192	PHE	0	0.009	-0.002	24.963	0.000	0.000	0.000	0.000	0.000	0.000
108	B	193	ALA	0	-0.032	-0.023	26.520	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	194	ASP	-1	-0.891	-0.956	27.677	-0.022	-0.022	0.000	0.000	0.000	0.000
110	B	195	ASP	-1	-0.879	-0.932	30.231	-0.059	-0.059	0.000	0.000	0.000	0.000
111	B	196	PRO	0	-0.041	-0.007	28.494	-0.011	-0.011	0.000	0.000	0.000	0.000
112	B	197	ASP	-1	-0.941	-0.959	28.610	-0.037	-0.037	0.000	0.000	0.000	0.000
113	B	198	ILE	0	-0.030	-0.018	26.169	-0.024	-0.024	0.000	0.000	0.000	0.000
114	B	199	PRO	0	-0.015	-0.009	23.277	0.008	0.008	0.000	0.000	0.000	0.000
115	B	200	LYS	1	0.819	0.934	21.850	0.055	0.055	0.000	0.000	0.000	0.000
116	B	201	THR	0	0.064	0.022	16.224	0.026	0.026	0.000	0.000	0.000	0.000
117	B	202	LEU	0	0.023	0.001	17.258	0.006	0.006	0.000	0.000	0.000	0.000
118	B	203	GLY	0	0.058	0.033	16.642	0.010	0.010	0.000	0.000	0.000	0.000
119	B	204	VAL	0	0.033	0.030	17.478	0.005	0.005	0.000	0.000	0.000	0.000
120	B	205	ILE	0	0.012	0.008	20.442	0.014	0.014	0.000	0.000	0.000	0.000
121	B	206	PHE	0	-0.032	-0.021	18.702	0.025	0.025	0.000	0.000	0.000	0.000
122	B	207	GLY	0	0.034	0.009	20.666	0.009	0.009	0.000	0.000	0.000	0.000
123	B	208	VAL	0	-0.005	-0.004	21.628	0.003	0.003	0.000	0.000	0.000	0.000
124	B	209	SER	0	0.012	0.021	24.846	0.016	0.016	0.000	0.000	0.000	0.000
125	B	210	TRP	0	-0.009	-0.008	23.088	0.000	0.000	0.000	0.000	0.000	0.000
126	B	211	PHE	0	0.025	-0.010	24.785	0.005	0.005	0.000	0.000	0.000	0.000
127	B	212	LEU	0	-0.014	-0.023	26.236	0.003	0.003	0.000	0.000	0.000	0.000
128	B	213	SER	0	-0.046	-0.019	28.118	0.013	0.013	0.000	0.000	0.000	0.000
129	B	214	GLN	0	-0.081	-0.036	26.179	0.017	0.017	0.000	0.000	0.000	0.000
130	B	215	VAL	0	-0.037	-0.021	26.124	0.000	0.000	0.000	0.000	0.000	0.000
131	B	216	ALA	0	-0.010	0.000	29.401	0.000	0.000	0.000	0.000	0.000	0.000
132	B	217	PRO	0	-0.006	0.005	31.693	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	218	ASN	0	-0.116	-0.047	31.841	0.010	0.010	0.000	0.000	0.000	0.000
134	B	219	LEU	0	-0.005	0.006	31.122	-0.008	-0.008	0.000	0.000	0.000	0.000
135	B	220	ASP	-1	-0.880	-0.910	34.718	-0.108	-0.108	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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