FMO DATABASE

FMODB ID: 52K7Z

Calculation Name: 3Q91-A-Xray372

Preferred Name: Uridine diphosphate glucose pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q91

Chain ID: A

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1309506.328212
FMO2-HF: Nuclear repulsion	1252939.500219
FMO2-HF: Total energy	-56566.827993
FMO2-MP2: Total energy	-56732.342049

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(A:39:THR)

Summations of interaction energy for fragment #1(A:39:THR)

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.
-5.7	-1.171	0.291	-2.093	-2.727	-0.002

Interaction energy analysis for fragmet #1(A:39:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.016

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	A	41	ASP	-1	-0.870	-0.915	3.712	-3.932	-1.445	-0.011	-1.325	-1.151	0.003
4	A	42	SER	0	-0.024	-0.003	6.174	0.192	0.192	0.000	0.000	0.000	0.000
5	A	43	VAL	0	-0.038	-0.017	8.926	0.027	0.027	0.000	0.000	0.000	0.000
6	A	44	THR	0	0.027	0.022	12.654	0.049	0.049	0.000	0.000	0.000	0.000
7	A	45	VAL	0	0.014	-0.004	15.426	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	46	LEU	0	-0.019	-0.002	19.100	0.026	0.026	0.000	0.000	0.000	0.000
9	A	47	LEU	0	0.026	0.008	22.249	0.002	0.002	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.006	0.000	25.370	0.013	0.013	0.000	0.000	0.000	0.000
11	A	49	ASN	0	0.009	-0.005	28.910	0.001	0.001	0.000	0.000	0.000	0.000
12	A	50	SER	0	0.059	0.023	31.661	0.010	0.010	0.000	0.000	0.000	0.000
13	A	51	SER	0	-0.028	-0.016	34.789	0.005	0.005	0.000	0.000	0.000	0.000
14	A	52	ARG	1	0.914	0.955	33.711	0.076	0.076	0.000	0.000	0.000	0.000
15	A	53	ARG	1	0.925	0.987	34.893	0.084	0.084	0.000	0.000	0.000	0.000
16	A	54	SER	0	-0.045	-0.033	31.636	0.007	0.007	0.000	0.000	0.000	0.000
17	A	55	LEU	0	-0.001	0.010	26.621	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	56	VAL	0	-0.031	-0.007	24.970	0.013	0.013	0.000	0.000	0.000	0.000
19	A	57	LEU	0	-0.025	-0.024	22.358	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	58	VAL	0	0.066	0.029	18.942	0.014	0.014	0.000	0.000	0.000	0.000
21	A	59	LYS	1	0.837	0.917	21.475	0.026	0.026	0.000	0.000	0.000	0.000
22	A	60	GLN	0	0.030	0.003	15.596	0.042	0.042	0.000	0.000	0.000	0.000
23	A	61	PHE	0	0.013	0.024	19.580	0.002	0.002	0.000	0.000	0.000	0.000
24	A	62	ARG	1	0.849	0.906	13.111	0.018	0.018	0.000	0.000	0.000	0.000
25	A	63	PRO	0	0.045	0.004	15.802	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	64	ALA	0	-0.009	0.006	15.127	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	65	VAL	0	0.032	0.024	17.238	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	66	TYR	0	0.000	0.001	19.958	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	67	ALA	0	-0.057	-0.047	19.857	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	68	GLY	0	0.016	0.020	21.106	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	69	GLU	-1	-0.935	-0.983	22.488	0.029	0.029	0.000	0.000	0.000	0.000
32	A	70	VAL	0	-0.135	-0.039	24.941	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	71	GLU	-1	-1.015	-1.000	23.473	0.139	0.139	0.000	0.000	0.000	0.000
34	A	97	ALA	0	0.065	0.013	26.081	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	98	GLY	0	0.015	0.002	22.084	0.011	0.011	0.000	0.000	0.000	0.000
36	A	99	VAL	0	-0.066	-0.019	20.948	0.004	0.004	0.000	0.000	0.000	0.000
37	A	100	THR	0	-0.027	-0.022	17.644	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	101	VAL	0	0.037	0.026	20.439	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	102	GLU	-1	-0.829	-0.928	15.920	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	103	LEU	0	-0.049	-0.029	17.369	0.013	0.013	0.000	0.000	0.000	0.000
41	A	104	CYS	0	-0.045	-0.001	17.134	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	105	ALA	0	-0.058	-0.055	13.143	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	106	GLY	0	0.096	0.064	11.693	0.068	0.068	0.000	0.000	0.000	0.000
44	A	107	LEU	0	-0.010	-0.020	5.349	-0.158	-0.158	0.000	0.000	0.000	0.000
45	A	108	VAL	0	-0.038	-0.014	8.200	0.208	0.208	0.000	0.000	0.000	0.000
46	A	109	ASP	-1	-0.895	-0.935	8.008	-0.916	-0.916	0.000	0.000	0.000	0.000
47	A	110	GLN	0	-0.038	-0.035	9.464	0.034	0.034	0.000	0.000	0.000	0.000
48	A	111	PRO	0	-0.039	-0.007	11.658	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	112	GLY	0	-0.037	-0.025	13.004	0.091	0.091	0.000	0.000	0.000	0.000
50	A	113	LEU	0	0.022	0.006	15.210	0.058	0.058	0.000	0.000	0.000	0.000
51	A	114	SER	0	-0.018	0.004	15.300	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	115	LEU	0	0.031	0.018	11.668	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	116	GLU	-1	-0.876	-0.958	15.092	-0.425	-0.425	0.000	0.000	0.000	0.000
54	A	117	GLU	-1	-0.884	-0.956	18.127	-0.279	-0.279	0.000	0.000	0.000	0.000
55	A	118	VAL	0	-0.002	0.002	12.601	0.034	0.034	0.000	0.000	0.000	0.000
56	A	119	ALA	0	-0.003	0.000	15.929	0.030	0.030	0.000	0.000	0.000	0.000
57	A	120	CYS	0	-0.053	-0.019	17.739	0.043	0.043	0.000	0.000	0.000	0.000
58	A	121	LYS	1	0.903	0.965	15.416	0.274	0.274	0.000	0.000	0.000	0.000
59	A	122	GLU	-1	-0.834	-0.921	14.705	-0.260	-0.260	0.000	0.000	0.000	0.000
60	A	123	ALA	0	-0.004	-0.018	18.049	0.033	0.033	0.000	0.000	0.000	0.000
61	A	124	TRP	0	-0.077	-0.035	21.316	0.031	0.031	0.000	0.000	0.000	0.000
62	A	125	GLU	-1	-0.929	-0.981	17.741	-0.148	-0.148	0.000	0.000	0.000	0.000
63	A	126	GLU	-1	-0.775	-0.862	16.569	-0.189	-0.189	0.000	0.000	0.000	0.000
64	A	127	CYS	0	-0.091	-0.048	20.697	0.019	0.019	0.000	0.000	0.000	0.000
65	A	128	GLY	0	0.002	0.023	23.734	0.013	0.013	0.000	0.000	0.000	0.000
66	A	129	TYR	0	-0.039	-0.048	25.026	0.013	0.013	0.000	0.000	0.000	0.000
67	A	130	HIS	0	-0.014	-0.009	25.296	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	131	LEU	0	0.007	-0.017	22.660	0.000	0.000	0.000	0.000	0.000	0.000
69	A	132	ALA	0	0.025	0.028	25.471	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	133	PRO	0	0.052	0.004	22.309	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	134	SER	0	-0.052	-0.030	23.750	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	135	ASP	-1	-0.879	-0.931	26.619	-0.169	-0.169	0.000	0.000	0.000	0.000
73	A	136	LEU	0	-0.091	-0.003	20.283	0.000	0.000	0.000	0.000	0.000	0.000
74	A	137	ARG	1	0.999	1.009	23.549	0.223	0.223	0.000	0.000	0.000	0.000
75	A	138	ARG	1	0.919	0.959	17.131	0.434	0.434	0.000	0.000	0.000	0.000
76	A	139	VAL	0	-0.060	-0.013	19.807	0.023	0.023	0.000	0.000	0.000	0.000
77	A	140	ALA	0	-0.005	-0.019	18.074	0.015	0.015	0.000	0.000	0.000	0.000
78	A	141	THR	0	-0.069	-0.028	13.049	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	142	TYR	0	-0.046	-0.026	12.161	0.069	0.069	0.000	0.000	0.000	0.000
80	A	143	TRP	0	0.047	0.013	8.108	-0.038	-0.038	0.000	0.000	0.000	0.000
81	A	144	SER	0	0.032	0.024	7.638	0.310	0.310	0.000	0.000	0.000	0.000
82	A	145	GLY	0	0.031	0.025	6.242	-0.432	-0.432	0.000	0.000	0.000	0.000
83	A	146	VAL	0	-0.031	-0.020	7.247	0.135	0.135	0.000	0.000	0.000	0.000
84	A	147	GLY	0	0.036	0.024	7.992	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	148	LEU	0	-0.015	-0.019	6.243	-0.570	-0.570	0.000	0.000	0.000	0.000
86	A	149	THR	0	-0.047	-0.051	3.201	0.594	0.942	0.048	-0.091	-0.305	0.000
87	A	150	GLY	0	-0.034	0.010	3.147	-0.706	0.215	0.221	-0.364	-0.778	-0.004
88	A	151	SER	0	-0.032	-0.037	3.228	-2.318	-1.620	0.034	-0.301	-0.431	-0.001
89	A	152	ARG	1	0.939	0.976	4.518	1.754	1.829	-0.001	-0.012	-0.062	0.000
90	A	153	GLN	0	0.057	0.022	7.431	0.024	0.024	0.000	0.000	0.000	0.000
91	A	154	THR	0	-0.056	-0.042	10.070	0.124	0.124	0.000	0.000	0.000	0.000
92	A	155	MET	0	0.025	0.040	13.591	0.012	0.012	0.000	0.000	0.000	0.000
93	A	156	PHE	0	0.026	-0.012	16.044	0.015	0.015	0.000	0.000	0.000	0.000
94	A	157	TYR	0	0.028	0.006	19.607	0.016	0.016	0.000	0.000	0.000	0.000
95	A	158	THR	0	-0.018	-0.044	23.183	0.001	0.001	0.000	0.000	0.000	0.000
96	A	159	GLU	-1	-0.953	-0.961	26.034	-0.125	-0.125	0.000	0.000	0.000	0.000
97	A	160	VAL	0	-0.008	0.000	27.668	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	161	THR	0	0.004	-0.004	30.564	0.009	0.009	0.000	0.000	0.000	0.000
99	A	162	ASP	-1	-0.839	-0.951	32.789	-0.083	-0.083	0.000	0.000	0.000	0.000
100	A	163	ALA	0	-0.061	-0.019	34.456	0.003	0.003	0.000	0.000	0.000	0.000
101	A	164	GLN	0	-0.010	-0.001	29.277	0.008	0.008	0.000	0.000	0.000	0.000
102	A	165	ARG	1	0.922	0.995	29.746	0.071	0.071	0.000	0.000	0.000	0.000
103	A	166	SER	0	-0.031	-0.008	28.752	0.013	0.013	0.000	0.000	0.000	0.000
104	A	176	GLY	0	-0.014	-0.010	18.958	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	177	GLU	-1	-0.929	-0.967	15.593	0.152	0.152	0.000	0.000	0.000	0.000
106	A	178	LEU	0	-0.065	-0.043	18.849	0.002	0.002	0.000	0.000	0.000	0.000
107	A	179	ILE	0	0.004	0.009	17.328	0.005	0.005	0.000	0.000	0.000	0.000
108	A	180	GLU	-1	-0.889	-0.916	21.404	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	181	VAL	0	0.024	0.013	24.348	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	182	VAL	0	-0.003	-0.012	25.254	0.014	0.014	0.000	0.000	0.000	0.000
111	A	183	HIS	0	-0.040	-0.015	27.176	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	184	LEU	0	0.010	0.018	27.339	0.010	0.010	0.000	0.000	0.000	0.000
113	A	185	PRO	0	0.021	0.004	30.302	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	186	LEU	0	0.025	0.001	31.553	0.000	0.000	0.000	0.000	0.000	0.000
115	A	187	GLU	-1	-0.972	-0.972	33.572	-0.061	-0.061	0.000	0.000	0.000	0.000
116	A	188	GLY	0	0.010	0.003	34.533	0.001	0.001	0.000	0.000	0.000	0.000
117	A	189	ALA	0	-0.021	-0.012	29.696	0.001	0.001	0.000	0.000	0.000	0.000
118	A	190	GLN	0	-0.030	-0.026	29.380	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	191	ALA	0	0.012	-0.001	30.699	0.001	0.001	0.000	0.000	0.000	0.000
120	A	192	PHE	0	0.004	0.000	24.845	0.002	0.002	0.000	0.000	0.000	0.000
121	A	193	ALA	0	-0.034	-0.032	26.343	0.001	0.001	0.000	0.000	0.000	0.000
122	A	194	ASP	-1	-0.873	-0.942	26.563	-0.097	-0.097	0.000	0.000	0.000	0.000
123	A	195	ASP	-1	-0.865	-0.919	29.183	-0.033	-0.033	0.000	0.000	0.000	0.000
124	A	196	PRO	0	-0.061	-0.023	26.865	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	197	ASP	-1	-0.903	-0.946	26.821	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	198	ILE	0	-0.040	-0.006	25.540	0.007	0.007	0.000	0.000	0.000	0.000
127	A	199	PRO	0	-0.005	-0.004	21.546	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	200	LYS	1	0.814	0.901	21.061	0.067	0.067	0.000	0.000	0.000	0.000
129	A	201	THR	0	0.032	0.020	15.892	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	202	LEU	0	0.044	0.005	16.424	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	203	GLY	0	0.026	0.019	16.749	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	204	VAL	0	0.054	0.043	17.829	0.002	0.002	0.000	0.000	0.000	0.000
133	A	205	ILE	0	0.025	0.030	20.819	0.006	0.006	0.000	0.000	0.000	0.000
134	A	206	PHE	0	-0.006	-0.019	19.238	0.008	0.008	0.000	0.000	0.000	0.000
135	A	207	GLY	0	0.009	0.001	21.375	0.003	0.003	0.000	0.000	0.000	0.000
136	A	208	VAL	0	-0.026	-0.029	22.734	0.008	0.008	0.000	0.000	0.000	0.000
137	A	209	SER	0	-0.011	0.016	25.097	0.007	0.007	0.000	0.000	0.000	0.000
138	A	210	TRP	0	-0.004	-0.032	24.161	0.007	0.007	0.000	0.000	0.000	0.000
139	A	211	PHE	0	0.052	0.015	26.076	0.007	0.007	0.000	0.000	0.000	0.000
140	A	212	LEU	0	-0.008	-0.006	27.895	0.007	0.007	0.000	0.000	0.000	0.000
141	A	213	SER	0	-0.035	-0.007	28.802	0.004	0.004	0.000	0.000	0.000	0.000
142	A	214	GLN	0	-0.063	-0.040	27.379	0.003	0.003	0.000	0.000	0.000	0.000
143	A	215	VAL	0	-0.035	-0.021	28.623	0.001	0.001	0.000	0.000	0.000	0.000
144	A	216	ALA	0	-0.018	-0.008	31.427	0.007	0.007	0.000	0.000	0.000	0.000
145	A	217	PRO	0	-0.025	-0.002	33.302	0.007	0.007	0.000	0.000	0.000	0.000
146	A	218	ASN	0	-0.068	-0.024	33.460	0.010	0.010	0.000	0.000	0.000	0.000
147	A	219	LEU	0	-0.051	-0.010	33.281	0.001	0.001	0.000	0.000	0.000	0.000
148	A	220	ASP	-1	-0.949	-0.968	37.341	-0.080	-0.080	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:THR)