FMO DATABASE

FMODB ID: V5131

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	OptAll
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	-1309573.180985
FMO2-HF: Nuclear repulsion	1253005.178362
FMO2-HF: Total energy	-56568.002622
FMO2-MP2: Total energy	-56733.477251

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.
-4.929	0.061	2.05	-2.648	-4.393	-0.014

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 : -0.043 / q_NPA : -0.025

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	-0.856	-0.930	3.864	-3.079	-1.361	-0.017	-0.829	-0.873	0.003
4	A	42	SER	0	-0.023	-0.001	6.721	0.508	0.508	0.000	0.000	0.000	0.000
5	A	43	VAL	0	-0.035	-0.022	8.811	-0.023	-0.023	0.000	0.000	0.000	0.000
6	A	44	THR	0	0.027	0.010	12.554	0.063	0.063	0.000	0.000	0.000	0.000
7	A	45	VAL	0	-0.014	-0.014	15.316	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	46	LEU	0	-0.013	0.017	19.101	0.024	0.024	0.000	0.000	0.000	0.000
9	A	47	LEU	0	0.030	0.011	22.294	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.006	-0.002	25.275	0.011	0.011	0.000	0.000	0.000	0.000
11	A	49	ASN	0	0.023	-0.010	28.907	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	50	SER	0	0.012	-0.017	31.521	0.008	0.008	0.000	0.000	0.000	0.000
13	A	51	SER	0	-0.051	-0.035	34.598	0.004	0.004	0.000	0.000	0.000	0.000
14	A	52	ARG	1	0.821	0.896	33.629	0.035	0.035	0.000	0.000	0.000	0.000
15	A	53	ARG	1	0.860	0.931	34.792	0.052	0.052	0.000	0.000	0.000	0.000
16	A	54	SER	0	-0.019	-0.013	31.433	0.004	0.004	0.000	0.000	0.000	0.000
17	A	55	LEU	0	-0.011	0.000	26.699	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	56	VAL	0	-0.052	-0.020	24.601	0.012	0.012	0.000	0.000	0.000	0.000
19	A	57	LEU	0	-0.008	-0.009	22.195	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	58	VAL	0	0.044	0.023	18.585	0.007	0.007	0.000	0.000	0.000	0.000
21	A	59	LYS	1	0.804	0.887	21.849	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	60	GLN	0	0.076	0.044	15.737	0.045	0.045	0.000	0.000	0.000	0.000
23	A	61	PHE	0	0.011	0.018	19.805	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	62	ARG	1	0.802	0.861	14.818	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	63	PRO	0	0.031	0.009	16.493	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	64	ALA	0	-0.006	0.000	15.459	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	65	VAL	0	0.023	0.013	17.599	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	66	TYR	0	0.005	-0.010	20.240	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	67	ALA	0	-0.042	-0.017	20.454	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	68	GLY	0	0.046	0.028	21.604	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	69	GLU	-1	-0.947	-0.981	23.180	0.058	0.058	0.000	0.000	0.000	0.000
32	A	70	VAL	0	-0.095	-0.037	25.617	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	71	GLU	-1	-1.057	-1.012	23.544	0.124	0.124	0.000	0.000	0.000	0.000
34	A	97	ALA	0	0.043	0.014	26.839	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	98	GLY	0	0.020	-0.005	22.599	0.010	0.010	0.000	0.000	0.000	0.000
36	A	99	VAL	0	-0.071	-0.024	21.531	0.015	0.015	0.000	0.000	0.000	0.000
37	A	100	THR	0	-0.033	-0.038	18.111	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	101	VAL	0	0.007	-0.004	21.244	0.001	0.001	0.000	0.000	0.000	0.000
39	A	102	GLU	-1	-0.829	-0.886	15.636	0.041	0.041	0.000	0.000	0.000	0.000
40	A	103	LEU	0	-0.025	-0.021	16.889	0.000	0.000	0.000	0.000	0.000	0.000
41	A	104	CYS	0	-0.046	-0.007	17.076	0.006	0.006	0.000	0.000	0.000	0.000
42	A	105	ALA	0	-0.016	-0.032	12.780	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	106	GLY	0	0.063	0.048	11.614	0.079	0.079	0.000	0.000	0.000	0.000
44	A	107	LEU	0	-0.010	-0.005	5.527	-0.189	-0.189	0.000	0.000	0.000	0.000
45	A	108	VAL	0	-0.033	-0.023	8.148	0.126	0.126	0.000	0.000	0.000	0.000
46	A	109	ASP	-1	-0.841	-0.916	7.760	0.134	0.134	0.000	0.000	0.000	0.000
47	A	110	GLN	0	-0.021	-0.007	9.692	0.077	0.077	0.000	0.000	0.000	0.000
48	A	111	PRO	0	-0.040	-0.024	12.037	-0.088	-0.088	0.000	0.000	0.000	0.000
49	A	112	GLY	0	-0.050	-0.037	13.600	0.071	0.071	0.000	0.000	0.000	0.000
50	A	113	LEU	0	-0.016	0.004	15.507	0.068	0.068	0.000	0.000	0.000	0.000
51	A	114	SER	0	-0.049	-0.040	15.556	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	115	LEU	0	-0.014	-0.008	12.097	0.005	0.005	0.000	0.000	0.000	0.000
53	A	116	GLU	-1	-0.810	-0.933	15.441	-0.387	-0.387	0.000	0.000	0.000	0.000
54	A	117	GLU	-1	-0.827	-0.897	18.397	-0.253	-0.253	0.000	0.000	0.000	0.000
55	A	118	VAL	0	-0.003	0.008	12.548	0.037	0.037	0.000	0.000	0.000	0.000
56	A	119	ALA	0	-0.004	0.001	15.982	0.047	0.047	0.000	0.000	0.000	0.000
57	A	120	CYS	0	-0.062	-0.033	17.570	0.042	0.042	0.000	0.000	0.000	0.000
58	A	121	LYS	1	0.789	0.895	15.417	0.069	0.069	0.000	0.000	0.000	0.000
59	A	122	GLU	-1	-0.800	-0.913	14.653	-0.078	-0.078	0.000	0.000	0.000	0.000
60	A	123	ALA	0	0.000	-0.010	18.060	0.027	0.027	0.000	0.000	0.000	0.000
61	A	124	TRP	0	-0.047	-0.012	21.311	0.018	0.018	0.000	0.000	0.000	0.000
62	A	125	GLU	-1	-0.865	-0.931	19.121	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	126	GLU	-1	-0.781	-0.887	17.188	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	127	CYS	0	-0.086	-0.046	20.758	0.005	0.005	0.000	0.000	0.000	0.000
65	A	128	GLY	0	0.026	0.036	23.711	0.001	0.001	0.000	0.000	0.000	0.000
66	A	129	TYR	0	-0.052	-0.035	25.175	0.003	0.003	0.000	0.000	0.000	0.000
67	A	130	HIS	0	0.000	0.002	25.330	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	131	LEU	0	-0.012	-0.019	22.715	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	132	ALA	0	-0.013	0.001	25.851	0.001	0.001	0.000	0.000	0.000	0.000
70	A	133	PRO	0	0.054	0.001	22.473	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	134	SER	0	-0.081	-0.047	24.032	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	135	ASP	-1	-0.832	-0.892	26.451	-0.132	-0.132	0.000	0.000	0.000	0.000
73	A	136	LEU	0	-0.039	0.002	20.652	0.006	0.006	0.000	0.000	0.000	0.000
74	A	137	ARG	1	0.930	0.980	23.597	0.144	0.144	0.000	0.000	0.000	0.000
75	A	138	ARG	1	0.956	0.971	17.643	0.369	0.369	0.000	0.000	0.000	0.000
76	A	139	VAL	0	-0.057	-0.019	20.250	0.016	0.016	0.000	0.000	0.000	0.000
77	A	140	ALA	0	0.005	-0.007	17.884	0.014	0.014	0.000	0.000	0.000	0.000
78	A	141	THR	0	-0.074	-0.042	13.602	-0.052	-0.052	0.000	0.000	0.000	0.000
79	A	142	TYR	0	-0.044	-0.028	12.456	0.067	0.067	0.000	0.000	0.000	0.000
80	A	143	TRP	0	0.052	0.018	7.356	-0.042	-0.042	0.000	0.000	0.000	0.000
81	A	144	SER	0	0.005	0.004	7.965	0.250	0.250	0.000	0.000	0.000	0.000
82	A	145	GLY	0	0.060	0.034	5.826	-0.308	-0.308	0.000	0.000	0.000	0.000
83	A	146	VAL	0	-0.041	-0.016	6.915	0.189	0.189	0.000	0.000	0.000	0.000
84	A	147	GLY	0	0.034	0.019	7.651	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	148	LEU	0	-0.023	-0.026	5.668	-0.169	-0.169	0.000	0.000	0.000	0.000
86	A	149	THR	0	-0.030	-0.026	2.726	0.381	0.775	0.323	-0.175	-0.542	0.001
87	A	150	GLY	0	-0.047	-0.005	2.975	-1.578	-0.679	0.772	-0.447	-1.224	-0.005
88	A	151	SER	0	-0.007	-0.017	2.683	-3.443	-1.539	0.973	-1.180	-1.697	-0.013
89	A	152	ARG	1	0.898	0.949	4.408	1.789	1.864	-0.001	-0.017	-0.057	0.000
90	A	153	GLN	0	0.037	0.037	7.633	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	154	THR	0	-0.020	-0.013	10.438	0.108	0.108	0.000	0.000	0.000	0.000
92	A	155	MET	0	0.028	0.044	13.907	0.024	0.024	0.000	0.000	0.000	0.000
93	A	156	PHE	0	0.011	-0.008	16.101	0.005	0.005	0.000	0.000	0.000	0.000
94	A	157	TYR	0	0.039	0.010	20.126	0.019	0.019	0.000	0.000	0.000	0.000
95	A	158	THR	0	-0.013	-0.027	23.604	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	159	GLU	-1	-0.888	-0.917	26.147	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	160	VAL	0	-0.011	-0.006	27.526	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	161	THR	0	0.032	0.007	30.501	0.007	0.007	0.000	0.000	0.000	0.000
99	A	162	ASP	-1	-0.749	-0.867	32.713	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	163	ALA	0	-0.040	-0.012	34.709	0.004	0.004	0.000	0.000	0.000	0.000
101	A	164	GLN	0	0.018	0.021	29.631	0.006	0.006	0.000	0.000	0.000	0.000
102	A	165	ARG	1	0.845	0.935	30.006	0.029	0.029	0.000	0.000	0.000	0.000
103	A	166	SER	0	-0.085	-0.050	28.629	0.011	0.011	0.000	0.000	0.000	0.000
104	A	176	GLY	0	-0.005	-0.009	19.579	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	177	GLU	-1	-0.941	-0.972	15.557	0.330	0.330	0.000	0.000	0.000	0.000
106	A	178	LEU	0	-0.052	-0.024	19.008	-0.025	-0.025	0.000	0.000	0.000	0.000
107	A	179	ILE	0	-0.021	-0.014	17.631	0.002	0.002	0.000	0.000	0.000	0.000
108	A	180	GLU	-1	-0.827	-0.881	21.456	0.026	0.026	0.000	0.000	0.000	0.000
109	A	181	VAL	0	0.017	0.018	23.996	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	182	VAL	0	0.010	0.001	25.187	0.005	0.005	0.000	0.000	0.000	0.000
111	A	183	HIS	0	-0.032	-0.018	26.811	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	184	LEU	0	0.018	0.020	27.485	0.006	0.006	0.000	0.000	0.000	0.000
113	A	185	PRO	0	0.019	0.009	30.343	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	186	LEU	0	0.020	-0.001	31.763	0.001	0.001	0.000	0.000	0.000	0.000
115	A	187	GLU	-1	-0.988	-0.988	33.636	-0.030	-0.030	0.000	0.000	0.000	0.000
116	A	188	GLY	0	0.025	0.016	34.731	0.001	0.001	0.000	0.000	0.000	0.000
117	A	189	ALA	0	-0.028	-0.014	29.757	0.002	0.002	0.000	0.000	0.000	0.000
118	A	190	GLN	0	-0.026	-0.036	29.699	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	191	ALA	0	0.029	0.011	30.781	0.001	0.001	0.000	0.000	0.000	0.000
120	A	192	PHE	0	0.036	0.010	25.082	0.003	0.003	0.000	0.000	0.000	0.000
121	A	193	ALA	0	-0.045	-0.031	26.549	0.003	0.003	0.000	0.000	0.000	0.000
122	A	194	ASP	-1	-0.877	-0.933	26.855	-0.042	-0.042	0.000	0.000	0.000	0.000
123	A	195	ASP	-1	-0.908	-0.945	29.407	0.004	0.004	0.000	0.000	0.000	0.000
124	A	196	PRO	0	-0.063	-0.038	27.259	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	197	ASP	-1	-0.893	-0.940	27.126	0.024	0.024	0.000	0.000	0.000	0.000
126	A	198	ILE	0	-0.059	-0.022	26.322	0.006	0.006	0.000	0.000	0.000	0.000
127	A	199	PRO	0	0.012	-0.001	22.288	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	200	LYS	1	0.841	0.938	21.242	0.017	0.017	0.000	0.000	0.000	0.000
129	A	201	THR	0	0.032	0.022	15.492	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	202	LEU	0	0.006	-0.006	16.528	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	203	GLY	0	0.033	0.013	16.987	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	204	VAL	0	0.038	0.035	18.121	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	205	ILE	0	0.020	0.020	21.330	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	206	PHE	0	-0.026	-0.017	19.872	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	207	GLY	0	0.033	0.008	21.729	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	208	VAL	0	-0.004	-0.004	23.026	0.002	0.002	0.000	0.000	0.000	0.000
137	A	209	SER	0	0.018	0.017	25.754	0.001	0.001	0.000	0.000	0.000	0.000
138	A	210	TRP	0	0.004	0.003	24.434	0.001	0.001	0.000	0.000	0.000	0.000
139	A	211	PHE	0	0.039	0.006	26.489	0.002	0.002	0.000	0.000	0.000	0.000
140	A	212	LEU	0	-0.011	-0.019	28.314	0.004	0.004	0.000	0.000	0.000	0.000
141	A	213	SER	0	-0.052	-0.019	29.322	0.002	0.002	0.000	0.000	0.000	0.000
142	A	214	GLN	0	-0.069	-0.036	27.307	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	215	VAL	0	-0.028	-0.017	28.713	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	216	ALA	0	0.022	0.017	31.663	0.005	0.005	0.000	0.000	0.000	0.000
145	A	217	PRO	0	-0.022	-0.003	33.749	0.005	0.005	0.000	0.000	0.000	0.000
146	A	218	ASN	0	-0.100	-0.045	34.142	0.004	0.004	0.000	0.000	0.000	0.000
147	A	219	LEU	0	-0.029	-0.006	33.930	0.000	0.000	0.000	0.000	0.000	0.000
148	A	220	ASP	-1	-0.891	-0.922	37.821	-0.050	-0.050	0.000	0.000	0.000	0.000

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