FMO DATABASE

FMODB ID: YZK52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1309948.726815
FMO2-HF: Nuclear repulsion	1253381.238453
FMO2-HF: Total energy	-56567.488362
FMO2-MP2: Total energy	-56732.990411

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.
-5.432	-0.734	0.284	-2.166	-2.815	0.001

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 : -0.021 / q_NPA : -0.012

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	-0.857	-0.908	3.740	-1.765	1.014	-0.014	-1.479	-1.285	0.005
4	A	42	SER	0	-0.013	0.000	6.207	-0.260	-0.260	0.000	0.000	0.000	0.000
5	A	43	VAL	0	-0.035	-0.019	8.950	0.199	0.199	0.000	0.000	0.000	0.000
6	A	44	THR	0	0.033	0.021	12.676	-0.021	-0.021	0.000	0.000	0.000	0.000
7	A	45	VAL	0	0.007	-0.004	15.441	0.031	0.031	0.000	0.000	0.000	0.000
8	A	46	LEU	0	-0.017	0.004	19.117	0.006	0.006	0.000	0.000	0.000	0.000
9	A	47	LEU	0	0.020	0.008	22.261	0.010	0.010	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.016	0.001	25.385	0.012	0.012	0.000	0.000	0.000	0.000
11	A	49	ASN	0	0.016	-0.006	28.924	0.003	0.003	0.000	0.000	0.000	0.000
12	A	50	SER	0	0.034	-0.010	31.676	0.006	0.006	0.000	0.000	0.000	0.000
13	A	51	SER	0	-0.067	-0.035	34.804	0.004	0.004	0.000	0.000	0.000	0.000
14	A	52	ARG	1	0.816	0.886	33.732	0.088	0.088	0.000	0.000	0.000	0.000
15	A	53	ARG	1	0.921	0.982	34.858	0.048	0.048	0.000	0.000	0.000	0.000
16	A	54	SER	0	-0.026	-0.013	31.504	0.005	0.005	0.000	0.000	0.000	0.000
17	A	55	LEU	0	-0.011	0.009	26.704	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	56	VAL	0	-0.032	-0.010	25.016	0.004	0.004	0.000	0.000	0.000	0.000
19	A	57	LEU	0	-0.023	-0.021	22.390	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	58	VAL	0	0.058	0.023	18.920	0.001	0.001	0.000	0.000	0.000	0.000
21	A	59	LYS	1	0.803	0.895	21.522	0.107	0.107	0.000	0.000	0.000	0.000
22	A	60	GLN	0	0.061	0.023	15.694	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	61	PHE	0	0.012	0.023	19.680	0.025	0.025	0.000	0.000	0.000	0.000
24	A	62	ARG	1	0.820	0.874	14.278	0.209	0.209	0.000	0.000	0.000	0.000
25	A	63	PRO	0	0.040	0.001	15.816	0.023	0.023	0.000	0.000	0.000	0.000
26	A	64	ALA	0	-0.017	0.002	15.092	0.014	0.014	0.000	0.000	0.000	0.000
27	A	65	VAL	0	0.042	0.021	17.229	0.012	0.012	0.000	0.000	0.000	0.000
28	A	66	TYR	0	0.006	0.005	19.956	0.002	0.002	0.000	0.000	0.000	0.000
29	A	67	ALA	0	-0.052	-0.045	19.812	0.003	0.003	0.000	0.000	0.000	0.000
30	A	68	GLY	0	0.009	0.016	21.102	0.006	0.006	0.000	0.000	0.000	0.000
31	A	69	GLU	-1	-0.933	-0.975	22.470	0.020	0.020	0.000	0.000	0.000	0.000
32	A	70	VAL	0	-0.140	-0.053	24.928	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	71	GLU	-1	-1.015	-0.993	23.649	0.102	0.102	0.000	0.000	0.000	0.000
34	A	97	ALA	0	0.048	0.009	26.120	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	98	GLY	0	0.036	0.010	22.094	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	99	VAL	0	-0.079	-0.026	20.967	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	100	THR	0	-0.018	-0.028	17.768	0.013	0.013	0.000	0.000	0.000	0.000
38	A	101	VAL	0	0.002	0.002	20.475	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	102	GLU	-1	-0.824	-0.891	15.581	-0.160	-0.160	0.000	0.000	0.000	0.000
40	A	103	LEU	0	-0.041	-0.029	17.313	0.001	0.001	0.000	0.000	0.000	0.000
41	A	104	CYS	0	-0.042	-0.008	17.190	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	105	ALA	0	-0.025	-0.033	13.174	0.013	0.013	0.000	0.000	0.000	0.000
43	A	106	GLY	0	0.070	0.046	11.712	0.011	0.011	0.000	0.000	0.000	0.000
44	A	107	LEU	0	-0.004	-0.009	5.340	0.047	0.047	0.000	0.000	0.000	0.000
45	A	108	VAL	0	-0.034	-0.015	8.228	0.216	0.216	0.000	0.000	0.000	0.000
46	A	109	ASP	-1	-0.865	-0.927	7.721	-2.493	-2.493	0.000	0.000	0.000	0.000
47	A	110	GLN	0	-0.021	-0.017	9.551	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	111	PRO	0	-0.040	-0.012	11.873	0.054	0.054	0.000	0.000	0.000	0.000
49	A	112	GLY	0	-0.035	-0.023	13.431	0.102	0.102	0.000	0.000	0.000	0.000
50	A	113	LEU	0	0.006	0.000	15.219	0.048	0.048	0.000	0.000	0.000	0.000
51	A	114	SER	0	-0.076	-0.050	15.342	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	115	LEU	0	0.016	0.008	11.726	-0.042	-0.042	0.000	0.000	0.000	0.000
53	A	116	GLU	-1	-0.834	-0.946	15.128	-0.289	-0.289	0.000	0.000	0.000	0.000
54	A	117	GLU	-1	-0.832	-0.903	18.200	-0.336	-0.336	0.000	0.000	0.000	0.000
55	A	118	VAL	0	-0.001	0.003	12.514	0.006	0.006	0.000	0.000	0.000	0.000
56	A	119	ALA	0	0.003	0.004	15.953	0.010	0.010	0.000	0.000	0.000	0.000
57	A	120	CYS	0	-0.051	-0.012	17.763	0.034	0.034	0.000	0.000	0.000	0.000
58	A	121	LYS	1	0.803	0.893	15.124	0.597	0.597	0.000	0.000	0.000	0.000
59	A	122	GLU	-1	-0.826	-0.918	14.719	-0.586	-0.586	0.000	0.000	0.000	0.000
60	A	123	ALA	0	-0.001	-0.022	18.069	0.039	0.039	0.000	0.000	0.000	0.000
61	A	124	TRP	0	-0.078	-0.033	21.336	0.040	0.040	0.000	0.000	0.000	0.000
62	A	125	GLU	-1	-0.848	-0.917	18.493	-0.442	-0.442	0.000	0.000	0.000	0.000
63	A	126	GLU	-1	-0.795	-0.878	17.103	-0.327	-0.327	0.000	0.000	0.000	0.000
64	A	127	CYS	0	-0.092	-0.047	20.712	0.037	0.037	0.000	0.000	0.000	0.000
65	A	128	GLY	0	0.016	0.031	23.751	0.023	0.023	0.000	0.000	0.000	0.000
66	A	129	TYR	0	-0.037	-0.049	25.045	0.030	0.030	0.000	0.000	0.000	0.000
67	A	130	HIS	0	-0.018	-0.011	25.317	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	131	LEU	0	-0.004	-0.017	22.681	0.015	0.015	0.000	0.000	0.000	0.000
69	A	132	ALA	0	-0.003	0.010	25.494	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	133	PRO	0	0.050	0.002	22.293	0.009	0.009	0.000	0.000	0.000	0.000
71	A	134	SER	0	-0.057	-0.025	23.784	0.005	0.005	0.000	0.000	0.000	0.000
72	A	135	ASP	-1	-0.845	-0.925	26.682	-0.134	-0.134	0.000	0.000	0.000	0.000
73	A	136	LEU	0	-0.091	-0.005	20.291	0.010	0.010	0.000	0.000	0.000	0.000
74	A	137	ARG	1	0.976	0.998	23.557	0.069	0.069	0.000	0.000	0.000	0.000
75	A	138	ARG	1	0.936	0.966	17.235	0.068	0.068	0.000	0.000	0.000	0.000
76	A	139	VAL	0	-0.044	-0.007	19.811	0.019	0.019	0.000	0.000	0.000	0.000
77	A	140	ALA	0	0.002	-0.014	18.040	0.027	0.027	0.000	0.000	0.000	0.000
78	A	141	THR	0	-0.064	-0.036	13.287	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	142	TYR	0	-0.047	-0.030	12.131	0.061	0.061	0.000	0.000	0.000	0.000
80	A	143	TRP	0	0.060	0.019	7.839	-0.154	-0.154	0.000	0.000	0.000	0.000
81	A	144	SER	0	0.025	0.022	7.834	-0.064	-0.064	0.000	0.000	0.000	0.000
82	A	145	GLY	0	0.038	0.028	6.275	0.167	0.167	0.000	0.000	0.000	0.000
83	A	146	VAL	0	-0.034	-0.019	7.278	0.133	0.133	0.000	0.000	0.000	0.000
84	A	147	GLY	0	0.033	0.021	7.762	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	148	LEU	0	-0.023	-0.023	6.288	0.319	0.319	0.000	0.000	0.000	0.000
86	A	149	THR	0	-0.050	-0.044	3.115	-0.032	0.331	0.059	-0.101	-0.321	0.000
87	A	150	GLY	0	-0.025	0.005	3.160	-1.360	-0.478	0.213	-0.336	-0.758	-0.003
88	A	151	SER	0	-0.032	-0.038	3.293	0.727	1.326	0.027	-0.239	-0.388	-0.001
89	A	152	ARG	1	0.911	0.961	4.512	-0.094	-0.019	-0.001	-0.011	-0.063	0.000
90	A	153	GLN	0	0.043	0.031	7.446	-0.174	-0.174	0.000	0.000	0.000	0.000
91	A	154	THR	0	-0.047	-0.033	10.082	0.156	0.156	0.000	0.000	0.000	0.000
92	A	155	MET	0	0.022	0.035	13.607	-0.040	-0.040	0.000	0.000	0.000	0.000
93	A	156	PHE	0	0.013	-0.014	15.575	0.033	0.033	0.000	0.000	0.000	0.000
94	A	157	TYR	0	0.039	0.014	19.626	0.003	0.003	0.000	0.000	0.000	0.000
95	A	158	THR	0	-0.005	-0.035	23.201	0.000	0.000	0.000	0.000	0.000	0.000
96	A	159	GLU	-1	-0.890	-0.910	26.055	-0.074	-0.074	0.000	0.000	0.000	0.000
97	A	160	VAL	0	-0.023	-0.012	27.699	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	161	THR	0	0.015	0.006	30.585	0.010	0.010	0.000	0.000	0.000	0.000
99	A	162	ASP	-1	-0.728	-0.873	32.811	-0.105	-0.105	0.000	0.000	0.000	0.000
100	A	163	ALA	0	-0.050	-0.011	34.476	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	164	GLN	0	-0.001	0.005	29.600	0.005	0.005	0.000	0.000	0.000	0.000
102	A	165	ARG	1	0.851	0.950	29.766	0.102	0.102	0.000	0.000	0.000	0.000
103	A	166	SER	0	-0.025	-0.008	28.694	0.007	0.007	0.000	0.000	0.000	0.000
104	A	176	GLY	0	-0.009	-0.008	18.961	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	177	GLU	-1	-0.941	-0.975	15.439	-0.393	-0.393	0.000	0.000	0.000	0.000
106	A	178	LEU	0	-0.058	-0.038	18.854	0.030	0.030	0.000	0.000	0.000	0.000
107	A	179	ILE	0	-0.016	-0.002	17.307	0.021	0.021	0.000	0.000	0.000	0.000
108	A	180	GLU	-1	-0.840	-0.884	21.413	-0.099	-0.099	0.000	0.000	0.000	0.000
109	A	181	VAL	0	0.031	0.017	24.364	0.008	0.008	0.000	0.000	0.000	0.000
110	A	182	VAL	0	0.012	-0.004	25.269	0.016	0.016	0.000	0.000	0.000	0.000
111	A	183	HIS	0	-0.043	-0.008	27.192	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	184	LEU	0	0.011	0.023	27.431	0.007	0.007	0.000	0.000	0.000	0.000
113	A	185	PRO	0	0.023	0.006	30.350	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	186	LEU	0	0.022	-0.001	31.693	0.004	0.004	0.000	0.000	0.000	0.000
115	A	187	GLU	-1	-0.974	-0.977	33.617	-0.024	-0.024	0.000	0.000	0.000	0.000
116	A	188	GLY	0	0.015	0.009	34.568	0.005	0.005	0.000	0.000	0.000	0.000
117	A	189	ALA	0	-0.017	-0.014	29.712	0.000	0.000	0.000	0.000	0.000	0.000
118	A	190	GLN	0	-0.031	-0.038	29.307	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	191	ALA	0	0.020	0.003	30.721	0.004	0.004	0.000	0.000	0.000	0.000
120	A	192	PHE	0	0.016	0.004	24.788	0.002	0.002	0.000	0.000	0.000	0.000
121	A	193	ALA	0	-0.023	-0.035	26.365	0.001	0.001	0.000	0.000	0.000	0.000
122	A	194	ASP	-1	-0.882	-0.934	26.579	0.019	0.019	0.000	0.000	0.000	0.000
123	A	195	ASP	-1	-0.872	-0.930	29.196	0.003	0.003	0.000	0.000	0.000	0.000
124	A	196	PRO	0	-0.064	-0.021	26.871	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	197	ASP	-1	-0.893	-0.939	26.824	0.018	0.018	0.000	0.000	0.000	0.000
126	A	198	ILE	0	-0.050	-0.015	25.596	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	199	PRO	0	-0.003	-0.001	21.558	0.001	0.001	0.000	0.000	0.000	0.000
128	A	200	LYS	1	0.804	0.916	21.102	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	201	THR	0	0.050	0.022	15.541	0.013	0.013	0.000	0.000	0.000	0.000
130	A	202	LEU	0	0.030	-0.001	16.335	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	203	GLY	0	0.029	0.020	16.772	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	204	VAL	0	0.055	0.047	17.861	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	205	ILE	0	0.017	0.026	20.842	0.003	0.003	0.000	0.000	0.000	0.000
134	A	206	PHE	0	0.001	-0.016	19.594	0.005	0.005	0.000	0.000	0.000	0.000
135	A	207	GLY	0	0.008	0.003	21.397	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	208	VAL	0	-0.032	-0.034	22.770	0.001	0.001	0.000	0.000	0.000	0.000
137	A	209	SER	0	-0.004	0.018	25.121	0.005	0.005	0.000	0.000	0.000	0.000
138	A	210	TRP	0	-0.013	-0.029	24.087	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	211	PHE	0	0.042	0.006	26.076	0.001	0.001	0.000	0.000	0.000	0.000
140	A	212	LEU	0	0.004	0.003	27.899	0.001	0.001	0.000	0.000	0.000	0.000
141	A	213	SER	0	-0.035	-0.003	28.828	0.003	0.003	0.000	0.000	0.000	0.000
142	A	214	GLN	0	-0.062	-0.041	27.353	0.002	0.002	0.000	0.000	0.000	0.000
143	A	215	VAL	0	-0.045	-0.029	28.448	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	216	ALA	0	-0.007	-0.002	31.436	0.000	0.000	0.000	0.000	0.000	0.000
145	A	217	PRO	0	-0.027	-0.001	33.352	0.000	0.000	0.000	0.000	0.000	0.000
146	A	218	ASN	0	-0.085	-0.036	33.571	0.003	0.003	0.000	0.000	0.000	0.000
147	A	219	LEU	0	-0.027	0.002	33.554	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	220	ASP	-1	-0.952	-0.971	37.352	-0.035	-0.035	0.000	0.000	0.000	0.000

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