FMO DATABASE

FMODB ID: 2J1YR

Calculation Name: 3Q91-D-Xray372

Preferred Name: Uridine diphosphate glucose pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q91

Chain ID: D

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1344630.275345
FMO2-HF: Nuclear repulsion	1286793.186648
FMO2-HF: Total energy	-57837.088698
FMO2-MP2: Total energy	-58006.564292

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(D:39:THR)

Summations of interaction energy for fragment #1(D: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.
-1.857	0.475	0.08	-0.827	-1.585	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.021

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	D	41	ASP	-1	-0.814	-0.899	3.793	-4.411	-3.013	-0.004	-0.569	-0.825	0.002
4	D	42	SER	0	-0.040	-0.010	6.594	0.715	0.715	0.000	0.000	0.000	0.000
5	D	43	VAL	0	-0.039	-0.024	8.675	0.048	0.048	0.000	0.000	0.000	0.000
6	D	44	THR	0	0.011	0.002	12.396	0.036	0.036	0.000	0.000	0.000	0.000
7	D	45	VAL	0	-0.008	-0.010	15.022	0.010	0.010	0.000	0.000	0.000	0.000
8	D	46	LEU	0	-0.015	0.017	18.793	0.016	0.016	0.000	0.000	0.000	0.000
9	D	47	LEU	0	0.016	0.007	21.975	0.004	0.004	0.000	0.000	0.000	0.000
10	D	48	PHE	0	0.018	-0.002	25.097	0.008	0.008	0.000	0.000	0.000	0.000
11	D	49	ASN	0	0.013	-0.013	28.738	0.008	0.008	0.000	0.000	0.000	0.000
12	D	50	SER	0	0.015	-0.013	31.311	0.008	0.008	0.000	0.000	0.000	0.000
13	D	51	SER	0	-0.043	-0.031	34.481	0.006	0.006	0.000	0.000	0.000	0.000
14	D	52	ARG	1	0.808	0.884	33.336	0.105	0.105	0.000	0.000	0.000	0.000
15	D	53	ARG	1	0.867	0.938	34.804	0.104	0.104	0.000	0.000	0.000	0.000
16	D	54	SER	0	-0.021	-0.021	31.098	0.002	0.002	0.000	0.000	0.000	0.000
17	D	55	LEU	0	-0.009	-0.001	26.450	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	56	VAL	0	-0.039	-0.015	24.554	0.013	0.013	0.000	0.000	0.000	0.000
19	D	57	LEU	0	-0.020	-0.015	21.880	-0.024	-0.024	0.000	0.000	0.000	0.000
20	D	58	VAL	0	0.055	0.036	18.394	0.021	0.021	0.000	0.000	0.000	0.000
21	D	59	LYS	1	0.827	0.915	20.759	0.105	0.105	0.000	0.000	0.000	0.000
22	D	60	GLN	0	0.054	0.024	15.833	-0.016	-0.016	0.000	0.000	0.000	0.000
23	D	61	PHE	0	0.004	0.008	20.391	-0.006	-0.006	0.000	0.000	0.000	0.000
24	D	62	ARG	1	0.829	0.885	14.323	0.245	0.245	0.000	0.000	0.000	0.000
25	D	63	PRO	0	0.025	0.003	17.327	0.002	0.002	0.000	0.000	0.000	0.000
26	D	64	ALA	0	0.006	0.005	16.737	0.008	0.008	0.000	0.000	0.000	0.000
27	D	65	VAL	0	0.045	0.028	18.503	0.002	0.002	0.000	0.000	0.000	0.000
28	D	66	TYR	0	-0.036	-0.029	20.868	0.011	0.011	0.000	0.000	0.000	0.000
29	D	67	ALA	0	-0.036	-0.015	21.685	0.007	0.007	0.000	0.000	0.000	0.000
30	D	68	GLY	0	0.056	0.029	22.510	0.007	0.007	0.000	0.000	0.000	0.000
31	D	69	GLU	-1	-0.807	-0.880	23.957	-0.092	-0.092	0.000	0.000	0.000	0.000
32	D	70	VAL	0	-0.053	-0.027	26.586	0.008	0.008	0.000	0.000	0.000	0.000
33	D	71	GLU	-1	-0.987	-0.989	24.850	-0.041	-0.041	0.000	0.000	0.000	0.000
34	D	72	ARG	1	0.715	0.834	27.880	0.092	0.092	0.000	0.000	0.000	0.000
35	D	73	ARG	1	0.828	0.919	30.385	0.030	0.030	0.000	0.000	0.000	0.000
36	D	93	LEU	0	0.030	0.011	28.445	0.002	0.002	0.000	0.000	0.000	0.000
37	D	94	PRO	0	-0.035	-0.025	32.278	-0.001	-0.001	0.000	0.000	0.000	0.000
38	D	95	GLY	0	0.043	0.043	29.999	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	96	SER	0	0.006	-0.012	29.203	0.003	0.003	0.000	0.000	0.000	0.000
40	D	97	ALA	0	0.049	0.023	27.334	-0.001	-0.001	0.000	0.000	0.000	0.000
41	D	98	GLY	0	0.022	0.020	23.946	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	99	VAL	0	-0.081	-0.050	22.154	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	100	THR	0	-0.024	-0.027	17.957	0.012	0.012	0.000	0.000	0.000	0.000
44	D	101	VAL	0	0.007	-0.004	21.025	0.002	0.002	0.000	0.000	0.000	0.000
45	D	102	GLU	-1	-0.829	-0.882	15.176	-0.340	-0.340	0.000	0.000	0.000	0.000
46	D	103	LEU	0	-0.017	-0.013	16.359	0.024	0.024	0.000	0.000	0.000	0.000
47	D	104	CYS	0	-0.045	-0.009	16.477	-0.014	-0.014	0.000	0.000	0.000	0.000
48	D	105	ALA	0	-0.022	-0.030	12.364	-0.058	-0.058	0.000	0.000	0.000	0.000
49	D	106	GLY	0	0.054	0.046	11.169	0.088	0.088	0.000	0.000	0.000	0.000
50	D	107	LEU	0	-0.031	-0.022	5.099	-0.248	-0.248	0.000	0.000	0.000	0.000
51	D	108	VAL	0	-0.019	-0.015	8.035	0.231	0.231	0.000	0.000	0.000	0.000
52	D	109	ASP	-1	-0.886	-0.951	7.701	-0.089	-0.089	0.000	0.000	0.000	0.000
53	D	110	GLN	0	-0.063	-0.026	8.742	0.130	0.130	0.000	0.000	0.000	0.000
54	D	111	PRO	0	0.001	-0.002	10.592	-0.098	-0.098	0.000	0.000	0.000	0.000
55	D	112	GLY	0	-0.011	-0.019	12.029	0.073	0.073	0.000	0.000	0.000	0.000
56	D	113	LEU	0	-0.011	0.007	14.268	0.047	0.047	0.000	0.000	0.000	0.000
57	D	114	SER	0	-0.001	0.004	14.424	-0.085	-0.085	0.000	0.000	0.000	0.000
58	D	115	LEU	0	0.004	0.008	12.142	-0.026	-0.026	0.000	0.000	0.000	0.000
59	D	116	GLU	-1	-0.806	-0.932	15.475	-0.475	-0.475	0.000	0.000	0.000	0.000
60	D	117	GLU	-1	-0.864	-0.945	17.752	-0.228	-0.228	0.000	0.000	0.000	0.000
61	D	118	VAL	0	-0.026	-0.004	12.381	0.033	0.033	0.000	0.000	0.000	0.000
62	D	119	ALA	0	-0.002	0.000	15.841	0.035	0.035	0.000	0.000	0.000	0.000
63	D	120	CYS	0	-0.046	-0.022	17.263	0.045	0.045	0.000	0.000	0.000	0.000
64	D	121	LYS	1	0.783	0.892	15.241	0.272	0.272	0.000	0.000	0.000	0.000
65	D	122	GLU	-1	-0.807	-0.905	14.290	-0.301	-0.301	0.000	0.000	0.000	0.000
66	D	123	ALA	0	0.006	-0.009	17.767	0.029	0.029	0.000	0.000	0.000	0.000
67	D	124	TRP	0	-0.036	-0.007	21.071	0.028	0.028	0.000	0.000	0.000	0.000
68	D	125	GLU	-1	-0.877	-0.948	18.269	-0.139	-0.139	0.000	0.000	0.000	0.000
69	D	126	GLU	-1	-0.805	-0.897	16.666	-0.283	-0.283	0.000	0.000	0.000	0.000
70	D	127	CYS	0	-0.101	-0.051	20.396	0.010	0.010	0.000	0.000	0.000	0.000
71	D	128	GLY	0	-0.010	0.017	23.377	0.011	0.011	0.000	0.000	0.000	0.000
72	D	129	TYR	0	-0.057	-0.064	24.870	0.016	0.016	0.000	0.000	0.000	0.000
73	D	130	HIS	0	0.001	0.001	25.018	-0.011	-0.011	0.000	0.000	0.000	0.000
74	D	131	LEU	0	-0.027	-0.027	22.463	-0.001	-0.001	0.000	0.000	0.000	0.000
75	D	132	ALA	0	0.004	0.004	25.369	0.006	0.006	0.000	0.000	0.000	0.000
76	D	133	PRO	0	0.038	0.002	22.125	-0.007	-0.007	0.000	0.000	0.000	0.000
77	D	134	SER	0	-0.090	-0.050	24.051	-0.008	-0.008	0.000	0.000	0.000	0.000
78	D	135	ASP	-1	-0.823	-0.891	26.282	-0.183	-0.183	0.000	0.000	0.000	0.000
79	D	136	LEU	0	-0.049	0.001	20.218	-0.002	-0.002	0.000	0.000	0.000	0.000
80	D	137	ARG	1	0.971	1.000	23.583	0.217	0.217	0.000	0.000	0.000	0.000
81	D	138	ARG	1	0.935	0.952	18.317	0.443	0.443	0.000	0.000	0.000	0.000
82	D	139	VAL	0	-0.059	-0.021	20.283	0.030	0.030	0.000	0.000	0.000	0.000
83	D	140	ALA	0	0.006	-0.008	18.426	0.025	0.025	0.000	0.000	0.000	0.000
84	D	141	THR	0	-0.041	-0.031	13.812	-0.002	-0.002	0.000	0.000	0.000	0.000
85	D	142	TYR	0	-0.079	-0.041	12.844	0.112	0.112	0.000	0.000	0.000	0.000
86	D	143	TRP	0	0.042	0.008	7.529	0.010	0.010	0.000	0.000	0.000	0.000
87	D	144	SER	0	0.039	0.021	8.187	0.273	0.273	0.000	0.000	0.000	0.000
88	D	145	GLY	0	0.018	0.020	7.856	-0.212	-0.212	0.000	0.000	0.000	0.000
89	D	146	VAL	0	-0.075	-0.054	8.942	0.208	0.208	0.000	0.000	0.000	0.000
90	D	147	GLY	0	0.037	0.032	9.861	0.063	0.063	0.000	0.000	0.000	0.000
91	D	148	DLE	0	-0.017	-0.013	8.183	0.144	0.144	0.000	0.000	0.000	0.000
92	D	149	THR	0	-0.062	-0.041	6.091	-0.187	-0.187	0.000	0.000	0.000	0.000
93	D	150	GLY	0	0.052	0.041	4.516	-0.171	-0.017	-0.001	-0.012	-0.141	0.000
94	D	151	SER	0	-0.056	-0.034	3.026	-0.157	0.547	0.086	-0.241	-0.550	-0.001
95	D	152	ARG	1	0.920	0.962	4.811	2.143	2.219	-0.001	-0.005	-0.069	0.000
96	D	153	GLN	0	0.025	0.025	8.136	-0.088	-0.088	0.000	0.000	0.000	0.000
97	D	154	THR	0	-0.037	-0.015	10.800	0.187	0.187	0.000	0.000	0.000	0.000
98	D	155	MET	0	0.019	0.042	14.301	0.001	0.001	0.000	0.000	0.000	0.000
99	D	156	PHE	0	0.021	-0.006	16.073	0.030	0.030	0.000	0.000	0.000	0.000
100	D	157	TYR	0	0.035	0.004	19.983	0.009	0.009	0.000	0.000	0.000	0.000
101	D	158	THR	0	-0.019	-0.037	23.404	0.007	0.007	0.000	0.000	0.000	0.000
102	D	159	GLU	-1	-0.882	-0.911	26.341	-0.142	-0.142	0.000	0.000	0.000	0.000
103	D	160	VAL	0	-0.017	-0.007	27.125	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	161	THR	0	0.034	0.010	30.292	0.010	0.010	0.000	0.000	0.000	0.000
105	D	162	ASP	-1	-0.721	-0.826	32.355	-0.107	-0.107	0.000	0.000	0.000	0.000
106	D	163	ALA	0	-0.019	0.001	33.995	0.002	0.002	0.000	0.000	0.000	0.000
107	D	164	GLN	0	0.021	0.018	29.032	0.010	0.010	0.000	0.000	0.000	0.000
108	D	165	ARG	1	0.785	0.900	29.382	0.115	0.115	0.000	0.000	0.000	0.000
109	D	178	LEU	0	-0.039	-0.030	19.178	0.002	0.002	0.000	0.000	0.000	0.000
110	D	179	ILE	0	0.007	-0.004	16.940	-0.003	-0.003	0.000	0.000	0.000	0.000
111	D	180	GLU	-1	-0.853	-0.908	21.150	-0.093	-0.093	0.000	0.000	0.000	0.000
112	D	181	VAL	0	0.041	0.022	23.303	-0.014	-0.014	0.000	0.000	0.000	0.000
113	D	182	VAL	0	-0.031	-0.024	24.530	0.016	0.016	0.000	0.000	0.000	0.000
114	D	183	HIS	0	0.022	0.024	26.384	-0.013	-0.013	0.000	0.000	0.000	0.000
115	D	184	LEU	0	-0.010	0.001	27.266	0.009	0.009	0.000	0.000	0.000	0.000
116	D	185	PRO	0	0.029	0.015	30.145	-0.006	-0.006	0.000	0.000	0.000	0.000
117	D	186	LEU	0	0.023	0.009	31.291	-0.002	-0.002	0.000	0.000	0.000	0.000
118	D	187	GLU	-1	-0.879	-0.936	33.505	-0.109	-0.109	0.000	0.000	0.000	0.000
119	D	188	GLY	0	-0.019	-0.001	34.678	0.004	0.004	0.000	0.000	0.000	0.000
120	D	189	ALA	0	-0.020	-0.012	29.604	-0.002	-0.002	0.000	0.000	0.000	0.000
121	D	190	GLN	0	-0.025	-0.028	29.802	-0.013	-0.013	0.000	0.000	0.000	0.000
122	D	191	ALA	0	0.037	0.013	30.937	-0.003	-0.003	0.000	0.000	0.000	0.000
123	D	192	PHE	0	0.027	0.007	24.844	-0.001	-0.001	0.000	0.000	0.000	0.000
124	D	193	ALA	0	-0.041	-0.029	26.743	-0.005	-0.005	0.000	0.000	0.000	0.000
125	D	194	ASP	-1	-0.870	-0.930	27.074	-0.145	-0.145	0.000	0.000	0.000	0.000
126	D	195	ASP	-1	-0.909	-0.943	29.462	-0.105	-0.105	0.000	0.000	0.000	0.000
127	D	196	PRO	0	-0.050	-0.032	27.636	-0.011	-0.011	0.000	0.000	0.000	0.000
128	D	197	ASP	-1	-0.834	-0.915	27.447	-0.092	-0.092	0.000	0.000	0.000	0.000
129	D	198	ILE	0	-0.040	-0.003	26.094	0.003	0.003	0.000	0.000	0.000	0.000
130	D	199	PRO	0	0.007	-0.004	22.379	-0.016	-0.016	0.000	0.000	0.000	0.000
131	D	200	LYS	1	0.848	0.940	20.959	0.161	0.161	0.000	0.000	0.000	0.000
132	D	201	THR	0	0.022	0.017	15.145	-0.012	-0.012	0.000	0.000	0.000	0.000
133	D	202	LEU	0	0.015	-0.003	17.143	0.010	0.010	0.000	0.000	0.000	0.000
134	D	203	GLY	0	0.031	0.012	17.026	0.013	0.013	0.000	0.000	0.000	0.000
135	D	204	VAL	0	0.036	0.034	17.993	0.015	0.015	0.000	0.000	0.000	0.000
136	D	205	ILE	0	0.015	0.017	21.058	0.016	0.016	0.000	0.000	0.000	0.000
137	D	206	PHE	0	-0.025	-0.017	19.839	0.015	0.015	0.000	0.000	0.000	0.000
138	D	207	GLY	0	0.031	0.009	21.621	0.012	0.012	0.000	0.000	0.000	0.000
139	D	208	VAL	0	-0.006	-0.006	22.896	0.015	0.015	0.000	0.000	0.000	0.000
140	D	209	SER	0	0.031	0.016	25.860	0.014	0.014	0.000	0.000	0.000	0.000
141	D	210	TRP	0	-0.028	-0.013	24.538	0.011	0.011	0.000	0.000	0.000	0.000
142	D	211	PHE	0	0.023	0.000	26.503	0.009	0.009	0.000	0.000	0.000	0.000
143	D	212	LEU	0	-0.008	-0.012	28.282	0.013	0.013	0.000	0.000	0.000	0.000
144	D	213	SER	0	-0.016	-0.019	29.831	0.007	0.007	0.000	0.000	0.000	0.000
145	D	214	GLN	0	-0.050	-0.008	27.902	0.013	0.013	0.000	0.000	0.000	0.000
146	D	215	VAL	0	-0.051	-0.023	28.682	0.001	0.001	0.000	0.000	0.000	0.000
147	D	216	ALA	0	-0.002	-0.003	31.782	0.009	0.009	0.000	0.000	0.000	0.000
148	D	217	PRO	0	-0.028	-0.002	33.887	0.007	0.007	0.000	0.000	0.000	0.000
149	D	218	ASN	0	-0.077	-0.038	33.929	0.012	0.012	0.000	0.000	0.000	0.000
150	D	219	LEU	0	-0.015	0.011	33.803	0.004	0.004	0.000	0.000	0.000	0.000
151	D	220	ASP	-1	-0.965	-0.972	36.811	-0.087	-0.087	0.000	0.000	0.000	0.000

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