FMO DATABASE

FMODB ID: 72R9K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1346492.714118
FMO2-HF: Nuclear repulsion	1288658.034793
FMO2-HF: Total energy	-57834.679326
FMO2-MP2: Total energy	-58004.402343

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.
-2.187	-0.11	0.012	-0.861	-1.229	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 : -0.042 / q_NPA : -0.040

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	-0.884	-0.946	3.546	-3.067	-1.467	0.007	-0.712	-0.896	0.002
4	D	42	SER	0	-0.043	-0.009	6.505	0.174	0.174	0.000	0.000	0.000	0.000
5	D	43	VAL	0	-0.012	-0.010	8.761	0.042	0.042	0.000	0.000	0.000	0.000
6	D	44	THR	0	0.010	0.006	12.500	0.013	0.013	0.000	0.000	0.000	0.000
7	D	45	VAL	0	-0.001	-0.010	15.070	0.011	0.011	0.000	0.000	0.000	0.000
8	D	46	LEU	0	-0.033	0.001	18.773	0.003	0.003	0.000	0.000	0.000	0.000
9	D	47	LEU	0	0.031	0.014	21.906	0.005	0.005	0.000	0.000	0.000	0.000
10	D	48	PHE	0	0.012	-0.005	24.878	0.000	0.000	0.000	0.000	0.000	0.000
11	D	49	ASN	0	0.010	-0.007	28.463	0.004	0.004	0.000	0.000	0.000	0.000
12	D	50	SER	0	0.047	0.012	31.110	0.001	0.001	0.000	0.000	0.000	0.000
13	D	51	SER	0	-0.037	-0.016	34.400	0.001	0.001	0.000	0.000	0.000	0.000
14	D	52	ARG	1	0.879	0.946	32.797	0.023	0.023	0.000	0.000	0.000	0.000
15	D	53	ARG	1	0.928	1.006	34.586	0.025	0.025	0.000	0.000	0.000	0.000
16	D	54	SER	0	-0.045	-0.053	31.217	0.000	0.000	0.000	0.000	0.000	0.000
17	D	55	LEU	0	-0.001	0.009	26.376	0.000	0.000	0.000	0.000	0.000	0.000
18	D	56	VAL	0	-0.032	-0.006	23.709	0.003	0.003	0.000	0.000	0.000	0.000
19	D	57	LEU	0	-0.034	-0.030	22.002	-0.009	-0.009	0.000	0.000	0.000	0.000
20	D	58	VAL	0	0.097	0.060	18.416	0.010	0.010	0.000	0.000	0.000	0.000
21	D	59	LYS	1	0.914	0.962	20.700	0.029	0.029	0.000	0.000	0.000	0.000
22	D	60	GLN	0	0.059	0.035	15.965	-0.001	-0.001	0.000	0.000	0.000	0.000
23	D	61	PHE	0	-0.002	0.011	20.587	-0.008	-0.008	0.000	0.000	0.000	0.000
24	D	62	ARG	1	0.869	0.932	12.943	0.103	0.103	0.000	0.000	0.000	0.000
25	D	63	PRO	0	0.033	0.002	17.326	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	64	ALA	0	0.007	0.006	16.828	0.002	0.002	0.000	0.000	0.000	0.000
27	D	65	VAL	0	0.041	0.027	18.584	-0.001	-0.001	0.000	0.000	0.000	0.000
28	D	66	TYR	0	-0.023	-0.013	20.825	0.006	0.006	0.000	0.000	0.000	0.000
29	D	67	ALA	0	-0.036	-0.020	21.494	0.003	0.003	0.000	0.000	0.000	0.000
30	D	68	GLY	0	0.037	0.008	22.305	0.004	0.004	0.000	0.000	0.000	0.000
31	D	69	GLU	-1	-0.847	-0.912	23.773	-0.048	-0.048	0.000	0.000	0.000	0.000
32	D	70	VAL	0	-0.042	-0.014	26.490	0.005	0.005	0.000	0.000	0.000	0.000
33	D	71	GLU	-1	-1.034	-1.027	24.955	-0.043	-0.043	0.000	0.000	0.000	0.000
34	D	72	ARG	1	0.824	0.915	28.173	0.047	0.047	0.000	0.000	0.000	0.000
35	D	73	ARG	1	0.930	0.981	30.680	0.028	0.028	0.000	0.000	0.000	0.000
36	D	93	LEU	0	-0.017	-0.031	28.372	0.000	0.000	0.000	0.000	0.000	0.000
37	D	94	PRO	0	0.002	-0.002	32.507	0.001	0.001	0.000	0.000	0.000	0.000
38	D	95	GLY	0	0.045	0.042	30.325	0.000	0.000	0.000	0.000	0.000	0.000
39	D	96	SER	0	-0.003	-0.013	29.619	0.001	0.001	0.000	0.000	0.000	0.000
40	D	97	ALA	0	0.014	0.005	27.025	0.000	0.000	0.000	0.000	0.000	0.000
41	D	98	GLY	0	0.062	0.041	23.811	-0.002	-0.002	0.000	0.000	0.000	0.000
42	D	99	VAL	0	-0.078	-0.048	22.135	-0.003	-0.003	0.000	0.000	0.000	0.000
43	D	100	THR	0	-0.019	-0.006	18.277	0.003	0.003	0.000	0.000	0.000	0.000
44	D	101	VAL	0	0.025	0.012	20.771	0.003	0.003	0.000	0.000	0.000	0.000
45	D	102	GLU	-1	-0.876	-0.950	15.497	-0.148	-0.148	0.000	0.000	0.000	0.000
46	D	103	LEU	0	-0.025	-0.016	16.666	0.017	0.017	0.000	0.000	0.000	0.000
47	D	104	CYS	0	-0.023	0.005	16.448	-0.010	-0.010	0.000	0.000	0.000	0.000
48	D	105	ALA	0	-0.050	-0.046	12.450	-0.024	-0.024	0.000	0.000	0.000	0.000
49	D	106	GLY	0	0.088	0.064	11.252	0.033	0.033	0.000	0.000	0.000	0.000
50	D	107	LEU	0	-0.046	-0.033	5.570	-0.122	-0.122	0.000	0.000	0.000	0.000
51	D	108	VAL	0	-0.010	-0.004	7.902	0.080	0.080	0.000	0.000	0.000	0.000
52	D	109	ASP	-1	-0.910	-0.949	7.169	0.400	0.400	0.000	0.000	0.000	0.000
53	D	110	GLN	0	-0.036	-0.024	8.320	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	111	PRO	0	0.006	0.011	10.582	-0.024	-0.024	0.000	0.000	0.000	0.000
55	D	112	GLY	0	-0.027	-0.030	11.874	0.003	0.003	0.000	0.000	0.000	0.000
56	D	113	LEU	0	0.003	0.000	13.924	0.002	0.002	0.000	0.000	0.000	0.000
57	D	114	SER	0	-0.018	0.000	14.223	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	115	LEU	0	0.045	0.020	12.080	-0.007	-0.007	0.000	0.000	0.000	0.000
59	D	116	GLU	-1	-0.862	-0.957	15.287	-0.066	-0.066	0.000	0.000	0.000	0.000
60	D	117	GLU	-1	-0.893	-0.955	17.187	-0.015	-0.015	0.000	0.000	0.000	0.000
61	D	118	VAL	0	-0.024	-0.004	12.318	0.008	0.008	0.000	0.000	0.000	0.000
62	D	119	ALA	0	-0.007	0.004	15.639	0.001	0.001	0.000	0.000	0.000	0.000
63	D	120	CYS	0	-0.050	-0.021	17.314	0.006	0.006	0.000	0.000	0.000	0.000
64	D	121	LYS	1	0.901	0.964	14.560	-0.022	-0.022	0.000	0.000	0.000	0.000
65	D	122	GLU	-1	-0.843	-0.927	14.204	-0.018	-0.018	0.000	0.000	0.000	0.000
66	D	123	ALA	0	0.011	-0.004	17.571	0.002	0.002	0.000	0.000	0.000	0.000
67	D	124	TRP	0	-0.053	-0.016	20.798	0.003	0.003	0.000	0.000	0.000	0.000
68	D	125	GLU	-1	-0.946	-0.991	17.617	0.026	0.026	0.000	0.000	0.000	0.000
69	D	126	GLU	-1	-0.832	-0.910	16.102	-0.070	-0.070	0.000	0.000	0.000	0.000
70	D	127	CYS	0	-0.097	-0.050	20.307	-0.002	-0.002	0.000	0.000	0.000	0.000
71	D	128	GLY	0	-0.015	0.018	23.234	0.002	0.002	0.000	0.000	0.000	0.000
72	D	129	TYR	0	-0.054	-0.067	24.540	0.002	0.002	0.000	0.000	0.000	0.000
73	D	130	HIS	0	-0.006	0.006	24.740	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	131	LEU	0	-0.006	-0.007	22.362	-0.002	-0.002	0.000	0.000	0.000	0.000
75	D	132	ALA	0	0.009	0.007	25.288	0.003	0.003	0.000	0.000	0.000	0.000
76	D	133	PRO	0	0.058	0.004	21.897	-0.004	-0.004	0.000	0.000	0.000	0.000
77	D	134	SER	0	-0.059	-0.026	23.737	-0.002	-0.002	0.000	0.000	0.000	0.000
78	D	135	ASP	-1	-0.849	-0.914	26.232	-0.027	-0.027	0.000	0.000	0.000	0.000
79	D	136	LEU	0	-0.093	-0.010	20.016	-0.004	-0.004	0.000	0.000	0.000	0.000
80	D	137	ARG	1	0.996	1.004	23.789	0.052	0.052	0.000	0.000	0.000	0.000
81	D	138	ARG	1	0.927	0.963	18.838	0.062	0.062	0.000	0.000	0.000	0.000
82	D	139	VAL	0	-0.047	-0.024	20.363	0.008	0.008	0.000	0.000	0.000	0.000
83	D	140	ALA	0	-0.012	-0.021	18.867	0.007	0.007	0.000	0.000	0.000	0.000
84	D	141	THR	0	-0.044	-0.028	14.032	0.000	0.000	0.000	0.000	0.000	0.000
85	D	142	TYR	0	-0.055	-0.012	13.104	0.051	0.051	0.000	0.000	0.000	0.000
86	D	143	TRP	0	0.052	0.011	8.086	-0.057	-0.057	0.000	0.000	0.000	0.000
87	D	144	SER	0	0.029	0.021	8.746	0.088	0.088	0.000	0.000	0.000	0.000
88	D	145	GLY	0	0.099	-0.059	7.965	-0.160	-0.160	0.000	0.000	0.000	0.000
89	D	146	VAL	0	0.331	0.313	9.042	0.058	0.058	0.000	0.000	0.000	0.000
90	D	147	GLY	0	0.520	0.365	9.873	0.041	0.041	0.000	0.000	0.000	0.000
91	D	148	DLE	1	-1.124	-0.531	6.221	0.695	0.695	0.000	0.000	0.000	0.000
92	D	149	THR	-1	0.263	-0.151	6.848	-0.393	-0.393	0.000	0.000	0.000	0.000
93	D	150	GLY	0	-0.129	0.025	4.820	-0.250	-0.250	0.000	0.000	0.000	0.000
94	D	151	SER	0	-0.039	0.004	3.697	-0.183	0.294	0.005	-0.149	-0.333	-0.001
95	D	152	ARG	1	0.949	0.993	5.446	0.480	0.480	0.000	0.000	0.000	0.000
96	D	153	GLN	0	0.041	-0.002	8.281	-0.063	-0.063	0.000	0.000	0.000	0.000
97	D	154	THR	0	-0.043	-0.024	10.872	0.086	0.086	0.000	0.000	0.000	0.000
98	D	155	MET	0	0.000	0.034	14.380	-0.008	-0.008	0.000	0.000	0.000	0.000
99	D	156	PHE	0	0.029	0.010	16.198	0.018	0.018	0.000	0.000	0.000	0.000
100	D	157	TYR	0	0.032	-0.006	19.918	-0.003	-0.003	0.000	0.000	0.000	0.000
101	D	158	THR	0	0.016	-0.022	23.302	0.005	0.005	0.000	0.000	0.000	0.000
102	D	159	GLU	-1	-0.940	-0.958	26.075	-0.032	-0.032	0.000	0.000	0.000	0.000
103	D	160	VAL	0	0.015	0.011	27.181	0.001	0.001	0.000	0.000	0.000	0.000
104	D	161	THR	0	0.034	0.017	30.261	0.001	0.001	0.000	0.000	0.000	0.000
105	D	162	ASP	-1	-0.803	-0.925	32.365	-0.021	-0.021	0.000	0.000	0.000	0.000
106	D	163	ALA	0	-0.073	-0.029	34.155	0.001	0.001	0.000	0.000	0.000	0.000
107	D	164	GLN	0	-0.072	-0.049	29.033	0.001	0.001	0.000	0.000	0.000	0.000
108	D	165	ARG	1	0.931	0.991	29.438	0.021	0.021	0.000	0.000	0.000	0.000
109	D	178	LEU	0	-0.056	-0.029	19.014	0.000	0.000	0.000	0.000	0.000	0.000
110	D	179	ILE	0	0.011	-0.016	16.641	-0.003	-0.003	0.000	0.000	0.000	0.000
111	D	180	GLU	-1	-0.929	-0.950	20.989	-0.025	-0.025	0.000	0.000	0.000	0.000
112	D	181	VAL	0	0.051	0.025	23.016	-0.006	-0.006	0.000	0.000	0.000	0.000
113	D	182	VAL	0	-0.046	-0.038	24.507	0.004	0.004	0.000	0.000	0.000	0.000
114	D	183	HIS	0	0.015	0.021	26.482	-0.002	-0.002	0.000	0.000	0.000	0.000
115	D	184	LEU	0	-0.011	0.000	27.285	0.002	0.002	0.000	0.000	0.000	0.000
116	D	185	PRO	0	0.018	0.007	30.041	-0.001	-0.001	0.000	0.000	0.000	0.000
117	D	186	LEU	0	0.022	0.006	31.536	-0.002	-0.002	0.000	0.000	0.000	0.000
118	D	187	GLU	-1	-0.922	-0.958	33.529	-0.030	-0.030	0.000	0.000	0.000	0.000
119	D	188	GLY	0	-0.010	-0.010	34.942	0.000	0.000	0.000	0.000	0.000	0.000
120	D	189	ALA	0	0.007	0.001	29.852	-0.002	-0.002	0.000	0.000	0.000	0.000
121	D	190	GLN	0	-0.011	-0.002	29.721	-0.004	-0.004	0.000	0.000	0.000	0.000
122	D	191	ALA	0	0.039	0.013	31.255	-0.002	-0.002	0.000	0.000	0.000	0.000
123	D	192	PHE	0	-0.005	0.003	25.069	-0.001	-0.001	0.000	0.000	0.000	0.000
124	D	193	ALA	0	-0.040	-0.040	26.690	-0.004	-0.004	0.000	0.000	0.000	0.000
125	D	194	ASP	-1	-0.890	-0.961	27.310	-0.053	-0.053	0.000	0.000	0.000	0.000
126	D	195	ASP	-1	-0.883	-0.931	30.001	-0.043	-0.043	0.000	0.000	0.000	0.000
127	D	196	PRO	0	-0.050	-0.030	27.588	-0.005	-0.005	0.000	0.000	0.000	0.000
128	D	197	ASP	-1	-0.934	-0.960	27.603	-0.043	-0.043	0.000	0.000	0.000	0.000
129	D	198	ILE	0	-0.076	-0.025	25.758	0.001	0.001	0.000	0.000	0.000	0.000
130	D	199	PRO	0	0.008	0.000	22.231	-0.007	-0.007	0.000	0.000	0.000	0.000
131	D	200	LYS	1	0.857	0.932	20.926	0.070	0.070	0.000	0.000	0.000	0.000
132	D	201	THR	0	-0.021	0.013	15.825	-0.009	-0.009	0.000	0.000	0.000	0.000
133	D	202	LEU	0	0.057	0.013	17.114	0.010	0.010	0.000	0.000	0.000	0.000
134	D	203	GLY	0	0.031	0.023	17.232	0.013	0.013	0.000	0.000	0.000	0.000
135	D	204	VAL	0	0.060	0.044	18.177	0.013	0.013	0.000	0.000	0.000	0.000
136	D	205	ILE	0	0.019	0.013	21.091	0.010	0.010	0.000	0.000	0.000	0.000
137	D	206	PHE	0	-0.067	-0.050	19.375	0.010	0.010	0.000	0.000	0.000	0.000
138	D	207	GLY	0	0.012	0.002	21.644	0.007	0.007	0.000	0.000	0.000	0.000
139	D	208	VAL	0	-0.008	-0.012	22.816	0.008	0.008	0.000	0.000	0.000	0.000
140	D	209	SER	0	0.016	0.010	25.805	0.008	0.008	0.000	0.000	0.000	0.000
141	D	210	TRP	0	0.004	0.005	24.560	0.006	0.006	0.000	0.000	0.000	0.000
142	D	211	PHE	0	-0.007	-0.009	26.492	0.005	0.005	0.000	0.000	0.000	0.000
143	D	212	LEU	0	0.016	0.003	28.132	0.005	0.005	0.000	0.000	0.000	0.000
144	D	213	SER	0	-0.015	-0.010	29.959	0.002	0.002	0.000	0.000	0.000	0.000
145	D	214	GLN	0	-0.052	-0.024	28.160	0.005	0.005	0.000	0.000	0.000	0.000
146	D	215	VAL	0	-0.065	-0.031	28.534	0.003	0.003	0.000	0.000	0.000	0.000
147	D	216	ALA	0	-0.041	-0.024	31.524	0.003	0.003	0.000	0.000	0.000	0.000
148	D	217	PRO	0	-0.014	0.006	33.774	0.002	0.002	0.000	0.000	0.000	0.000
149	D	218	ASN	0	-0.052	-0.024	34.130	0.003	0.003	0.000	0.000	0.000	0.000
150	D	219	LEU	0	-0.022	0.007	33.861	0.002	0.002	0.000	0.000	0.000	0.000
151	D	220	ASP	-1	-0.954	-0.970	36.797	-0.019	-0.019	0.000	0.000	0.000	0.000

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