FMO DATABASE

FMODB ID: R9JZ8

Calculation Name: 3Q91-C-Xray372

Preferred Name: Uridine diphosphate glucose pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q91

Chain ID: C

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	-1314680.286041
FMO2-HF: Nuclear repulsion	1257944.574888
FMO2-HF: Total energy	-56735.711153
FMO2-MP2: Total energy	-56901.710418

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(C:40:HIS)

Summations of interaction energy for fragment #1(C:40:HIS)

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.
-2.025	4.295	3.108	-2.963	-6.463	0.013

Interaction energy analysis for fragmet #1(C:40:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.019

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	C	42	SER	0	-0.028	-0.003	3.708	-0.412	1.743	-0.003	-1.147	-1.004	0.005
4	C	43	VAL	0	-0.041	-0.025	6.077	-0.110	-0.110	0.000	0.000	0.000	0.000
5	C	44	THR	0	0.016	0.005	9.737	0.052	0.052	0.000	0.000	0.000	0.000
6	C	45	VAL	0	-0.010	-0.010	12.773	-0.023	-0.023	0.000	0.000	0.000	0.000
7	C	46	LEU	0	-0.016	0.008	16.287	-0.003	-0.003	0.000	0.000	0.000	0.000
8	C	47	LEU	0	0.040	0.018	19.204	-0.006	-0.006	0.000	0.000	0.000	0.000
9	C	48	PHE	0	0.009	0.001	22.441	-0.009	-0.009	0.000	0.000	0.000	0.000
10	C	49	ASN	0	0.022	-0.016	26.119	-0.004	-0.004	0.000	0.000	0.000	0.000
11	C	50	SER	0	0.030	-0.021	28.533	-0.007	-0.007	0.000	0.000	0.000	0.000
12	C	51	SER	0	-0.069	-0.037	31.744	-0.003	-0.003	0.000	0.000	0.000	0.000
13	C	52	ARG	1	0.789	0.873	30.642	-0.079	-0.079	0.000	0.000	0.000	0.000
14	C	53	ARG	1	0.960	0.999	32.181	-0.044	-0.044	0.000	0.000	0.000	0.000
15	C	54	SER	0	-0.014	-0.017	28.798	-0.004	-0.004	0.000	0.000	0.000	0.000
16	C	55	LEU	0	-0.009	0.002	24.417	0.006	0.006	0.000	0.000	0.000	0.000
17	C	56	VAL	0	-0.031	-0.011	21.766	-0.003	-0.003	0.000	0.000	0.000	0.000
18	C	57	LEU	0	-0.028	-0.021	20.237	-0.001	-0.001	0.000	0.000	0.000	0.000
19	C	58	VAL	0	0.041	0.032	16.730	-0.001	-0.001	0.000	0.000	0.000	0.000
20	C	59	LYS	1	0.930	0.971	19.494	-0.107	-0.107	0.000	0.000	0.000	0.000
21	C	60	GLN	0	0.089	0.039	14.264	0.038	0.038	0.000	0.000	0.000	0.000
22	C	61	PHE	0	-0.012	-0.001	18.816	-0.024	-0.024	0.000	0.000	0.000	0.000
23	C	62	ARG	1	0.848	0.904	12.907	-0.225	-0.225	0.000	0.000	0.000	0.000
24	C	63	PRO	0	0.021	0.004	16.336	-0.025	-0.025	0.000	0.000	0.000	0.000
25	C	64	ALA	0	0.006	0.005	16.632	-0.014	-0.014	0.000	0.000	0.000	0.000
26	C	65	VAL	0	0.031	0.020	18.561	-0.013	-0.013	0.000	0.000	0.000	0.000
27	C	66	TYR	0	-0.004	-0.013	20.917	-0.006	-0.006	0.000	0.000	0.000	0.000
28	C	67	ALA	0	-0.045	-0.010	21.728	-0.005	-0.005	0.000	0.000	0.000	0.000
29	C	68	GLY	0	0.081	0.043	22.510	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	69	GLU	-1	-0.810	-0.884	24.096	0.006	0.006	0.000	0.000	0.000	0.000
31	C	70	VAL	0	-0.053	-0.006	26.584	-0.003	-0.003	0.000	0.000	0.000	0.000
32	C	71	GLU	-1	-1.000	-0.999	24.469	-0.006	-0.006	0.000	0.000	0.000	0.000
33	C	72	ARG	1	0.677	0.804	25.076	-0.006	-0.006	0.000	0.000	0.000	0.000
34	C	97	ALA	0	0.018	-0.005	26.631	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	98	GLY	0	0.049	0.018	23.213	0.004	0.004	0.000	0.000	0.000	0.000
36	C	99	VAL	0	-0.073	-0.022	21.352	0.012	0.012	0.000	0.000	0.000	0.000
37	C	100	THR	0	0.028	0.011	18.079	-0.014	-0.014	0.000	0.000	0.000	0.000
38	C	101	VAL	0	-0.022	-0.017	19.803	0.019	0.019	0.000	0.000	0.000	0.000
39	C	102	GLU	-1	-0.854	-0.926	14.841	0.147	0.147	0.000	0.000	0.000	0.000
40	C	103	LEU	0	-0.031	-0.019	15.107	0.002	0.002	0.000	0.000	0.000	0.000
41	C	104	CYS	0	-0.047	-0.010	14.854	0.018	0.018	0.000	0.000	0.000	0.000
42	C	105	ALA	0	-0.026	-0.033	10.377	-0.063	-0.063	0.000	0.000	0.000	0.000
43	C	106	GLY	0	0.065	0.053	8.290	0.042	0.042	0.000	0.000	0.000	0.000
44	C	107	LEU	0	-0.032	-0.022	2.505	-2.663	-0.838	0.749	-0.687	-1.886	0.003
45	C	108	VAL	0	-0.017	-0.014	4.105	-0.462	-0.215	-0.001	-0.029	-0.216	0.000
46	C	109	ASP	-1	-0.889	-0.942	2.411	2.467	3.910	2.295	-1.410	-2.328	0.004
47	C	110	GLN	0	-0.039	-0.022	3.220	-3.190	-3.572	0.029	0.712	-0.359	0.000
48	C	111	PRO	0	-0.048	-0.037	5.875	0.030	0.030	0.000	0.000	0.000	0.000
49	C	112	GLY	0	-0.017	-0.007	8.787	-0.123	-0.123	0.000	0.000	0.000	0.000
50	C	113	LEU	0	-0.003	0.017	9.996	-0.086	-0.086	0.000	0.000	0.000	0.000
51	C	114	SER	0	-0.037	-0.045	11.028	0.097	0.097	0.000	0.000	0.000	0.000
52	C	115	LEU	0	0.007	-0.012	8.950	0.075	0.075	0.000	0.000	0.000	0.000
53	C	116	GLU	-1	-0.805	-0.892	11.623	0.293	0.293	0.000	0.000	0.000	0.000
54	C	117	GLU	-1	-0.862	-0.937	13.825	0.318	0.318	0.000	0.000	0.000	0.000
55	C	118	VAL	0	-0.021	-0.001	8.473	-0.012	-0.012	0.000	0.000	0.000	0.000
56	C	119	ALA	0	0.002	-0.002	11.817	-0.029	-0.029	0.000	0.000	0.000	0.000
57	C	120	CYS	0	-0.054	-0.027	13.739	-0.055	-0.055	0.000	0.000	0.000	0.000
58	C	121	LYS	1	0.793	0.896	10.229	-0.908	-0.908	0.000	0.000	0.000	0.000
59	C	122	GLU	-1	-0.784	-0.890	10.292	0.972	0.972	0.000	0.000	0.000	0.000
60	C	123	ALA	0	0.000	-0.012	14.255	-0.064	-0.064	0.000	0.000	0.000	0.000
61	C	124	TRP	0	-0.032	-0.007	17.683	-0.054	-0.054	0.000	0.000	0.000	0.000
62	C	125	GLU	-1	-0.877	-0.951	13.833	0.513	0.513	0.000	0.000	0.000	0.000
63	C	126	GLU	-1	-0.769	-0.878	14.215	0.364	0.364	0.000	0.000	0.000	0.000
64	C	127	CYS	0	-0.070	-0.042	17.416	-0.049	-0.049	0.000	0.000	0.000	0.000
65	C	128	GLY	0	-0.003	0.020	20.401	-0.028	-0.028	0.000	0.000	0.000	0.000
66	C	129	TYR	0	-0.066	-0.061	21.470	-0.034	-0.034	0.000	0.000	0.000	0.000
67	C	130	HIS	0	-0.001	0.002	21.416	0.028	0.028	0.000	0.000	0.000	0.000
68	C	131	LEU	0	-0.015	-0.021	18.931	-0.017	-0.017	0.000	0.000	0.000	0.000
69	C	132	ALA	0	-0.008	0.002	21.820	0.012	0.012	0.000	0.000	0.000	0.000
70	C	133	PRO	0	0.055	0.008	18.388	-0.013	-0.013	0.000	0.000	0.000	0.000
71	C	134	SER	0	-0.079	-0.046	20.014	-0.008	-0.008	0.000	0.000	0.000	0.000
72	C	135	ASP	-1	-0.838	-0.899	22.647	0.128	0.128	0.000	0.000	0.000	0.000
73	C	136	LEU	0	-0.031	0.006	16.871	-0.012	-0.012	0.000	0.000	0.000	0.000
74	C	137	ARG	1	0.950	0.987	20.325	-0.049	-0.049	0.000	0.000	0.000	0.000
75	C	138	ARG	1	0.967	0.978	16.312	-0.025	-0.025	0.000	0.000	0.000	0.000
76	C	139	VAL	0	-0.061	-0.022	18.357	-0.010	-0.010	0.000	0.000	0.000	0.000
77	C	140	ALA	0	0.000	-0.011	17.330	-0.013	-0.013	0.000	0.000	0.000	0.000
78	C	141	THR	0	-0.072	-0.045	12.398	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	142	TYR	0	-0.054	-0.036	12.462	0.045	0.045	0.000	0.000	0.000	0.000
80	C	143	TRP	0	0.025	0.006	6.119	-0.096	-0.096	0.000	0.000	0.000	0.000
81	C	144	SER	0	0.001	0.002	8.783	0.201	0.201	0.000	0.000	0.000	0.000
82	C	145	GLY	0	0.067	0.022	8.131	-0.259	-0.259	0.000	0.000	0.000	0.000
83	C	146	VAL	0	-0.071	-0.039	10.125	0.064	0.064	0.000	0.000	0.000	0.000
84	C	147	GLY	0	0.039	0.028	8.839	0.126	0.126	0.000	0.000	0.000	0.000
85	C	148	LEU	0	-0.047	-0.016	6.655	-0.105	-0.105	0.000	0.000	0.000	0.000
86	C	149	THR	0	0.011	0.002	5.444	-0.048	-0.048	0.000	0.000	0.000	0.000
87	C	150	GLY	0	-0.023	-0.015	5.845	0.187	0.187	0.000	0.000	0.000	0.000
88	C	151	SER	0	-0.048	-0.012	3.056	-0.292	0.641	0.040	-0.397	-0.577	0.001
89	C	152	ARG	1	0.952	0.981	5.061	1.040	1.139	-0.001	-0.005	-0.093	0.000
90	C	153	GLN	0	0.016	0.021	6.791	-0.241	-0.241	0.000	0.000	0.000	0.000
91	C	154	THR	0	-0.038	-0.019	9.460	0.072	0.072	0.000	0.000	0.000	0.000
92	C	155	MET	0	0.031	0.045	12.316	0.057	0.057	0.000	0.000	0.000	0.000
93	C	156	PHE	0	-0.002	-0.011	13.063	-0.014	-0.014	0.000	0.000	0.000	0.000
94	C	157	TYR	0	0.003	-0.010	17.568	0.000	0.000	0.000	0.000	0.000	0.000
95	C	158	THR	0	-0.008	-0.023	21.008	0.006	0.006	0.000	0.000	0.000	0.000
96	C	159	GLU	-1	-0.859	-0.904	23.031	0.060	0.060	0.000	0.000	0.000	0.000
97	C	160	VAL	0	-0.002	0.007	24.227	0.005	0.005	0.000	0.000	0.000	0.000
98	C	161	THR	0	0.012	-0.002	27.401	-0.011	-0.011	0.000	0.000	0.000	0.000
99	C	162	ASP	-1	-0.760	-0.868	29.145	0.092	0.092	0.000	0.000	0.000	0.000
100	C	163	ALA	0	-0.026	-0.004	30.860	0.002	0.002	0.000	0.000	0.000	0.000
101	C	164	GLN	0	0.007	0.007	25.579	-0.009	-0.009	0.000	0.000	0.000	0.000
102	C	165	ARG	1	0.892	0.974	26.174	-0.094	-0.094	0.000	0.000	0.000	0.000
103	C	166	SER	0	-0.029	-0.009	25.570	-0.011	-0.011	0.000	0.000	0.000	0.000
104	C	176	GLY	0	0.017	0.006	17.387	-0.002	-0.002	0.000	0.000	0.000	0.000
105	C	177	GLU	-1	-0.988	-0.997	12.917	0.519	0.519	0.000	0.000	0.000	0.000
106	C	178	LEU	0	-0.051	-0.031	17.621	-0.005	-0.005	0.000	0.000	0.000	0.000
107	C	179	ILE	0	-0.001	0.012	15.254	-0.011	-0.011	0.000	0.000	0.000	0.000
108	C	180	GLU	-1	-0.926	-0.964	19.290	0.101	0.101	0.000	0.000	0.000	0.000
109	C	181	VAL	0	-0.003	0.007	21.476	0.004	0.004	0.000	0.000	0.000	0.000
110	C	182	VAL	0	-0.019	-0.015	22.975	-0.018	-0.018	0.000	0.000	0.000	0.000
111	C	183	HIS	0	-0.042	-0.019	24.381	0.004	0.004	0.000	0.000	0.000	0.000
112	C	184	LEU	0	0.008	0.015	25.918	-0.006	-0.006	0.000	0.000	0.000	0.000
113	C	185	PRO	0	0.029	0.013	28.247	-0.001	-0.001	0.000	0.000	0.000	0.000
114	C	186	LEU	0	0.019	-0.005	29.466	-0.003	-0.003	0.000	0.000	0.000	0.000
115	C	187	GLU	-1	-0.991	-0.988	32.013	0.030	0.030	0.000	0.000	0.000	0.000
116	C	188	GLY	0	0.003	0.008	33.125	-0.003	-0.003	0.000	0.000	0.000	0.000
117	C	189	ALA	0	-0.024	-0.008	28.351	-0.001	-0.001	0.000	0.000	0.000	0.000
118	C	190	GLN	0	-0.010	-0.020	28.765	0.000	0.000	0.000	0.000	0.000	0.000
119	C	191	ALA	0	0.039	0.016	30.358	-0.002	-0.002	0.000	0.000	0.000	0.000
120	C	192	PHE	0	0.030	0.013	24.144	-0.001	-0.001	0.000	0.000	0.000	0.000
121	C	193	ALA	0	-0.003	0.001	26.163	-0.001	-0.001	0.000	0.000	0.000	0.000
122	C	194	ASP	-1	-0.870	-0.913	26.863	0.000	0.000	0.000	0.000	0.000	0.000
123	C	195	ASP	-1	-0.916	-0.974	29.405	0.019	0.019	0.000	0.000	0.000	0.000
124	C	196	PRO	0	-0.065	-0.029	28.118	0.002	0.002	0.000	0.000	0.000	0.000
125	C	197	ASP	-1	-0.908	-0.943	28.068	0.014	0.014	0.000	0.000	0.000	0.000
126	C	198	ILE	0	-0.060	-0.023	25.411	0.007	0.007	0.000	0.000	0.000	0.000
127	C	199	PRO	0	-0.007	-0.007	22.588	-0.003	-0.003	0.000	0.000	0.000	0.000
128	C	200	LYS	1	0.809	0.893	20.753	-0.002	-0.002	0.000	0.000	0.000	0.000
129	C	201	THR	0	0.032	0.017	15.173	-0.019	-0.019	0.000	0.000	0.000	0.000
130	C	202	LEU	0	0.010	-0.002	17.535	0.004	0.004	0.000	0.000	0.000	0.000
131	C	203	GLY	0	0.028	0.013	16.448	0.000	0.000	0.000	0.000	0.000	0.000
132	C	204	VAL	0	0.038	0.030	17.411	0.012	0.012	0.000	0.000	0.000	0.000
133	C	205	ILE	0	0.013	0.018	20.229	0.001	0.001	0.000	0.000	0.000	0.000
134	C	206	PHE	0	-0.023	-0.016	18.978	-0.001	-0.001	0.000	0.000	0.000	0.000
135	C	207	GLY	0	0.033	0.010	20.696	0.003	0.003	0.000	0.000	0.000	0.000
136	C	208	VAL	0	-0.008	-0.005	21.621	0.006	0.006	0.000	0.000	0.000	0.000
137	C	209	SER	0	0.025	0.012	25.000	-0.001	-0.001	0.000	0.000	0.000	0.000
138	C	210	TRP	0	-0.028	-0.015	23.261	0.004	0.004	0.000	0.000	0.000	0.000
139	C	211	PHE	0	0.022	0.001	25.133	0.002	0.002	0.000	0.000	0.000	0.000
140	C	212	LEU	0	-0.013	-0.018	26.581	0.001	0.001	0.000	0.000	0.000	0.000
141	C	213	SER	0	-0.017	-0.019	28.870	-0.001	-0.001	0.000	0.000	0.000	0.000
142	C	214	GLN	0	-0.069	-0.014	26.547	-0.003	-0.003	0.000	0.000	0.000	0.000
143	C	215	VAL	0	-0.025	-0.014	26.467	0.004	0.004	0.000	0.000	0.000	0.000
144	C	216	ALA	0	0.021	0.013	29.667	0.000	0.000	0.000	0.000	0.000	0.000
145	C	217	PRO	0	-0.043	-0.018	32.094	0.001	0.001	0.000	0.000	0.000	0.000
146	C	218	ASN	0	-0.081	-0.043	32.191	-0.003	-0.003	0.000	0.000	0.000	0.000
147	C	219	LEU	0	-0.044	-0.003	31.551	0.002	0.002	0.000	0.000	0.000	0.000
148	C	220	ASP	-1	-0.985	-0.979	35.557	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:40:HIS)