FMO DATABASE

FMODB ID: 4942N

Calculation Name: 3Q91-B-Xray372

Preferred Name: Uridine diphosphate glucose pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q91

Chain ID: B

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1140388.386394
FMO2-HF: Nuclear repulsion	1088817.702501
FMO2-HF: Total energy	-51570.683893
FMO2-MP2: Total energy	-51721.204137

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(B:40:HIS)

Summations of interaction energy for fragment #1(B: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.
-42.292	-36.356	11.305	-7.05	-10.189	-0.054

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.013

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	B	42	SER	0	-0.023	-0.014	2.902	-5.772	-2.874	0.235	-1.542	-1.592	-0.004
4	B	43	VAL	0	-0.022	-0.013	5.481	0.817	0.817	0.000	0.000	0.000	0.000
5	B	44	THR	0	0.021	0.010	9.163	-0.159	-0.159	0.000	0.000	0.000	0.000
6	B	45	VAL	0	-0.012	-0.013	12.340	0.127	0.127	0.000	0.000	0.000	0.000
7	B	46	LEU	0	-0.007	0.019	15.878	-0.012	-0.012	0.000	0.000	0.000	0.000
8	B	47	LEU	0	0.030	0.011	18.678	0.029	0.029	0.000	0.000	0.000	0.000
9	B	48	PHE	0	0.004	0.000	21.991	0.018	0.018	0.000	0.000	0.000	0.000
10	B	49	ASN	0	0.017	-0.016	25.761	0.026	0.026	0.000	0.000	0.000	0.000
11	B	50	SER	0	0.021	-0.024	28.192	0.022	0.022	0.000	0.000	0.000	0.000
12	B	51	SER	0	-0.048	-0.035	31.288	0.009	0.009	0.000	0.000	0.000	0.000
13	B	52	ARG	1	0.815	0.894	30.824	0.278	0.278	0.000	0.000	0.000	0.000
14	B	53	ARG	1	0.836	0.914	31.692	0.147	0.147	0.000	0.000	0.000	0.000
15	B	54	SER	0	-0.010	-0.009	28.728	0.015	0.015	0.000	0.000	0.000	0.000
16	B	55	LEU	0	-0.014	-0.001	24.189	-0.015	-0.015	0.000	0.000	0.000	0.000
17	B	56	VAL	0	-0.051	-0.021	21.538	0.004	0.004	0.000	0.000	0.000	0.000
18	B	57	LEU	0	-0.024	-0.017	20.232	0.001	0.001	0.000	0.000	0.000	0.000
19	B	58	VAL	0	0.052	0.026	16.438	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	59	LYS	1	0.855	0.935	19.558	0.443	0.443	0.000	0.000	0.000	0.000
21	B	60	GLN	0	-0.023	-0.020	13.359	-0.092	-0.092	0.000	0.000	0.000	0.000
22	B	97	ALA	0	0.016	-0.013	27.899	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	98	GLY	0	-0.020	0.003	23.649	0.018	0.018	0.000	0.000	0.000	0.000
24	B	99	VAL	0	-0.034	-0.023	22.311	-0.040	-0.040	0.000	0.000	0.000	0.000
25	B	100	THR	0	-0.019	-0.013	18.230	0.045	0.045	0.000	0.000	0.000	0.000
26	B	101	VAL	0	-0.002	0.003	20.438	-0.052	-0.052	0.000	0.000	0.000	0.000
27	B	102	GLU	-1	-0.850	-0.927	15.049	-0.564	-0.564	0.000	0.000	0.000	0.000
28	B	103	LEU	0	-0.034	-0.021	15.036	0.023	0.023	0.000	0.000	0.000	0.000
29	B	104	CYS	0	-0.041	-0.014	14.660	-0.059	-0.059	0.000	0.000	0.000	0.000
30	B	105	ALA	0	-0.029	-0.035	10.392	0.127	0.127	0.000	0.000	0.000	0.000
31	B	106	GLY	0	0.064	0.051	7.950	-0.069	-0.069	0.000	0.000	0.000	0.000
32	B	107	LEU	0	-0.018	-0.018	2.262	-1.394	0.119	1.802	-0.943	-2.372	0.003
33	B	108	VAL	0	-0.033	-0.020	3.715	-0.250	0.113	0.001	-0.075	-0.289	0.000
34	B	109	ASP	-1	-0.919	-0.959	1.899	-31.652	-31.240	9.243	-4.771	-4.884	-0.052
35	B	110	GLN	0	-0.007	0.004	3.313	0.361	0.061	0.025	0.629	-0.353	-0.001
36	B	111	PRO	0	-0.035	-0.034	5.611	1.293	1.293	0.000	0.000	0.000	0.000
37	B	112	GLY	0	-0.023	-0.017	7.953	0.011	0.011	0.000	0.000	0.000	0.000
38	B	113	LEU	0	0.001	0.023	9.081	0.123	0.123	0.000	0.000	0.000	0.000
39	B	114	SER	0	-0.059	-0.063	10.616	0.144	0.144	0.000	0.000	0.000	0.000
40	B	115	LEU	0	0.007	-0.004	8.769	-0.230	-0.230	0.000	0.000	0.000	0.000
41	B	116	GLU	-1	-0.782	-0.878	11.217	-0.505	-0.505	0.000	0.000	0.000	0.000
42	B	117	GLU	-1	-0.851	-0.928	13.167	-0.853	-0.853	0.000	0.000	0.000	0.000
43	B	118	VAL	0	-0.012	0.000	7.522	-0.075	-0.075	0.000	0.000	0.000	0.000
44	B	119	ALA	0	-0.001	0.000	10.776	-0.043	-0.043	0.000	0.000	0.000	0.000
45	B	120	CYS	0	-0.058	-0.029	13.070	0.089	0.089	0.000	0.000	0.000	0.000
46	B	121	LYS	1	0.778	0.881	9.384	2.537	2.537	0.000	0.000	0.000	0.000
47	B	122	GLU	-1	-0.786	-0.883	9.117	-2.577	-2.577	0.000	0.000	0.000	0.000
48	B	123	ALA	0	0.012	-0.007	13.276	0.137	0.137	0.000	0.000	0.000	0.000
49	B	124	TRP	0	-0.038	-0.011	16.713	0.148	0.148	0.000	0.000	0.000	0.000
50	B	125	GLU	-1	-0.905	-0.963	13.147	-1.769	-1.769	0.000	0.000	0.000	0.000
51	B	126	GLU	-1	-0.787	-0.883	13.729	-1.174	-1.174	0.000	0.000	0.000	0.000
52	B	127	CYS	0	-0.078	-0.040	16.587	0.135	0.135	0.000	0.000	0.000	0.000
53	B	128	GLY	0	-0.013	0.018	19.606	0.084	0.084	0.000	0.000	0.000	0.000
54	B	129	TYR	0	-0.045	-0.042	20.517	0.103	0.103	0.000	0.000	0.000	0.000
55	B	130	HIS	0	-0.020	-0.006	20.389	-0.091	-0.091	0.000	0.000	0.000	0.000
56	B	131	LEU	0	-0.015	-0.022	18.359	0.055	0.055	0.000	0.000	0.000	0.000
57	B	132	ALA	0	-0.010	-0.001	20.537	-0.051	-0.051	0.000	0.000	0.000	0.000
58	B	133	PRO	0	0.046	-0.002	17.336	0.033	0.033	0.000	0.000	0.000	0.000
59	B	134	SER	0	-0.083	-0.047	19.350	0.042	0.042	0.000	0.000	0.000	0.000
60	B	135	ASP	-1	-0.839	-0.902	22.090	-0.333	-0.333	0.000	0.000	0.000	0.000
61	B	136	LEU	0	-0.040	-0.009	16.287	0.023	0.023	0.000	0.000	0.000	0.000
62	B	137	ARG	1	0.927	0.968	19.656	0.105	0.105	0.000	0.000	0.000	0.000
63	B	138	ARG	1	0.951	0.977	15.380	-0.173	-0.173	0.000	0.000	0.000	0.000
64	B	139	VAL	0	-0.053	-0.027	17.705	0.045	0.045	0.000	0.000	0.000	0.000
65	B	140	ALA	0	-0.009	-0.005	16.564	0.059	0.059	0.000	0.000	0.000	0.000
66	B	141	THR	0	-0.078	-0.052	11.946	0.023	0.023	0.000	0.000	0.000	0.000
67	B	142	TYR	0	-0.060	-0.038	12.179	0.067	0.067	0.000	0.000	0.000	0.000
68	B	143	TRP	0	0.004	0.003	5.897	-0.029	-0.029	0.000	0.000	0.000	0.000
69	B	144	SER	0	0.041	0.019	8.730	-0.188	-0.188	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.036	0.017	8.280	0.372	0.372	0.000	0.000	0.000	0.000
71	B	146	VAL	0	-0.067	-0.043	9.403	0.032	0.032	0.000	0.000	0.000	0.000
72	B	147	GLY	0	0.080	0.037	9.031	-0.200	-0.200	0.000	0.000	0.000	0.000
73	B	148	LEU	0	-0.051	-0.038	8.719	0.296	0.296	0.000	0.000	0.000	0.000
74	B	149	THR	0	0.005	0.008	3.854	-0.355	-0.137	0.001	-0.039	-0.179	0.000
75	B	150	GLY	0	-0.066	-0.027	5.175	0.937	0.947	-0.001	-0.003	-0.005	0.000
76	B	151	SER	0	0.006	0.005	3.905	0.006	0.687	0.000	-0.294	-0.388	0.000
77	B	152	ARG	1	0.931	0.983	4.818	-2.100	-1.959	-0.001	-0.012	-0.127	0.000
78	B	153	GLN	0	0.031	0.040	6.438	-0.562	-0.562	0.000	0.000	0.000	0.000
79	B	154	THR	0	-0.028	-0.014	8.915	0.340	0.340	0.000	0.000	0.000	0.000
80	B	155	MET	0	0.017	0.038	11.555	-0.170	-0.170	0.000	0.000	0.000	0.000
81	B	156	PHE	0	0.007	-0.012	12.291	0.120	0.120	0.000	0.000	0.000	0.000
82	B	157	TYR	0	0.034	0.007	16.898	-0.025	-0.025	0.000	0.000	0.000	0.000
83	B	158	THR	0	0.028	0.004	20.343	0.012	0.012	0.000	0.000	0.000	0.000
84	B	159	GLU	-1	-0.878	-0.908	22.706	-0.196	-0.196	0.000	0.000	0.000	0.000
85	B	160	VAL	0	-0.003	0.001	23.491	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	161	THR	0	0.011	-0.009	26.711	0.029	0.029	0.000	0.000	0.000	0.000
87	B	162	ASP	-1	-0.753	-0.860	28.393	-0.333	-0.333	0.000	0.000	0.000	0.000
88	B	163	ALA	0	-0.035	-0.010	30.311	-0.010	-0.010	0.000	0.000	0.000	0.000
89	B	164	GLN	0	-0.007	0.012	25.375	0.018	0.018	0.000	0.000	0.000	0.000
90	B	165	ARG	1	0.864	0.935	25.030	0.345	0.345	0.000	0.000	0.000	0.000
91	B	166	SER	0	0.025	0.024	24.041	0.034	0.034	0.000	0.000	0.000	0.000
92	B	167	GLY	0	-0.046	-0.022	26.096	0.034	0.034	0.000	0.000	0.000	0.000
93	B	178	LEU	0	-0.023	-0.009	17.189	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	179	ILE	0	0.001	0.005	15.346	0.039	0.039	0.000	0.000	0.000	0.000
95	B	180	GLU	-1	-0.899	-0.948	19.229	-0.402	-0.402	0.000	0.000	0.000	0.000
96	B	181	VAL	0	0.019	0.015	20.954	0.012	0.012	0.000	0.000	0.000	0.000
97	B	182	VAL	0	-0.009	-0.005	22.557	0.051	0.051	0.000	0.000	0.000	0.000
98	B	183	HIS	0	-0.041	-0.024	24.451	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	184	LEU	0	0.018	0.020	26.069	0.017	0.017	0.000	0.000	0.000	0.000
100	B	185	PRO	0	0.023	0.012	28.292	0.006	0.006	0.000	0.000	0.000	0.000
101	B	186	LEU	0	0.029	-0.003	28.867	0.011	0.011	0.000	0.000	0.000	0.000
102	B	187	GLU	-1	-0.996	-0.988	31.604	-0.099	-0.099	0.000	0.000	0.000	0.000
103	B	188	GLY	0	0.016	0.014	33.333	0.011	0.011	0.000	0.000	0.000	0.000
104	B	189	ALA	0	-0.036	-0.019	28.169	0.002	0.002	0.000	0.000	0.000	0.000
105	B	190	GLN	0	-0.028	-0.031	28.788	-0.005	-0.005	0.000	0.000	0.000	0.000
106	B	191	ALA	0	0.044	0.020	30.150	0.004	0.004	0.000	0.000	0.000	0.000
107	B	192	PHE	0	0.006	-0.001	24.874	0.000	0.000	0.000	0.000	0.000	0.000
108	B	193	ALA	0	-0.014	-0.020	26.003	-0.008	-0.008	0.000	0.000	0.000	0.000
109	B	194	ASP	-1	-0.890	-0.945	27.074	-0.026	-0.026	0.000	0.000	0.000	0.000
110	B	195	ASP	-1	-0.891	-0.939	29.779	-0.078	-0.078	0.000	0.000	0.000	0.000
111	B	196	PRO	0	-0.052	-0.016	28.565	-0.009	-0.009	0.000	0.000	0.000	0.000
112	B	197	ASP	-1	-0.912	-0.954	28.338	-0.060	-0.060	0.000	0.000	0.000	0.000
113	B	198	ILE	0	-0.039	-0.005	26.030	-0.024	-0.024	0.000	0.000	0.000	0.000
114	B	199	PRO	0	-0.025	-0.020	23.253	0.009	0.009	0.000	0.000	0.000	0.000
115	B	200	LYS	1	0.832	0.929	21.528	0.075	0.075	0.000	0.000	0.000	0.000
116	B	201	THR	0	0.029	0.014	15.777	0.036	0.036	0.000	0.000	0.000	0.000
117	B	202	LEU	0	0.011	-0.008	17.609	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	203	GLY	0	0.030	0.015	16.408	0.017	0.017	0.000	0.000	0.000	0.000
119	B	204	VAL	0	0.042	0.032	17.337	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	205	ILE	0	0.014	0.014	20.310	0.014	0.014	0.000	0.000	0.000	0.000
121	B	206	PHE	0	-0.022	-0.016	18.832	0.023	0.023	0.000	0.000	0.000	0.000
122	B	207	GLY	0	0.028	0.008	20.512	0.010	0.010	0.000	0.000	0.000	0.000
123	B	208	VAL	0	-0.001	0.000	21.429	0.002	0.002	0.000	0.000	0.000	0.000
124	B	209	SER	0	0.015	0.016	24.929	0.015	0.015	0.000	0.000	0.000	0.000
125	B	210	TRP	0	0.009	0.010	22.895	0.001	0.001	0.000	0.000	0.000	0.000
126	B	211	PHE	0	0.049	0.009	24.771	0.007	0.007	0.000	0.000	0.000	0.000
127	B	212	LEU	0	-0.019	-0.024	26.210	0.005	0.005	0.000	0.000	0.000	0.000
128	B	213	SER	0	-0.048	-0.023	28.005	0.016	0.016	0.000	0.000	0.000	0.000
129	B	214	GLN	0	-0.073	-0.036	25.703	0.019	0.019	0.000	0.000	0.000	0.000
130	B	215	VAL	0	-0.032	-0.019	26.009	-0.004	-0.004	0.000	0.000	0.000	0.000
131	B	216	ALA	0	0.004	0.011	29.156	0.003	0.003	0.000	0.000	0.000	0.000
132	B	217	PRO	0	-0.032	-0.008	31.530	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	218	ASN	0	-0.091	-0.038	31.823	0.013	0.013	0.000	0.000	0.000	0.000
134	B	219	LEU	0	-0.017	0.000	30.865	-0.006	-0.006	0.000	0.000	0.000	0.000
135	B	220	ASP	-1	-0.858	-0.895	34.551	-0.106	-0.106	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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