FMO DATABASE

FMODB ID: 6NQMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1315239.261369
FMO2-HF: Nuclear repulsion	1258504.85117
FMO2-HF: Total energy	-56734.4102
FMO2-MP2: Total energy	-56900.488363

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.
0.082	4.466	2.893	-1.866	-5.414	0

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 : 0.005 / 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	-0.015	0.014	3.829	0.475	1.797	-0.009	-0.569	-0.744	0.002
4	C	43	VAL	0	-0.028	-0.023	5.914	-0.084	-0.084	0.000	0.000	0.000	0.000
5	C	44	THR	0	0.022	0.015	9.588	0.023	0.023	0.000	0.000	0.000	0.000
6	C	45	VAL	0	0.013	-0.006	12.525	-0.020	-0.020	0.000	0.000	0.000	0.000
7	C	46	LEU	0	-0.015	0.009	16.004	-0.007	-0.007	0.000	0.000	0.000	0.000
8	C	47	LEU	0	0.037	0.013	18.958	-0.007	-0.007	0.000	0.000	0.000	0.000
9	C	48	PHE	0	0.001	0.000	22.197	-0.004	-0.004	0.000	0.000	0.000	0.000
10	C	49	ASN	0	0.028	0.005	25.852	-0.007	-0.007	0.000	0.000	0.000	0.000
11	C	50	SER	0	0.046	0.007	28.391	-0.002	-0.002	0.000	0.000	0.000	0.000
12	C	51	SER	0	-0.036	-0.013	31.635	-0.003	-0.003	0.000	0.000	0.000	0.000
13	C	52	ARG	1	0.892	0.953	30.582	-0.065	-0.065	0.000	0.000	0.000	0.000
14	C	53	ARG	1	0.949	0.992	31.890	-0.063	-0.063	0.000	0.000	0.000	0.000
15	C	54	SER	0	-0.035	-0.023	28.447	-0.001	-0.001	0.000	0.000	0.000	0.000
16	C	55	LEU	0	0.006	0.012	24.061	0.001	0.001	0.000	0.000	0.000	0.000
17	C	56	VAL	0	-0.039	-0.023	21.379	-0.006	-0.006	0.000	0.000	0.000	0.000
18	C	57	LEU	0	-0.060	-0.038	20.081	0.017	0.017	0.000	0.000	0.000	0.000
19	C	58	VAL	0	0.068	0.034	17.018	-0.018	-0.018	0.000	0.000	0.000	0.000
20	C	59	LYS	1	0.935	0.992	19.279	-0.084	-0.084	0.000	0.000	0.000	0.000
21	C	60	GLN	0	0.086	0.034	14.058	-0.018	-0.018	0.000	0.000	0.000	0.000
22	C	61	PHE	0	-0.002	0.012	19.082	0.007	0.007	0.000	0.000	0.000	0.000
23	C	62	ARG	1	0.867	0.928	11.269	-0.327	-0.327	0.000	0.000	0.000	0.000
24	C	63	PRO	0	0.044	0.002	16.103	-0.006	-0.006	0.000	0.000	0.000	0.000
25	C	64	ALA	0	-0.013	-0.004	16.407	-0.009	-0.009	0.000	0.000	0.000	0.000
26	C	65	VAL	0	0.028	0.019	18.419	-0.009	-0.009	0.000	0.000	0.000	0.000
27	C	66	TYR	0	0.024	0.002	20.683	-0.015	-0.015	0.000	0.000	0.000	0.000
28	C	67	ALA	0	-0.039	-0.011	21.705	-0.011	-0.011	0.000	0.000	0.000	0.000
29	C	68	GLY	0	0.030	0.015	22.654	-0.007	-0.007	0.000	0.000	0.000	0.000
30	C	69	GLU	-1	-0.922	-0.968	24.345	0.111	0.111	0.000	0.000	0.000	0.000
31	C	70	VAL	0	-0.044	0.005	26.716	-0.009	-0.009	0.000	0.000	0.000	0.000
32	C	71	GLU	-1	-1.018	-0.996	24.855	0.101	0.101	0.000	0.000	0.000	0.000
33	C	72	ARG	1	0.843	0.913	25.333	-0.133	-0.133	0.000	0.000	0.000	0.000
34	C	97	ALA	0	-0.007	-0.012	26.126	0.002	0.002	0.000	0.000	0.000	0.000
35	C	98	GLY	0	0.043	0.012	23.575	-0.005	-0.005	0.000	0.000	0.000	0.000
36	C	99	VAL	0	-0.057	-0.030	21.571	0.003	0.003	0.000	0.000	0.000	0.000
37	C	100	THR	0	0.009	-0.003	17.010	-0.007	-0.007	0.000	0.000	0.000	0.000
38	C	101	VAL	0	0.003	-0.001	19.270	0.000	0.000	0.000	0.000	0.000	0.000
39	C	102	GLU	-1	-0.862	-0.950	14.840	0.326	0.326	0.000	0.000	0.000	0.000
40	C	103	LEU	0	-0.025	-0.016	15.093	-0.023	-0.023	0.000	0.000	0.000	0.000
41	C	104	CYS	0	-0.024	0.011	14.495	0.021	0.021	0.000	0.000	0.000	0.000
42	C	105	ALA	0	-0.059	-0.044	10.109	0.012	0.012	0.000	0.000	0.000	0.000
43	C	106	GLY	0	0.099	0.066	8.292	-0.054	-0.054	0.000	0.000	0.000	0.000
44	C	107	LEU	0	-0.050	-0.036	2.761	-1.979	-0.288	0.312	-0.494	-1.510	0.002
45	C	108	VAL	0	-0.003	0.001	4.277	-0.916	-0.662	-0.001	-0.036	-0.217	0.000
46	C	109	ASP	-1	-0.909	-0.963	2.313	2.458	3.717	2.588	-1.460	-2.387	-0.003
47	C	110	GLN	0	-0.036	-0.025	3.023	-0.827	-1.459	0.001	0.838	-0.208	-0.001
48	C	111	PRO	0	-0.035	-0.014	6.110	0.419	0.419	0.000	0.000	0.000	0.000
49	C	112	GLY	0	-0.037	-0.021	8.141	-0.065	-0.065	0.000	0.000	0.000	0.000
50	C	113	LEU	0	0.029	0.023	9.672	-0.039	-0.039	0.000	0.000	0.000	0.000
51	C	114	SER	0	0.013	0.011	10.702	0.126	0.126	0.000	0.000	0.000	0.000
52	C	115	LEU	0	0.025	-0.003	8.751	0.025	0.025	0.000	0.000	0.000	0.000
53	C	116	GLU	-1	-0.894	-0.957	11.429	0.259	0.259	0.000	0.000	0.000	0.000
54	C	117	GLU	-1	-0.913	-0.960	13.211	0.098	0.098	0.000	0.000	0.000	0.000
55	C	118	VAL	0	-0.012	-0.008	8.556	-0.032	-0.032	0.000	0.000	0.000	0.000
56	C	119	ALA	0	-0.010	0.000	11.719	-0.016	-0.016	0.000	0.000	0.000	0.000
57	C	120	CYS	0	-0.027	-0.012	13.786	-0.038	-0.038	0.000	0.000	0.000	0.000
58	C	121	LYS	1	0.897	0.975	9.824	-0.248	-0.248	0.000	0.000	0.000	0.000
59	C	122	GLU	-1	-0.821	-0.912	10.696	0.386	0.386	0.000	0.000	0.000	0.000
60	C	123	ALA	0	-0.002	-0.013	14.250	-0.034	-0.034	0.000	0.000	0.000	0.000
61	C	124	TRP	0	-0.060	-0.026	17.420	-0.025	-0.025	0.000	0.000	0.000	0.000
62	C	125	GLU	-1	-0.955	-0.999	13.859	0.039	0.039	0.000	0.000	0.000	0.000
63	C	126	GLU	-1	-0.809	-0.893	13.175	0.293	0.293	0.000	0.000	0.000	0.000
64	C	127	CYS	0	-0.072	-0.043	17.414	-0.014	-0.014	0.000	0.000	0.000	0.000
65	C	128	GLY	0	0.002	0.020	20.320	-0.014	-0.014	0.000	0.000	0.000	0.000
66	C	129	TYR	0	-0.057	-0.080	21.306	-0.015	-0.015	0.000	0.000	0.000	0.000
67	C	130	HIS	0	0.001	0.008	21.289	0.010	0.010	0.000	0.000	0.000	0.000
68	C	131	LEU	0	-0.006	-0.013	18.770	0.003	0.003	0.000	0.000	0.000	0.000
69	C	132	ALA	0	0.011	0.007	21.568	-0.007	-0.007	0.000	0.000	0.000	0.000
70	C	133	PRO	0	0.059	0.011	18.221	0.008	0.008	0.000	0.000	0.000	0.000
71	C	134	SER	0	-0.048	-0.026	19.914	0.008	0.008	0.000	0.000	0.000	0.000
72	C	135	ASP	-1	-0.854	-0.920	22.667	0.096	0.096	0.000	0.000	0.000	0.000
73	C	136	LEU	0	-0.092	-0.025	16.681	0.005	0.005	0.000	0.000	0.000	0.000
74	C	137	ARG	1	0.990	1.004	20.670	-0.145	-0.145	0.000	0.000	0.000	0.000
75	C	138	ARG	1	0.939	0.966	15.625	-0.210	-0.210	0.000	0.000	0.000	0.000
76	C	139	VAL	0	-0.062	-0.031	18.101	-0.016	-0.016	0.000	0.000	0.000	0.000
77	C	140	ALA	0	0.004	-0.012	17.362	-0.010	-0.010	0.000	0.000	0.000	0.000
78	C	141	THR	0	-0.080	-0.020	11.648	0.013	0.013	0.000	0.000	0.000	0.000
79	C	142	TYR	0	-0.060	-0.064	12.021	-0.035	-0.035	0.000	0.000	0.000	0.000
80	C	143	TRP	0	0.012	0.001	6.293	-0.042	-0.042	0.000	0.000	0.000	0.000
81	C	144	SER	0	-0.007	-0.002	8.757	-0.072	-0.072	0.000	0.000	0.000	0.000
82	C	145	GLY	0	0.061	0.024	8.433	0.297	0.297	0.000	0.000	0.000	0.000
83	C	146	VAL	0	-0.037	-0.020	9.660	-0.109	-0.109	0.000	0.000	0.000	0.000
84	C	147	GLY	0	0.046	0.028	9.354	-0.159	-0.159	0.000	0.000	0.000	0.000
85	C	148	LEU	0	-0.057	-0.050	6.398	-0.172	-0.172	0.000	0.000	0.000	0.000
86	C	149	THR	0	0.006	0.007	5.536	1.083	1.083	0.000	0.000	0.000	0.000
87	C	150	GLY	0	-0.069	-0.004	7.187	-0.129	-0.129	0.000	0.000	0.000	0.000
88	C	151	SER	0	0.023	0.011	3.706	0.135	0.625	0.002	-0.145	-0.348	0.000
89	C	152	ARG	1	0.985	1.010	4.844	-0.558	-0.558	0.000	0.000	0.000	0.000
90	C	153	GLN	0	0.052	0.033	6.624	-0.257	-0.257	0.000	0.000	0.000	0.000
91	C	154	THR	0	-0.041	-0.028	9.226	-0.017	-0.017	0.000	0.000	0.000	0.000
92	C	155	MET	0	0.037	0.040	12.064	0.028	0.028	0.000	0.000	0.000	0.000
93	C	156	PHE	0	0.006	-0.010	13.094	-0.027	-0.027	0.000	0.000	0.000	0.000
94	C	157	TYR	0	0.023	-0.007	17.157	0.001	0.001	0.000	0.000	0.000	0.000
95	C	158	THR	0	-0.006	-0.004	20.605	-0.008	-0.008	0.000	0.000	0.000	0.000
96	C	159	GLU	-1	-0.919	-0.943	22.986	0.090	0.090	0.000	0.000	0.000	0.000
97	C	160	VAL	0	0.024	0.008	23.954	-0.002	-0.002	0.000	0.000	0.000	0.000
98	C	161	THR	0	0.008	-0.006	27.222	-0.005	-0.005	0.000	0.000	0.000	0.000
99	C	162	ASP	-1	-0.842	-0.945	29.120	0.061	0.061	0.000	0.000	0.000	0.000
100	C	163	ALA	0	-0.057	-0.014	30.761	-0.003	-0.003	0.000	0.000	0.000	0.000
101	C	164	GLN	0	-0.048	-0.029	25.423	-0.004	-0.004	0.000	0.000	0.000	0.000
102	C	165	ARG	1	0.931	0.978	26.141	-0.058	-0.058	0.000	0.000	0.000	0.000
103	C	166	SER	0	-0.028	-0.001	25.562	-0.013	-0.013	0.000	0.000	0.000	0.000
104	C	176	GLY	0	-0.022	-0.027	18.117	-0.013	-0.013	0.000	0.000	0.000	0.000
105	C	177	GLU	-1	-0.961	-0.964	13.566	0.126	0.126	0.000	0.000	0.000	0.000
106	C	178	LEU	0	-0.040	-0.026	17.778	0.001	0.001	0.000	0.000	0.000	0.000
107	C	179	ILE	0	0.029	0.017	15.525	0.017	0.017	0.000	0.000	0.000	0.000
108	C	180	GLU	-1	-0.978	-0.975	19.586	0.042	0.042	0.000	0.000	0.000	0.000
109	C	181	VAL	0	0.010	0.005	21.748	0.015	0.015	0.000	0.000	0.000	0.000
110	C	182	VAL	0	-0.025	-0.024	22.851	-0.011	-0.011	0.000	0.000	0.000	0.000
111	C	183	HIS	0	-0.023	0.016	24.233	0.008	0.008	0.000	0.000	0.000	0.000
112	C	184	LEU	0	0.012	0.016	25.983	-0.008	-0.008	0.000	0.000	0.000	0.000
113	C	185	PRO	0	0.014	0.001	27.975	0.003	0.003	0.000	0.000	0.000	0.000
114	C	186	LEU	0	0.024	0.000	29.286	0.004	0.004	0.000	0.000	0.000	0.000
115	C	187	GLU	-1	-0.971	-0.977	31.684	0.066	0.066	0.000	0.000	0.000	0.000
116	C	188	GLY	0	0.016	0.011	33.272	-0.001	-0.001	0.000	0.000	0.000	0.000
117	C	189	ALA	0	-0.011	-0.003	28.216	0.004	0.004	0.000	0.000	0.000	0.000
118	C	190	GLN	0	-0.001	-0.010	28.679	0.009	0.009	0.000	0.000	0.000	0.000
119	C	191	ALA	0	0.026	0.007	30.329	0.003	0.003	0.000	0.000	0.000	0.000
120	C	192	PHE	0	0.034	0.021	24.060	0.001	0.001	0.000	0.000	0.000	0.000
121	C	193	ALA	0	0.003	0.001	25.999	0.007	0.007	0.000	0.000	0.000	0.000
122	C	194	ASP	-1	-0.919	-0.963	26.633	0.130	0.130	0.000	0.000	0.000	0.000
123	C	195	ASP	-1	-0.858	-0.939	29.384	0.100	0.100	0.000	0.000	0.000	0.000
124	C	196	PRO	0	-0.099	-0.037	27.511	0.007	0.007	0.000	0.000	0.000	0.000
125	C	197	ASP	-1	-0.905	-0.936	27.867	0.096	0.096	0.000	0.000	0.000	0.000
126	C	198	ILE	0	-0.091	-0.042	25.317	-0.002	-0.002	0.000	0.000	0.000	0.000
127	C	199	PRO	0	0.007	-0.006	22.188	0.012	0.012	0.000	0.000	0.000	0.000
128	C	200	LYS	1	0.817	0.907	20.605	-0.143	-0.143	0.000	0.000	0.000	0.000
129	C	201	THR	0	0.016	0.011	15.172	0.012	0.012	0.000	0.000	0.000	0.000
130	C	202	LEU	0	0.034	0.007	16.899	-0.014	-0.014	0.000	0.000	0.000	0.000
131	C	203	GLY	0	0.040	0.028	16.113	-0.015	-0.015	0.000	0.000	0.000	0.000
132	C	204	VAL	0	0.024	0.033	17.055	-0.018	-0.018	0.000	0.000	0.000	0.000
133	C	205	ILE	0	0.020	0.015	19.783	-0.013	-0.013	0.000	0.000	0.000	0.000
134	C	206	PHE	0	-0.027	-0.027	18.496	-0.014	-0.014	0.000	0.000	0.000	0.000
135	C	207	GLY	0	0.030	0.004	20.157	-0.014	-0.014	0.000	0.000	0.000	0.000
136	C	208	VAL	0	-0.007	-0.010	21.314	-0.014	-0.014	0.000	0.000	0.000	0.000
137	C	209	SER	0	0.008	0.002	24.315	-0.014	-0.014	0.000	0.000	0.000	0.000
138	C	210	TRP	0	-0.017	-0.016	22.944	-0.008	-0.008	0.000	0.000	0.000	0.000
139	C	211	PHE	0	0.016	-0.004	24.874	-0.008	-0.008	0.000	0.000	0.000	0.000
140	C	212	LEU	0	-0.020	-0.016	26.322	-0.010	-0.010	0.000	0.000	0.000	0.000
141	C	213	SER	0	-0.005	-0.010	28.607	-0.005	-0.005	0.000	0.000	0.000	0.000
142	C	214	GLN	0	-0.087	-0.023	26.471	-0.007	-0.007	0.000	0.000	0.000	0.000
143	C	215	VAL	0	-0.054	-0.028	26.259	-0.003	-0.003	0.000	0.000	0.000	0.000
144	C	216	ALA	0	0.003	0.001	29.534	-0.006	-0.006	0.000	0.000	0.000	0.000
145	C	217	PRO	0	-0.018	-0.011	32.063	-0.006	-0.006	0.000	0.000	0.000	0.000
146	C	218	ASN	0	-0.052	-0.024	31.859	-0.007	-0.007	0.000	0.000	0.000	0.000
147	C	219	LEU	0	-0.070	-0.017	31.754	-0.002	-0.002	0.000	0.000	0.000	0.000
148	C	220	ASP	-1	-0.964	-0.963	35.518	0.059	0.059	0.000	0.000	0.000	0.000

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