FMO DATABASE

FMODB ID: 524MZ

Calculation Name: 3PV6-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 3PV6

Chain ID: B

ChEMBL ID:

UniProt ID: O14931

Base Structure: X-ray

Registration Date: 2023-09-19

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-854390.60345
FMO2-HF: Nuclear repulsion	811639.003665
FMO2-HF: Total energy	-42751.599785
FMO2-MP2: Total energy	-42878.02942

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:19:LEU)

Summations of interaction energy for fragment #1(B:19:LEU)

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.
-20.929	-4.772	10.46	-7.92	-18.696	-0.049

Interaction energy analysis for fragmet #1(B:19:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.016

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	21	VAL	0	0.004	-0.007	2.628	-2.864	0.227	0.644	-1.451	-2.283	-0.004
4	B	22	SER	0	-0.057	-0.017	4.642	0.218	0.294	-0.001	-0.014	-0.060	0.000
5	B	23	GLN	0	0.076	0.010	8.411	-0.126	-0.126	0.000	0.000	0.000	0.000
6	B	24	PRO	0	0.010	0.033	11.596	0.025	0.025	0.000	0.000	0.000	0.000
7	B	25	PRO	0	0.077	0.034	15.300	-0.026	-0.026	0.000	0.000	0.000	0.000
8	B	26	GLU	-1	-0.862	-0.905	17.473	-0.100	-0.100	0.000	0.000	0.000	0.000
9	B	27	ILE	0	-0.026	-0.006	18.133	0.007	0.007	0.000	0.000	0.000	0.000
10	B	28	ARG	1	0.781	0.858	20.954	0.062	0.062	0.000	0.000	0.000	0.000
11	B	29	THR	0	-0.027	-0.015	24.383	0.005	0.005	0.000	0.000	0.000	0.000
12	B	30	LEU	0	0.062	0.043	26.374	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	31	GLU	-1	-0.834	-0.937	28.999	-0.073	-0.073	0.000	0.000	0.000	0.000
14	B	32	GLY	0	-0.001	0.011	30.294	0.005	0.005	0.000	0.000	0.000	0.000
15	B	33	SER	0	-0.028	-0.005	27.545	0.003	0.003	0.000	0.000	0.000	0.000
16	B	34	SER	0	-0.049	-0.029	23.559	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	35	ALA	0	-0.024	-0.006	21.773	0.006	0.006	0.000	0.000	0.000	0.000
18	B	36	PHE	0	0.013	-0.004	18.126	-0.009	-0.009	0.000	0.000	0.000	0.000
19	B	37	LEU	0	0.003	0.006	15.208	0.009	0.009	0.000	0.000	0.000	0.000
20	B	38	PRO	0	0.015	0.002	13.519	-0.034	-0.034	0.000	0.000	0.000	0.000
21	B	39	CYS	0	-0.020	-0.008	7.976	-0.080	-0.080	0.000	0.000	0.000	0.000
22	B	40	SER	0	-0.012	0.014	7.743	0.073	0.073	0.000	0.000	0.000	0.000
23	B	41	PHE	0	0.037	0.010	2.319	-1.823	-0.610	1.531	-0.602	-2.142	-0.002
24	B	42	ASN	0	-0.007	0.002	3.717	-0.348	0.137	0.017	-0.105	-0.397	0.000
25	B	43	ALA	0	0.003	0.006	3.609	-0.049	0.631	0.030	-0.197	-0.513	-0.001
26	B	44	SER	0	-0.008	-0.023	4.548	-0.255	-0.217	0.000	-0.010	-0.027	0.000
27	B	45	GLN	0	0.008	-0.002	8.108	-0.122	-0.122	0.000	0.000	0.000	0.000
28	B	46	GLY	0	0.048	0.033	11.237	-0.054	-0.054	0.000	0.000	0.000	0.000
29	B	47	ARG	1	0.800	0.903	6.696	-0.166	-0.166	0.000	0.000	0.000	0.000
30	B	48	LEU	0	0.038	0.018	9.461	0.023	0.023	0.000	0.000	0.000	0.000
31	B	49	ALA	0	-0.025	-0.007	6.014	-0.007	-0.007	0.000	0.000	0.000	0.000
32	B	50	ILE	0	0.013	-0.005	7.720	-0.074	-0.074	0.000	0.000	0.000	0.000
33	B	51	GLY	0	0.018	-0.006	6.053	-0.086	-0.086	0.000	0.000	0.000	0.000
34	B	52	SER	0	-0.060	-0.006	6.091	0.106	0.106	0.000	0.000	0.000	0.000
35	B	53	VAL	0	0.071	0.025	5.821	-0.129	-0.129	0.000	0.000	0.000	0.000
36	B	54	THR	0	-0.112	-0.048	7.882	0.095	0.095	0.000	0.000	0.000	0.000
37	B	55	TRP	0	0.021	0.007	9.822	-0.095	-0.095	0.000	0.000	0.000	0.000
38	B	56	PHE	0	-0.040	-0.010	10.483	0.024	0.024	0.000	0.000	0.000	0.000
39	B	57	ARG	1	0.842	0.900	14.513	0.192	0.192	0.000	0.000	0.000	0.000
40	B	58	ASP	-1	-0.781	-0.865	17.929	-0.207	-0.207	0.000	0.000	0.000	0.000
41	B	59	GLU	-1	-0.873	-0.918	17.266	-0.241	-0.241	0.000	0.000	0.000	0.000
42	B	60	VAL	0	-0.011	-0.013	11.661	-0.016	-0.016	0.000	0.000	0.000	0.000
43	B	61	VAL	0	0.048	0.025	14.773	-0.014	-0.014	0.000	0.000	0.000	0.000
44	B	62	PRO	0	0.068	0.019	16.388	0.005	0.005	0.000	0.000	0.000	0.000
45	B	63	GLY	0	-0.024	-0.012	17.339	0.012	0.012	0.000	0.000	0.000	0.000
46	B	64	LYS	1	0.790	0.874	18.357	0.263	0.263	0.000	0.000	0.000	0.000
47	B	65	GLU	-1	-0.855	-0.909	13.530	-0.536	-0.536	0.000	0.000	0.000	0.000
48	B	66	VAL	0	0.016	-0.009	15.198	0.040	0.040	0.000	0.000	0.000	0.000
49	B	67	ARG	1	0.912	0.955	13.777	0.389	0.389	0.000	0.000	0.000	0.000
50	B	68	ASN	0	-0.022	-0.005	18.248	0.035	0.035	0.000	0.000	0.000	0.000
51	B	69	GLY	0	0.039	0.033	20.854	0.012	0.012	0.000	0.000	0.000	0.000
52	B	70	THR	0	0.037	0.004	22.684	0.005	0.005	0.000	0.000	0.000	0.000
53	B	71	PRO	0	0.029	-0.002	25.518	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	72	GLU	-1	-0.761	-0.862	27.370	-0.118	-0.118	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.040	0.025	19.918	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.877	0.922	20.985	0.189	0.189	0.000	0.000	0.000	0.000
57	B	75	GLY	0	-0.010	0.005	23.152	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	76	ARG	1	0.718	0.842	24.717	0.131	0.131	0.000	0.000	0.000	0.000
59	B	77	LEU	0	-0.007	0.016	18.172	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	78	ALA	0	-0.043	-0.014	19.696	0.012	0.012	0.000	0.000	0.000	0.000
61	B	79	PRO	0	-0.043	-0.019	17.123	-0.018	-0.018	0.000	0.000	0.000	0.000
62	B	80	LEU	0	0.019	0.020	10.245	0.015	0.015	0.000	0.000	0.000	0.000
63	B	81	ALA	0	0.012	0.005	14.729	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	82	SER	0	0.047	0.010	13.130	0.007	0.007	0.000	0.000	0.000	0.000
65	B	83	SER	0	0.042	0.020	12.387	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	84	ARG	1	0.833	0.891	12.479	0.091	0.091	0.000	0.000	0.000	0.000
67	B	85	PHE	0	0.024	0.041	4.630	-0.025	0.041	-0.001	-0.003	-0.063	0.000
68	B	86	LEU	0	-0.030	-0.033	8.381	0.076	0.076	0.000	0.000	0.000	0.000
69	B	87	HIS	0	0.008	-0.009	10.174	0.049	0.049	0.000	0.000	0.000	0.000
70	B	88	ASP	-1	-0.809	-0.891	10.496	0.070	0.070	0.000	0.000	0.000	0.000
71	B	89	HIS	1	0.783	0.918	5.693	-0.289	-0.289	0.000	0.000	0.000	0.000
72	B	90	GLN	0	-0.024	-0.019	7.050	-0.065	-0.065	0.000	0.000	0.000	0.000
73	B	91	ALA	0	0.021	-0.019	6.717	-0.013	-0.013	0.000	0.000	0.000	0.000
74	B	92	GLU	-1	-0.806	-0.880	8.844	-0.206	-0.206	0.000	0.000	0.000	0.000
75	B	93	LEU	0	-0.022	0.007	12.285	-0.012	-0.012	0.000	0.000	0.000	0.000
76	B	94	HIS	0	0.013	-0.006	14.828	0.017	0.017	0.000	0.000	0.000	0.000
77	B	95	ILE	0	0.006	0.008	18.396	-0.010	-0.010	0.000	0.000	0.000	0.000
78	B	96	ARG	1	0.904	0.934	21.453	0.134	0.134	0.000	0.000	0.000	0.000
79	B	97	ASP	-1	-0.807	-0.889	24.897	-0.092	-0.092	0.000	0.000	0.000	0.000
80	B	98	VAL	0	-0.030	-0.017	24.318	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	99	ARG	1	0.809	0.890	27.135	0.103	0.103	0.000	0.000	0.000	0.000
82	B	100	GLY	0	0.075	0.042	28.360	0.006	0.006	0.000	0.000	0.000	0.000
83	B	101	HIS	0	-0.031	-0.021	26.955	0.000	0.000	0.000	0.000	0.000	0.000
84	B	102	ASP	-1	-0.759	-0.862	23.480	-0.144	-0.144	0.000	0.000	0.000	0.000
85	B	103	ALA	0	0.018	0.028	23.202	-0.016	-0.016	0.000	0.000	0.000	0.000
86	B	104	SER	0	-0.022	-0.032	20.938	0.006	0.006	0.000	0.000	0.000	0.000
87	B	105	ILE	0	-0.024	0.005	17.099	0.006	0.006	0.000	0.000	0.000	0.000
88	B	106	TYR	0	-0.038	-0.037	15.527	-0.014	-0.014	0.000	0.000	0.000	0.000
89	B	107	VAL	0	0.003	0.000	10.726	0.005	0.005	0.000	0.000	0.000	0.000
90	B	109	ARG	1	0.935	0.970	6.262	0.796	0.796	0.000	0.000	0.000	0.000
91	B	110	VAL	0	-0.010	-0.017	2.294	-0.150	0.050	1.476	-0.337	-1.338	0.001
92	B	111	GLU	-1	-0.919	-0.959	2.643	-4.435	-3.097	1.165	-0.954	-1.549	-0.012
93	B	112	VAL	0	-0.004	-0.004	2.466	-0.685	0.364	2.129	-0.521	-2.657	0.000
94	B	113	LEU	0	0.049	0.023	3.770	-0.489	-0.385	0.001	0.048	-0.154	0.000
95	B	114	GLY	0	0.014	0.007	7.150	0.225	0.225	0.000	0.000	0.000	0.000
96	B	115	LEU	0	-0.068	-0.037	2.260	-0.350	0.279	1.319	-0.366	-1.583	0.002
97	B	116	GLY	0	0.027	0.026	2.863	-4.193	-1.590	0.250	-1.264	-1.589	-0.012
98	B	117	VAL	0	0.010	0.002	2.747	-2.473	-0.346	0.949	-1.009	-2.067	-0.010
99	B	118	GLY	0	0.030	0.020	2.844	-4.287	-1.972	0.937	-1.321	-1.931	-0.011
100	B	119	THR	0	-0.050	-0.046	3.416	0.927	1.070	0.014	0.186	-0.343	0.000
101	B	120	GLY	0	0.019	0.031	6.629	0.095	0.095	0.000	0.000	0.000	0.000
102	B	121	ASN	0	-0.030	-0.036	8.702	0.001	0.001	0.000	0.000	0.000	0.000
103	B	122	GLY	0	0.009	0.015	12.066	0.059	0.059	0.000	0.000	0.000	0.000
104	B	123	THR	0	-0.054	-0.033	14.116	0.018	0.018	0.000	0.000	0.000	0.000
105	B	124	ARG	1	0.870	0.923	16.524	0.107	0.107	0.000	0.000	0.000	0.000
106	B	125	LEU	0	-0.004	0.004	20.265	0.009	0.009	0.000	0.000	0.000	0.000
107	B	126	VAL	0	-0.013	-0.020	21.698	0.001	0.001	0.000	0.000	0.000	0.000
108	B	127	VAL	0	-0.012	-0.004	25.365	0.004	0.004	0.000	0.000	0.000	0.000
109	B	128	GLU	-1	-0.822	-0.888	27.497	-0.060	-0.060	0.000	0.000	0.000	0.000
110	B	129	LYS	1	0.790	0.885	30.866	0.058	0.058	0.000	0.000	0.000	0.000
111	B	130	GLU	-1	-0.861	-0.916	34.353	-0.049	-0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:19:LEU)