FMO DATABASE

FMODB ID: K9JN3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-853887.027565
FMO2-HF: Nuclear repulsion	811136.787741
FMO2-HF: Total energy	-42750.239824
FMO2-MP2: Total energy	-42876.814695

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.
-17.764	-3.576	10.473	-7.322	-17.337	-0.037

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 : -0.029 / q_NPA : -0.021

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	0.013	-0.003	2.779	-1.651	0.953	0.261	-1.084	-1.781	-0.001
4	B	22	SER	0	-0.056	-0.014	4.792	0.123	0.192	-0.001	-0.010	-0.058	0.000
5	B	23	GLN	0	0.085	0.027	8.440	-0.096	-0.096	0.000	0.000	0.000	0.000
6	B	24	PRO	0	0.012	0.027	11.508	0.023	0.023	0.000	0.000	0.000	0.000
7	B	25	PRO	0	0.067	0.036	15.195	-0.031	-0.031	0.000	0.000	0.000	0.000
8	B	26	GLU	-1	-0.964	-0.982	17.453	-0.133	-0.133	0.000	0.000	0.000	0.000
9	B	27	ILE	0	0.015	0.018	18.357	0.009	0.009	0.000	0.000	0.000	0.000
10	B	28	ARG	1	0.910	0.978	21.150	0.082	0.082	0.000	0.000	0.000	0.000
11	B	29	THR	0	-0.005	-0.004	24.142	0.009	0.009	0.000	0.000	0.000	0.000
12	B	30	LEU	0	0.056	0.029	26.104	0.001	0.001	0.000	0.000	0.000	0.000
13	B	31	GLU	-1	-0.902	-0.955	29.007	-0.091	-0.091	0.000	0.000	0.000	0.000
14	B	32	GLY	0	0.009	0.026	29.903	0.007	0.007	0.000	0.000	0.000	0.000
15	B	33	SER	0	-0.034	-0.038	27.351	0.004	0.004	0.000	0.000	0.000	0.000
16	B	34	SER	0	-0.047	-0.015	23.398	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	35	ALA	0	-0.011	0.011	21.193	0.006	0.006	0.000	0.000	0.000	0.000
18	B	36	PHE	0	0.005	-0.007	18.212	-0.010	-0.010	0.000	0.000	0.000	0.000
19	B	37	LEU	0	-0.015	-0.014	15.359	0.006	0.006	0.000	0.000	0.000	0.000
20	B	38	PRO	0	0.017	0.007	13.662	-0.031	-0.031	0.000	0.000	0.000	0.000
21	B	39	CYS	0	-0.005	0.012	8.016	-0.087	-0.087	0.000	0.000	0.000	0.000
22	B	40	SER	0	-0.042	0.010	7.738	0.086	0.086	0.000	0.000	0.000	0.000
23	B	41	PHE	0	0.029	0.011	2.498	-1.974	-0.452	0.754	-0.517	-1.760	-0.002
24	B	42	ASN	0	-0.020	-0.014	3.757	-0.316	0.085	0.007	-0.087	-0.321	0.000
25	B	43	ALA	0	0.038	0.028	3.053	-0.469	0.762	0.176	-0.562	-0.844	-0.005
26	B	44	SER	0	-0.031	-0.031	4.724	-0.218	-0.194	-0.001	-0.007	-0.016	0.000
27	B	45	GLN	0	-0.001	-0.004	8.225	-0.132	-0.132	0.000	0.000	0.000	0.000
28	B	46	GLY	0	0.060	0.038	11.138	-0.061	-0.061	0.000	0.000	0.000	0.000
29	B	47	ARG	1	0.880	0.957	6.299	-0.576	-0.576	0.000	0.000	0.000	0.000
30	B	48	LEU	0	0.031	0.019	9.689	0.008	0.008	0.000	0.000	0.000	0.000
31	B	49	ALA	0	-0.041	-0.026	5.731	0.036	0.036	0.000	0.000	0.000	0.000
32	B	50	ILE	0	0.024	0.009	7.563	-0.086	-0.086	0.000	0.000	0.000	0.000
33	B	51	GLY	0	0.036	0.005	6.350	-0.062	-0.062	0.000	0.000	0.000	0.000
34	B	52	SER	0	-0.048	-0.001	6.509	0.101	0.101	0.000	0.000	0.000	0.000
35	B	53	VAL	0	0.048	0.017	6.130	-0.170	-0.170	0.000	0.000	0.000	0.000
36	B	54	THR	0	-0.050	-0.018	8.089	0.134	0.134	0.000	0.000	0.000	0.000
37	B	55	TRP	0	0.018	0.000	9.726	-0.123	-0.123	0.000	0.000	0.000	0.000
38	B	56	PHE	0	-0.041	-0.024	10.579	0.039	0.039	0.000	0.000	0.000	0.000
39	B	57	ARG	1	0.846	0.901	14.672	0.214	0.214	0.000	0.000	0.000	0.000
40	B	58	ASP	-1	-0.805	-0.891	17.886	-0.238	-0.238	0.000	0.000	0.000	0.000
41	B	59	GLU	-1	-0.932	-0.960	17.645	-0.289	-0.289	0.000	0.000	0.000	0.000
42	B	60	VAL	0	-0.031	-0.024	11.774	-0.018	-0.018	0.000	0.000	0.000	0.000
43	B	61	VAL	0	0.012	0.013	15.013	-0.020	-0.020	0.000	0.000	0.000	0.000
44	B	62	PRO	0	0.106	0.046	16.548	0.009	0.009	0.000	0.000	0.000	0.000
45	B	63	GLY	0	-0.033	-0.018	17.484	0.013	0.013	0.000	0.000	0.000	0.000
46	B	64	LYS	1	0.918	0.955	17.843	0.282	0.282	0.000	0.000	0.000	0.000
47	B	65	GLU	-1	-0.925	-0.952	14.327	-0.474	-0.474	0.000	0.000	0.000	0.000
48	B	66	VAL	0	0.075	0.023	15.893	0.042	0.042	0.000	0.000	0.000	0.000
49	B	67	ARG	1	0.845	0.921	14.453	0.361	0.361	0.000	0.000	0.000	0.000
50	B	68	ASN	0	0.016	0.006	18.410	0.037	0.037	0.000	0.000	0.000	0.000
51	B	69	GLY	0	-0.008	0.011	20.924	0.010	0.010	0.000	0.000	0.000	0.000
52	B	70	THR	0	0.025	0.010	23.099	0.006	0.006	0.000	0.000	0.000	0.000
53	B	71	PRO	0	0.043	0.002	25.468	-0.007	-0.007	0.000	0.000	0.000	0.000
54	B	72	GLU	-1	-0.823	-0.906	27.117	-0.132	-0.132	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.024	0.022	20.171	0.000	0.000	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.907	0.951	21.065	0.192	0.192	0.000	0.000	0.000	0.000
57	B	75	GLY	0	-0.021	0.002	22.948	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	76	ARG	1	0.730	0.832	24.883	0.143	0.143	0.000	0.000	0.000	0.000
59	B	77	LEU	0	-0.032	0.005	18.855	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	78	ALA	0	-0.065	-0.024	19.823	0.009	0.009	0.000	0.000	0.000	0.000
61	B	79	PRO	0	-0.030	-0.021	17.549	-0.018	-0.018	0.000	0.000	0.000	0.000
62	B	80	LEU	0	0.023	0.030	10.553	0.008	0.008	0.000	0.000	0.000	0.000
63	B	81	ALA	0	0.004	0.000	14.924	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	82	SER	0	0.068	0.011	13.012	0.001	0.001	0.000	0.000	0.000	0.000
65	B	83	SER	0	0.029	0.017	12.619	0.009	0.009	0.000	0.000	0.000	0.000
66	B	84	ARG	1	0.842	0.897	12.654	0.074	0.074	0.000	0.000	0.000	0.000
67	B	85	PHE	0	0.010	0.017	4.868	0.052	0.052	0.000	0.000	0.000	0.000
68	B	86	LEU	0	-0.047	-0.047	8.634	0.085	0.085	0.000	0.000	0.000	0.000
69	B	87	HIS	0	-0.026	-0.032	9.940	0.066	0.066	0.000	0.000	0.000	0.000
70	B	88	ASP	-1	-0.819	-0.898	10.777	0.118	0.118	0.000	0.000	0.000	0.000
71	B	89	HIS	1	0.774	0.906	6.149	-0.379	-0.379	0.000	0.000	0.000	0.000
72	B	90	GLN	0	0.025	0.003	7.640	-0.091	-0.091	0.000	0.000	0.000	0.000
73	B	91	ALA	0	0.006	-0.030	7.141	0.003	0.003	0.000	0.000	0.000	0.000
74	B	92	GLU	-1	-0.825	-0.876	9.218	-0.177	-0.177	0.000	0.000	0.000	0.000
75	B	93	LEU	0	0.006	0.022	12.572	-0.009	-0.009	0.000	0.000	0.000	0.000
76	B	94	HIS	0	-0.011	-0.016	14.965	0.012	0.012	0.000	0.000	0.000	0.000
77	B	95	ILE	0	0.020	0.018	18.516	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	96	ARG	1	0.945	0.960	21.473	0.129	0.129	0.000	0.000	0.000	0.000
79	B	97	ASP	-1	-0.911	-0.960	24.796	-0.097	-0.097	0.000	0.000	0.000	0.000
80	B	98	VAL	0	-0.027	-0.028	24.535	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	99	ARG	1	0.976	0.972	26.726	0.111	0.111	0.000	0.000	0.000	0.000
82	B	100	GLY	0	0.096	0.060	27.976	0.006	0.006	0.000	0.000	0.000	0.000
83	B	101	HIS	0	-0.035	-0.008	27.075	0.000	0.000	0.000	0.000	0.000	0.000
84	B	102	ASP	-1	-0.786	-0.866	23.745	-0.162	-0.162	0.000	0.000	0.000	0.000
85	B	103	ALA	0	0.003	0.017	23.247	-0.018	-0.018	0.000	0.000	0.000	0.000
86	B	104	SER	0	-0.001	-0.020	20.637	0.006	0.006	0.000	0.000	0.000	0.000
87	B	105	ILE	0	-0.027	0.004	16.888	0.008	0.008	0.000	0.000	0.000	0.000
88	B	106	TYR	0	-0.080	-0.067	15.397	-0.023	-0.023	0.000	0.000	0.000	0.000
89	B	107	VAL	0	0.021	0.011	10.681	-0.010	-0.010	0.000	0.000	0.000	0.000
90	B	109	ARG	1	1.006	1.005	5.951	0.987	0.987	0.000	0.000	0.000	0.000
91	B	110	VAL	0	-0.027	-0.016	2.263	-0.068	-0.067	1.739	-0.361	-1.379	0.001
92	B	111	GLU	-1	-0.910	-0.952	2.622	-4.229	-2.952	1.016	-0.893	-1.400	-0.011
93	B	112	VAL	0	-0.023	-0.003	2.367	-0.467	0.543	2.133	-0.649	-2.494	0.001
94	B	113	LEU	0	0.056	0.010	3.815	-0.453	-0.347	-0.001	0.036	-0.141	0.000
95	B	114	GLY	0	-0.032	-0.025	7.008	0.256	0.256	0.000	0.000	0.000	0.000
96	B	115	LEU	0	-0.069	-0.034	2.187	-0.777	-0.160	2.506	-0.773	-2.350	0.002
97	B	116	GLY	0	0.029	0.018	3.234	-2.795	-1.059	0.073	-0.825	-0.983	-0.006
98	B	117	VAL	0	0.004	-0.003	2.620	-2.454	-0.645	1.105	-1.012	-1.902	-0.012
99	B	118	GLY	0	0.031	0.026	2.675	-3.250	-1.491	0.679	-0.880	-1.558	-0.004
100	B	119	THR	0	-0.051	-0.047	3.284	1.134	1.156	0.027	0.302	-0.350	0.000
101	B	120	GLY	0	0.024	0.017	6.753	0.021	0.021	0.000	0.000	0.000	0.000
102	B	121	ASN	0	-0.009	-0.020	8.933	-0.066	-0.066	0.000	0.000	0.000	0.000
103	B	122	GLY	0	-0.036	-0.014	12.079	0.077	0.077	0.000	0.000	0.000	0.000
104	B	123	THR	0	-0.040	-0.037	13.974	0.020	0.020	0.000	0.000	0.000	0.000
105	B	124	ARG	1	0.928	0.973	16.558	0.168	0.168	0.000	0.000	0.000	0.000
106	B	125	LEU	0	-0.040	-0.014	20.233	0.013	0.013	0.000	0.000	0.000	0.000
107	B	126	VAL	0	-0.010	-0.023	21.788	0.002	0.002	0.000	0.000	0.000	0.000
108	B	127	VAL	0	-0.011	-0.011	25.410	0.002	0.002	0.000	0.000	0.000	0.000
109	B	128	GLU	-1	-0.891	-0.940	27.789	-0.078	-0.078	0.000	0.000	0.000	0.000
110	B	129	LYS	1	0.830	0.909	31.098	0.072	0.072	0.000	0.000	0.000	0.000
111	B	130	GLU	-1	-0.867	-0.927	34.523	-0.060	-0.060	0.000	0.000	0.000	0.000

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