FMO DATABASE

FMODB ID: 4957N

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	OptHSide
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	-854381.206499
FMO2-HF: Nuclear repulsion	811630.117417
FMO2-HF: Total energy	-42751.089082
FMO2-MP2: Total energy	-42877.55149

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.
-18.387	-3.281	9.631	-7.181	-17.553	-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 : -0.033 / 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	B	21	VAL	0	0.011	-0.006	2.600	-1.811	0.912	0.602	-1.152	-2.172	-0.001
4	B	22	SER	0	-0.036	-0.006	4.595	0.086	0.170	-0.001	-0.016	-0.067	0.000
5	B	23	GLN	0	0.055	0.003	8.263	-0.097	-0.097	0.000	0.000	0.000	0.000
6	B	24	PRO	0	0.020	0.032	11.338	0.024	0.024	0.000	0.000	0.000	0.000
7	B	25	PRO	0	0.066	0.031	15.026	-0.031	-0.031	0.000	0.000	0.000	0.000
8	B	26	GLU	-1	-0.882	-0.922	17.249	-0.121	-0.121	0.000	0.000	0.000	0.000
9	B	27	ILE	0	0.007	0.011	18.009	0.009	0.009	0.000	0.000	0.000	0.000
10	B	28	ARG	1	0.796	0.887	20.996	0.071	0.071	0.000	0.000	0.000	0.000
11	B	29	THR	0	-0.011	-0.009	23.804	0.008	0.008	0.000	0.000	0.000	0.000
12	B	30	LEU	0	0.053	0.025	25.798	0.001	0.001	0.000	0.000	0.000	0.000
13	B	31	GLU	-1	-0.873	-0.948	28.719	-0.079	-0.079	0.000	0.000	0.000	0.000
14	B	32	GLY	0	0.029	0.035	29.588	0.007	0.007	0.000	0.000	0.000	0.000
15	B	33	SER	0	-0.025	-0.016	27.495	0.003	0.003	0.000	0.000	0.000	0.000
16	B	34	SER	0	-0.035	-0.013	23.182	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	35	ALA	0	-0.011	0.014	20.877	0.006	0.006	0.000	0.000	0.000	0.000
18	B	36	PHE	0	-0.004	-0.011	17.998	-0.010	-0.010	0.000	0.000	0.000	0.000
19	B	37	LEU	0	-0.013	-0.013	14.998	0.007	0.007	0.000	0.000	0.000	0.000
20	B	38	PRO	0	0.015	0.007	13.365	-0.030	-0.030	0.000	0.000	0.000	0.000
21	B	39	CYS	0	0.000	0.012	7.775	-0.088	-0.088	0.000	0.000	0.000	0.000
22	B	40	SER	0	-0.024	0.023	7.556	0.073	0.073	0.000	0.000	0.000	0.000
23	B	41	PHE	0	0.032	0.002	2.286	-1.904	-0.693	1.798	-0.669	-2.339	-0.003
24	B	42	ASN	0	-0.031	-0.018	3.560	-0.492	0.078	0.029	-0.146	-0.452	-0.001
25	B	43	ALA	0	0.036	0.026	3.045	-0.507	0.725	0.196	-0.568	-0.860	-0.005
26	B	44	SER	0	-0.027	-0.030	4.786	-0.266	-0.242	-0.001	-0.006	-0.017	0.000
27	B	45	GLN	0	0.005	-0.001	8.273	-0.120	-0.120	0.000	0.000	0.000	0.000
28	B	46	GLY	0	0.053	0.034	11.134	-0.056	-0.056	0.000	0.000	0.000	0.000
29	B	47	ARG	1	0.844	0.931	6.631	-0.394	-0.394	0.000	0.000	0.000	0.000
30	B	48	LEU	0	0.020	0.022	9.876	0.013	0.013	0.000	0.000	0.000	0.000
31	B	49	ALA	0	-0.020	-0.015	5.853	0.018	0.018	0.000	0.000	0.000	0.000
32	B	50	ILE	0	0.028	0.007	7.807	-0.073	-0.073	0.000	0.000	0.000	0.000
33	B	51	GLY	0	0.025	0.001	6.366	-0.085	-0.085	0.000	0.000	0.000	0.000
34	B	52	SER	0	-0.049	-0.004	6.478	0.122	0.122	0.000	0.000	0.000	0.000
35	B	53	VAL	0	0.046	0.016	6.104	-0.166	-0.166	0.000	0.000	0.000	0.000
36	B	54	THR	0	-0.066	-0.019	7.965	0.127	0.127	0.000	0.000	0.000	0.000
37	B	55	TRP	0	0.018	-0.005	9.616	-0.113	-0.113	0.000	0.000	0.000	0.000
38	B	56	PHE	0	-0.054	-0.023	10.480	0.031	0.031	0.000	0.000	0.000	0.000
39	B	57	ARG	1	0.859	0.915	14.530	0.202	0.202	0.000	0.000	0.000	0.000
40	B	58	ASP	-1	-0.809	-0.895	17.706	-0.223	-0.223	0.000	0.000	0.000	0.000
41	B	59	GLU	-1	-0.862	-0.905	17.456	-0.269	-0.269	0.000	0.000	0.000	0.000
42	B	60	VAL	0	-0.024	-0.022	11.592	-0.017	-0.017	0.000	0.000	0.000	0.000
43	B	61	VAL	0	0.031	0.018	14.866	-0.020	-0.020	0.000	0.000	0.000	0.000
44	B	62	PRO	0	0.098	0.045	16.420	0.009	0.009	0.000	0.000	0.000	0.000
45	B	63	GLY	0	-0.039	-0.018	17.400	0.012	0.012	0.000	0.000	0.000	0.000
46	B	64	LYS	1	0.796	0.867	18.132	0.285	0.285	0.000	0.000	0.000	0.000
47	B	65	GLU	-1	-0.912	-0.947	14.063	-0.493	-0.493	0.000	0.000	0.000	0.000
48	B	66	VAL	0	0.062	0.016	15.425	0.041	0.041	0.000	0.000	0.000	0.000
49	B	67	ARG	1	0.859	0.933	14.189	0.370	0.370	0.000	0.000	0.000	0.000
50	B	68	ASN	0	0.003	-0.007	18.415	0.027	0.027	0.000	0.000	0.000	0.000
51	B	69	GLY	0	0.009	0.019	20.850	0.010	0.010	0.000	0.000	0.000	0.000
52	B	70	THR	0	0.026	0.007	23.005	0.006	0.006	0.000	0.000	0.000	0.000
53	B	71	PRO	0	0.051	0.008	25.386	-0.007	-0.007	0.000	0.000	0.000	0.000
54	B	72	GLU	-1	-0.787	-0.887	26.936	-0.124	-0.124	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.032	0.026	20.147	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.922	0.961	21.161	0.189	0.189	0.000	0.000	0.000	0.000
57	B	75	GLY	0	-0.012	0.005	22.775	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	76	ARG	1	0.711	0.834	24.681	0.133	0.133	0.000	0.000	0.000	0.000
59	B	77	LEU	0	-0.038	0.001	18.433	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	78	ALA	0	-0.058	-0.025	19.717	0.008	0.008	0.000	0.000	0.000	0.000
61	B	79	PRO	0	-0.022	-0.014	17.430	-0.018	-0.018	0.000	0.000	0.000	0.000
62	B	80	LEU	0	0.008	0.024	10.373	0.010	0.010	0.000	0.000	0.000	0.000
63	B	81	ALA	0	-0.002	-0.002	14.874	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	82	SER	0	0.078	0.016	13.037	0.000	0.000	0.000	0.000	0.000	0.000
65	B	83	SER	0	0.028	0.017	12.680	0.006	0.006	0.000	0.000	0.000	0.000
66	B	84	ARG	1	0.841	0.888	12.671	0.065	0.065	0.000	0.000	0.000	0.000
67	B	85	PHE	0	0.013	0.021	5.030	0.058	0.058	0.000	0.000	0.000	0.000
68	B	86	LEU	0	-0.037	-0.039	8.491	0.079	0.079	0.000	0.000	0.000	0.000
69	B	87	HIS	0	-0.014	-0.029	9.964	0.065	0.065	0.000	0.000	0.000	0.000
70	B	88	ASP	-1	-0.805	-0.882	10.619	0.116	0.116	0.000	0.000	0.000	0.000
71	B	89	HIS	1	0.770	0.918	5.577	-0.344	-0.344	0.000	0.000	0.000	0.000
72	B	90	GLN	0	-0.004	-0.014	7.150	-0.063	-0.063	0.000	0.000	0.000	0.000
73	B	91	ALA	0	0.011	-0.029	6.950	-0.007	-0.007	0.000	0.000	0.000	0.000
74	B	92	GLU	-1	-0.831	-0.885	9.029	-0.170	-0.170	0.000	0.000	0.000	0.000
75	B	93	LEU	0	0.013	0.020	12.337	-0.011	-0.011	0.000	0.000	0.000	0.000
76	B	94	HIS	0	-0.010	-0.010	14.719	0.013	0.013	0.000	0.000	0.000	0.000
77	B	95	ILE	0	0.011	0.009	18.285	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	96	ARG	1	0.932	0.964	21.227	0.129	0.129	0.000	0.000	0.000	0.000
79	B	97	ASP	-1	-0.832	-0.915	24.567	-0.092	-0.092	0.000	0.000	0.000	0.000
80	B	98	VAL	0	-0.033	-0.032	23.930	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	99	ARG	1	0.829	0.888	26.452	0.106	0.106	0.000	0.000	0.000	0.000
82	B	100	GLY	0	0.088	0.043	27.797	0.007	0.007	0.000	0.000	0.000	0.000
83	B	101	HIS	0	-0.030	-0.003	27.037	0.002	0.002	0.000	0.000	0.000	0.000
84	B	102	ASP	-1	-0.757	-0.858	23.554	-0.151	-0.151	0.000	0.000	0.000	0.000
85	B	103	ALA	0	-0.002	0.018	23.091	-0.017	-0.017	0.000	0.000	0.000	0.000
86	B	104	SER	0	0.017	-0.007	20.511	0.006	0.006	0.000	0.000	0.000	0.000
87	B	105	ILE	0	-0.024	0.000	16.741	0.008	0.008	0.000	0.000	0.000	0.000
88	B	106	TYR	0	-0.070	-0.058	15.261	-0.024	-0.024	0.000	0.000	0.000	0.000
89	B	107	VAL	0	0.020	0.009	10.531	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	109	ARG	1	0.990	1.002	6.123	0.902	0.902	0.000	0.000	0.000	0.000
91	B	110	VAL	0	-0.018	-0.017	2.471	-0.349	0.062	1.320	-0.324	-1.406	0.002
92	B	111	GLU	-1	-0.900	-0.943	2.595	-4.130	-2.939	1.199	-0.911	-1.479	-0.012
93	B	112	VAL	0	-0.025	-0.009	2.520	-0.648	0.553	1.568	-0.555	-2.214	0.001
94	B	113	LEU	0	0.058	0.015	3.937	-0.420	-0.305	-0.001	0.017	-0.132	0.000
95	B	114	GLY	0	-0.011	-0.016	7.103	0.230	0.230	0.000	0.000	0.000	0.000
96	B	115	LEU	0	-0.065	-0.032	2.266	-0.771	0.106	1.431	-0.501	-1.807	0.002
97	B	116	GLY	0	0.029	0.021	3.236	-2.727	-1.078	0.067	-0.805	-0.911	-0.006
98	B	117	VAL	0	0.004	-0.003	2.780	-2.340	-0.421	0.651	-0.911	-1.660	-0.009
99	B	118	GLY	0	0.031	0.026	2.684	-3.501	-1.668	0.752	-0.917	-1.667	-0.005
100	B	119	THR	0	-0.046	-0.046	3.349	1.119	1.185	0.021	0.283	-0.370	0.000
101	B	120	GLY	0	0.020	0.020	6.561	0.042	0.042	0.000	0.000	0.000	0.000
102	B	121	ASN	0	-0.026	-0.031	8.695	-0.031	-0.031	0.000	0.000	0.000	0.000
103	B	122	GLY	0	-0.018	-0.006	11.856	0.069	0.069	0.000	0.000	0.000	0.000
104	B	123	THR	0	-0.044	-0.028	13.777	0.022	0.022	0.000	0.000	0.000	0.000
105	B	124	ARG	1	0.881	0.939	16.358	0.140	0.140	0.000	0.000	0.000	0.000
106	B	125	LEU	0	-0.033	-0.012	20.046	0.014	0.014	0.000	0.000	0.000	0.000
107	B	126	VAL	0	-0.016	-0.022	21.617	0.001	0.001	0.000	0.000	0.000	0.000
108	B	127	VAL	0	-0.007	-0.014	25.235	0.002	0.002	0.000	0.000	0.000	0.000
109	B	128	GLU	-1	-0.818	-0.880	27.544	-0.068	-0.068	0.000	0.000	0.000	0.000
110	B	129	LYS	1	0.805	0.902	30.797	0.065	0.065	0.000	0.000	0.000	0.000
111	B	130	GLU	-1	-0.873	-0.933	34.208	-0.054	-0.054	0.000	0.000	0.000	0.000

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