FMO DATABASE

FMODB ID: G5ZK1

Calculation Name: 4DOH-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4DOH

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UHF4

Base Structure: X-ray

Registration Date: 2023-09-23

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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1570558.67461
FMO2-HF: Nuclear repulsion	1507858.1774
FMO2-HF: Total energy	-62700.49721
FMO2-MP2: Total energy	-62879.858066

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(A:24:DAL)

Summations of interaction energy for fragment #1(A:24:DAL)

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.
-0.619	1.358	-0.019	-1.105	-0.854	0.004

Interaction energy analysis for fragmet #1(A:24:DAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.012

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	A	26	LYS	1	0.847	0.953	3.869	-0.131	1.846	-0.019	-1.105	-0.854	0.004
4	A	27	THR	0	0.013	-0.005	6.622	0.108	0.108	0.000	0.000	0.000	0.000
5	A	28	LEU	0	-0.033	-0.002	9.090	0.122	0.122	0.000	0.000	0.000	0.000
6	A	29	ASN	0	0.013	-0.010	12.563	0.042	0.042	0.000	0.000	0.000	0.000
7	A	30	LEU	0	-0.016	-0.024	15.549	0.023	0.023	0.000	0.000	0.000	0.000
8	A	31	GLY	0	0.022	0.002	18.577	0.018	0.018	0.000	0.000	0.000	0.000
9	A	32	SER	0	-0.004	-0.014	19.700	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	33	CYS	0	-0.028	0.022	18.638	0.005	0.005	0.000	0.000	0.000	0.000
11	A	34	VAL	0	0.017	0.004	12.929	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	35	ILE	0	0.009	0.008	13.042	0.012	0.012	0.000	0.000	0.000	0.000
13	A	36	ALA	0	0.030	0.021	7.848	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	37	THR	0	0.011	-0.001	8.618	0.062	0.062	0.000	0.000	0.000	0.000
15	A	38	ASN	0	0.044	0.010	6.585	-1.166	-1.166	0.000	0.000	0.000	0.000
16	A	39	LEU	0	0.038	0.008	7.715	0.296	0.296	0.000	0.000	0.000	0.000
17	A	40	GLN	0	-0.025	-0.011	5.275	0.310	0.310	0.000	0.000	0.000	0.000
18	A	41	GLU	-1	-0.870	-0.910	7.297	-0.649	-0.649	0.000	0.000	0.000	0.000
19	A	42	ILE	0	0.017	0.002	9.524	0.253	0.253	0.000	0.000	0.000	0.000
20	A	43	ARG	1	0.861	0.912	10.066	0.881	0.881	0.000	0.000	0.000	0.000
21	A	44	ASN	0	0.014	0.015	8.886	0.133	0.133	0.000	0.000	0.000	0.000
22	A	45	GLY	0	0.046	0.028	12.446	0.099	0.099	0.000	0.000	0.000	0.000
23	A	46	PHE	0	0.010	-0.008	15.015	0.071	0.071	0.000	0.000	0.000	0.000
24	A	47	SER	0	-0.071	-0.025	15.345	0.069	0.069	0.000	0.000	0.000	0.000
25	A	48	GLU	-1	-0.792	-0.877	16.716	-0.256	-0.256	0.000	0.000	0.000	0.000
26	A	49	ILE	0	-0.016	-0.015	19.287	0.029	0.029	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.919	0.990	18.120	0.244	0.244	0.000	0.000	0.000	0.000
28	A	51	GLY	0	0.051	0.025	21.905	0.014	0.014	0.000	0.000	0.000	0.000
29	A	52	SER	0	0.001	-0.005	24.795	0.016	0.016	0.000	0.000	0.000	0.000
30	A	53	VAL	0	-0.004	-0.009	24.037	0.011	0.011	0.000	0.000	0.000	0.000
31	A	54	GLN	0	-0.009	-0.034	22.612	0.021	0.021	0.000	0.000	0.000	0.000
32	A	55	ALA	0	-0.026	0.004	27.155	0.010	0.010	0.000	0.000	0.000	0.000
33	A	56	LYS	1	0.821	0.914	29.579	0.138	0.138	0.000	0.000	0.000	0.000
34	A	57	ASP	-1	-0.805	-0.890	29.899	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	58	GLY	0	0.018	0.014	31.799	0.003	0.003	0.000	0.000	0.000	0.000
36	A	59	ASN	0	-0.033	-0.007	34.053	0.005	0.005	0.000	0.000	0.000	0.000
37	A	60	ILE	0	-0.022	-0.014	32.414	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	61	ASP	-1	-0.867	-0.930	33.218	-0.091	-0.091	0.000	0.000	0.000	0.000
39	A	62	ILE	0	-0.049	-0.017	32.540	0.000	0.000	0.000	0.000	0.000	0.000
40	A	63	ARG	1	0.880	0.927	23.468	0.161	0.161	0.000	0.000	0.000	0.000
41	A	64	ILE	0	-0.013	-0.012	27.387	0.005	0.005	0.000	0.000	0.000	0.000
42	A	65	LEU	0	-0.024	-0.012	21.795	0.002	0.002	0.000	0.000	0.000	0.000
43	A	66	ARG	1	0.856	0.913	25.394	0.117	0.117	0.000	0.000	0.000	0.000
44	A	67	ARG	1	0.935	0.964	24.714	0.114	0.114	0.000	0.000	0.000	0.000
45	A	68	THR	0	-0.019	-0.016	25.862	0.005	0.005	0.000	0.000	0.000	0.000
46	A	69	GLU	-1	-0.837	-0.914	26.324	-0.134	-0.134	0.000	0.000	0.000	0.000
47	A	70	SER	0	0.007	0.025	20.446	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	71	LEU	0	0.045	0.007	17.444	0.016	0.016	0.000	0.000	0.000	0.000
49	A	72	GLN	0	-0.032	-0.017	18.115	0.007	0.007	0.000	0.000	0.000	0.000
50	A	73	ASP	-1	-0.839	-0.903	19.910	-0.123	-0.123	0.000	0.000	0.000	0.000
51	A	74	THR	0	-0.118	-0.061	22.612	0.022	0.022	0.000	0.000	0.000	0.000
52	A	75	LYS	1	0.861	0.923	23.135	0.110	0.110	0.000	0.000	0.000	0.000
53	A	76	PRO	0	0.069	0.033	21.137	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	77	ALA	0	0.006	-0.004	22.654	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	78	ASN	0	-0.029	-0.036	25.108	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.754	0.887	17.609	0.220	0.220	0.000	0.000	0.000	0.000
57	A	80	CYS	0	-0.029	-0.005	20.537	-0.045	-0.045	0.000	0.000	0.000	0.000
58	A	81	CYS	0	-0.032	-0.018	21.490	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	82	LEU	0	0.017	-0.002	23.054	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.024	0.016	16.488	0.000	0.000	0.000	0.000	0.000	0.000
61	A	84	ARG	1	0.908	0.943	21.142	0.216	0.216	0.000	0.000	0.000	0.000
62	A	85	HIS	0	0.020	0.017	22.756	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	86	LEU	0	0.040	0.029	21.879	0.007	0.007	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.006	0.002	17.711	0.000	0.000	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.863	0.931	22.056	0.206	0.206	0.000	0.000	0.000	0.000
66	A	89	LEU	0	-0.015	0.007	25.493	0.010	0.010	0.000	0.000	0.000	0.000
67	A	90	TYR	0	-0.003	-0.032	22.542	0.007	0.007	0.000	0.000	0.000	0.000
68	A	91	LEU	0	-0.055	-0.038	21.222	0.007	0.007	0.000	0.000	0.000	0.000
69	A	92	ASP	-1	-0.916	-0.960	24.986	-0.184	-0.184	0.000	0.000	0.000	0.000
70	A	93	ARG	1	0.747	0.840	28.217	0.166	0.166	0.000	0.000	0.000	0.000
71	A	94	VAL	0	0.026	0.041	25.312	0.010	0.010	0.000	0.000	0.000	0.000
72	A	95	PHE	0	0.035	0.006	19.891	0.010	0.010	0.000	0.000	0.000	0.000
73	A	96	LYS	1	0.866	0.932	25.405	0.185	0.185	0.000	0.000	0.000	0.000
74	A	97	ASN	0	-0.020	-0.017	28.407	0.016	0.016	0.000	0.000	0.000	0.000
75	A	98	TYR	0	0.023	0.027	27.412	0.011	0.011	0.000	0.000	0.000	0.000
76	A	99	GLN	0	-0.013	0.001	29.444	0.004	0.004	0.000	0.000	0.000	0.000
77	A	100	THR	0	0.001	-0.015	28.008	0.007	0.007	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.016	0.012	31.454	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	102	ASP	-1	-0.806	-0.875	27.431	-0.150	-0.150	0.000	0.000	0.000	0.000
80	A	103	HIS	0	0.077	0.012	28.392	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	104	TYR	0	-0.099	-0.067	20.176	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	105	THR	0	-0.017	-0.046	23.849	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	106	LEU	0	0.019	0.013	23.781	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	107	ARG	1	0.934	0.977	22.388	0.162	0.162	0.000	0.000	0.000	0.000
85	A	108	LYS	1	0.847	0.934	17.391	0.281	0.281	0.000	0.000	0.000	0.000
86	A	109	ILE	0	0.010	0.014	19.623	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	110	SER	0	0.003	0.006	21.386	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	111	SER	0	-0.035	-0.010	16.505	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	112	LEU	0	0.013	0.010	15.901	-0.049	-0.049	0.000	0.000	0.000	0.000
90	A	113	ALA	0	0.017	0.017	17.737	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.041	-0.041	18.180	0.005	0.005	0.000	0.000	0.000	0.000
92	A	115	SER	0	0.015	-0.014	13.332	0.024	0.024	0.000	0.000	0.000	0.000
93	A	116	PHE	0	0.006	-0.015	15.293	-0.058	-0.058	0.000	0.000	0.000	0.000
94	A	117	LEU	0	-0.006	0.007	17.466	0.017	0.017	0.000	0.000	0.000	0.000
95	A	118	THR	0	-0.082	-0.047	14.180	0.000	0.000	0.000	0.000	0.000	0.000
96	A	119	ILE	0	0.074	0.042	13.040	0.018	0.018	0.000	0.000	0.000	0.000
97	A	120	LYN	0	-0.008	0.009	15.911	0.066	0.066	0.000	0.000	0.000	0.000
98	A	121	LYS	1	0.885	0.927	18.135	0.411	0.411	0.000	0.000	0.000	0.000
99	A	122	ASP	-1	-0.811	-0.893	14.099	-0.521	-0.521	0.000	0.000	0.000	0.000
100	A	123	LEU	0	0.001	-0.008	17.701	0.053	0.053	0.000	0.000	0.000	0.000
101	A	124	ARG	1	0.874	0.936	19.795	0.267	0.267	0.000	0.000	0.000	0.000
102	A	125	LEU	0	0.023	0.027	18.696	0.032	0.032	0.000	0.000	0.000	0.000
103	A	127	HIS	0	0.027	0.007	21.637	0.016	0.016	0.000	0.000	0.000	0.000
104	A	128	ALA	0	-0.029	-0.010	24.775	0.018	0.018	0.000	0.000	0.000	0.000
105	A	129	HIS	0	-0.016	-0.004	21.611	0.024	0.024	0.000	0.000	0.000	0.000
106	A	130	MET	0	-0.038	-0.018	25.566	0.008	0.008	0.000	0.000	0.000	0.000
107	A	131	THR	0	-0.019	-0.012	22.521	0.001	0.001	0.000	0.000	0.000	0.000
108	A	133	HIS	0	0.049	0.031	24.692	0.001	0.001	0.000	0.000	0.000	0.000
109	A	135	GLY	0	0.055	0.045	29.367	0.011	0.011	0.000	0.000	0.000	0.000
110	A	136	GLU	-1	-0.788	-0.902	30.998	-0.101	-0.101	0.000	0.000	0.000	0.000
111	A	137	GLU	-1	-0.704	-0.834	27.647	-0.134	-0.134	0.000	0.000	0.000	0.000
112	A	138	ALA	0	-0.005	-0.001	27.123	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	139	MET	0	0.018	0.003	28.482	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	140	LYS	1	0.826	0.919	31.269	0.094	0.094	0.000	0.000	0.000	0.000
115	A	141	LYS	1	0.885	0.928	25.895	0.148	0.148	0.000	0.000	0.000	0.000
116	A	142	TYR	0	0.013	0.002	26.938	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	143	SER	0	0.004	-0.008	29.112	0.000	0.000	0.000	0.000	0.000	0.000
118	A	144	GLN	0	-0.047	-0.019	31.135	0.007	0.007	0.000	0.000	0.000	0.000
119	A	145	ILE	0	-0.010	0.000	25.450	0.001	0.001	0.000	0.000	0.000	0.000
120	A	146	LEU	0	-0.030	-0.024	29.705	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	147	SER	0	0.021	0.010	31.572	0.006	0.006	0.000	0.000	0.000	0.000
122	A	148	HIS	0	-0.010	-0.017	30.793	0.002	0.002	0.000	0.000	0.000	0.000
123	A	149	PHE	0	-0.024	-0.019	28.993	0.001	0.001	0.000	0.000	0.000	0.000
124	A	150	GLU	-1	-0.825	-0.907	32.220	-0.125	-0.125	0.000	0.000	0.000	0.000
125	A	151	LYN	0	-0.036	0.021	34.857	0.005	0.005	0.000	0.000	0.000	0.000
126	A	152	LEU	0	-0.014	0.002	32.995	0.005	0.005	0.000	0.000	0.000	0.000
127	A	153	GLU	-1	-0.881	-0.935	36.652	-0.090	-0.090	0.000	0.000	0.000	0.000
128	A	154	PRO	0	0.056	0.001	35.631	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	155	GLN	0	-0.006	-0.006	32.357	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	156	ALA	0	0.071	0.036	32.894	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	157	ALA	0	0.013	0.019	32.182	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	158	VAL	0	-0.062	-0.038	29.230	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	159	VAL	0	-0.046	-0.023	27.992	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	160	LYS	1	0.831	0.913	27.756	0.125	0.125	0.000	0.000	0.000	0.000
135	A	161	ALA	0	-0.010	0.000	25.840	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	162	LEU	0	-0.026	-0.006	22.402	-0.029	-0.029	0.000	0.000	0.000	0.000
137	A	163	GLY	0	0.010	-0.004	22.603	-0.023	-0.023	0.000	0.000	0.000	0.000
138	A	164	GLU	-1	-0.757	-0.870	22.867	-0.186	-0.186	0.000	0.000	0.000	0.000
139	A	165	LEU	0	0.000	-0.002	18.110	-0.022	-0.022	0.000	0.000	0.000	0.000
140	A	166	ASP	-1	-0.872	-0.936	17.182	-0.302	-0.302	0.000	0.000	0.000	0.000
141	A	167	ILE	0	-0.027	0.000	17.329	-0.017	-0.017	0.000	0.000	0.000	0.000
142	A	168	LEU	0	0.022	0.011	17.577	-0.017	-0.017	0.000	0.000	0.000	0.000
143	A	169	LEU	0	-0.023	-0.029	12.818	-0.045	-0.045	0.000	0.000	0.000	0.000
144	A	170	GLN	0	0.025	0.031	13.437	-0.113	-0.113	0.000	0.000	0.000	0.000
145	A	171	TRP	0	-0.010	0.002	15.134	0.009	0.009	0.000	0.000	0.000	0.000
146	A	172	MET	0	-0.035	-0.015	13.043	0.011	0.011	0.000	0.000	0.000	0.000
147	A	173	GLU	-1	-0.852	-0.933	8.288	-1.214	-1.214	0.000	0.000	0.000	0.000
148	A	174	GLU	-1	-0.864	-0.950	11.717	-0.204	-0.204	0.000	0.000	0.000	0.000
149	A	175	THR	0	-0.077	-0.016	13.873	0.048	0.048	0.000	0.000	0.000	0.000
150	A	176	GLU	-1	-0.791	-0.874	11.497	-0.372	-0.372	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:DAL)