FMO DATABASE

FMODB ID: 894ZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1578686.619927
FMO2-HF: Nuclear repulsion	1515985.799418
FMO2-HF: Total energy	-62700.82051
FMO2-MP2: Total energy	-62880.193436

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.
-0.304	1.417	-0.016	-0.933	-0.771	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 : 0.022 / q_NPA : 0.013

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	0.838	0.950	3.876	0.317	2.038	-0.016	-0.933	-0.771	0.004
4	A	27	THR	0	0.030	0.002	6.550	0.133	0.133	0.000	0.000	0.000	0.000
5	A	28	LEU	0	-0.024	0.001	9.047	0.078	0.078	0.000	0.000	0.000	0.000
6	A	29	ASN	0	0.016	-0.002	12.619	0.047	0.047	0.000	0.000	0.000	0.000
7	A	30	LEU	0	-0.033	-0.032	15.468	0.019	0.019	0.000	0.000	0.000	0.000
8	A	31	GLY	0	0.017	0.008	18.432	0.019	0.019	0.000	0.000	0.000	0.000
9	A	32	SER	0	0.016	-0.010	19.658	0.001	0.001	0.000	0.000	0.000	0.000
10	A	33	CYS	0	-0.025	0.023	18.294	0.006	0.006	0.000	0.000	0.000	0.000
11	A	34	VAL	0	0.026	0.005	12.862	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	35	ILE	0	0.015	0.012	12.755	0.023	0.023	0.000	0.000	0.000	0.000
13	A	36	ALA	0	0.020	0.010	7.287	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	37	THR	0	0.002	-0.004	8.193	0.087	0.087	0.000	0.000	0.000	0.000
15	A	38	ASN	0	0.045	0.005	6.400	-1.196	-1.196	0.000	0.000	0.000	0.000
16	A	39	LEU	0	0.036	0.009	7.763	0.312	0.312	0.000	0.000	0.000	0.000
17	A	40	GLN	0	-0.018	-0.008	5.754	0.301	0.301	0.000	0.000	0.000	0.000
18	A	41	GLU	-1	-0.854	-0.886	7.755	-0.721	-0.721	0.000	0.000	0.000	0.000
19	A	42	ILE	0	0.006	0.001	9.975	0.240	0.240	0.000	0.000	0.000	0.000
20	A	43	ARG	1	0.836	0.885	10.521	0.871	0.871	0.000	0.000	0.000	0.000
21	A	44	ASN	0	0.009	0.016	9.490	0.126	0.126	0.000	0.000	0.000	0.000
22	A	45	GLY	0	0.041	0.032	12.826	0.103	0.103	0.000	0.000	0.000	0.000
23	A	46	PHE	0	0.019	0.004	15.439	0.067	0.067	0.000	0.000	0.000	0.000
24	A	47	SER	0	-0.078	-0.046	15.593	0.073	0.073	0.000	0.000	0.000	0.000
25	A	48	GLU	-1	-0.767	-0.857	17.168	-0.284	-0.284	0.000	0.000	0.000	0.000
26	A	49	ILE	0	-0.013	-0.008	19.685	0.032	0.032	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.913	0.992	18.723	0.271	0.271	0.000	0.000	0.000	0.000
28	A	51	GLY	0	0.041	0.016	21.924	0.016	0.016	0.000	0.000	0.000	0.000
29	A	52	SER	0	-0.010	-0.004	24.761	0.019	0.019	0.000	0.000	0.000	0.000
30	A	53	VAL	0	0.004	0.002	24.105	0.013	0.013	0.000	0.000	0.000	0.000
31	A	54	GLN	0	0.000	-0.029	22.537	0.024	0.024	0.000	0.000	0.000	0.000
32	A	55	ALA	0	-0.041	-0.006	27.312	0.011	0.011	0.000	0.000	0.000	0.000
33	A	56	LYS	1	0.840	0.914	29.560	0.154	0.154	0.000	0.000	0.000	0.000
34	A	57	ASP	-1	-0.819	-0.898	29.739	-0.148	-0.148	0.000	0.000	0.000	0.000
35	A	58	GLY	0	0.002	0.004	31.747	0.003	0.003	0.000	0.000	0.000	0.000
36	A	59	ASN	0	-0.048	-0.023	34.224	0.005	0.005	0.000	0.000	0.000	0.000
37	A	60	ILE	0	-0.004	-0.012	32.485	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	61	ASP	-1	-0.863	-0.910	33.482	-0.100	-0.100	0.000	0.000	0.000	0.000
39	A	62	ILE	0	-0.038	-0.011	32.589	0.000	0.000	0.000	0.000	0.000	0.000
40	A	63	ARG	1	0.853	0.920	23.437	0.182	0.182	0.000	0.000	0.000	0.000
41	A	64	ILE	0	-0.013	-0.013	27.182	0.006	0.006	0.000	0.000	0.000	0.000
42	A	65	LEU	0	-0.015	-0.012	21.723	0.004	0.004	0.000	0.000	0.000	0.000
43	A	66	ARG	1	0.814	0.881	25.249	0.123	0.123	0.000	0.000	0.000	0.000
44	A	67	ARG	1	0.942	0.963	24.809	0.128	0.128	0.000	0.000	0.000	0.000
45	A	68	THR	0	-0.023	-0.014	25.716	0.001	0.001	0.000	0.000	0.000	0.000
46	A	69	GLU	-1	-0.790	-0.885	26.230	-0.140	-0.140	0.000	0.000	0.000	0.000
47	A	70	SER	0	0.025	0.029	20.279	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	71	LEU	0	0.027	0.010	17.101	0.020	0.020	0.000	0.000	0.000	0.000
49	A	72	GLN	0	-0.041	-0.023	18.117	0.004	0.004	0.000	0.000	0.000	0.000
50	A	73	ASP	-1	-0.804	-0.894	19.723	-0.140	-0.140	0.000	0.000	0.000	0.000
51	A	74	THR	0	-0.116	-0.057	22.621	0.027	0.027	0.000	0.000	0.000	0.000
52	A	75	LYS	1	0.848	0.909	22.733	0.114	0.114	0.000	0.000	0.000	0.000
53	A	76	PRO	0	0.060	0.013	21.008	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	77	ALA	0	0.022	0.001	22.197	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	78	ASN	0	-0.032	-0.019	24.630	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.741	0.865	17.341	0.232	0.232	0.000	0.000	0.000	0.000
57	A	80	CYS	0	-0.048	-0.001	20.434	-0.045	-0.045	0.000	0.000	0.000	0.000
58	A	81	CYS	0	-0.022	-0.011	21.395	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	82	LEU	0	0.000	0.003	23.182	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.044	0.022	16.573	0.000	0.000	0.000	0.000	0.000	0.000
61	A	84	ARG	1	0.845	0.905	21.170	0.216	0.216	0.000	0.000	0.000	0.000
62	A	85	HIS	0	0.015	0.007	22.724	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	86	LEU	0	0.023	0.015	22.034	0.008	0.008	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.009	-0.001	17.620	0.001	0.001	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.866	0.933	22.087	0.205	0.205	0.000	0.000	0.000	0.000
66	A	89	LEU	0	-0.013	0.006	25.504	0.009	0.009	0.000	0.000	0.000	0.000
67	A	90	TYR	0	0.004	-0.030	22.902	0.008	0.008	0.000	0.000	0.000	0.000
68	A	91	LEU	0	-0.041	-0.021	21.257	0.010	0.010	0.000	0.000	0.000	0.000
69	A	92	ASP	-1	-0.916	-0.966	25.162	-0.181	-0.181	0.000	0.000	0.000	0.000
70	A	93	ARG	1	0.743	0.841	28.523	0.167	0.167	0.000	0.000	0.000	0.000
71	A	94	VAL	0	0.036	0.038	25.792	0.010	0.010	0.000	0.000	0.000	0.000
72	A	95	PHE	0	0.029	-0.008	19.886	0.008	0.008	0.000	0.000	0.000	0.000
73	A	96	LYS	1	0.847	0.933	25.631	0.186	0.186	0.000	0.000	0.000	0.000
74	A	97	ASN	0	-0.004	-0.001	28.567	0.015	0.015	0.000	0.000	0.000	0.000
75	A	98	TYR	0	0.047	0.038	27.861	0.012	0.012	0.000	0.000	0.000	0.000
76	A	99	GLN	0	-0.025	-0.008	29.934	0.004	0.004	0.000	0.000	0.000	0.000
77	A	100	THR	0	0.011	-0.011	28.642	0.005	0.005	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.024	0.017	32.097	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	102	ASP	-1	-0.800	-0.866	27.466	-0.164	-0.164	0.000	0.000	0.000	0.000
80	A	103	HIS	0	0.080	0.014	28.441	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	104	TYR	0	-0.102	-0.077	20.371	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	105	THR	0	0.006	-0.035	23.850	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	106	LEU	0	-0.007	0.007	24.253	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	107	ARG	1	0.921	0.975	22.412	0.171	0.171	0.000	0.000	0.000	0.000
85	A	108	LYS	1	0.809	0.918	17.773	0.297	0.297	0.000	0.000	0.000	0.000
86	A	109	ILE	0	0.026	0.016	19.878	-0.042	-0.042	0.000	0.000	0.000	0.000
87	A	110	SER	0	-0.005	-0.001	21.610	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	111	SER	0	-0.029	-0.021	16.809	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	112	LEU	0	0.000	0.001	15.972	-0.045	-0.045	0.000	0.000	0.000	0.000
90	A	113	ALA	0	0.009	0.013	17.942	-0.036	-0.036	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.041	-0.037	18.038	0.004	0.004	0.000	0.000	0.000	0.000
92	A	115	SER	0	0.015	-0.019	13.419	0.027	0.027	0.000	0.000	0.000	0.000
93	A	116	PHE	0	0.030	0.006	15.168	-0.064	-0.064	0.000	0.000	0.000	0.000
94	A	117	LEU	0	-0.020	-0.002	17.227	0.018	0.018	0.000	0.000	0.000	0.000
95	A	118	THR	0	-0.083	-0.052	13.832	0.002	0.002	0.000	0.000	0.000	0.000
96	A	119	ILE	0	0.078	0.041	12.904	0.037	0.037	0.000	0.000	0.000	0.000
97	A	120	LYN	0	0.001	0.022	15.745	0.069	0.069	0.000	0.000	0.000	0.000
98	A	121	LYS	1	0.900	0.946	17.723	0.415	0.415	0.000	0.000	0.000	0.000
99	A	122	ASP	-1	-0.842	-0.914	14.048	-0.490	-0.490	0.000	0.000	0.000	0.000
100	A	123	LEU	0	0.024	-0.004	17.459	0.048	0.048	0.000	0.000	0.000	0.000
101	A	124	ARG	1	0.891	0.944	19.552	0.256	0.256	0.000	0.000	0.000	0.000
102	A	125	LEU	0	0.005	0.013	18.253	0.031	0.031	0.000	0.000	0.000	0.000
103	A	127	HIS	0	0.035	0.016	21.208	0.014	0.014	0.000	0.000	0.000	0.000
104	A	128	ALA	0	-0.029	-0.010	24.542	0.018	0.018	0.000	0.000	0.000	0.000
105	A	129	HIS	0	0.003	0.002	21.043	0.025	0.025	0.000	0.000	0.000	0.000
106	A	130	MET	0	-0.029	-0.011	25.068	0.007	0.007	0.000	0.000	0.000	0.000
107	A	131	THR	0	-0.040	-0.024	21.916	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	133	HIS	0	0.065	0.033	24.195	0.000	0.000	0.000	0.000	0.000	0.000
109	A	135	GLY	0	0.053	0.036	29.065	0.011	0.011	0.000	0.000	0.000	0.000
110	A	136	GLU	-1	-0.800	-0.903	30.637	-0.107	-0.107	0.000	0.000	0.000	0.000
111	A	137	GLU	-1	-0.706	-0.825	27.304	-0.142	-0.142	0.000	0.000	0.000	0.000
112	A	138	ALA	0	0.002	0.006	26.958	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	139	MET	0	0.029	0.014	28.085	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	140	LYS	1	0.840	0.930	31.111	0.099	0.099	0.000	0.000	0.000	0.000
115	A	141	LYS	1	0.849	0.922	25.577	0.158	0.158	0.000	0.000	0.000	0.000
116	A	142	TYR	0	0.008	-0.004	26.759	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	143	SER	0	0.000	-0.022	28.794	0.001	0.001	0.000	0.000	0.000	0.000
118	A	144	GLN	0	-0.072	-0.038	30.837	0.008	0.008	0.000	0.000	0.000	0.000
119	A	145	ILE	0	-0.002	0.006	25.236	0.001	0.001	0.000	0.000	0.000	0.000
120	A	146	LEU	0	-0.022	-0.011	29.483	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	147	SER	0	0.008	0.005	31.550	0.005	0.005	0.000	0.000	0.000	0.000
122	A	148	HIS	0	0.002	-0.020	30.935	0.002	0.002	0.000	0.000	0.000	0.000
123	A	149	PHE	0	-0.031	-0.017	29.324	0.001	0.001	0.000	0.000	0.000	0.000
124	A	150	GLU	-1	-0.820	-0.904	32.261	-0.127	-0.127	0.000	0.000	0.000	0.000
125	A	151	LYN	0	-0.018	0.029	35.058	0.006	0.006	0.000	0.000	0.000	0.000
126	A	152	LEU	0	-0.027	-0.001	33.321	0.005	0.005	0.000	0.000	0.000	0.000
127	A	153	GLU	-1	-0.887	-0.939	36.952	-0.095	-0.095	0.000	0.000	0.000	0.000
128	A	154	PRO	0	0.009	-0.009	35.738	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	155	GLN	0	-0.004	-0.022	32.783	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	156	ALA	0	0.073	0.035	33.123	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	157	ALA	0	0.025	0.025	32.374	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	158	VAL	0	-0.052	-0.025	29.374	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	159	VAL	0	-0.023	-0.009	28.168	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	160	LYS	1	0.805	0.903	27.940	0.134	0.134	0.000	0.000	0.000	0.000
135	A	161	ALA	0	-0.004	-0.003	26.348	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	162	LEU	0	-0.027	-0.011	22.899	-0.028	-0.028	0.000	0.000	0.000	0.000
137	A	163	GLY	0	0.037	0.013	22.976	-0.022	-0.022	0.000	0.000	0.000	0.000
138	A	164	GLU	-1	-0.768	-0.870	23.208	-0.205	-0.205	0.000	0.000	0.000	0.000
139	A	165	LEU	0	0.021	0.005	18.740	-0.024	-0.024	0.000	0.000	0.000	0.000
140	A	166	ASP	-1	-0.860	-0.936	17.244	-0.341	-0.341	0.000	0.000	0.000	0.000
141	A	167	ILE	0	-0.017	0.000	17.199	-0.030	-0.030	0.000	0.000	0.000	0.000
142	A	168	LEU	0	0.000	0.006	17.882	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	169	LEU	0	-0.028	-0.025	13.060	-0.044	-0.044	0.000	0.000	0.000	0.000
144	A	170	GLN	0	0.037	0.035	13.629	-0.120	-0.120	0.000	0.000	0.000	0.000
145	A	171	TRP	0	0.010	-0.004	15.112	0.009	0.009	0.000	0.000	0.000	0.000
146	A	172	MET	0	-0.027	0.003	12.944	0.017	0.017	0.000	0.000	0.000	0.000
147	A	173	GLU	-1	-0.828	-0.916	8.701	-1.246	-1.246	0.000	0.000	0.000	0.000
148	A	174	GLU	-1	-0.848	-0.936	11.952	-0.238	-0.238	0.000	0.000	0.000	0.000
149	A	175	THR	0	-0.056	-0.002	13.681	0.062	0.062	0.000	0.000	0.000	0.000
150	A	176	GLU	-1	-0.835	-0.907	10.833	-0.410	-0.410	0.000	0.000	0.000	0.000

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