FMO DATABASE

FMODB ID: K9ZR3

Calculation Name: 4HG4-P-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: P

ChEMBL ID:

UniProt ID: P03451

Base Structure: X-ray

Registration Date: 2023-06-26

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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1419210.030181
FMO2-HF: Nuclear repulsion	1357870.620391
FMO2-HF: Total energy	-61339.40979
FMO2-MP2: Total energy	-61519.986249

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(P:1:GLU)

Summations of interaction energy for fragment #1(P:1:GLU)

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.
-3.408	0.912	2.303	-2.665	-3.958	-0.006

Interaction energy analysis for fragmet #1(P:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.970 / q_NPA : -0.992

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	P	3	GLN	0	0.002	0.018	3.655	-8.894	-6.972	-0.019	-0.790	-1.113	0.000
4	P	4	LEU	0	0.013	-0.013	6.465	-0.374	-0.374	0.000	0.000	0.000	0.000
5	P	5	VAL	0	-0.032	-0.011	10.211	-1.005	-1.005	0.000	0.000	0.000	0.000
6	P	6	GLU	-1	-0.756	-0.884	13.040	16.631	16.631	0.000	0.000	0.000	0.000
7	P	7	SER	0	-0.021	0.002	16.378	-0.313	-0.313	0.000	0.000	0.000	0.000
8	P	8	GLY	0	-0.004	0.009	19.913	0.024	0.024	0.000	0.000	0.000	0.000
9	P	9	ALA	0	-0.012	-0.014	22.300	-0.230	-0.230	0.000	0.000	0.000	0.000
10	P	10	GLU	-1	-0.811	-0.892	24.672	10.585	10.585	0.000	0.000	0.000	0.000
11	P	11	VAL	0	-0.020	-0.017	27.962	-0.112	-0.112	0.000	0.000	0.000	0.000
12	P	12	LYS	1	0.800	0.900	29.811	-10.370	-10.370	0.000	0.000	0.000	0.000
13	P	13	LYS	1	0.886	0.935	33.930	-7.988	-7.988	0.000	0.000	0.000	0.000
14	P	14	PRO	0	0.000	-0.007	37.168	0.129	0.129	0.000	0.000	0.000	0.000
15	P	15	GLY	0	0.060	0.048	37.578	-0.225	-0.225	0.000	0.000	0.000	0.000
16	P	16	SER	0	-0.108	-0.060	35.529	0.108	0.108	0.000	0.000	0.000	0.000
17	P	17	SER	0	0.019	-0.007	31.538	0.023	0.023	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.057	-0.017	27.069	-0.064	-0.064	0.000	0.000	0.000	0.000
19	P	19	LYS	1	0.920	0.948	24.226	-11.709	-11.709	0.000	0.000	0.000	0.000
20	P	20	VAL	0	0.013	0.033	21.561	0.105	0.105	0.000	0.000	0.000	0.000
21	P	21	SER	0	0.022	-0.012	17.845	-0.066	-0.066	0.000	0.000	0.000	0.000
22	P	22	CYS	0	-0.076	-0.010	14.269	0.434	0.434	0.000	0.000	0.000	0.000
23	P	23	LYS	1	0.893	0.956	10.995	-25.104	-25.104	0.000	0.000	0.000	0.000
24	P	24	ALA	0	0.032	0.030	8.642	0.891	0.891	0.000	0.000	0.000	0.000
25	P	25	SER	0	-0.045	-0.038	6.750	-1.494	-1.494	0.000	0.000	0.000	0.000
26	P	26	GLY	0	0.079	0.041	2.783	-2.792	-1.286	0.309	-0.982	-0.834	0.007
27	P	27	GLY	0	-0.006	0.001	2.479	7.116	7.889	2.014	-0.887	-1.900	-0.013
28	P	28	THR	0	-0.002	-0.002	5.019	-4.522	-4.403	-0.001	-0.006	-0.111	0.000
29	P	29	PHE	0	0.078	0.024	8.593	-0.260	-0.260	0.000	0.000	0.000	0.000
30	P	30	ILE	0	0.046	0.015	11.217	-0.551	-0.551	0.000	0.000	0.000	0.000
31	P	31	THR	0	-0.072	-0.028	8.567	-0.027	-0.027	0.000	0.000	0.000	0.000
32	P	32	HIS	0	0.003	0.025	6.693	-0.540	-0.540	0.000	0.000	0.000	0.000
33	P	33	VAL	0	0.006	-0.001	11.279	-1.434	-1.434	0.000	0.000	0.000	0.000
34	P	34	PHE	0	0.008	0.014	12.332	0.521	0.521	0.000	0.000	0.000	0.000
35	P	35	THR	0	-0.035	-0.013	15.505	-1.208	-1.208	0.000	0.000	0.000	0.000
36	P	36	TRP	0	0.048	0.015	17.472	0.517	0.517	0.000	0.000	0.000	0.000
37	P	37	VAL	0	0.005	0.015	19.437	-0.777	-0.777	0.000	0.000	0.000	0.000
38	P	38	ARG	1	0.806	0.896	21.523	-9.973	-9.973	0.000	0.000	0.000	0.000
39	P	39	GLN	0	-0.009	-0.010	24.123	0.293	0.293	0.000	0.000	0.000	0.000
40	P	40	ALA	0	0.022	0.015	26.143	-0.042	-0.042	0.000	0.000	0.000	0.000
41	P	41	PRO	0	0.032	0.003	28.831	0.050	0.050	0.000	0.000	0.000	0.000
42	P	42	GLY	0	-0.018	0.004	29.142	-0.332	-0.332	0.000	0.000	0.000	0.000
43	P	43	GLN	0	-0.024	-0.009	30.775	-0.225	-0.225	0.000	0.000	0.000	0.000
44	P	44	GLY	0	0.025	0.008	27.902	0.281	0.281	0.000	0.000	0.000	0.000
45	P	45	LEU	0	-0.008	-0.004	21.808	0.058	0.058	0.000	0.000	0.000	0.000
46	P	46	GLU	-1	-0.774	-0.868	25.489	9.536	9.536	0.000	0.000	0.000	0.000
47	P	47	TRP	0	-0.021	-0.013	20.434	-0.008	-0.008	0.000	0.000	0.000	0.000
48	P	48	VAL	0	-0.046	-0.035	23.474	-0.507	-0.507	0.000	0.000	0.000	0.000
49	P	49	GLY	0	0.037	0.003	23.047	-0.425	-0.425	0.000	0.000	0.000	0.000
50	P	50	GLY	0	-0.027	-0.009	20.085	0.545	0.545	0.000	0.000	0.000	0.000
51	P	51	PHE	0	0.010	-0.003	16.681	-0.603	-0.603	0.000	0.000	0.000	0.000
52	P	52	ILE	0	0.004	0.016	17.293	1.103	1.103	0.000	0.000	0.000	0.000
53	P	52	ALA	0	0.009	0.016	14.331	-0.625	-0.625	0.000	0.000	0.000	0.000
54	P	53	ILE	0	-0.033	-0.015	16.048	-0.541	-0.541	0.000	0.000	0.000	0.000
55	P	54	PHE	0	-0.031	-0.017	17.623	-0.568	-0.568	0.000	0.000	0.000	0.000
56	P	55	GLY	0	0.010	0.018	19.766	-0.576	-0.576	0.000	0.000	0.000	0.000
57	P	56	THR	0	-0.005	-0.004	21.153	-0.448	-0.448	0.000	0.000	0.000	0.000
58	P	57	SER	0	0.002	0.001	21.850	0.413	0.413	0.000	0.000	0.000	0.000
59	P	58	ASN	0	-0.030	0.012	23.499	-0.088	-0.088	0.000	0.000	0.000	0.000
60	P	59	TYR	0	0.061	0.009	24.795	0.190	0.190	0.000	0.000	0.000	0.000
61	P	60	ALA	0	0.064	0.044	27.394	-0.063	-0.063	0.000	0.000	0.000	0.000
62	P	61	GLN	0	0.005	-0.017	29.347	0.095	0.095	0.000	0.000	0.000	0.000
63	P	62	LYS	1	0.848	0.912	31.691	-9.533	-9.533	0.000	0.000	0.000	0.000
64	P	63	PHE	0	-0.027	-0.012	28.374	-0.200	-0.200	0.000	0.000	0.000	0.000
65	P	64	GLN	0	0.048	0.029	32.181	0.333	0.333	0.000	0.000	0.000	0.000
66	P	65	GLY	0	-0.036	-0.013	33.837	-0.249	-0.249	0.000	0.000	0.000	0.000
67	P	66	ARG	1	0.812	0.869	32.839	-9.037	-9.037	0.000	0.000	0.000	0.000
68	P	67	VAL	0	0.006	0.007	26.757	0.102	0.102	0.000	0.000	0.000	0.000
69	P	68	THR	0	-0.010	-0.002	27.869	-0.193	-0.193	0.000	0.000	0.000	0.000
70	P	69	ILE	0	-0.041	-0.015	21.559	0.270	0.270	0.000	0.000	0.000	0.000
71	P	70	THR	0	0.000	0.005	22.663	-0.194	-0.194	0.000	0.000	0.000	0.000
72	P	71	ALA	0	0.000	-0.002	17.474	0.522	0.522	0.000	0.000	0.000	0.000
73	P	72	ASP	-1	-0.797	-0.868	17.623	15.570	15.570	0.000	0.000	0.000	0.000
74	P	73	GLU	-1	-0.917	-0.957	15.227	19.248	19.248	0.000	0.000	0.000	0.000
75	P	74	SER	0	-0.068	-0.032	14.602	1.266	1.266	0.000	0.000	0.000	0.000
76	P	75	THR	0	-0.062	-0.064	14.605	1.121	1.121	0.000	0.000	0.000	0.000
77	P	76	SER	0	-0.011	0.001	10.233	1.785	1.785	0.000	0.000	0.000	0.000
78	P	77	THR	0	-0.027	-0.026	12.334	1.539	1.539	0.000	0.000	0.000	0.000
79	P	78	ALA	0	-0.008	0.011	15.101	-0.911	-0.911	0.000	0.000	0.000	0.000
80	P	79	TYR	0	0.003	-0.029	17.394	0.077	0.077	0.000	0.000	0.000	0.000
81	P	80	MET	0	-0.027	0.013	20.791	-0.586	-0.586	0.000	0.000	0.000	0.000
82	P	81	GLU	-1	-0.820	-0.911	23.158	10.619	10.619	0.000	0.000	0.000	0.000
83	P	82	LEU	0	-0.015	0.000	26.777	-0.184	-0.184	0.000	0.000	0.000	0.000
84	P	82	THR	0	0.003	-0.009	29.586	-0.215	-0.215	0.000	0.000	0.000	0.000
85	P	82	SER	0	-0.002	-0.017	33.194	-0.086	-0.086	0.000	0.000	0.000	0.000
86	P	82	LEU	0	-0.051	-0.006	31.251	-0.102	-0.102	0.000	0.000	0.000	0.000
87	P	83	THR	0	0.031	-0.005	35.125	-0.292	-0.292	0.000	0.000	0.000	0.000
88	P	84	SER	0	0.018	-0.002	34.972	0.188	0.188	0.000	0.000	0.000	0.000
89	P	85	GLU	-1	-0.929	-0.949	35.114	8.172	8.172	0.000	0.000	0.000	0.000
90	P	86	ASP	-1	-0.791	-0.858	31.244	9.528	9.528	0.000	0.000	0.000	0.000
91	P	87	THR	0	-0.018	0.015	30.148	0.398	0.398	0.000	0.000	0.000	0.000
92	P	88	ALA	0	-0.031	-0.016	27.182	-0.115	-0.115	0.000	0.000	0.000	0.000
93	P	89	VAL	0	0.010	0.022	21.842	0.074	0.074	0.000	0.000	0.000	0.000
94	P	90	TYR	0	-0.040	-0.057	22.505	-0.061	-0.061	0.000	0.000	0.000	0.000
95	P	91	TYR	0	0.011	0.026	17.698	0.396	0.396	0.000	0.000	0.000	0.000
96	P	93	ALA	0	0.044	0.005	13.100	0.568	0.568	0.000	0.000	0.000	0.000
97	P	94	ARG	1	0.882	0.937	7.803	-30.666	-30.666	0.000	0.000	0.000	0.000
98	P	95	GLY	0	0.025	0.019	11.668	0.012	0.012	0.000	0.000	0.000	0.000
99	P	96	ILE	0	-0.004	-0.008	11.521	1.240	1.240	0.000	0.000	0.000	0.000
100	P	97	SER	0	0.041	0.008	13.976	-1.610	-1.610	0.000	0.000	0.000	0.000
101	P	98	GLY	0	0.057	0.017	16.959	0.300	0.300	0.000	0.000	0.000	0.000
102	P	99	SER	0	-0.051	-0.034	19.685	-0.616	-0.616	0.000	0.000	0.000	0.000
103	P	100	TYR	0	-0.061	-0.050	17.682	-0.152	-0.152	0.000	0.000	0.000	0.000
104	P	100	GLY	0	-0.053	-0.015	16.593	-0.389	-0.389	0.000	0.000	0.000	0.000
105	P	100	TRP	0	0.025	0.015	11.932	-1.379	-1.379	0.000	0.000	0.000	0.000
106	P	100	PHE	0	-0.036	-0.041	13.691	0.829	0.829	0.000	0.000	0.000	0.000
107	P	101	ASP	-1	-0.907	-0.949	8.085	26.169	26.169	0.000	0.000	0.000	0.000
108	P	102	PRO	0	0.010	0.029	7.109	-0.017	-0.017	0.000	0.000	0.000	0.000
109	P	103	TRP	0	-0.039	-0.048	9.696	-1.953	-1.953	0.000	0.000	0.000	0.000
110	P	104	GLY	0	-0.009	0.000	12.226	0.938	0.938	0.000	0.000	0.000	0.000
111	P	105	GLN	0	-0.013	-0.018	13.821	-0.383	-0.383	0.000	0.000	0.000	0.000
112	P	106	GLY	0	-0.001	0.000	15.930	-0.950	-0.950	0.000	0.000	0.000	0.000
113	P	107	THR	0	-0.032	-0.025	18.894	0.184	0.184	0.000	0.000	0.000	0.000
114	P	108	LEU	0	-0.019	0.004	21.562	-0.317	-0.317	0.000	0.000	0.000	0.000
115	P	109	VAL	0	0.002	0.006	25.170	-0.145	-0.145	0.000	0.000	0.000	0.000
116	P	110	THR	0	0.028	-0.008	27.773	-0.271	-0.271	0.000	0.000	0.000	0.000
117	P	111	VAL	0	-0.018	-0.006	31.233	-0.098	-0.098	0.000	0.000	0.000	0.000
118	P	112	SER	0	0.051	0.027	34.408	-0.290	-0.290	0.000	0.000	0.000	0.000
119	P	113	SER	0	0.034	0.007	37.611	0.099	0.099	0.000	0.000	0.000	0.000
120	P	114	ALA	0	0.009	0.016	38.556	-0.099	-0.099	0.000	0.000	0.000	0.000
121	P	115	SER	0	-0.018	-0.010	38.996	0.192	0.192	0.000	0.000	0.000	0.000
122	P	116	THR	0	0.023	-0.001	35.007	-0.018	-0.018	0.000	0.000	0.000	0.000
123	P	117	LYS	1	0.940	1.002	37.301	-7.042	-7.042	0.000	0.000	0.000	0.000
124	P	118	GLY	0	0.079	0.042	37.885	0.136	0.136	0.000	0.000	0.000	0.000
125	P	119	PRO	0	-0.051	-0.031	37.866	-0.332	-0.332	0.000	0.000	0.000	0.000
126	P	142	VAL	0	0.001	-0.015	37.843	-0.079	-0.079	0.000	0.000	0.000	0.000
127	P	143	LYS	1	0.849	0.903	39.729	-6.560	-6.560	0.000	0.000	0.000	0.000
128	P	144	ASP	-1	-0.810	-0.895	41.760	6.831	6.831	0.000	0.000	0.000	0.000
129	P	145	TYR	0	-0.071	-0.052	33.330	-0.193	-0.193	0.000	0.000	0.000	0.000
130	P	146	PHE	0	0.003	0.013	35.490	-0.011	-0.011	0.000	0.000	0.000	0.000
131	P	147	PRO	0	-0.063	-0.026	30.985	-0.015	-0.015	0.000	0.000	0.000	0.000
132	P	148	GLU	-1	-0.849	-1.009	29.932	9.293	9.293	0.000	0.000	0.000	0.000
133	P	149	PRO	0	0.118	0.129	26.055	0.055	0.055	0.000	0.000	0.000	0.000
134	P	150	VAL	0	-0.022	0.001	27.106	0.288	0.288	0.000	0.000	0.000	0.000
135	P	151	THR	0	0.022	0.003	27.482	-0.310	-0.310	0.000	0.000	0.000	0.000
136	P	152	VAL	0	-0.018	-0.009	29.927	0.095	0.095	0.000	0.000	0.000	0.000
137	P	153	SER	0	0.010	-0.018	31.292	-0.024	-0.024	0.000	0.000	0.000	0.000
138	P	154	TRP	0	0.000	0.022	33.289	0.072	0.072	0.000	0.000	0.000	0.000
139	P	155	ASN	0	-0.004	-0.025	36.149	0.033	0.033	0.000	0.000	0.000	0.000
140	P	156	SER	0	-0.035	-0.025	34.469	-0.020	-0.020	0.000	0.000	0.000	0.000
141	P	157	GLY	0	0.039	0.030	32.614	0.206	0.206	0.000	0.000	0.000	0.000
142	P	158	ALA	0	-0.059	-0.006	33.551	0.043	0.043	0.000	0.000	0.000	0.000
143	P	159	LEU	0	-0.012	0.008	35.851	0.048	0.048	0.000	0.000	0.000	0.000
144	P	160	THR	0	0.085	0.029	31.819	0.122	0.122	0.000	0.000	0.000	0.000
145	P	161	SER	0	-0.010	-0.019	33.900	-0.137	-0.137	0.000	0.000	0.000	0.000
146	P	162	GLY	0	0.054	0.031	35.284	-0.180	-0.180	0.000	0.000	0.000	0.000
147	P	163	VAL	0	-0.066	-0.025	34.174	-0.173	-0.173	0.000	0.000	0.000	0.000
148	P	164	HIS	0	-0.046	-0.053	35.560	-0.013	-0.013	0.000	0.000	0.000	0.000
149	P	165	THR	0	0.009	0.008	32.005	-0.240	-0.240	0.000	0.000	0.000	0.000
150	P	166	PHE	0	-0.018	-0.008	34.499	0.039	0.039	0.000	0.000	0.000	0.000
151	P	167	PRO	0	-0.004	0.003	32.999	0.162	0.162	0.000	0.000	0.000	0.000
152	P	168	ALA	0	0.025	0.026	33.564	-0.267	-0.267	0.000	0.000	0.000	0.000
153	P	169	VAL	0	0.013	0.008	35.522	0.047	0.047	0.000	0.000	0.000	0.000
154	P	170	LEU	0	0.018	-0.007	37.655	0.030	0.030	0.000	0.000	0.000	0.000
155	P	171	GLN	0	0.021	0.012	39.691	-0.167	-0.167	0.000	0.000	0.000	0.000
156	P	172	SER	0	-0.021	-0.021	42.938	0.043	0.043	0.000	0.000	0.000	0.000
157	P	173	SER	0	-0.012	0.007	44.585	-0.010	-0.010	0.000	0.000	0.000	0.000
158	P	174	GLY	0	0.035	0.006	40.883	0.041	0.041	0.000	0.000	0.000	0.000
159	P	175	LEU	0	-0.107	-0.032	39.398	0.150	0.150	0.000	0.000	0.000	0.000
160	P	176	TYR	0	0.007	0.018	33.831	-0.040	-0.040	0.000	0.000	0.000	0.000
161	P	177	SER	0	-0.047	-0.042	38.192	-0.148	-0.148	0.000	0.000	0.000	0.000
162	P	178	LEU	0	0.004	0.025	34.109	-0.065	-0.065	0.000	0.000	0.000	0.000
163	P	179	SER	0	-0.001	-0.012	37.837	-0.312	-0.312	0.000	0.000	0.000	0.000
164	P	180	SER	0	-0.007	-0.016	37.159	0.244	0.244	0.000	0.000	0.000	0.000
165	P	181	VAL	0	0.026	0.048	38.528	-0.041	-0.041	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:1:GLU)