FMO DATABASE

FMODB ID: 3943L

Calculation Name: 4GG6-B-Xray372

Preferred Name: HLA class II histocompatibility antigen, DQ alpha 1 chain

Target Type: SINGLE PROTEIN

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

ligand 3-letter code: NAG

PDB ID: 4GG6

Chain ID: B

ChEMBL ID: CHEMBL4105884

UniProt ID: P01909

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	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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1559535.154521
FMO2-HF: Nuclear repulsion	1490034.125164
FMO2-HF: Total energy	-69501.029356
FMO2-MP2: Total energy	-69703.476006

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:3:SER)

Summations of interaction energy for fragment #1(B:3:SER)

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.
-4.494	-2.974	0.011	-0.815	-0.716	-0.002

Interaction energy analysis for fragmet #1(B:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.040

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	5	GLU	-1	-0.914	-0.947	3.325	-5.056	-3.536	0.011	-0.815	-0.716	-0.002
4	B	6	ASP	-1	-0.919	-0.967	5.611	-0.063	-0.063	0.000	0.000	0.000	0.000
5	B	7	PHE	0	-0.065	-0.006	7.856	0.165	0.165	0.000	0.000	0.000	0.000
6	B	8	VAL	0	0.025	0.019	10.536	0.155	0.155	0.000	0.000	0.000	0.000
7	B	9	TYR	0	-0.003	-0.030	13.188	0.047	0.047	0.000	0.000	0.000	0.000
8	B	10	GLN	0	-0.052	-0.027	15.910	0.067	0.067	0.000	0.000	0.000	0.000
9	B	11	PHE	0	0.033	0.010	19.429	0.000	0.000	0.000	0.000	0.000	0.000
10	B	12	LYS	1	0.932	0.966	20.696	0.092	0.092	0.000	0.000	0.000	0.000
11	B	13	GLY	0	0.033	0.019	25.254	0.003	0.003	0.000	0.000	0.000	0.000
12	B	14	MET	0	-0.025	0.002	27.366	0.005	0.005	0.000	0.000	0.000	0.000
13	B	15	CYS	0	-0.040	-0.012	30.501	0.000	0.000	0.000	0.000	0.000	0.000
14	B	16	TYR	0	-0.029	-0.015	29.952	0.001	0.001	0.000	0.000	0.000	0.000
15	B	17	PHE	0	0.025	0.007	35.831	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.039	-0.029	39.060	0.002	0.002	0.000	0.000	0.000	0.000
17	B	19	ASN	0	0.001	0.006	41.677	0.000	0.000	0.000	0.000	0.000	0.000
18	B	20	GLY	0	0.064	0.047	43.859	0.000	0.000	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.052	-0.053	42.321	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	22	GLU	-1	-0.916	-0.949	44.439	-0.018	-0.018	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.934	0.974	38.565	0.031	0.031	0.000	0.000	0.000	0.000
22	B	24	VAL	0	-0.032	-0.010	39.377	0.001	0.001	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.817	0.909	34.908	0.049	0.049	0.000	0.000	0.000	0.000
24	B	26	LEU	0	0.027	0.018	33.578	0.002	0.002	0.000	0.000	0.000	0.000
25	B	27	VAL	0	-0.051	-0.036	29.439	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	28	THR	0	0.005	0.021	29.033	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	29	ARG	1	0.831	0.901	24.802	0.078	0.078	0.000	0.000	0.000	0.000
28	B	30	TYR	0	0.045	0.029	23.530	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	31	ILE	0	-0.019	-0.017	18.073	0.009	0.009	0.000	0.000	0.000	0.000
30	B	32	TYR	0	0.048	0.035	14.405	-0.016	-0.016	0.000	0.000	0.000	0.000
31	B	33	ASN	0	0.073	0.022	12.273	-0.017	-0.017	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.911	0.937	13.532	0.105	0.105	0.000	0.000	0.000	0.000
33	B	35	GLU	-1	-0.859	-0.896	16.280	-0.226	-0.226	0.000	0.000	0.000	0.000
34	B	36	GLU	-1	-0.759	-0.894	18.987	-0.123	-0.123	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.080	0.053	21.127	0.003	0.003	0.000	0.000	0.000	0.000
36	B	38	ALA	0	0.017	0.017	23.883	0.011	0.011	0.000	0.000	0.000	0.000
37	B	39	ARG	1	0.831	0.917	26.560	0.097	0.097	0.000	0.000	0.000	0.000
38	B	40	PHE	0	0.003	0.012	29.156	0.002	0.002	0.000	0.000	0.000	0.000
39	B	41	ASP	-1	-0.766	-0.868	32.462	-0.057	-0.057	0.000	0.000	0.000	0.000
40	B	42	SER	0	0.033	0.005	34.675	0.000	0.000	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.888	-0.948	37.608	-0.042	-0.042	0.000	0.000	0.000	0.000
42	B	44	VAL	0	-0.107	-0.039	36.440	0.001	0.001	0.000	0.000	0.000	0.000
43	B	45	GLY	0	0.027	0.017	38.145	0.002	0.002	0.000	0.000	0.000	0.000
44	B	46	VAL	0	-0.034	-0.034	37.053	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	47	TYR	0	0.014	-0.008	30.533	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	48	ARG	1	0.929	0.959	31.981	0.081	0.081	0.000	0.000	0.000	0.000
47	B	49	ALA	0	0.015	0.019	28.748	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	50	VAL	0	-0.106	-0.055	25.759	0.010	0.010	0.000	0.000	0.000	0.000
49	B	51	THR	0	0.022	-0.005	22.588	0.009	0.009	0.000	0.000	0.000	0.000
50	B	52	PRO	0	0.005	-0.011	24.736	0.001	0.001	0.000	0.000	0.000	0.000
51	B	53	LEU	0	0.025	0.016	19.584	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	54	GLY	0	-0.037	-0.019	23.906	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	55	PRO	0	-0.023	-0.009	26.608	0.006	0.006	0.000	0.000	0.000	0.000
54	B	56	PRO	0	0.051	0.026	27.195	0.009	0.009	0.000	0.000	0.000	0.000
55	B	57	ALA	0	0.013	0.012	26.862	0.005	0.005	0.000	0.000	0.000	0.000
56	B	58	ALA	0	-0.014	-0.016	28.987	0.010	0.010	0.000	0.000	0.000	0.000
57	B	59	GLU	-1	-0.978	-1.002	31.530	-0.114	-0.114	0.000	0.000	0.000	0.000
58	B	60	TYR	0	-0.004	0.008	31.628	0.006	0.006	0.000	0.000	0.000	0.000
59	B	61	TRP	0	0.024	0.021	26.737	0.004	0.004	0.000	0.000	0.000	0.000
60	B	62	ASN	0	-0.012	-0.017	34.135	0.010	0.010	0.000	0.000	0.000	0.000
61	B	63	SER	0	-0.094	-0.039	36.837	0.006	0.006	0.000	0.000	0.000	0.000
62	B	64	GLN	0	0.059	0.030	35.339	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	65	LYS	1	0.968	0.998	39.119	0.060	0.060	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.898	-0.962	39.561	-0.085	-0.085	0.000	0.000	0.000	0.000
65	B	67	VAL	0	0.026	0.017	34.172	0.002	0.002	0.000	0.000	0.000	0.000
66	B	68	LEU	0	0.012	0.016	36.774	0.001	0.001	0.000	0.000	0.000	0.000
67	B	69	GLU	-1	-0.909	-0.972	38.697	-0.059	-0.059	0.000	0.000	0.000	0.000
68	B	70	ARG	1	0.889	0.950	34.040	0.092	0.092	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.023	-0.020	33.540	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	72	ARG	1	0.854	0.926	36.430	0.069	0.069	0.000	0.000	0.000	0.000
71	B	73	ALA	0	0.031	0.017	39.403	0.004	0.004	0.000	0.000	0.000	0.000
72	B	74	GLU	-1	-0.863	-0.919	33.876	-0.083	-0.083	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.009	-0.007	37.654	0.002	0.002	0.000	0.000	0.000	0.000
74	B	76	ASP	-1	-0.852	-0.928	39.464	-0.038	-0.038	0.000	0.000	0.000	0.000
75	B	77	THR	0	-0.015	-0.025	38.305	0.002	0.002	0.000	0.000	0.000	0.000
76	B	78	VAL	0	-0.019	0.008	33.762	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	80	ARG	1	0.898	0.925	38.067	0.041	0.041	0.000	0.000	0.000	0.000
78	B	81	HIS	0	0.002	0.010	39.493	0.004	0.004	0.000	0.000	0.000	0.000
79	B	82	ASN	0	0.052	0.015	35.106	0.002	0.002	0.000	0.000	0.000	0.000
80	B	83	TYR	0	0.025	0.024	39.044	0.004	0.004	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.003	0.002	40.632	0.005	0.005	0.000	0.000	0.000	0.000
82	B	85	LEU	0	0.010	0.005	39.755	0.003	0.003	0.000	0.000	0.000	0.000
83	B	86	GLU	-1	-0.854	-0.871	35.653	-0.018	-0.018	0.000	0.000	0.000	0.000
84	B	87	LEU	0	-0.069	-0.044	39.862	0.003	0.003	0.000	0.000	0.000	0.000
85	B	88	ARG	1	0.870	0.937	43.356	0.019	0.019	0.000	0.000	0.000	0.000
86	B	89	THR	0	0.008	0.003	39.611	0.002	0.002	0.000	0.000	0.000	0.000
87	B	90	THR	0	0.013	-0.037	36.006	0.003	0.003	0.000	0.000	0.000	0.000
88	B	91	LEU	0	-0.025	-0.015	38.947	0.003	0.003	0.000	0.000	0.000	0.000
89	B	92	GLN	0	-0.039	-0.006	41.473	0.001	0.001	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.901	0.973	36.029	-0.015	-0.015	0.000	0.000	0.000	0.000
91	B	94	ARG	1	0.793	0.882	40.896	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	95	VAL	0	0.002	0.000	38.920	0.000	0.000	0.000	0.000	0.000	0.000
93	B	96	GLU	-1	-0.864	-0.942	41.923	0.017	0.017	0.000	0.000	0.000	0.000
94	B	97	PRO	0	-0.038	-0.005	40.983	0.002	0.002	0.000	0.000	0.000	0.000
95	B	98	THR	0	-0.009	0.008	40.956	-0.002	-0.002	0.000	0.000	0.000	0.000
96	B	99	VAL	0	-0.012	-0.012	41.417	0.003	0.003	0.000	0.000	0.000	0.000
97	B	100	THR	0	-0.020	-0.006	42.109	0.000	0.000	0.000	0.000	0.000	0.000
98	B	101	ILE	0	-0.007	-0.012	43.425	0.001	0.001	0.000	0.000	0.000	0.000
99	B	102	SER	0	0.009	0.005	41.394	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	103	PRO	0	0.013	-0.002	42.244	0.002	0.002	0.000	0.000	0.000	0.000
101	B	104	SER	0	-0.070	-0.018	39.040	0.004	0.004	0.000	0.000	0.000	0.000
102	B	114	LEU	0	0.041	0.014	38.917	0.001	0.001	0.000	0.000	0.000	0.000
103	B	115	LEU	0	-0.058	-0.035	43.620	0.001	0.001	0.000	0.000	0.000	0.000
104	B	116	VAL	0	-0.030	-0.009	38.073	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	117	CYS	0	-0.060	-0.032	41.536	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	118	SER	0	-0.037	-0.013	37.787	0.001	0.001	0.000	0.000	0.000	0.000
107	B	119	VAL	0	0.014	0.003	38.678	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	120	THR	0	-0.029	-0.039	35.568	0.002	0.002	0.000	0.000	0.000	0.000
109	B	121	ASP	-1	-0.856	-0.935	35.226	0.043	0.043	0.000	0.000	0.000	0.000
110	B	122	PHE	0	0.031	0.020	36.849	-0.003	-0.003	0.000	0.000	0.000	0.000
111	B	123	TYR	0	-0.010	0.001	34.059	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	124	PRO	0	-0.017	-0.015	37.481	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	125	ALA	0	0.049	-0.003	34.900	0.002	0.002	0.000	0.000	0.000	0.000
114	B	126	GLN	0	-0.044	-0.019	36.868	0.003	0.003	0.000	0.000	0.000	0.000
115	B	127	ILE	0	0.023	0.013	38.830	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	128	LYS	1	0.817	0.900	41.436	-0.011	-0.011	0.000	0.000	0.000	0.000
117	B	129	VAL	0	0.040	0.030	41.345	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	130	ARG	1	0.836	0.938	43.994	-0.017	-0.017	0.000	0.000	0.000	0.000
119	B	131	TRP	0	0.020	0.004	43.943	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	132	PHE	0	0.039	0.021	48.545	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	133	ARG	1	0.684	0.823	52.333	-0.019	-0.019	0.000	0.000	0.000	0.000
122	B	134	ASN	0	0.030	0.001	55.259	0.000	0.000	0.000	0.000	0.000	0.000
123	B	135	ASP	-1	-0.862	-0.913	58.016	0.019	0.019	0.000	0.000	0.000	0.000
124	B	136	GLN	0	-0.033	-0.019	59.251	0.000	0.000	0.000	0.000	0.000	0.000
125	B	137	GLU	-1	-0.859	-0.921	56.666	0.018	0.018	0.000	0.000	0.000	0.000
126	B	138	GLU	-1	-0.909	-0.974	50.904	0.018	0.018	0.000	0.000	0.000	0.000
127	B	139	THR	0	-0.010	0.014	50.432	0.000	0.000	0.000	0.000	0.000	0.000
128	B	140	THR	0	0.008	-0.002	46.835	0.000	0.000	0.000	0.000	0.000	0.000
129	B	141	GLY	0	0.006	0.008	46.336	-0.001	-0.001	0.000	0.000	0.000	0.000
130	B	142	VAL	0	-0.033	-0.012	42.569	0.002	0.002	0.000	0.000	0.000	0.000
131	B	143	VAL	0	0.020	0.008	36.877	0.000	0.000	0.000	0.000	0.000	0.000
132	B	144	SER	0	0.020	0.006	36.916	0.000	0.000	0.000	0.000	0.000	0.000
133	B	145	THR	0	-0.058	-0.008	32.337	0.001	0.001	0.000	0.000	0.000	0.000
134	B	146	PRO	0	0.031	-0.007	29.589	-0.005	-0.005	0.000	0.000	0.000	0.000
135	B	147	LEU	0	-0.015	0.000	32.188	0.002	0.002	0.000	0.000	0.000	0.000
136	B	148	ILE	0	0.009	0.020	28.246	0.000	0.000	0.000	0.000	0.000	0.000
137	B	149	ARG	1	0.933	0.962	26.789	-0.037	-0.037	0.000	0.000	0.000	0.000
138	B	150	ASN	0	0.036	0.009	27.203	0.014	0.014	0.000	0.000	0.000	0.000
139	B	151	GLY	0	-0.044	-0.017	26.249	0.005	0.005	0.000	0.000	0.000	0.000
140	B	152	ASP	-1	-0.854	-0.924	27.234	0.040	0.040	0.000	0.000	0.000	0.000
141	B	153	TRP	0	-0.081	-0.045	30.138	-0.004	-0.004	0.000	0.000	0.000	0.000
142	B	154	THR	0	0.031	0.042	32.264	-0.002	-0.002	0.000	0.000	0.000	0.000
143	B	155	PHE	0	-0.076	-0.057	30.834	0.002	0.002	0.000	0.000	0.000	0.000
144	B	156	GLN	0	0.026	0.016	31.243	-0.001	-0.001	0.000	0.000	0.000	0.000
145	B	157	ILE	0	-0.033	-0.017	33.714	0.000	0.000	0.000	0.000	0.000	0.000
146	B	158	LEU	0	0.027	0.021	33.688	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	159	VAL	0	0.007	0.004	37.032	0.001	0.001	0.000	0.000	0.000	0.000
148	B	160	MET	0	-0.016	-0.018	35.370	0.001	0.001	0.000	0.000	0.000	0.000
149	B	161	LEU	0	0.040	0.012	40.540	-0.003	-0.003	0.000	0.000	0.000	0.000
150	B	162	GLU	-1	-0.931	-0.942	42.125	0.048	0.048	0.000	0.000	0.000	0.000
151	B	172	THR	0	-0.020	-0.014	50.971	0.000	0.000	0.000	0.000	0.000	0.000
152	B	174	HIS	0	0.038	0.021	48.457	-0.001	-0.001	0.000	0.000	0.000	0.000
153	B	175	VAL	0	0.001	-0.006	43.528	0.000	0.000	0.000	0.000	0.000	0.000
154	B	176	GLU	-1	-0.801	-0.903	46.050	0.012	0.012	0.000	0.000	0.000	0.000
155	B	177	HIS	0	0.029	0.024	40.404	0.000	0.000	0.000	0.000	0.000	0.000
156	B	178	PRO	0	-0.056	-0.041	42.994	-0.001	-0.001	0.000	0.000	0.000	0.000
157	B	179	SER	0	-0.044	-0.040	44.227	-0.001	-0.001	0.000	0.000	0.000	0.000
158	B	180	LEU	0	-0.013	0.010	46.384	0.000	0.000	0.000	0.000	0.000	0.000
159	B	181	GLN	0	-0.017	-0.001	48.951	-0.001	-0.001	0.000	0.000	0.000	0.000
160	B	182	ASN	0	-0.017	-0.011	52.610	-0.001	-0.001	0.000	0.000	0.000	0.000
161	B	183	PRO	0	0.004	-0.004	50.340	0.001	0.001	0.000	0.000	0.000	0.000
162	B	184	ILE	0	0.027	0.023	47.236	0.000	0.000	0.000	0.000	0.000	0.000
163	B	185	ILE	0	-0.016	-0.008	49.623	0.001	0.001	0.000	0.000	0.000	0.000
164	B	186	VAL	0	-0.012	0.000	47.718	0.000	0.000	0.000	0.000	0.000	0.000
165	B	187	GLU	-1	-0.816	-0.899	50.151	0.024	0.024	0.000	0.000	0.000	0.000
166	B	188	TRP	0	0.001	0.004	49.353	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:SER)