FMO DATABASE

FMODB ID: 942N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1563114.404217
FMO2-HF: Nuclear repulsion	1493612.301786
FMO2-HF: Total energy	-69502.102431
FMO2-MP2: Total energy	-69704.533448

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.
-7.912	-5.343	0.027	-1.505	-1.09	-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 : 0.020 / q_NPA : 0.004

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	-0.920	-0.949	3.175	-7.833	-5.264	0.027	-1.505	-1.090	-0.002
4	B	6	ASP	-1	-0.904	-0.958	5.522	-0.961	-0.961	0.000	0.000	0.000	0.000
5	B	7	PHE	0	-0.082	-0.035	7.884	0.202	0.202	0.000	0.000	0.000	0.000
6	B	8	VAL	0	0.036	0.036	10.359	0.238	0.238	0.000	0.000	0.000	0.000
7	B	9	TYR	0	0.012	-0.016	12.853	0.082	0.082	0.000	0.000	0.000	0.000
8	B	10	GLN	0	-0.038	-0.027	15.715	0.079	0.079	0.000	0.000	0.000	0.000
9	B	11	PHE	0	0.041	0.024	19.284	0.011	0.011	0.000	0.000	0.000	0.000
10	B	12	LYS	1	0.874	0.936	19.564	0.161	0.161	0.000	0.000	0.000	0.000
11	B	13	GLY	0	0.060	0.031	25.351	0.007	0.007	0.000	0.000	0.000	0.000
12	B	14	MET	0	-0.041	0.007	27.272	0.007	0.007	0.000	0.000	0.000	0.000
13	B	15	CYS	0	-0.022	-0.005	30.187	0.001	0.001	0.000	0.000	0.000	0.000
14	B	16	TYR	0	0.001	0.003	29.577	0.002	0.002	0.000	0.000	0.000	0.000
15	B	17	PHE	0	0.045	0.019	35.566	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.041	-0.037	39.033	0.004	0.004	0.000	0.000	0.000	0.000
17	B	19	ASN	0	0.001	-0.006	41.895	0.000	0.000	0.000	0.000	0.000	0.000
18	B	20	GLY	0	0.038	0.032	43.592	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.061	-0.051	42.445	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	22	GLU	-1	-0.867	-0.908	44.447	-0.016	-0.016	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.860	0.923	38.642	0.029	0.029	0.000	0.000	0.000	0.000
22	B	24	VAL	0	-0.040	-0.018	39.273	0.001	0.001	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.713	0.830	34.734	0.051	0.051	0.000	0.000	0.000	0.000
24	B	26	LEU	0	0.005	0.006	33.576	0.002	0.002	0.000	0.000	0.000	0.000
25	B	27	VAL	0	-0.044	-0.027	29.768	0.001	0.001	0.000	0.000	0.000	0.000
26	B	28	THR	0	0.005	0.017	29.121	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	29	ARG	1	0.837	0.890	24.861	0.093	0.093	0.000	0.000	0.000	0.000
28	B	30	TYR	0	0.026	0.005	23.423	-0.012	-0.012	0.000	0.000	0.000	0.000
29	B	31	ILE	0	-0.020	-0.017	17.857	0.018	0.018	0.000	0.000	0.000	0.000
30	B	32	TYR	0	0.047	0.029	13.862	-0.016	-0.016	0.000	0.000	0.000	0.000
31	B	33	ASN	0	0.052	0.017	11.374	-0.053	-0.053	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.898	0.931	13.278	0.011	0.011	0.000	0.000	0.000	0.000
33	B	35	GLU	-1	-0.833	-0.870	16.035	-0.212	-0.212	0.000	0.000	0.000	0.000
34	B	36	GLU	-1	-0.756	-0.853	18.694	-0.147	-0.147	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.089	0.063	20.605	0.014	0.014	0.000	0.000	0.000	0.000
36	B	38	ALA	0	0.012	-0.005	23.346	0.014	0.014	0.000	0.000	0.000	0.000
37	B	39	ARG	1	0.824	0.890	26.148	0.096	0.096	0.000	0.000	0.000	0.000
38	B	40	PHE	0	0.014	0.019	28.906	0.003	0.003	0.000	0.000	0.000	0.000
39	B	41	ASP	-1	-0.771	-0.869	32.160	-0.066	-0.066	0.000	0.000	0.000	0.000
40	B	42	SER	0	0.076	0.037	34.537	0.001	0.001	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.799	-0.873	37.671	-0.043	-0.043	0.000	0.000	0.000	0.000
42	B	44	VAL	0	-0.073	-0.038	36.012	0.003	0.003	0.000	0.000	0.000	0.000
43	B	45	GLY	0	0.020	0.020	38.391	0.000	0.000	0.000	0.000	0.000	0.000
44	B	46	VAL	0	-0.026	-0.021	37.017	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	47	TYR	0	0.020	0.001	30.418	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	48	ARG	1	0.902	0.956	31.781	0.090	0.090	0.000	0.000	0.000	0.000
47	B	49	ALA	0	0.043	0.033	28.272	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	50	VAL	0	-0.113	-0.053	25.563	0.019	0.019	0.000	0.000	0.000	0.000
49	B	51	THR	0	-0.017	-0.042	22.266	0.016	0.016	0.000	0.000	0.000	0.000
50	B	52	PRO	0	0.029	-0.012	24.174	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	53	LEU	0	0.006	0.020	19.227	-0.007	-0.007	0.000	0.000	0.000	0.000
52	B	54	GLY	0	-0.004	-0.003	23.393	-0.017	-0.017	0.000	0.000	0.000	0.000
53	B	55	PRO	0	-0.060	-0.018	26.065	0.005	0.005	0.000	0.000	0.000	0.000
54	B	56	PRO	0	0.084	0.038	27.347	0.006	0.006	0.000	0.000	0.000	0.000
55	B	57	ALA	0	0.007	0.012	26.745	0.003	0.003	0.000	0.000	0.000	0.000
56	B	58	ALA	0	-0.009	-0.004	28.880	0.011	0.011	0.000	0.000	0.000	0.000
57	B	59	GLU	-1	-0.942	-0.983	31.331	-0.150	-0.150	0.000	0.000	0.000	0.000
58	B	60	TYR	0	-0.021	-0.009	30.753	0.003	0.003	0.000	0.000	0.000	0.000
59	B	61	TRP	0	-0.003	-0.003	26.251	0.007	0.007	0.000	0.000	0.000	0.000
60	B	62	ASN	0	-0.010	-0.031	33.808	0.013	0.013	0.000	0.000	0.000	0.000
61	B	63	SER	0	-0.094	-0.048	36.421	0.007	0.007	0.000	0.000	0.000	0.000
62	B	64	GLN	0	0.025	0.019	35.851	-0.007	-0.007	0.000	0.000	0.000	0.000
63	B	65	LYS	1	0.924	0.962	38.794	0.088	0.088	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.838	-0.928	39.248	-0.126	-0.126	0.000	0.000	0.000	0.000
65	B	67	VAL	0	0.007	0.012	33.823	0.001	0.001	0.000	0.000	0.000	0.000
66	B	68	LEU	0	-0.004	0.016	36.531	0.002	0.002	0.000	0.000	0.000	0.000
67	B	69	GLU	-1	-0.834	-0.908	38.428	-0.083	-0.083	0.000	0.000	0.000	0.000
68	B	70	ARG	1	0.811	0.877	34.155	0.144	0.144	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.018	-0.006	33.546	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	72	ARG	1	0.801	0.877	36.397	0.095	0.095	0.000	0.000	0.000	0.000
71	B	73	ALA	0	0.026	0.018	39.512	0.005	0.005	0.000	0.000	0.000	0.000
72	B	74	GLU	-1	-0.781	-0.849	34.164	-0.128	-0.128	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.001	-0.001	37.756	0.003	0.003	0.000	0.000	0.000	0.000
74	B	76	ASP	-1	-0.867	-0.925	39.506	-0.053	-0.053	0.000	0.000	0.000	0.000
75	B	77	THR	0	0.007	-0.020	38.517	0.002	0.002	0.000	0.000	0.000	0.000
76	B	78	VAL	0	-0.008	0.007	33.674	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	80	ARG	1	0.902	0.921	37.599	0.057	0.057	0.000	0.000	0.000	0.000
78	B	81	HIS	0	0.000	0.010	38.519	0.007	0.007	0.000	0.000	0.000	0.000
79	B	82	ASN	0	0.039	0.005	34.390	0.003	0.003	0.000	0.000	0.000	0.000
80	B	83	TYR	0	0.036	0.023	38.278	0.006	0.006	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.025	0.027	40.060	0.008	0.008	0.000	0.000	0.000	0.000
82	B	85	LEU	0	0.018	0.017	38.444	0.004	0.004	0.000	0.000	0.000	0.000
83	B	86	GLU	-1	-0.844	-0.898	34.814	-0.034	-0.034	0.000	0.000	0.000	0.000
84	B	87	LEU	0	-0.064	-0.031	39.126	0.006	0.006	0.000	0.000	0.000	0.000
85	B	88	ARG	1	0.860	0.910	42.549	0.035	0.035	0.000	0.000	0.000	0.000
86	B	89	THR	0	-0.002	-0.004	39.124	0.002	0.002	0.000	0.000	0.000	0.000
87	B	90	THR	0	-0.012	-0.020	35.280	0.007	0.007	0.000	0.000	0.000	0.000
88	B	91	LEU	0	-0.030	-0.022	38.166	0.006	0.006	0.000	0.000	0.000	0.000
89	B	92	GLN	0	-0.041	-0.019	40.864	0.005	0.005	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.872	0.945	35.320	-0.013	-0.013	0.000	0.000	0.000	0.000
91	B	94	ARG	1	0.806	0.899	40.646	-0.006	-0.006	0.000	0.000	0.000	0.000
92	B	95	VAL	0	0.024	0.007	38.450	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	96	GLU	-1	-0.847	-0.930	41.208	0.027	0.027	0.000	0.000	0.000	0.000
94	B	97	PRO	0	-0.049	-0.013	40.866	0.002	0.002	0.000	0.000	0.000	0.000
95	B	98	THR	0	0.025	0.027	40.427	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	99	VAL	0	-0.019	-0.019	41.319	0.004	0.004	0.000	0.000	0.000	0.000
97	B	100	THR	0	-0.012	-0.004	41.791	0.000	0.000	0.000	0.000	0.000	0.000
98	B	101	ILE	0	0.009	-0.002	43.203	0.002	0.002	0.000	0.000	0.000	0.000
99	B	102	SER	0	-0.001	0.005	41.214	-0.002	-0.002	0.000	0.000	0.000	0.000
100	B	103	PRO	0	0.011	0.005	42.527	0.003	0.003	0.000	0.000	0.000	0.000
101	B	104	SER	0	-0.042	-0.006	38.758	0.008	0.008	0.000	0.000	0.000	0.000
102	B	114	LEU	0	0.014	0.018	38.551	0.001	0.001	0.000	0.000	0.000	0.000
103	B	115	LEU	0	-0.059	-0.049	43.307	0.000	0.000	0.000	0.000	0.000	0.000
104	B	116	VAL	0	0.000	0.003	37.756	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	117	CYS	0	-0.069	-0.030	41.148	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	118	SER	0	-0.018	-0.004	38.303	0.004	0.004	0.000	0.000	0.000	0.000
107	B	119	VAL	0	-0.005	-0.005	38.632	-0.006	-0.006	0.000	0.000	0.000	0.000
108	B	120	THR	0	-0.017	-0.046	36.147	0.004	0.004	0.000	0.000	0.000	0.000
109	B	121	ASP	-1	-0.817	-0.908	34.839	0.070	0.070	0.000	0.000	0.000	0.000
110	B	122	PHE	0	0.005	0.023	36.579	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	123	TYR	0	-0.009	-0.021	33.641	0.001	0.001	0.000	0.000	0.000	0.000
112	B	124	PRO	0	-0.018	-0.010	37.115	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	125	ALA	0	0.036	0.005	34.511	0.003	0.003	0.000	0.000	0.000	0.000
114	B	126	GLN	0	-0.053	-0.024	36.475	0.005	0.005	0.000	0.000	0.000	0.000
115	B	127	ILE	0	0.037	0.018	38.748	-0.003	-0.003	0.000	0.000	0.000	0.000
116	B	128	LYS	1	0.831	0.904	41.317	-0.031	-0.031	0.000	0.000	0.000	0.000
117	B	129	VAL	0	0.014	0.015	41.066	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	130	ARG	1	0.754	0.870	43.759	-0.042	-0.042	0.000	0.000	0.000	0.000
119	B	131	TRP	0	0.032	0.010	43.542	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	132	PHE	0	0.004	0.009	48.326	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	133	ARG	1	0.756	0.857	52.090	-0.047	-0.047	0.000	0.000	0.000	0.000
122	B	134	ASN	0	0.029	-0.006	54.958	0.000	0.000	0.000	0.000	0.000	0.000
123	B	135	ASP	-1	-0.860	-0.913	57.837	0.045	0.045	0.000	0.000	0.000	0.000
124	B	136	GLN	0	-0.037	-0.016	58.992	0.000	0.000	0.000	0.000	0.000	0.000
125	B	137	GLU	-1	-0.869	-0.913	56.336	0.048	0.048	0.000	0.000	0.000	0.000
126	B	138	GLU	-1	-0.841	-0.936	50.734	0.048	0.048	0.000	0.000	0.000	0.000
127	B	139	THR	0	-0.026	-0.005	50.177	0.000	0.000	0.000	0.000	0.000	0.000
128	B	140	THR	0	0.022	-0.002	46.559	0.000	0.000	0.000	0.000	0.000	0.000
129	B	141	GLY	0	-0.016	0.010	46.244	0.002	0.002	0.000	0.000	0.000	0.000
130	B	142	VAL	0	-0.016	-0.013	42.882	0.003	0.003	0.000	0.000	0.000	0.000
131	B	143	VAL	0	0.012	0.008	36.668	0.002	0.002	0.000	0.000	0.000	0.000
132	B	144	SER	0	0.000	-0.017	36.249	-0.005	-0.005	0.000	0.000	0.000	0.000
133	B	145	THR	0	-0.015	0.010	32.032	0.006	0.006	0.000	0.000	0.000	0.000
134	B	146	PRO	0	0.006	0.000	29.027	-0.010	-0.010	0.000	0.000	0.000	0.000
135	B	147	LEU	0	-0.002	0.000	32.052	0.001	0.001	0.000	0.000	0.000	0.000
136	B	148	ILE	0	0.007	0.017	28.363	0.000	0.000	0.000	0.000	0.000	0.000
137	B	149	ARG	1	0.939	0.959	27.113	-0.062	-0.062	0.000	0.000	0.000	0.000
138	B	150	ASN	0	0.028	0.036	27.281	0.021	0.021	0.000	0.000	0.000	0.000
139	B	151	GLY	0	-0.033	-0.011	26.239	0.004	0.004	0.000	0.000	0.000	0.000
140	B	152	ASP	-1	-0.827	-0.889	27.171	0.042	0.042	0.000	0.000	0.000	0.000
141	B	153	TRP	0	-0.051	-0.034	30.041	-0.004	-0.004	0.000	0.000	0.000	0.000
142	B	154	THR	0	-0.038	-0.013	31.882	-0.001	-0.001	0.000	0.000	0.000	0.000
143	B	155	PHE	0	-0.049	-0.040	31.118	0.002	0.002	0.000	0.000	0.000	0.000
144	B	156	GLN	0	-0.017	-0.019	31.416	0.000	0.000	0.000	0.000	0.000	0.000
145	B	157	ILE	0	-0.076	-0.031	33.683	0.003	0.003	0.000	0.000	0.000	0.000
146	B	158	LEU	0	0.042	0.017	33.822	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	159	VAL	0	0.012	-0.002	36.928	0.005	0.005	0.000	0.000	0.000	0.000
148	B	160	MET	0	-0.018	0.000	35.364	0.000	0.000	0.000	0.000	0.000	0.000
149	B	161	LEU	0	0.025	0.024	40.597	-0.003	-0.003	0.000	0.000	0.000	0.000
150	B	162	GLU	-1	-0.919	-0.964	41.131	0.110	0.110	0.000	0.000	0.000	0.000
151	B	172	THR	0	-0.024	-0.023	50.630	0.001	0.001	0.000	0.000	0.000	0.000
152	B	174	HIS	0	-0.024	-0.006	47.903	-0.004	-0.004	0.000	0.000	0.000	0.000
153	B	175	VAL	0	0.016	-0.007	43.791	0.002	0.002	0.000	0.000	0.000	0.000
154	B	176	GLU	-1	-0.774	-0.860	45.874	0.032	0.032	0.000	0.000	0.000	0.000
155	B	177	HIS	0	0.046	0.015	39.947	0.001	0.001	0.000	0.000	0.000	0.000
156	B	178	PRO	0	-0.044	-0.026	42.836	-0.002	-0.002	0.000	0.000	0.000	0.000
157	B	179	SER	0	-0.025	-0.020	44.028	-0.003	-0.003	0.000	0.000	0.000	0.000
158	B	180	LEU	0	-0.053	-0.020	46.005	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	181	GLN	0	-0.036	-0.017	48.632	0.000	0.000	0.000	0.000	0.000	0.000
160	B	182	ASN	0	-0.022	-0.009	52.104	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	183	PRO	0	-0.013	-0.010	49.805	0.001	0.001	0.000	0.000	0.000	0.000
162	B	184	ILE	0	0.045	0.031	47.242	-0.001	-0.001	0.000	0.000	0.000	0.000
163	B	185	ILE	0	0.005	-0.004	49.655	0.001	0.001	0.000	0.000	0.000	0.000
164	B	186	VAL	0	-0.035	-0.012	47.497	-0.001	-0.001	0.000	0.000	0.000	0.000
165	B	187	GLU	-1	-0.798	-0.886	49.993	0.052	0.052	0.000	0.000	0.000	0.000
166	B	188	TRP	0	-0.022	-0.004	49.377	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)