FMO DATABASE

FMODB ID: LZ6M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1559756.977917
FMO2-HF: Nuclear repulsion	1490255.492596
FMO2-HF: Total energy	-69501.485321
FMO2-MP2: Total energy	-69703.940865

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.
-5.909	-4.171	-0.006	-0.959	-0.773	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 : 0.014 / q_NPA : 0.000

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	-0.927	-0.952	3.622	-6.033	-4.295	-0.006	-0.959	-0.773	0.002
4	B	6	ASP	-1	-0.918	-0.969	5.838	-0.907	-0.907	0.000	0.000	0.000	0.000
5	B	7	PHE	0	-0.058	-0.006	8.055	0.267	0.267	0.000	0.000	0.000	0.000
6	B	8	VAL	0	0.028	0.018	10.622	0.190	0.190	0.000	0.000	0.000	0.000
7	B	9	TYR	0	-0.008	-0.025	13.311	0.099	0.099	0.000	0.000	0.000	0.000
8	B	10	GLN	0	-0.024	-0.018	16.173	0.086	0.086	0.000	0.000	0.000	0.000
9	B	11	PHE	0	0.034	0.014	19.524	0.014	0.014	0.000	0.000	0.000	0.000
10	B	12	LYS	1	0.897	0.950	19.679	0.220	0.220	0.000	0.000	0.000	0.000
11	B	13	GLY	0	0.040	0.021	25.321	0.011	0.011	0.000	0.000	0.000	0.000
12	B	14	MET	0	-0.026	0.001	27.477	0.005	0.005	0.000	0.000	0.000	0.000
13	B	15	CYS	0	-0.045	-0.017	30.546	0.003	0.003	0.000	0.000	0.000	0.000
14	B	16	TYR	0	-0.015	-0.005	29.845	0.000	0.000	0.000	0.000	0.000	0.000
15	B	17	PHE	0	0.024	0.007	35.865	0.000	0.000	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.036	-0.029	39.144	0.003	0.003	0.000	0.000	0.000	0.000
17	B	19	ASN	0	-0.002	0.003	41.769	0.000	0.000	0.000	0.000	0.000	0.000
18	B	20	GLY	0	0.051	0.041	44.027	0.000	0.000	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.048	-0.053	42.477	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	22	GLU	-1	-0.894	-0.933	44.506	-0.031	-0.031	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.914	0.959	38.768	0.051	0.051	0.000	0.000	0.000	0.000
22	B	24	VAL	0	-0.050	-0.011	39.470	0.000	0.000	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.739	0.838	34.808	0.076	0.076	0.000	0.000	0.000	0.000
24	B	26	LEU	0	0.015	0.009	33.513	0.001	0.001	0.000	0.000	0.000	0.000
25	B	27	VAL	0	-0.045	-0.031	29.821	0.001	0.001	0.000	0.000	0.000	0.000
26	B	28	THR	0	-0.003	0.016	29.075	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	29	ARG	1	0.843	0.899	24.824	0.131	0.131	0.000	0.000	0.000	0.000
28	B	30	TYR	0	0.035	0.023	23.595	-0.016	-0.016	0.000	0.000	0.000	0.000
29	B	31	ILE	0	-0.020	-0.018	18.016	0.021	0.021	0.000	0.000	0.000	0.000
30	B	32	TYR	0	0.039	0.031	14.494	-0.031	-0.031	0.000	0.000	0.000	0.000
31	B	33	ASN	0	0.069	0.022	12.123	-0.062	-0.062	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.921	0.947	13.347	0.148	0.148	0.000	0.000	0.000	0.000
33	B	35	GLU	-1	-0.852	-0.877	16.225	-0.257	-0.257	0.000	0.000	0.000	0.000
34	B	36	GLU	-1	-0.745	-0.854	18.917	-0.188	-0.188	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.086	0.049	21.034	0.011	0.011	0.000	0.000	0.000	0.000
36	B	38	ALA	0	0.009	0.013	23.853	0.020	0.020	0.000	0.000	0.000	0.000
37	B	39	ARG	1	0.808	0.882	26.569	0.131	0.131	0.000	0.000	0.000	0.000
38	B	40	PHE	0	0.012	0.011	29.161	0.006	0.006	0.000	0.000	0.000	0.000
39	B	41	ASP	-1	-0.757	-0.855	32.483	-0.090	-0.090	0.000	0.000	0.000	0.000
40	B	42	SER	0	0.042	0.016	34.674	0.001	0.001	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.825	-0.902	37.601	-0.063	-0.063	0.000	0.000	0.000	0.000
42	B	44	VAL	0	-0.082	-0.028	36.179	0.003	0.003	0.000	0.000	0.000	0.000
43	B	45	GLY	0	0.041	0.025	38.132	0.003	0.003	0.000	0.000	0.000	0.000
44	B	46	VAL	0	-0.042	-0.033	37.257	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	47	TYR	0	0.017	-0.007	30.607	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	48	ARG	1	0.921	0.959	31.980	0.110	0.110	0.000	0.000	0.000	0.000
47	B	49	ALA	0	0.022	0.021	28.782	-0.009	-0.009	0.000	0.000	0.000	0.000
48	B	50	VAL	0	-0.104	-0.057	25.662	0.016	0.016	0.000	0.000	0.000	0.000
49	B	51	THR	0	0.018	-0.025	22.510	0.016	0.016	0.000	0.000	0.000	0.000
50	B	52	PRO	0	0.003	-0.011	24.630	-0.004	-0.004	0.000	0.000	0.000	0.000
51	B	53	LEU	0	0.027	0.019	19.559	-0.008	-0.008	0.000	0.000	0.000	0.000
52	B	54	GLY	0	-0.030	-0.015	23.867	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	55	PRO	0	-0.029	-0.007	26.593	0.003	0.003	0.000	0.000	0.000	0.000
54	B	56	PRO	0	0.059	0.029	27.290	0.008	0.008	0.000	0.000	0.000	0.000
55	B	57	ALA	0	0.008	0.010	26.898	0.004	0.004	0.000	0.000	0.000	0.000
56	B	58	ALA	0	-0.016	-0.018	29.035	0.011	0.011	0.000	0.000	0.000	0.000
57	B	59	GLU	-1	-0.964	-0.998	31.555	-0.158	-0.158	0.000	0.000	0.000	0.000
58	B	60	TYR	0	-0.045	-0.016	31.302	0.005	0.005	0.000	0.000	0.000	0.000
59	B	61	TRP	0	0.015	0.008	26.718	0.005	0.005	0.000	0.000	0.000	0.000
60	B	62	ASN	0	0.004	-0.015	34.207	0.011	0.011	0.000	0.000	0.000	0.000
61	B	63	SER	0	-0.092	-0.040	36.900	0.009	0.009	0.000	0.000	0.000	0.000
62	B	64	GLN	0	0.041	0.026	35.811	-0.008	-0.008	0.000	0.000	0.000	0.000
63	B	65	LYS	1	0.951	0.992	39.212	0.094	0.094	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.842	-0.929	39.689	-0.137	-0.137	0.000	0.000	0.000	0.000
65	B	67	VAL	0	0.019	0.012	34.285	0.001	0.001	0.000	0.000	0.000	0.000
66	B	68	LEU	0	-0.011	0.010	36.870	0.000	0.000	0.000	0.000	0.000	0.000
67	B	69	GLU	-1	-0.859	-0.935	38.776	-0.095	-0.095	0.000	0.000	0.000	0.000
68	B	70	ARG	1	0.841	0.897	34.378	0.159	0.159	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.027	-0.003	33.783	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	72	ARG	1	0.824	0.889	36.520	0.108	0.108	0.000	0.000	0.000	0.000
71	B	73	ALA	0	0.020	0.016	39.472	0.005	0.005	0.000	0.000	0.000	0.000
72	B	74	GLU	-1	-0.801	-0.863	34.399	-0.149	-0.149	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.007	-0.004	37.745	0.002	0.002	0.000	0.000	0.000	0.000
74	B	76	ASP	-1	-0.861	-0.931	39.536	-0.069	-0.069	0.000	0.000	0.000	0.000
75	B	77	THR	0	-0.003	-0.014	38.532	0.002	0.002	0.000	0.000	0.000	0.000
76	B	78	VAL	0	-0.017	0.001	33.845	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	80	ARG	1	0.887	0.913	38.147	0.072	0.072	0.000	0.000	0.000	0.000
78	B	81	HIS	0	-0.006	0.012	39.315	0.008	0.008	0.000	0.000	0.000	0.000
79	B	82	ASN	0	0.048	0.013	35.083	0.004	0.004	0.000	0.000	0.000	0.000
80	B	83	TYR	0	0.031	0.021	39.057	0.006	0.006	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.036	0.025	40.696	0.008	0.008	0.000	0.000	0.000	0.000
82	B	85	LEU	0	0.023	0.010	39.418	0.005	0.005	0.000	0.000	0.000	0.000
83	B	86	GLU	-1	-0.873	-0.901	35.408	-0.059	-0.059	0.000	0.000	0.000	0.000
84	B	87	LEU	0	-0.053	-0.031	39.757	0.005	0.005	0.000	0.000	0.000	0.000
85	B	88	ARG	1	0.835	0.911	43.278	0.050	0.050	0.000	0.000	0.000	0.000
86	B	89	THR	0	0.027	0.018	39.369	0.003	0.003	0.000	0.000	0.000	0.000
87	B	90	THR	0	0.017	-0.010	36.001	0.007	0.007	0.000	0.000	0.000	0.000
88	B	91	LEU	0	-0.029	-0.020	38.736	0.006	0.006	0.000	0.000	0.000	0.000
89	B	92	GLN	0	-0.053	-0.022	41.366	0.005	0.005	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.873	0.951	35.769	0.011	0.011	0.000	0.000	0.000	0.000
91	B	94	ARG	1	0.809	0.891	40.717	0.013	0.013	0.000	0.000	0.000	0.000
92	B	95	VAL	0	-0.002	-0.008	38.884	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	96	GLU	-1	-0.864	-0.942	41.801	0.008	0.008	0.000	0.000	0.000	0.000
94	B	97	PRO	0	-0.026	0.003	40.910	0.002	0.002	0.000	0.000	0.000	0.000
95	B	98	THR	0	-0.035	-0.008	40.873	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	99	VAL	0	-0.005	-0.005	41.397	0.004	0.004	0.000	0.000	0.000	0.000
97	B	100	THR	0	-0.022	-0.008	42.165	0.000	0.000	0.000	0.000	0.000	0.000
98	B	101	ILE	0	0.001	-0.010	43.447	0.002	0.002	0.000	0.000	0.000	0.000
99	B	102	SER	0	0.010	0.009	41.459	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	103	PRO	0	0.011	0.000	42.322	0.003	0.003	0.000	0.000	0.000	0.000
101	B	104	SER	0	-0.072	-0.022	38.964	0.006	0.006	0.000	0.000	0.000	0.000
102	B	114	LEU	0	0.040	0.020	38.835	0.001	0.001	0.000	0.000	0.000	0.000
103	B	115	LEU	0	-0.054	-0.041	43.565	0.001	0.001	0.000	0.000	0.000	0.000
104	B	116	VAL	0	-0.026	-0.011	38.119	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	117	CYS	0	-0.066	-0.034	41.574	-0.003	-0.003	0.000	0.000	0.000	0.000
106	B	118	SER	0	-0.036	-0.009	37.996	0.001	0.001	0.000	0.000	0.000	0.000
107	B	119	VAL	0	0.010	-0.001	38.636	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	120	THR	0	0.008	-0.021	36.043	0.003	0.003	0.000	0.000	0.000	0.000
109	B	121	ASP	-1	-0.880	-0.948	34.986	0.038	0.038	0.000	0.000	0.000	0.000
110	B	122	PHE	0	0.034	0.024	36.750	-0.004	-0.004	0.000	0.000	0.000	0.000
111	B	123	TYR	0	-0.005	0.000	33.845	-0.002	-0.002	0.000	0.000	0.000	0.000
112	B	124	PRO	0	-0.017	-0.013	37.371	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	125	ALA	0	0.052	0.008	34.969	0.004	0.004	0.000	0.000	0.000	0.000
114	B	126	GLN	0	-0.040	-0.022	36.887	0.006	0.006	0.000	0.000	0.000	0.000
115	B	127	ILE	0	0.025	0.013	38.831	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	128	LYS	1	0.835	0.904	41.546	-0.013	-0.013	0.000	0.000	0.000	0.000
117	B	129	VAL	0	0.018	0.026	41.227	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	130	ARG	1	0.786	0.895	44.038	-0.024	-0.024	0.000	0.000	0.000	0.000
119	B	131	TRP	0	0.014	0.001	43.923	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	132	PHE	0	0.033	0.021	48.599	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	133	ARG	1	0.692	0.826	52.380	-0.034	-0.034	0.000	0.000	0.000	0.000
122	B	134	ASN	0	0.033	0.000	55.301	0.000	0.000	0.000	0.000	0.000	0.000
123	B	135	ASP	-1	-0.865	-0.912	57.919	0.034	0.034	0.000	0.000	0.000	0.000
124	B	136	GLN	0	-0.033	-0.020	59.352	0.000	0.000	0.000	0.000	0.000	0.000
125	B	137	GLU	-1	-0.862	-0.922	56.772	0.035	0.035	0.000	0.000	0.000	0.000
126	B	138	GLU	-1	-0.894	-0.966	51.136	0.030	0.030	0.000	0.000	0.000	0.000
127	B	139	THR	0	-0.007	0.015	50.484	0.000	0.000	0.000	0.000	0.000	0.000
128	B	140	THR	0	0.002	-0.008	46.816	0.000	0.000	0.000	0.000	0.000	0.000
129	B	141	GLY	0	0.004	0.011	46.343	0.000	0.000	0.000	0.000	0.000	0.000
130	B	142	VAL	0	-0.020	-0.011	42.835	0.003	0.003	0.000	0.000	0.000	0.000
131	B	143	VAL	0	0.021	0.012	36.902	0.002	0.002	0.000	0.000	0.000	0.000
132	B	144	SER	0	0.022	0.007	36.915	-0.003	-0.003	0.000	0.000	0.000	0.000
133	B	145	THR	0	-0.022	0.006	32.292	0.003	0.003	0.000	0.000	0.000	0.000
134	B	146	PRO	0	0.002	-0.009	29.467	-0.008	-0.008	0.000	0.000	0.000	0.000
135	B	147	LEU	0	-0.013	-0.009	32.321	0.002	0.002	0.000	0.000	0.000	0.000
136	B	148	ILE	0	0.013	0.023	28.309	-0.003	-0.003	0.000	0.000	0.000	0.000
137	B	149	ARG	1	0.941	0.961	27.131	-0.015	-0.015	0.000	0.000	0.000	0.000
138	B	150	ASN	0	0.054	0.038	27.106	0.018	0.018	0.000	0.000	0.000	0.000
139	B	151	GLY	0	-0.047	-0.015	26.131	0.002	0.002	0.000	0.000	0.000	0.000
140	B	152	ASP	-1	-0.833	-0.898	27.110	0.009	0.009	0.000	0.000	0.000	0.000
141	B	153	TRP	0	-0.061	-0.039	30.024	0.000	0.000	0.000	0.000	0.000	0.000
142	B	154	THR	0	-0.019	0.008	32.155	0.001	0.001	0.000	0.000	0.000	0.000
143	B	155	PHE	0	-0.059	-0.045	31.176	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	156	GLN	0	0.000	-0.005	31.032	0.003	0.003	0.000	0.000	0.000	0.000
145	B	157	ILE	0	-0.037	-0.026	33.634	0.001	0.001	0.000	0.000	0.000	0.000
146	B	158	LEU	0	0.033	0.025	33.677	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	159	VAL	0	-0.001	0.000	37.014	0.004	0.004	0.000	0.000	0.000	0.000
148	B	160	MET	0	-0.020	-0.017	35.473	0.001	0.001	0.000	0.000	0.000	0.000
149	B	161	LEU	0	0.032	0.013	40.547	-0.004	-0.004	0.000	0.000	0.000	0.000
150	B	162	GLU	-1	-0.926	-0.943	41.974	0.088	0.088	0.000	0.000	0.000	0.000
151	B	172	THR	0	-0.016	-0.027	50.973	0.001	0.001	0.000	0.000	0.000	0.000
152	B	174	HIS	0	0.021	0.016	48.426	-0.003	-0.003	0.000	0.000	0.000	0.000
153	B	175	VAL	0	0.013	-0.001	43.572	0.000	0.000	0.000	0.000	0.000	0.000
154	B	176	GLU	-1	-0.792	-0.881	46.033	0.015	0.015	0.000	0.000	0.000	0.000
155	B	177	HIS	0	0.034	0.015	40.139	0.000	0.000	0.000	0.000	0.000	0.000
156	B	178	PRO	0	-0.039	-0.032	43.291	-0.001	-0.001	0.000	0.000	0.000	0.000
157	B	179	SER	0	-0.044	-0.030	44.074	-0.002	-0.002	0.000	0.000	0.000	0.000
158	B	180	LEU	0	-0.028	0.004	46.231	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	181	GLN	0	-0.018	-0.005	48.823	-0.001	-0.001	0.000	0.000	0.000	0.000
160	B	182	ASN	0	-0.012	-0.007	52.471	-0.001	-0.001	0.000	0.000	0.000	0.000
161	B	183	PRO	0	-0.001	-0.010	50.235	0.001	0.001	0.000	0.000	0.000	0.000
162	B	184	ILE	0	0.034	0.027	47.251	0.000	0.000	0.000	0.000	0.000	0.000
163	B	185	ILE	0	-0.019	-0.011	49.556	0.002	0.002	0.000	0.000	0.000	0.000
164	B	186	VAL	0	-0.018	-0.002	47.662	-0.001	-0.001	0.000	0.000	0.000	0.000
165	B	187	GLU	-1	-0.797	-0.883	50.147	0.037	0.037	0.000	0.000	0.000	0.000
166	B	188	TRP	0	-0.009	0.002	49.474	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)