FMO DATABASE

FMODB ID: G6LZ1

Calculation Name: 4GRW-A-Xray372

Preferred Name: Interleukin-12 subunit beta

Target Type: SINGLE PROTEIN

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

ligand 3-letter code: NAG

PDB ID: 4GRW

Chain ID: A

ChEMBL ID: CHEMBL3580484

UniProt ID: P29460

Base Structure: X-ray

Registration Date: 2023-06-21

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	129
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1085837.781062
FMO2-HF: Nuclear repulsion	1035350.432755
FMO2-HF: Total energy	-50487.348306
FMO2-MP2: Total energy	-50634.363352

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:8:SER)

Summations of interaction energy for fragment #1(A:8: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.
-1.42	-0.019999999999998	-0.017	-0.598	-0.786	0.003

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.015

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

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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	10	ALA	0	0.054	0.033	3.825	-1.455	-0.151	-0.016	-0.594	-0.695	0.003
4	A	11	TRP	0	0.031	0.008	4.752	-0.087	0.009	-0.001	-0.004	-0.091	0.000
5	A	12	THR	0	0.074	0.030	8.120	0.061	0.061	0.000	0.000	0.000	0.000
6	A	13	GLN	0	-0.006	0.002	10.401	-0.134	-0.134	0.000	0.000	0.000	0.000
7	A	14	CYS	0	0.021	0.013	9.280	0.117	0.117	0.000	0.000	0.000	0.000
8	A	15	GLN	0	0.036	0.037	11.898	0.019	0.019	0.000	0.000	0.000	0.000
9	A	16	GLN	0	-0.029	-0.022	13.941	0.029	0.029	0.000	0.000	0.000	0.000
10	A	17	LEU	0	-0.017	0.002	14.950	0.016	0.016	0.000	0.000	0.000	0.000
11	A	18	SER	0	0.006	-0.011	15.182	0.032	0.032	0.000	0.000	0.000	0.000
12	A	19	GLN	0	0.033	0.016	17.333	0.011	0.011	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.960	0.975	19.794	0.050	0.050	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.022	0.008	18.252	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	22	CYS	0	-0.030	0.002	21.136	0.011	0.011	0.000	0.000	0.000	0.000
16	A	23	THR	0	-0.025	-0.011	23.829	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	24	LEU	0	-0.042	-0.019	23.582	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	25	ALA	0	0.060	0.021	25.358	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	26	TRP	0	-0.009	0.011	27.248	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	27	SER	0	-0.053	-0.040	29.535	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.015	0.003	30.356	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	29	HIS	0	-0.066	-0.054	31.947	0.006	0.006	0.000	0.000	0.000	0.000
23	A	30	PRO	0	0.086	0.077	33.010	0.009	0.009	0.000	0.000	0.000	0.000
24	A	31	LEU	0	-0.048	-0.017	32.919	0.002	0.002	0.000	0.000	0.000	0.000
25	A	47	ASN	0	-0.021	-0.047	33.957	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	48	ASP	-1	-0.975	-0.968	30.524	0.123	0.123	0.000	0.000	0.000	0.000
27	A	49	VAL	0	-0.009	0.005	26.102	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	50	PRO	0	-0.010	0.015	21.785	0.010	0.010	0.000	0.000	0.000	0.000
29	A	51	HIS	0	-0.021	-0.029	23.069	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	52	ILE	0	-0.012	-0.002	17.700	0.016	0.016	0.000	0.000	0.000	0.000
31	A	53	GLN	0	-0.036	-0.034	20.595	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	54	CYM	-1	-0.871	-0.947	20.687	0.437	0.437	0.000	0.000	0.000	0.000
33	A	55	GLY	0	-0.020	-0.003	20.870	0.038	0.038	0.000	0.000	0.000	0.000
34	A	56	ASP	-1	-0.888	-0.946	17.082	0.565	0.565	0.000	0.000	0.000	0.000
35	A	57	GLY	0	0.021	0.020	15.526	0.114	0.114	0.000	0.000	0.000	0.000
36	A	58	CYS	0	-0.045	-0.011	11.715	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.832	-0.911	15.702	0.687	0.687	0.000	0.000	0.000	0.000
38	A	60	PRO	0	-0.021	-0.040	15.215	0.112	0.112	0.000	0.000	0.000	0.000
39	A	61	GLN	0	-0.018	-0.001	14.473	0.084	0.084	0.000	0.000	0.000	0.000
40	A	62	GLY	0	0.060	0.038	14.660	0.081	0.081	0.000	0.000	0.000	0.000
41	A	63	LEU	0	-0.051	-0.039	10.469	0.249	0.249	0.000	0.000	0.000	0.000
42	A	64	ARG	1	0.893	0.954	9.828	-0.566	-0.566	0.000	0.000	0.000	0.000
43	A	65	ASP	-1	-0.897	-0.936	10.521	1.107	1.107	0.000	0.000	0.000	0.000
44	A	66	ASN	0	0.005	-0.020	8.815	0.615	0.615	0.000	0.000	0.000	0.000
45	A	67	SER	0	0.019	0.020	5.917	0.031	0.031	0.000	0.000	0.000	0.000
46	A	68	GLN	0	-0.005	-0.013	4.910	-1.130	-1.130	0.000	0.000	0.000	0.000
47	A	69	PHE	0	0.019	0.022	8.390	-0.373	-0.373	0.000	0.000	0.000	0.000
48	A	71	LEU	0	0.000	-0.021	6.494	-0.256	-0.256	0.000	0.000	0.000	0.000
49	A	72	GLN	0	0.016	0.021	10.400	-0.363	-0.363	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.918	0.980	12.061	-0.662	-0.662	0.000	0.000	0.000	0.000
51	A	74	ILE	0	-0.020	-0.015	12.636	-0.130	-0.130	0.000	0.000	0.000	0.000
52	A	75	HIS	0	0.019	0.003	11.997	-0.076	-0.076	0.000	0.000	0.000	0.000
53	A	76	GLN	0	0.011	-0.001	14.169	-0.064	-0.064	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.001	-0.009	17.315	-0.059	-0.059	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.028	-0.019	14.783	-0.047	-0.047	0.000	0.000	0.000	0.000
56	A	79	ILE	0	-0.005	0.011	16.736	-0.051	-0.051	0.000	0.000	0.000	0.000
57	A	80	PHE	0	-0.012	-0.003	19.815	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	81	TYR	0	0.043	-0.005	22.014	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	82	GLU	-1	-0.898	-0.942	20.988	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	83	LYS	1	0.979	0.996	22.930	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	84	LEU	0	0.002	-0.001	25.866	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	85	LEU	0	-0.049	-0.027	25.761	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	86	GLY	0	0.029	0.026	28.031	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	87	SER	0	-0.060	-0.030	29.362	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	88	ASP	-1	-0.866	-0.951	31.944	0.022	0.022	0.000	0.000	0.000	0.000
66	A	89	ILE	0	-0.036	-0.011	32.671	0.000	0.000	0.000	0.000	0.000	0.000
67	A	90	PHE	0	-0.026	-0.015	30.934	0.001	0.001	0.000	0.000	0.000	0.000
68	A	91	THR	0	0.011	0.006	33.148	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	92	GLY	0	-0.009	0.017	35.819	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	93	GLU	-1	-0.958	-0.961	39.137	0.005	0.005	0.000	0.000	0.000	0.000
71	A	94	PRO	0	-0.020	-0.025	41.153	0.005	0.005	0.000	0.000	0.000	0.000
72	A	95	SER	0	0.028	0.006	39.621	0.002	0.002	0.000	0.000	0.000	0.000
73	A	96	LEU	0	-0.027	-0.005	33.609	0.002	0.002	0.000	0.000	0.000	0.000
74	A	97	LEU	0	0.032	0.015	37.737	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	98	PRO	0	0.012	-0.014	36.336	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.924	-0.946	34.642	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	100	SER	0	0.003	0.009	33.491	0.004	0.004	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.030	0.013	29.773	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	102	VAL	0	0.001	-0.010	28.504	0.000	0.000	0.000	0.000	0.000	0.000
80	A	103	GLY	0	0.051	0.036	28.180	0.000	0.000	0.000	0.000	0.000	0.000
81	A	104	GLN	0	0.016	-0.001	24.884	0.000	0.000	0.000	0.000	0.000	0.000
82	A	105	LEU	0	-0.042	-0.018	23.943	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	106	HIS	0	0.014	0.001	23.328	0.008	0.008	0.000	0.000	0.000	0.000
84	A	107	ALA	0	-0.003	-0.002	22.814	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	108	SER	0	-0.051	-0.040	20.043	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	109	LEU	0	-0.032	-0.005	18.639	0.004	0.004	0.000	0.000	0.000	0.000
87	A	110	LEU	0	0.024	0.021	17.806	0.015	0.015	0.000	0.000	0.000	0.000
88	A	111	GLY	0	0.023	0.019	16.537	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	112	LEU	0	-0.025	-0.015	12.697	-0.069	-0.069	0.000	0.000	0.000	0.000
90	A	113	SER	0	0.003	-0.011	12.850	0.010	0.010	0.000	0.000	0.000	0.000
91	A	114	GLN	0	0.006	-0.011	12.762	0.011	0.011	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.041	-0.017	9.621	-0.145	-0.145	0.000	0.000	0.000	0.000
93	A	116	LEU	0	-0.078	-0.020	8.226	-0.216	-0.216	0.000	0.000	0.000	0.000
94	A	117	GLN	0	-0.033	-0.034	7.964	0.202	0.202	0.000	0.000	0.000	0.000
95	A	118	PRO	0	-0.018	0.020	9.034	0.088	0.088	0.000	0.000	0.000	0.000
96	A	135	GLN	0	0.050	0.017	39.265	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.015	0.013	43.330	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	137	TRP	0	-0.022	0.014	43.710	0.004	0.004	0.000	0.000	0.000	0.000
99	A	138	GLN	0	0.089	-0.005	43.301	0.000	0.000	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.891	0.979	38.231	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	140	LEU	0	-0.005	-0.010	38.138	0.002	0.002	0.000	0.000	0.000	0.000
102	A	141	LEU	0	0.027	0.008	37.665	0.005	0.005	0.000	0.000	0.000	0.000
103	A	142	LEU	0	0.019	0.003	34.281	0.006	0.006	0.000	0.000	0.000	0.000
104	A	143	ARG	1	0.878	0.923	33.646	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	144	PHE	0	0.009	-0.002	32.890	0.005	0.005	0.000	0.000	0.000	0.000
106	A	145	LYS	1	0.945	0.981	33.612	-0.084	-0.084	0.000	0.000	0.000	0.000
107	A	146	ILE	0	0.026	0.029	28.563	0.013	0.013	0.000	0.000	0.000	0.000
108	A	147	LEU	0	0.015	-0.003	28.814	0.012	0.012	0.000	0.000	0.000	0.000
109	A	148	ARG	1	0.982	1.007	28.987	-0.095	-0.095	0.000	0.000	0.000	0.000
110	A	149	SER	0	-0.046	-0.033	27.827	0.014	0.014	0.000	0.000	0.000	0.000
111	A	150	LEU	0	0.014	0.010	23.030	0.022	0.022	0.000	0.000	0.000	0.000
112	A	151	GLN	0	-0.056	-0.049	24.135	0.024	0.024	0.000	0.000	0.000	0.000
113	A	152	ALA	0	-0.019	0.001	24.877	0.013	0.013	0.000	0.000	0.000	0.000
114	A	153	PHE	0	-0.026	-0.007	17.615	0.025	0.025	0.000	0.000	0.000	0.000
115	A	154	VAL	0	0.022	-0.013	19.857	0.042	0.042	0.000	0.000	0.000	0.000
116	A	155	ALA	0	0.013	0.013	19.943	0.014	0.014	0.000	0.000	0.000	0.000
117	A	156	VAL	0	-0.043	-0.018	18.142	0.020	0.020	0.000	0.000	0.000	0.000
118	A	157	ALA	0	0.059	0.028	15.911	0.061	0.061	0.000	0.000	0.000	0.000
119	A	158	ALA	0	0.002	-0.005	15.364	0.059	0.059	0.000	0.000	0.000	0.000
120	A	159	ARG	1	0.903	0.957	16.451	-0.292	-0.292	0.000	0.000	0.000	0.000
121	A	160	VAL	0	0.038	0.028	12.054	0.028	0.028	0.000	0.000	0.000	0.000
122	A	161	PHE	0	0.004	-0.015	9.809	0.094	0.094	0.000	0.000	0.000	0.000
123	A	162	ALA	0	-0.006	0.001	12.031	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	163	HIS	0	0.028	0.015	13.627	-0.086	-0.086	0.000	0.000	0.000	0.000
125	A	164	GLY	0	0.039	0.004	9.851	0.022	0.022	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.045	-0.038	9.646	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	166	ALA	0	-0.041	-0.004	10.791	-0.104	-0.104	0.000	0.000	0.000	0.000
128	A	167	THR	0	-0.078	-0.039	12.065	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	168	LEU	0	-0.057	-0.009	6.295	0.101	0.101	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)