FMO DATABASE

FMODB ID: 1728Z

Calculation Name: 4GRW-C-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: C

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	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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1078115.883576
FMO2-HF: Nuclear repulsion	1028040.184332
FMO2-HF: Total energy	-50075.699244
FMO2-MP2: Total energy	-50221.540477

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(C:9:PRO)

Summations of interaction energy for fragment #1(C:9:PRO)

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.
-3.417	3.82	3.189	-2.877	-7.549	-0.012

Interaction energy analysis for fragmet #1(C:9:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.023

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	C	11	TRP	0	0.048	0.010	2.840	-4.192	1.547	1.577	-2.352	-4.964	-0.010
4	C	12	THR	0	0.042	0.024	4.244	0.671	0.852	0.000	-0.021	-0.160	0.000
5	C	13	GLN	0	0.053	0.023	7.745	0.289	0.289	0.000	0.000	0.000	0.000
6	C	14	CYS	0	-0.011	0.000	4.933	0.258	0.389	0.001	-0.026	-0.106	0.000
7	C	15	GLN	0	0.041	0.043	7.323	0.145	0.145	0.000	0.000	0.000	0.000
8	C	16	GLN	0	-0.056	-0.031	9.510	0.169	0.169	0.000	0.000	0.000	0.000
9	C	17	LEU	0	-0.011	0.002	10.378	0.077	0.077	0.000	0.000	0.000	0.000
10	C	18	SER	0	0.027	-0.015	10.002	0.061	0.061	0.000	0.000	0.000	0.000
11	C	19	GLN	0	0.060	0.036	12.042	0.005	0.005	0.000	0.000	0.000	0.000
12	C	20	LYS	1	0.923	0.972	14.860	0.110	0.110	0.000	0.000	0.000	0.000
13	C	21	LEU	0	-0.012	-0.003	12.561	0.026	0.026	0.000	0.000	0.000	0.000
14	C	22	CYS	0	-0.053	-0.023	15.313	0.018	0.018	0.000	0.000	0.000	0.000
15	C	23	THR	0	-0.014	-0.009	18.030	0.016	0.016	0.000	0.000	0.000	0.000
16	C	24	LEU	0	-0.009	0.002	18.706	0.013	0.013	0.000	0.000	0.000	0.000
17	C	25	ALA	0	0.041	0.015	19.506	0.013	0.013	0.000	0.000	0.000	0.000
18	C	26	TRP	0	-0.029	-0.001	21.437	0.008	0.008	0.000	0.000	0.000	0.000
19	C	27	SER	0	-0.024	-0.038	23.802	0.006	0.006	0.000	0.000	0.000	0.000
20	C	28	ALA	0	-0.033	-0.009	24.504	0.006	0.006	0.000	0.000	0.000	0.000
21	C	29	HIS	0	-0.035	-0.019	26.260	0.007	0.007	0.000	0.000	0.000	0.000
22	C	30	PRO	0	0.058	0.064	27.390	-0.005	-0.005	0.000	0.000	0.000	0.000
23	C	31	LEU	0	-0.082	-0.050	28.449	0.006	0.006	0.000	0.000	0.000	0.000
24	C	48	ASP	-1	-0.923	-0.969	25.362	0.057	0.057	0.000	0.000	0.000	0.000
25	C	49	VAL	0	-0.055	-0.034	21.607	0.003	0.003	0.000	0.000	0.000	0.000
26	C	50	PRO	0	-0.057	-0.002	17.345	-0.006	-0.006	0.000	0.000	0.000	0.000
27	C	51	HIS	0	0.004	-0.009	18.280	-0.017	-0.017	0.000	0.000	0.000	0.000
28	C	52	ILE	0	0.003	-0.001	12.519	0.011	0.011	0.000	0.000	0.000	0.000
29	C	53	GLN	0	-0.015	-0.008	16.371	0.001	0.001	0.000	0.000	0.000	0.000
30	C	54	CYS	0	-0.015	-0.029	16.720	-0.009	-0.009	0.000	0.000	0.000	0.000
31	C	55	GLY	0	0.032	0.034	17.358	-0.012	-0.012	0.000	0.000	0.000	0.000
32	C	56	ASP	-1	-0.781	-0.867	13.026	0.041	0.041	0.000	0.000	0.000	0.000
33	C	57	GLY	0	0.031	0.019	11.643	-0.002	-0.002	0.000	0.000	0.000	0.000
34	C	58	CYS	0	-0.027	-0.005	7.772	-0.007	-0.007	0.000	0.000	0.000	0.000
35	C	59	ASP	-1	-0.797	-0.885	11.419	-0.284	-0.284	0.000	0.000	0.000	0.000
36	C	60	PRO	0	-0.003	-0.034	11.593	-0.043	-0.043	0.000	0.000	0.000	0.000
37	C	61	GLN	0	-0.037	-0.016	11.970	-0.087	-0.087	0.000	0.000	0.000	0.000
38	C	62	GLY	0	0.068	0.027	11.776	-0.023	-0.023	0.000	0.000	0.000	0.000
39	C	63	LEU	0	-0.039	-0.028	6.597	-0.018	-0.018	0.000	0.000	0.000	0.000
40	C	64	ARG	1	0.826	0.906	6.921	0.462	0.462	0.000	0.000	0.000	0.000
41	C	65	ASP	-1	-0.871	-0.904	9.312	-0.229	-0.229	0.000	0.000	0.000	0.000
42	C	66	ASN	0	-0.022	-0.034	8.061	0.096	0.096	0.000	0.000	0.000	0.000
43	C	67	SER	0	0.027	0.000	3.749	-0.223	-0.071	0.001	-0.026	-0.126	0.000
44	C	68	GLN	0	-0.026	-0.016	4.551	0.042	0.213	-0.001	-0.013	-0.157	0.000
45	C	69	PHE	0	-0.003	0.016	6.350	0.099	0.099	0.000	0.000	0.000	0.000
46	C	71	LEU	0	0.008	0.000	2.395	-0.519	-0.300	1.596	-0.319	-1.496	-0.001
47	C	72	GLN	0	0.026	0.017	6.810	0.264	0.264	0.000	0.000	0.000	0.000
48	C	73	ARG	1	0.789	0.876	9.295	-0.082	-0.082	0.000	0.000	0.000	0.000
49	C	74	ILE	0	-0.003	-0.018	7.889	-0.022	-0.022	0.000	0.000	0.000	0.000
50	C	75	HIS	0	-0.008	-0.005	8.738	-0.108	-0.108	0.000	0.000	0.000	0.000
51	C	76	GLN	0	0.029	0.008	10.529	-0.058	-0.058	0.000	0.000	0.000	0.000
52	C	77	GLY	0	0.019	0.006	13.542	-0.020	-0.020	0.000	0.000	0.000	0.000
53	C	78	LEU	0	-0.040	-0.025	9.783	-0.027	-0.027	0.000	0.000	0.000	0.000
54	C	79	ILE	0	0.015	0.004	13.388	-0.021	-0.021	0.000	0.000	0.000	0.000
55	C	80	PHE	0	0.002	0.005	15.881	-0.013	-0.013	0.000	0.000	0.000	0.000
56	C	81	TYR	0	0.038	-0.008	16.993	-0.015	-0.015	0.000	0.000	0.000	0.000
57	C	82	GLU	-1	-0.881	-0.936	17.007	0.143	0.143	0.000	0.000	0.000	0.000
58	C	83	LYS	1	0.956	0.983	19.100	-0.210	-0.210	0.000	0.000	0.000	0.000
59	C	84	LEU	0	-0.012	0.005	21.991	-0.010	-0.010	0.000	0.000	0.000	0.000
60	C	85	LEU	0	-0.039	-0.016	20.469	-0.009	-0.009	0.000	0.000	0.000	0.000
61	C	86	GLY	0	0.018	0.022	23.469	-0.006	-0.006	0.000	0.000	0.000	0.000
62	C	87	SER	0	-0.040	-0.028	25.038	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	88	ASP	-1	-0.781	-0.863	27.779	0.031	0.031	0.000	0.000	0.000	0.000
64	C	89	ILE	0	0.002	0.005	28.284	-0.006	-0.006	0.000	0.000	0.000	0.000
65	C	90	PHE	0	-0.008	-0.014	25.792	-0.009	-0.009	0.000	0.000	0.000	0.000
66	C	91	THR	0	-0.017	-0.017	28.450	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	92	GLY	0	0.029	0.030	30.989	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	93	GLU	-1	-0.833	-0.892	34.490	0.013	0.013	0.000	0.000	0.000	0.000
69	C	94	PRO	0	-0.061	-0.033	35.743	0.001	0.001	0.000	0.000	0.000	0.000
70	C	95	SER	0	0.039	-0.004	34.542	-0.001	-0.001	0.000	0.000	0.000	0.000
71	C	96	LEU	0	-0.053	-0.022	28.426	-0.005	-0.005	0.000	0.000	0.000	0.000
72	C	97	LEU	0	0.032	0.016	31.946	0.002	0.002	0.000	0.000	0.000	0.000
73	C	98	PRO	0	0.014	-0.005	30.824	0.001	0.001	0.000	0.000	0.000	0.000
74	C	99	ASP	-1	-0.891	-0.936	29.202	-0.009	-0.009	0.000	0.000	0.000	0.000
75	C	100	SER	0	-0.005	-0.001	28.035	-0.009	-0.009	0.000	0.000	0.000	0.000
76	C	101	PRO	0	0.025	0.004	24.090	0.004	0.004	0.000	0.000	0.000	0.000
77	C	102	VAL	0	0.027	0.001	22.919	0.000	0.000	0.000	0.000	0.000	0.000
78	C	103	GLY	0	0.048	0.031	22.700	0.009	0.009	0.000	0.000	0.000	0.000
79	C	104	GLN	0	-0.012	-0.006	21.367	0.000	0.000	0.000	0.000	0.000	0.000
80	C	105	LEU	0	-0.043	0.004	18.068	-0.003	-0.003	0.000	0.000	0.000	0.000
81	C	106	HIS	0	-0.020	-0.015	17.773	-0.002	-0.002	0.000	0.000	0.000	0.000
82	C	107	ALA	0	0.058	0.024	17.745	0.020	0.020	0.000	0.000	0.000	0.000
83	C	108	SER	0	-0.046	-0.046	15.091	0.008	0.008	0.000	0.000	0.000	0.000
84	C	109	LEU	0	-0.029	-0.007	13.357	-0.002	-0.002	0.000	0.000	0.000	0.000
85	C	110	LEU	0	0.027	0.035	12.877	0.045	0.045	0.000	0.000	0.000	0.000
86	C	111	GLY	0	0.018	0.014	12.530	0.064	0.064	0.000	0.000	0.000	0.000
87	C	112	LEU	0	-0.024	-0.023	7.375	0.040	0.040	0.000	0.000	0.000	0.000
88	C	113	SER	0	-0.003	-0.016	7.884	0.104	0.104	0.000	0.000	0.000	0.000
89	C	114	GLN	0	-0.020	-0.026	9.002	0.145	0.145	0.000	0.000	0.000	0.000
90	C	115	LEU	0	-0.058	-0.021	5.814	0.159	0.159	0.000	0.000	0.000	0.000
91	C	116	LEU	0	-0.064	-0.015	3.305	-0.033	0.420	0.017	-0.103	-0.368	-0.001
92	C	117	GLN	0	0.012	0.014	5.470	0.548	0.548	0.000	0.000	0.000	0.000
93	C	135	GLN	0	0.073	0.031	38.284	0.000	0.000	0.000	0.000	0.000	0.000
94	C	136	PRO	0	0.029	0.015	37.882	-0.001	-0.001	0.000	0.000	0.000	0.000
95	C	137	TRP	0	0.067	0.015	37.428	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	138	GLN	0	0.000	-0.005	36.788	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	139	ARG	1	0.788	0.866	33.468	-0.028	-0.028	0.000	0.000	0.000	0.000
98	C	140	LEU	0	-0.005	0.010	32.503	-0.001	-0.001	0.000	0.000	0.000	0.000
99	C	141	LEU	0	-0.008	-0.006	32.684	-0.003	-0.003	0.000	0.000	0.000	0.000
100	C	142	LEU	0	-0.016	-0.012	30.393	-0.002	-0.002	0.000	0.000	0.000	0.000
101	C	143	ARG	1	0.836	0.902	28.323	-0.015	-0.015	0.000	0.000	0.000	0.000
102	C	144	PHE	0	0.024	0.015	27.628	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	145	LYS	1	0.933	0.972	27.910	-0.001	-0.001	0.000	0.000	0.000	0.000
104	C	146	ILE	0	0.030	0.031	23.603	-0.004	-0.004	0.000	0.000	0.000	0.000
105	C	147	LEU	0	0.031	0.014	23.345	-0.002	-0.002	0.000	0.000	0.000	0.000
106	C	148	ARG	1	0.905	0.948	23.043	0.051	0.051	0.000	0.000	0.000	0.000
107	C	149	SER	0	-0.046	-0.028	22.688	-0.010	-0.010	0.000	0.000	0.000	0.000
108	C	150	LEU	0	0.013	0.011	17.293	-0.008	-0.008	0.000	0.000	0.000	0.000
109	C	151	GLN	0	-0.043	-0.037	18.378	-0.016	-0.016	0.000	0.000	0.000	0.000
110	C	152	ALA	0	-0.017	-0.001	18.925	-0.020	-0.020	0.000	0.000	0.000	0.000
111	C	153	PHE	0	-0.007	0.007	12.699	-0.025	-0.025	0.000	0.000	0.000	0.000
112	C	154	VAL	0	0.028	-0.002	13.995	-0.021	-0.021	0.000	0.000	0.000	0.000
113	C	155	ALA	0	0.040	0.016	14.069	-0.046	-0.046	0.000	0.000	0.000	0.000
114	C	156	VAL	0	-0.056	-0.007	13.463	-0.039	-0.039	0.000	0.000	0.000	0.000
115	C	157	ALA	0	0.058	0.022	10.142	-0.052	-0.052	0.000	0.000	0.000	0.000
116	C	158	ALA	0	0.002	0.000	10.016	-0.097	-0.097	0.000	0.000	0.000	0.000
117	C	159	ARG	1	0.863	0.927	11.456	0.143	0.143	0.000	0.000	0.000	0.000
118	C	160	VAL	0	0.030	0.020	7.237	-0.067	-0.067	0.000	0.000	0.000	0.000
119	C	161	PHE	0	0.027	-0.004	3.996	-0.325	-0.186	-0.001	-0.013	-0.126	0.000
120	C	162	ALA	0	-0.024	-0.004	7.487	-0.222	-0.222	0.000	0.000	0.000	0.000
121	C	163	HIS	0	-0.006	-0.001	9.747	-0.059	-0.059	0.000	0.000	0.000	0.000
122	C	164	GLY	0	0.042	0.024	5.900	-0.011	-0.011	0.000	0.000	0.000	0.000
123	C	165	ALA	0	-0.035	-0.040	6.800	-0.222	-0.222	0.000	0.000	0.000	0.000
124	C	166	ALA	0	-0.027	-0.005	7.856	0.076	0.076	0.000	0.000	0.000	0.000
125	C	167	THR	0	-0.052	-0.023	9.520	0.116	0.116	0.000	0.000	0.000	0.000
126	C	168	LEU	0	-0.029	0.000	5.351	0.168	0.168	0.000	0.000	0.000	0.000
127	C	169	SER	0	-0.002	0.004	5.002	-0.903	-0.851	-0.001	-0.004	-0.046	0.000
128	C	170	PRO	0	-0.019	0.011	5.294	0.278	0.278	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:9:PRO)