FMO DATABASE

FMODB ID: 49RRN

Calculation Name: 3DUH-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: 3DUH

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	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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1214316.076922
FMO2-HF: Nuclear repulsion	1159396.079692
FMO2-HF: Total energy	-54919.99723
FMO2-MP2: Total energy	-55080.20343

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:0:LEU)

Summations of interaction energy for fragment #1(C:0:LEU)

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.
-1.303	1.219	-0.047	-1.302	-1.173	0.002

Interaction energy analysis for fragmet #1(C:0:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.007

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	C	2	ALA	0	0.028	0.017	3.742	-1.609	0.913	-0.047	-1.302	-1.173	0.002
4	C	3	VAL	0	-0.017	-0.011	6.371	0.058	0.058	0.000	0.000	0.000	0.000
5	C	4	PRO	0	0.016	0.004	9.792	0.005	0.005	0.000	0.000	0.000	0.000
6	C	5	GLY	0	0.043	0.021	13.203	0.068	0.068	0.000	0.000	0.000	0.000
7	C	6	GLY	0	0.000	0.011	14.795	0.022	0.022	0.000	0.000	0.000	0.000
8	C	7	SER	0	-0.017	-0.012	18.093	-0.031	-0.031	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.006	0.006	19.685	0.014	0.014	0.000	0.000	0.000	0.000
10	C	9	PRO	0	0.033	0.018	21.025	0.000	0.000	0.000	0.000	0.000	0.000
11	C	10	ALA	0	0.064	0.034	24.252	-0.013	-0.013	0.000	0.000	0.000	0.000
12	C	11	TRP	0	0.032	0.010	22.275	0.004	0.004	0.000	0.000	0.000	0.000
13	C	12	THR	0	0.052	0.020	27.179	0.005	0.005	0.000	0.000	0.000	0.000
14	C	13	GLN	0	0.047	0.017	29.591	0.007	0.007	0.000	0.000	0.000	0.000
15	C	14	CYS	0	0.023	0.029	29.824	0.005	0.005	0.000	0.000	0.000	0.000
16	C	15	GLN	0	0.008	0.017	30.926	0.001	0.001	0.000	0.000	0.000	0.000
17	C	16	GLN	0	-0.043	-0.025	32.698	0.003	0.003	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.028	0.000	35.058	0.002	0.002	0.000	0.000	0.000	0.000
19	C	18	SER	0	-0.017	-0.020	34.348	0.003	0.003	0.000	0.000	0.000	0.000
20	C	19	GLN	0	0.037	0.020	36.877	0.004	0.004	0.000	0.000	0.000	0.000
21	C	20	LYS	1	0.946	0.975	38.759	0.017	0.017	0.000	0.000	0.000	0.000
22	C	21	LEU	0	0.018	0.005	38.549	0.001	0.001	0.000	0.000	0.000	0.000
23	C	22	CYS	0	-0.068	-0.011	39.767	0.002	0.002	0.000	0.000	0.000	0.000
24	C	23	THR	0	-0.010	-0.006	42.763	0.000	0.000	0.000	0.000	0.000	0.000
25	C	24	LEU	0	-0.015	-0.016	43.931	0.001	0.001	0.000	0.000	0.000	0.000
26	C	25	ALA	0	-0.011	-0.013	45.181	0.001	0.001	0.000	0.000	0.000	0.000
27	C	26	TRP	0	-0.029	-0.015	45.481	0.002	0.002	0.000	0.000	0.000	0.000
28	C	27	SER	0	-0.016	0.008	49.037	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	28	ALA	0	-0.051	-0.020	50.781	0.000	0.000	0.000	0.000	0.000	0.000
30	C	29	HIS	0	-0.023	0.005	51.342	0.001	0.001	0.000	0.000	0.000	0.000
31	C	47	ASN	0	-0.034	-0.021	48.582	-0.003	-0.003	0.000	0.000	0.000	0.000
32	C	48	ASP	-1	-0.936	-0.980	45.050	0.037	0.037	0.000	0.000	0.000	0.000
33	C	49	VAL	0	-0.042	-0.013	43.731	0.001	0.001	0.000	0.000	0.000	0.000
34	C	50	PRO	0	-0.018	0.019	38.992	0.002	0.002	0.000	0.000	0.000	0.000
35	C	51	HIS	0	-0.001	-0.014	39.783	-0.004	-0.004	0.000	0.000	0.000	0.000
36	C	52	ILE	0	0.019	0.002	34.039	0.004	0.004	0.000	0.000	0.000	0.000
37	C	53	GLN	0	-0.029	-0.007	35.944	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	54	CYS	0	0.007	-0.017	34.485	0.000	0.000	0.000	0.000	0.000	0.000
39	C	55	GLY	0	-0.004	0.003	32.122	0.003	0.003	0.000	0.000	0.000	0.000
40	C	56	ASP	-1	-0.846	-0.929	30.489	0.069	0.069	0.000	0.000	0.000	0.000
41	C	57	GLY	0	0.038	0.023	27.659	0.001	0.001	0.000	0.000	0.000	0.000
42	C	58	CYS	0	-0.052	-0.013	26.689	-0.013	-0.013	0.000	0.000	0.000	0.000
43	C	59	ASP	-1	-0.843	-0.916	28.888	0.049	0.049	0.000	0.000	0.000	0.000
44	C	60	PRO	0	0.003	-0.022	28.138	0.002	0.002	0.000	0.000	0.000	0.000
45	C	61	GLN	0	-0.030	-0.022	25.123	0.003	0.003	0.000	0.000	0.000	0.000
46	C	62	GLY	0	0.052	0.039	24.016	0.007	0.007	0.000	0.000	0.000	0.000
47	C	63	LEU	0	-0.048	-0.020	24.387	0.006	0.006	0.000	0.000	0.000	0.000
48	C	64	ARG	1	0.887	0.942	17.880	-0.005	-0.005	0.000	0.000	0.000	0.000
49	C	65	ASP	-1	-0.922	-0.938	19.297	0.118	0.118	0.000	0.000	0.000	0.000
50	C	66	ASN	0	-0.002	-0.023	19.044	0.005	0.005	0.000	0.000	0.000	0.000
51	C	67	SER	0	0.046	0.038	21.360	-0.005	-0.005	0.000	0.000	0.000	0.000
52	C	68	GLN	0	0.004	-0.001	21.948	0.007	0.007	0.000	0.000	0.000	0.000
53	C	69	PHE	0	0.041	0.025	22.735	-0.005	-0.005	0.000	0.000	0.000	0.000
54	C	71	LEU	0	0.020	-0.013	25.711	-0.006	-0.006	0.000	0.000	0.000	0.000
55	C	72	GLN	0	0.002	0.030	27.675	0.000	0.000	0.000	0.000	0.000	0.000
56	C	73	ARG	1	0.833	0.925	29.828	-0.057	-0.057	0.000	0.000	0.000	0.000
57	C	74	ILE	0	-0.013	-0.025	31.141	-0.005	-0.005	0.000	0.000	0.000	0.000
58	C	75	HIS	0	-0.053	-0.048	32.149	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	76	GLN	0	0.039	0.010	33.955	-0.003	-0.003	0.000	0.000	0.000	0.000
60	C	77	GLY	0	0.003	-0.001	36.108	-0.002	-0.002	0.000	0.000	0.000	0.000
61	C	78	LEU	0	-0.042	-0.022	35.151	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	79	ILE	0	0.029	0.019	37.381	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	80	PHE	0	-0.001	0.006	39.923	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	81	TYR	0	0.038	0.009	41.591	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	82	GLU	-1	-0.889	-0.949	41.906	0.013	0.013	0.000	0.000	0.000	0.000
66	C	83	LYS	1	1.003	1.006	44.040	-0.027	-0.027	0.000	0.000	0.000	0.000
67	C	84	LEU	0	-0.036	-0.022	45.954	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	85	LEU	0	-0.059	-0.038	46.426	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	86	GLY	0	0.027	0.029	48.264	-0.002	-0.002	0.000	0.000	0.000	0.000
70	C	87	SER	0	-0.078	-0.026	49.807	0.000	0.000	0.000	0.000	0.000	0.000
71	C	88	ASP	-1	-0.778	-0.889	51.978	0.012	0.012	0.000	0.000	0.000	0.000
72	C	89	ILE	0	-0.056	-0.028	52.363	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	90	PHE	0	0.008	-0.028	51.237	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	91	THR	0	-0.019	0.018	54.072	-0.001	-0.001	0.000	0.000	0.000	0.000
75	C	92	GLY	0	0.075	0.046	56.790	0.000	0.000	0.000	0.000	0.000	0.000
76	C	93	GLU	-1	-0.798	-0.940	60.112	0.008	0.008	0.000	0.000	0.000	0.000
77	C	94	PRO	0	-0.131	-0.121	60.778	0.000	0.000	0.000	0.000	0.000	0.000
78	C	95	SER	0	0.177	0.171	59.485	0.000	0.000	0.000	0.000	0.000	0.000
79	C	96	LEU	0	-0.006	-0.022	60.194	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	97	LEU	0	-0.019	-0.006	62.367	0.000	0.000	0.000	0.000	0.000	0.000
81	C	98	PRO	0	-0.036	-0.013	59.780	-0.001	-0.001	0.000	0.000	0.000	0.000
82	C	99	ASP	-1	-0.843	-0.899	55.595	-0.005	-0.005	0.000	0.000	0.000	0.000
83	C	100	SER	0	-0.046	-0.051	54.497	0.001	0.001	0.000	0.000	0.000	0.000
84	C	101	PRO	0	0.031	0.030	49.907	-0.001	-0.001	0.000	0.000	0.000	0.000
85	C	102	VAL	0	0.000	-0.015	49.282	0.000	0.000	0.000	0.000	0.000	0.000
86	C	103	GLY	0	0.040	0.025	49.092	0.001	0.001	0.000	0.000	0.000	0.000
87	C	104	GLN	0	0.013	-0.007	44.834	0.000	0.000	0.000	0.000	0.000	0.000
88	C	105	LEU	0	0.014	-0.004	44.405	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	106	HIS	0	-0.008	0.007	44.085	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	107	ALA	0	0.049	0.024	43.681	0.001	0.001	0.000	0.000	0.000	0.000
91	C	108	SER	0	-0.044	-0.022	41.020	-0.002	-0.002	0.000	0.000	0.000	0.000
92	C	109	LEU	0	-0.046	-0.022	39.543	0.000	0.000	0.000	0.000	0.000	0.000
93	C	110	LEU	0	0.040	0.016	38.791	0.002	0.002	0.000	0.000	0.000	0.000
94	C	111	GLY	0	-0.005	0.019	37.838	0.001	0.001	0.000	0.000	0.000	0.000
95	C	112	LEU	0	-0.028	-0.024	33.273	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	113	SER	0	-0.029	-0.016	33.766	0.002	0.002	0.000	0.000	0.000	0.000
97	C	114	GLN	0	0.050	0.001	33.619	0.000	0.000	0.000	0.000	0.000	0.000
98	C	115	LEU	0	-0.042	-0.016	30.645	-0.001	-0.001	0.000	0.000	0.000	0.000
99	C	116	LEU	0	-0.070	-0.033	29.299	-0.001	-0.001	0.000	0.000	0.000	0.000
100	C	117	GLN	0	0.012	0.029	28.790	0.008	0.008	0.000	0.000	0.000	0.000
101	C	118	PRO	0	0.005	0.024	25.106	-0.007	-0.007	0.000	0.000	0.000	0.000
102	C	119	GLU	-1	-0.907	-0.962	25.877	0.011	0.011	0.000	0.000	0.000	0.000
103	C	120	GLY	0	-0.020	-0.020	25.641	0.007	0.007	0.000	0.000	0.000	0.000
104	C	121	HIS	0	-0.085	-0.055	23.045	0.020	0.020	0.000	0.000	0.000	0.000
105	C	122	HIS	0	-0.008	-0.001	28.133	0.001	0.001	0.000	0.000	0.000	0.000
106	C	123	TRP	0	0.031	0.011	26.317	-0.001	-0.001	0.000	0.000	0.000	0.000
107	C	124	GLU	-1	-0.956	-0.959	32.391	0.029	0.029	0.000	0.000	0.000	0.000
108	C	125	THR	0	-0.037	-0.010	35.935	0.005	0.005	0.000	0.000	0.000	0.000
109	C	137	TRP	0	0.024	0.019	60.418	0.000	0.000	0.000	0.000	0.000	0.000
110	C	138	GLN	0	-0.009	-0.020	60.412	0.000	0.000	0.000	0.000	0.000	0.000
111	C	139	ARG	1	0.821	0.912	58.426	-0.011	-0.011	0.000	0.000	0.000	0.000
112	C	140	LEU	0	0.034	0.018	57.785	0.000	0.000	0.000	0.000	0.000	0.000
113	C	141	LEU	0	-0.024	0.003	58.411	0.000	0.000	0.000	0.000	0.000	0.000
114	C	142	LEU	0	0.027	-0.001	54.525	0.000	0.000	0.000	0.000	0.000	0.000
115	C	143	ARG	1	0.819	0.895	53.671	-0.007	-0.007	0.000	0.000	0.000	0.000
116	C	144	PHE	0	0.018	0.022	53.279	0.000	0.000	0.000	0.000	0.000	0.000
117	C	145	LYS	1	0.875	0.927	52.826	-0.014	-0.014	0.000	0.000	0.000	0.000
118	C	146	ILE	0	0.014	0.009	48.294	0.001	0.001	0.000	0.000	0.000	0.000
119	C	147	LEU	0	0.051	0.025	48.337	0.000	0.000	0.000	0.000	0.000	0.000
120	C	148	ARG	1	0.956	0.975	48.235	-0.014	-0.014	0.000	0.000	0.000	0.000
121	C	149	SER	0	-0.054	-0.029	45.558	0.000	0.000	0.000	0.000	0.000	0.000
122	C	150	LEU	0	0.017	0.010	42.822	0.001	0.001	0.000	0.000	0.000	0.000
123	C	151	GLN	0	-0.011	-0.007	43.277	-0.001	-0.001	0.000	0.000	0.000	0.000
124	C	152	ALA	0	-0.013	-0.001	43.140	-0.001	-0.001	0.000	0.000	0.000	0.000
125	C	153	PHE	0	-0.005	0.002	36.842	0.000	0.000	0.000	0.000	0.000	0.000
126	C	154	VAL	0	0.029	-0.008	38.586	0.000	0.000	0.000	0.000	0.000	0.000
127	C	155	ALA	0	0.012	0.021	38.383	-0.002	-0.002	0.000	0.000	0.000	0.000
128	C	156	VAL	0	-0.041	-0.026	35.033	-0.002	-0.002	0.000	0.000	0.000	0.000
129	C	157	ALA	0	0.038	0.023	34.149	-0.001	-0.001	0.000	0.000	0.000	0.000
130	C	158	ALA	0	0.003	-0.007	33.507	-0.002	-0.002	0.000	0.000	0.000	0.000
131	C	159	ARG	1	0.913	0.962	33.936	-0.010	-0.010	0.000	0.000	0.000	0.000
132	C	160	VAL	0	0.044	0.031	28.879	-0.003	-0.003	0.000	0.000	0.000	0.000
133	C	161	PHE	0	0.003	-0.017	29.184	-0.004	-0.004	0.000	0.000	0.000	0.000
134	C	162	ALA	0	-0.015	0.000	29.450	-0.007	-0.007	0.000	0.000	0.000	0.000
135	C	163	HIS	0	0.014	0.005	26.154	-0.004	-0.004	0.000	0.000	0.000	0.000
136	C	164	GLY	0	0.041	0.007	25.213	-0.005	-0.005	0.000	0.000	0.000	0.000
137	C	165	ALA	0	-0.011	-0.019	24.715	-0.009	-0.009	0.000	0.000	0.000	0.000
138	C	166	ALA	0	-0.043	-0.010	26.137	-0.011	-0.011	0.000	0.000	0.000	0.000
139	C	167	THR	0	-0.084	-0.037	23.738	-0.007	-0.007	0.000	0.000	0.000	0.000
140	C	168	LEU	0	-0.015	-0.003	20.476	-0.003	-0.003	0.000	0.000	0.000	0.000
141	C	169	SER	0	-0.076	-0.018	19.796	-0.018	-0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:0:LEU)