FMO DATABASE

FMODB ID: YY222

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:

Apendix: None

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1217596.486912
FMO2-HF: Nuclear repulsion	1162675.013307
FMO2-HF: Total energy	-54921.473605
FMO2-MP2: Total energy	-55081.566882

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.
-0.686	1.116	-0.017	-0.946	-0.838	0.001

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 : 0.000 / q_NPA : -0.005

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	0.031	0.026	3.888	-0.993	0.809	-0.017	-0.946	-0.838	0.001
4	C	3	VAL	0	-0.001	-0.013	6.793	0.072	0.072	0.000	0.000	0.000	0.000
5	C	4	PRO	0	0.001	-0.002	10.069	-0.006	-0.006	0.000	0.000	0.000	0.000
6	C	5	GLY	0	0.035	0.023	13.776	0.050	0.050	0.000	0.000	0.000	0.000
7	C	6	GLY	0	0.013	0.015	14.924	0.015	0.015	0.000	0.000	0.000	0.000
8	C	7	SER	0	-0.019	-0.011	18.383	-0.025	-0.025	0.000	0.000	0.000	0.000
9	C	8	SER	0	-0.019	-0.014	20.382	0.011	0.011	0.000	0.000	0.000	0.000
10	C	9	PRO	0	0.050	0.027	21.427	-0.001	-0.001	0.000	0.000	0.000	0.000
11	C	10	ALA	0	0.069	0.050	24.746	-0.010	-0.010	0.000	0.000	0.000	0.000
12	C	11	TRP	0	0.030	0.008	22.595	-0.001	-0.001	0.000	0.000	0.000	0.000
13	C	12	THR	0	0.056	0.022	27.562	0.003	0.003	0.000	0.000	0.000	0.000
14	C	13	GLN	0	0.044	0.024	30.006	0.004	0.004	0.000	0.000	0.000	0.000
15	C	14	CYS	0	-0.002	0.009	30.084	0.003	0.003	0.000	0.000	0.000	0.000
16	C	15	GLN	0	0.023	0.026	31.392	0.001	0.001	0.000	0.000	0.000	0.000
17	C	16	GLN	0	-0.029	-0.018	33.217	0.001	0.001	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.020	0.004	35.398	0.001	0.001	0.000	0.000	0.000	0.000
19	C	18	SER	0	0.002	-0.012	34.751	0.001	0.001	0.000	0.000	0.000	0.000
20	C	19	GLN	0	0.054	0.032	37.263	0.003	0.003	0.000	0.000	0.000	0.000
21	C	20	LYS	1	0.851	0.927	39.150	-0.001	-0.001	0.000	0.000	0.000	0.000
22	C	21	LEU	0	0.001	-0.003	38.846	0.000	0.000	0.000	0.000	0.000	0.000
23	C	22	CYS	0	-0.055	-0.021	39.901	0.001	0.001	0.000	0.000	0.000	0.000
24	C	23	THR	0	-0.031	-0.024	42.861	0.000	0.000	0.000	0.000	0.000	0.000
25	C	24	LEU	0	-0.015	-0.019	44.260	0.000	0.000	0.000	0.000	0.000	0.000
26	C	25	ALA	0	-0.010	-0.001	45.276	0.001	0.001	0.000	0.000	0.000	0.000
27	C	26	TRP	0	-0.008	-0.012	45.276	0.001	0.001	0.000	0.000	0.000	0.000
28	C	27	SER	0	-0.033	0.000	49.049	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	28	ALA	0	-0.033	-0.001	50.750	0.000	0.000	0.000	0.000	0.000	0.000
30	C	29	HIS	0	-0.037	-0.018	52.021	0.001	0.001	0.000	0.000	0.000	0.000
31	C	47	ASN	0	-0.050	-0.036	48.773	-0.002	-0.002	0.000	0.000	0.000	0.000
32	C	48	ASP	-1	-0.897	-0.965	45.202	0.037	0.037	0.000	0.000	0.000	0.000
33	C	49	VAL	0	-0.044	-0.009	43.851	0.002	0.002	0.000	0.000	0.000	0.000
34	C	50	PRO	0	-0.006	0.022	38.998	0.001	0.001	0.000	0.000	0.000	0.000
35	C	51	HIS	0	-0.016	-0.016	40.011	-0.004	-0.004	0.000	0.000	0.000	0.000
36	C	52	ILE	0	-0.004	-0.009	34.246	0.004	0.004	0.000	0.000	0.000	0.000
37	C	53	GLN	0	-0.076	-0.047	35.744	-0.005	-0.005	0.000	0.000	0.000	0.000
38	C	54	CYS	0	-0.020	-0.032	33.390	0.000	0.000	0.000	0.000	0.000	0.000
39	C	55	GLY	0	0.010	0.016	32.137	0.002	0.002	0.000	0.000	0.000	0.000
40	C	56	ASP	-1	-0.779	-0.863	30.822	0.064	0.064	0.000	0.000	0.000	0.000
41	C	57	GLY	0	0.036	0.016	27.776	0.002	0.002	0.000	0.000	0.000	0.000
42	C	58	CYS	0	-0.039	-0.001	26.923	-0.010	-0.010	0.000	0.000	0.000	0.000
43	C	59	ASP	-1	-0.808	-0.891	28.666	0.048	0.048	0.000	0.000	0.000	0.000
44	C	60	PRO	0	-0.017	-0.033	27.862	0.003	0.003	0.000	0.000	0.000	0.000
45	C	61	GLN	0	-0.019	-0.001	24.900	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	62	GLY	0	0.066	0.031	23.898	0.007	0.007	0.000	0.000	0.000	0.000
47	C	63	LEU	0	-0.052	-0.035	24.002	0.009	0.009	0.000	0.000	0.000	0.000
48	C	64	ARG	1	0.862	0.928	18.007	-0.025	-0.025	0.000	0.000	0.000	0.000
49	C	65	ASP	-1	-0.899	-0.923	19.308	0.113	0.113	0.000	0.000	0.000	0.000
50	C	66	ASN	0	-0.036	-0.036	19.027	0.007	0.007	0.000	0.000	0.000	0.000
51	C	67	SER	0	0.054	0.033	21.389	-0.002	-0.002	0.000	0.000	0.000	0.000
52	C	68	GLN	0	-0.012	-0.004	21.391	0.004	0.004	0.000	0.000	0.000	0.000
53	C	69	PHE	0	0.028	0.019	22.883	-0.004	-0.004	0.000	0.000	0.000	0.000
54	C	71	LEU	0	0.011	-0.011	25.610	-0.006	-0.006	0.000	0.000	0.000	0.000
55	C	72	GLN	0	0.010	0.019	28.284	-0.001	-0.001	0.000	0.000	0.000	0.000
56	C	73	ARG	1	0.820	0.900	30.068	-0.059	-0.059	0.000	0.000	0.000	0.000
57	C	74	ILE	0	-0.002	-0.019	31.340	-0.005	-0.005	0.000	0.000	0.000	0.000
58	C	75	HIS	0	-0.034	-0.017	32.303	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	76	GLN	0	0.053	0.027	34.135	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	77	GLY	0	0.013	0.005	36.116	-0.002	-0.002	0.000	0.000	0.000	0.000
61	C	78	LEU	0	-0.060	-0.031	35.315	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	79	ILE	0	0.019	0.006	36.908	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	80	PHE	0	0.002	0.014	39.976	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	81	TYR	0	0.034	0.000	41.303	-0.003	-0.003	0.000	0.000	0.000	0.000
65	C	82	GLU	-1	-0.868	-0.935	41.790	0.023	0.023	0.000	0.000	0.000	0.000
66	C	83	LYS	1	0.987	1.010	44.181	-0.033	-0.033	0.000	0.000	0.000	0.000
67	C	84	LEU	0	-0.017	-0.006	46.072	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	85	LEU	0	-0.039	-0.015	46.518	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	86	GLY	0	0.011	0.020	48.367	-0.002	-0.002	0.000	0.000	0.000	0.000
70	C	87	SER	0	-0.048	-0.033	49.878	0.000	0.000	0.000	0.000	0.000	0.000
71	C	88	ASP	-1	-0.752	-0.843	52.218	0.016	0.016	0.000	0.000	0.000	0.000
72	C	89	ILE	0	0.000	-0.001	52.432	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	90	PHE	0	0.001	-0.026	51.327	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	91	THR	0	-0.020	-0.014	54.231	-0.001	-0.001	0.000	0.000	0.000	0.000
75	C	92	GLY	0	0.023	0.030	56.999	-0.001	-0.001	0.000	0.000	0.000	0.000
76	C	93	GLU	-1	-0.744	-0.882	60.340	0.013	0.013	0.000	0.000	0.000	0.000
77	C	94	PRO	0	-0.043	-0.039	60.382	0.000	0.000	0.000	0.000	0.000	0.000
78	C	95	SER	0	0.025	0.023	59.473	0.000	0.000	0.000	0.000	0.000	0.000
79	C	96	LEU	0	0.009	0.006	60.146	0.000	0.000	0.000	0.000	0.000	0.000
80	C	97	LEU	0	-0.017	-0.002	62.274	0.000	0.000	0.000	0.000	0.000	0.000
81	C	98	PRO	0	-0.032	-0.014	59.739	-0.001	-0.001	0.000	0.000	0.000	0.000
82	C	99	ASP	-1	-0.842	-0.899	55.526	0.003	0.003	0.000	0.000	0.000	0.000
83	C	100	SER	0	-0.037	-0.045	54.340	0.001	0.001	0.000	0.000	0.000	0.000
84	C	101	PRO	0	0.031	0.025	49.614	0.000	0.000	0.000	0.000	0.000	0.000
85	C	102	VAL	0	0.009	-0.003	49.209	0.001	0.001	0.000	0.000	0.000	0.000
86	C	103	GLY	0	0.064	0.037	48.933	0.001	0.001	0.000	0.000	0.000	0.000
87	C	104	GLN	0	0.041	0.022	45.368	0.000	0.000	0.000	0.000	0.000	0.000
88	C	105	LEU	0	-0.018	0.002	44.965	0.000	0.000	0.000	0.000	0.000	0.000
89	C	106	HIS	0	-0.031	-0.017	43.987	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	107	ALA	0	0.053	0.022	43.620	0.001	0.001	0.000	0.000	0.000	0.000
91	C	108	SER	0	-0.029	-0.033	40.972	-0.001	-0.001	0.000	0.000	0.000	0.000
92	C	109	LEU	0	-0.031	-0.010	39.461	0.000	0.000	0.000	0.000	0.000	0.000
93	C	110	LEU	0	0.023	0.025	38.735	0.002	0.002	0.000	0.000	0.000	0.000
94	C	111	GLY	0	0.022	0.027	37.892	0.002	0.002	0.000	0.000	0.000	0.000
95	C	112	LEU	0	-0.037	-0.028	33.217	0.000	0.000	0.000	0.000	0.000	0.000
96	C	113	SER	0	-0.053	-0.042	33.864	0.003	0.003	0.000	0.000	0.000	0.000
97	C	114	GLN	0	0.052	0.004	33.515	0.002	0.002	0.000	0.000	0.000	0.000
98	C	115	LEU	0	-0.037	-0.009	30.913	0.000	0.000	0.000	0.000	0.000	0.000
99	C	116	LEU	0	-0.091	-0.045	29.244	0.000	0.000	0.000	0.000	0.000	0.000
100	C	117	GLN	0	-0.010	0.002	28.762	0.004	0.004	0.000	0.000	0.000	0.000
101	C	118	PRO	0	0.011	0.024	25.070	-0.005	-0.005	0.000	0.000	0.000	0.000
102	C	119	GLU	-1	-0.908	-0.960	25.374	0.044	0.044	0.000	0.000	0.000	0.000
103	C	120	GLY	0	-0.025	-0.010	25.810	0.010	0.010	0.000	0.000	0.000	0.000
104	C	121	HIS	0	-0.089	-0.058	22.787	0.018	0.018	0.000	0.000	0.000	0.000
105	C	122	HIS	0	-0.031	-0.008	27.932	-0.002	-0.002	0.000	0.000	0.000	0.000
106	C	123	TRP	0	0.056	0.026	26.369	0.000	0.000	0.000	0.000	0.000	0.000
107	C	124	GLU	-1	-0.888	-0.953	32.634	0.047	0.047	0.000	0.000	0.000	0.000
108	C	125	THR	0	-0.056	-0.010	36.240	0.001	0.001	0.000	0.000	0.000	0.000
109	C	137	TRP	0	0.037	0.023	60.842	0.000	0.000	0.000	0.000	0.000	0.000
110	C	138	GLN	0	-0.040	-0.038	60.418	0.000	0.000	0.000	0.000	0.000	0.000
111	C	139	ARG	1	0.748	0.843	57.877	-0.016	-0.016	0.000	0.000	0.000	0.000
112	C	140	LEU	0	0.020	0.001	57.742	0.000	0.000	0.000	0.000	0.000	0.000
113	C	141	LEU	0	-0.022	-0.002	58.299	0.000	0.000	0.000	0.000	0.000	0.000
114	C	142	LEU	0	0.025	0.004	54.865	0.000	0.000	0.000	0.000	0.000	0.000
115	C	143	ARG	1	0.850	0.926	53.668	-0.012	-0.012	0.000	0.000	0.000	0.000
116	C	144	PHE	0	0.035	0.020	52.950	0.000	0.000	0.000	0.000	0.000	0.000
117	C	145	LYS	1	0.864	0.933	52.342	-0.017	-0.017	0.000	0.000	0.000	0.000
118	C	146	ILE	0	0.036	0.018	48.191	0.000	0.000	0.000	0.000	0.000	0.000
119	C	147	LEU	0	0.014	0.014	48.145	0.001	0.001	0.000	0.000	0.000	0.000
120	C	148	ARG	1	0.961	0.988	47.952	-0.016	-0.016	0.000	0.000	0.000	0.000
121	C	149	SER	0	-0.018	-0.015	45.192	0.000	0.000	0.000	0.000	0.000	0.000
122	C	150	LEU	0	0.016	0.015	42.541	0.001	0.001	0.000	0.000	0.000	0.000
123	C	151	GLN	0	-0.011	-0.019	43.232	0.001	0.001	0.000	0.000	0.000	0.000
124	C	152	ALA	0	-0.030	-0.008	43.550	-0.001	-0.001	0.000	0.000	0.000	0.000
125	C	153	PHE	0	-0.005	0.001	37.011	0.000	0.000	0.000	0.000	0.000	0.000
126	C	154	VAL	0	0.013	-0.009	38.720	0.001	0.001	0.000	0.000	0.000	0.000
127	C	155	ALA	0	0.046	0.023	38.315	-0.001	-0.001	0.000	0.000	0.000	0.000
128	C	156	VAL	0	-0.051	-0.006	34.941	-0.002	-0.002	0.000	0.000	0.000	0.000
129	C	157	ALA	0	0.046	0.022	34.130	0.000	0.000	0.000	0.000	0.000	0.000
130	C	158	ALA	0	0.018	0.002	33.528	-0.001	-0.001	0.000	0.000	0.000	0.000
131	C	159	ARG	1	0.859	0.922	33.878	-0.015	-0.015	0.000	0.000	0.000	0.000
132	C	160	VAL	0	0.039	0.025	29.045	-0.002	-0.002	0.000	0.000	0.000	0.000
133	C	161	PHE	0	0.010	-0.010	29.146	-0.001	-0.001	0.000	0.000	0.000	0.000
134	C	162	ALA	0	0.004	0.003	29.337	-0.005	-0.005	0.000	0.000	0.000	0.000
135	C	163	HIS	0	-0.007	0.001	25.549	-0.003	-0.003	0.000	0.000	0.000	0.000
136	C	164	GLY	0	0.054	0.029	25.194	-0.004	-0.004	0.000	0.000	0.000	0.000
137	C	165	ALA	0	-0.009	-0.019	24.679	-0.006	-0.006	0.000	0.000	0.000	0.000
138	C	166	ALA	0	-0.039	-0.009	25.719	-0.009	-0.009	0.000	0.000	0.000	0.000
139	C	167	THR	0	-0.082	-0.050	23.770	-0.004	-0.004	0.000	0.000	0.000	0.000
140	C	168	LEU	0	-0.018	-0.001	20.219	0.001	0.001	0.000	0.000	0.000	0.000
141	C	169	SER	0	-0.075	-0.022	20.019	-0.009	-0.009	0.000	0.000	0.000	0.000

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