FMO DATABASE

FMODB ID: R9NN8

Calculation Name: 3DUH-D-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: D

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	-1194903.547757
FMO2-HF: Nuclear repulsion	1140159.247298
FMO2-HF: Total energy	-54744.300459
FMO2-MP2: Total energy	-54904.021137

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(D:0:LEU)

Summations of interaction energy for fragment #1(D: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.
-0.86	1.293	-0.042	-1.036	-1.074	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.008

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	D	2	ALA	0	0.020	0.018	3.762	-0.568	1.585	-0.042	-1.036	-1.074	0.004
4	D	3	VAL	0	0.000	-0.012	6.472	-0.204	-0.204	0.000	0.000	0.000	0.000
5	D	4	PRO	0	-0.004	0.000	9.752	0.037	0.037	0.000	0.000	0.000	0.000
6	D	5	GLY	0	0.039	0.023	13.274	0.078	0.078	0.000	0.000	0.000	0.000
7	D	6	GLY	0	0.008	0.001	14.588	-0.061	-0.061	0.000	0.000	0.000	0.000
8	D	7	SER	0	-0.058	-0.026	18.037	0.011	0.011	0.000	0.000	0.000	0.000
9	D	8	SER	0	0.042	0.015	19.309	-0.008	-0.008	0.000	0.000	0.000	0.000
10	D	9	PRO	0	0.044	0.004	21.101	-0.013	-0.013	0.000	0.000	0.000	0.000
11	D	10	ALA	0	0.012	0.035	23.655	-0.015	-0.015	0.000	0.000	0.000	0.000
12	D	11	TRP	0	0.060	0.040	22.679	-0.026	-0.026	0.000	0.000	0.000	0.000
13	D	12	THR	0	0.032	0.000	25.017	-0.006	-0.006	0.000	0.000	0.000	0.000
14	D	13	GLN	0	0.047	0.020	26.430	-0.016	-0.016	0.000	0.000	0.000	0.000
15	D	14	CYS	0	0.053	0.039	28.923	-0.009	-0.009	0.000	0.000	0.000	0.000
16	D	15	GLN	0	-0.034	0.010	29.326	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	16	GLN	0	0.008	0.004	30.446	-0.004	-0.004	0.000	0.000	0.000	0.000
18	D	17	LEU	0	-0.008	-0.002	33.525	-0.007	-0.007	0.000	0.000	0.000	0.000
19	D	18	SER	0	-0.006	-0.024	34.009	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	19	GLN	0	0.033	0.010	35.921	-0.006	-0.006	0.000	0.000	0.000	0.000
21	D	20	LYS	1	0.935	0.963	36.958	-0.060	-0.060	0.000	0.000	0.000	0.000
22	D	21	LEU	0	0.023	0.017	38.594	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	22	CYS	0	-0.046	-0.002	39.737	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	23	THR	0	-0.008	-0.005	41.973	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	24	LEU	0	-0.006	-0.009	42.733	-0.002	-0.002	0.000	0.000	0.000	0.000
26	D	25	ALA	0	0.012	0.013	45.259	-0.002	-0.002	0.000	0.000	0.000	0.000
27	D	26	TRP	0	-0.019	-0.005	45.688	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.081	-0.022	48.479	-0.002	-0.002	0.000	0.000	0.000	0.000
29	D	28	ALA	0	-0.002	0.004	50.258	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	47	ASN	0	-0.062	-0.042	52.460	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	48	ASP	-1	-0.876	-0.936	51.315	0.049	0.049	0.000	0.000	0.000	0.000
32	D	49	VAL	0	-0.070	-0.023	48.178	0.002	0.002	0.000	0.000	0.000	0.000
33	D	50	PRO	0	-0.011	0.007	43.401	0.000	0.000	0.000	0.000	0.000	0.000
34	D	51	HIS	0	-0.024	-0.021	44.217	-0.001	-0.001	0.000	0.000	0.000	0.000
35	D	52	ILE	0	-0.003	-0.022	37.861	0.003	0.003	0.000	0.000	0.000	0.000
36	D	53	GLN	0	-0.047	-0.023	40.858	-0.002	-0.002	0.000	0.000	0.000	0.000
37	D	54	CYS	0	-0.002	-0.020	39.815	0.004	0.004	0.000	0.000	0.000	0.000
38	D	55	GLY	0	0.017	0.012	38.989	0.002	0.002	0.000	0.000	0.000	0.000
39	D	56	ASP	-1	-0.818	-0.919	37.089	0.095	0.095	0.000	0.000	0.000	0.000
40	D	57	GLY	0	0.049	0.029	33.787	0.007	0.007	0.000	0.000	0.000	0.000
41	D	58	CYS	0	-0.036	-0.003	31.213	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	59	ASP	-1	-0.849	-0.917	34.256	0.096	0.096	0.000	0.000	0.000	0.000
43	D	60	PRO	0	0.010	-0.023	31.285	0.007	0.007	0.000	0.000	0.000	0.000
44	D	61	GLN	0	-0.004	0.003	29.794	0.004	0.004	0.000	0.000	0.000	0.000
45	D	62	GLY	0	0.048	0.021	29.498	0.010	0.010	0.000	0.000	0.000	0.000
46	D	63	LEU	0	-0.042	-0.018	28.141	0.013	0.013	0.000	0.000	0.000	0.000
47	D	64	ARG	1	0.927	0.964	19.358	-0.206	-0.206	0.000	0.000	0.000	0.000
48	D	65	ASP	-1	-0.934	-0.960	24.433	0.175	0.175	0.000	0.000	0.000	0.000
49	D	66	ASN	0	-0.009	-0.019	25.350	0.031	0.031	0.000	0.000	0.000	0.000
50	D	67	SER	0	0.033	0.025	25.015	-0.011	-0.011	0.000	0.000	0.000	0.000
51	D	68	GLN	0	-0.010	0.003	26.538	-0.004	-0.004	0.000	0.000	0.000	0.000
52	D	69	PHE	0	0.008	0.007	28.254	-0.008	-0.008	0.000	0.000	0.000	0.000
53	D	71	LEU	0	-0.010	-0.019	27.412	-0.010	-0.010	0.000	0.000	0.000	0.000
54	D	72	GLN	0	0.044	0.037	31.678	0.000	0.000	0.000	0.000	0.000	0.000
55	D	73	ARG	1	0.869	0.959	33.521	-0.094	-0.094	0.000	0.000	0.000	0.000
56	D	74	ILE	0	-0.010	-0.013	33.367	-0.008	-0.008	0.000	0.000	0.000	0.000
57	D	75	HIS	0	0.075	0.030	34.178	-0.005	-0.005	0.000	0.000	0.000	0.000
58	D	76	GLN	0	-0.007	-0.010	36.189	-0.011	-0.011	0.000	0.000	0.000	0.000
59	D	77	GLY	0	-0.006	-0.009	39.230	-0.005	-0.005	0.000	0.000	0.000	0.000
60	D	78	LEU	0	-0.017	-0.012	36.217	-0.006	-0.006	0.000	0.000	0.000	0.000
61	D	79	ILE	0	0.002	0.008	38.469	-0.005	-0.005	0.000	0.000	0.000	0.000
62	D	80	PHE	0	0.008	-0.005	41.646	-0.005	-0.005	0.000	0.000	0.000	0.000
63	D	81	TYR	0	0.013	-0.011	43.558	-0.004	-0.004	0.000	0.000	0.000	0.000
64	D	82	GLU	-1	-0.920	-0.960	42.303	0.064	0.064	0.000	0.000	0.000	0.000
65	D	83	LYS	1	0.990	1.003	44.718	-0.073	-0.073	0.000	0.000	0.000	0.000
66	D	84	LEU	0	-0.018	-0.024	47.466	-0.003	-0.003	0.000	0.000	0.000	0.000
67	D	85	LEU	0	-0.074	-0.050	46.710	-0.003	-0.003	0.000	0.000	0.000	0.000
68	D	86	GLY	0	0.024	0.031	49.162	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	87	SER	0	-0.065	-0.029	50.315	-0.002	-0.002	0.000	0.000	0.000	0.000
70	D	88	ASP	-1	-0.837	-0.931	53.063	0.038	0.038	0.000	0.000	0.000	0.000
71	D	89	ILE	0	-0.073	-0.026	54.301	-0.002	-0.002	0.000	0.000	0.000	0.000
72	D	90	PHE	0	-0.036	-0.029	52.401	-0.002	-0.002	0.000	0.000	0.000	0.000
73	D	91	THR	0	-0.028	0.005	54.064	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	92	GLY	0	0.039	0.012	56.710	0.000	0.000	0.000	0.000	0.000	0.000
75	D	93	GLU	-1	-0.912	-0.952	59.673	0.030	0.030	0.000	0.000	0.000	0.000
76	D	94	PRO	0	0.016	-0.010	58.600	0.000	0.000	0.000	0.000	0.000	0.000
77	D	95	SER	0	-0.019	0.005	60.134	0.000	0.000	0.000	0.000	0.000	0.000
78	D	96	LEU	0	-0.024	-0.025	62.127	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	97	LEU	0	-0.095	-0.042	55.118	0.001	0.001	0.000	0.000	0.000	0.000
80	D	98	PRO	0	-0.006	0.006	57.994	0.000	0.000	0.000	0.000	0.000	0.000
81	D	99	ASP	-1	-0.883	-0.939	54.015	0.029	0.029	0.000	0.000	0.000	0.000
82	D	100	SER	0	-0.026	0.006	53.577	0.001	0.001	0.000	0.000	0.000	0.000
83	D	101	PRO	0	0.041	0.012	48.144	0.001	0.001	0.000	0.000	0.000	0.000
84	D	102	VAL	0	0.009	-0.018	48.124	0.003	0.003	0.000	0.000	0.000	0.000
85	D	103	GLY	0	0.063	0.041	48.541	0.002	0.002	0.000	0.000	0.000	0.000
86	D	104	GLN	0	0.013	0.000	43.332	0.005	0.005	0.000	0.000	0.000	0.000
87	D	105	LEU	0	-0.027	-0.023	43.815	0.004	0.004	0.000	0.000	0.000	0.000
88	D	106	HIS	0	-0.005	0.010	43.768	0.003	0.003	0.000	0.000	0.000	0.000
89	D	107	ALA	0	0.045	0.027	42.640	0.004	0.004	0.000	0.000	0.000	0.000
90	D	108	SER	0	-0.029	-0.027	39.745	0.005	0.005	0.000	0.000	0.000	0.000
91	D	109	LEU	0	-0.059	-0.019	38.799	0.005	0.005	0.000	0.000	0.000	0.000
92	D	110	LEU	0	0.059	0.044	38.910	0.006	0.006	0.000	0.000	0.000	0.000
93	D	111	GLY	0	0.010	0.020	36.754	0.006	0.006	0.000	0.000	0.000	0.000
94	D	112	LEU	0	-0.020	-0.028	33.169	0.007	0.007	0.000	0.000	0.000	0.000
95	D	113	SER	0	-0.055	-0.043	33.833	0.007	0.007	0.000	0.000	0.000	0.000
96	D	114	GLN	0	0.000	-0.001	34.019	0.007	0.007	0.000	0.000	0.000	0.000
97	D	115	LEU	0	-0.044	-0.025	29.710	0.008	0.008	0.000	0.000	0.000	0.000
98	D	116	LEU	0	-0.059	-0.012	29.070	0.012	0.012	0.000	0.000	0.000	0.000
99	D	117	GLN	0	-0.053	-0.035	29.446	0.012	0.012	0.000	0.000	0.000	0.000
100	D	118	PRO	0	0.041	0.030	28.341	-0.009	-0.009	0.000	0.000	0.000	0.000
101	D	119	GLU	-1	-0.903	-0.961	30.596	0.145	0.145	0.000	0.000	0.000	0.000
102	D	120	GLY	0	-0.080	-0.044	32.694	-0.003	-0.003	0.000	0.000	0.000	0.000
103	D	121	HIS	0	-0.053	-0.018	34.675	-0.009	-0.009	0.000	0.000	0.000	0.000
104	D	122	HIS	0	-0.024	0.007	34.139	-0.012	-0.012	0.000	0.000	0.000	0.000
105	D	137	TRP	0	0.078	0.020	60.906	0.000	0.000	0.000	0.000	0.000	0.000
106	D	138	GLN	0	-0.010	0.005	63.835	-0.001	-0.001	0.000	0.000	0.000	0.000
107	D	139	ARG	1	0.951	0.964	62.804	-0.031	-0.031	0.000	0.000	0.000	0.000
108	D	140	LEU	0	0.012	0.014	59.073	0.001	0.001	0.000	0.000	0.000	0.000
109	D	141	LEU	0	0.062	0.021	59.518	0.000	0.000	0.000	0.000	0.000	0.000
110	D	142	LEU	0	-0.039	-0.007	56.084	0.000	0.000	0.000	0.000	0.000	0.000
111	D	143	ARG	1	0.971	0.976	54.721	-0.034	-0.034	0.000	0.000	0.000	0.000
112	D	144	PHE	0	0.048	0.030	53.914	0.002	0.002	0.000	0.000	0.000	0.000
113	D	145	LYS	1	0.945	0.964	54.250	-0.036	-0.036	0.000	0.000	0.000	0.000
114	D	146	ILE	0	-0.009	-0.001	50.096	0.001	0.001	0.000	0.000	0.000	0.000
115	D	147	LEU	0	0.038	0.010	49.715	0.002	0.002	0.000	0.000	0.000	0.000
116	D	148	ARG	1	0.978	1.009	49.380	-0.043	-0.043	0.000	0.000	0.000	0.000
117	D	149	SER	0	-0.078	-0.042	48.592	0.002	0.002	0.000	0.000	0.000	0.000
118	D	150	LEU	0	0.050	0.037	44.124	0.002	0.002	0.000	0.000	0.000	0.000
119	D	151	GLN	0	0.015	-0.013	44.554	0.003	0.003	0.000	0.000	0.000	0.000
120	D	152	ALA	0	-0.046	-0.011	44.482	0.001	0.001	0.000	0.000	0.000	0.000
121	D	153	PHE	0	-0.023	-0.013	39.143	0.002	0.002	0.000	0.000	0.000	0.000
122	D	154	VAL	0	0.057	0.003	39.995	0.005	0.005	0.000	0.000	0.000	0.000
123	D	155	ALA	0	0.013	0.016	39.349	0.002	0.002	0.000	0.000	0.000	0.000
124	D	156	VAL	0	-0.054	-0.028	37.642	0.001	0.001	0.000	0.000	0.000	0.000
125	D	157	ALA	0	0.036	0.015	35.880	0.005	0.005	0.000	0.000	0.000	0.000
126	D	158	ALA	0	0.024	0.006	34.591	0.005	0.005	0.000	0.000	0.000	0.000
127	D	159	ARG	1	0.923	0.964	34.232	-0.060	-0.060	0.000	0.000	0.000	0.000
128	D	160	VAL	0	0.037	0.034	31.135	0.003	0.003	0.000	0.000	0.000	0.000
129	D	161	PHE	0	0.001	-0.014	29.828	0.008	0.008	0.000	0.000	0.000	0.000
130	D	162	ALA	0	-0.015	-0.004	29.360	0.004	0.004	0.000	0.000	0.000	0.000
131	D	163	HIS	0	0.032	0.012	28.627	-0.003	-0.003	0.000	0.000	0.000	0.000
132	D	164	GLY	0	0.037	0.003	26.280	0.006	0.006	0.000	0.000	0.000	0.000
133	D	165	ALA	0	-0.041	-0.040	24.811	0.012	0.012	0.000	0.000	0.000	0.000
134	D	166	ALA	0	-0.043	-0.017	24.338	0.004	0.004	0.000	0.000	0.000	0.000
135	D	167	THR	0	-0.067	-0.025	23.536	0.000	0.000	0.000	0.000	0.000	0.000
136	D	168	LEU	0	-0.025	-0.017	21.814	0.014	0.014	0.000	0.000	0.000	0.000
137	D	169	SER	0	-0.028	0.006	21.104	0.033	0.033	0.000	0.000	0.000	0.000
138	D	170	PRO	0	-0.008	-0.009	16.566	0.004	0.004	0.000	0.000	0.000	0.000
139	D	171	HIS	0	-0.016	-0.001	16.218	0.009	0.009	0.000	0.000	0.000	0.000
140	D	172	HIS	1	0.899	0.934	14.285	-0.230	-0.230	0.000	0.000	0.000	0.000
141	D	173	HIS	0	0.053	0.051	17.386	-0.029	-0.029	0.000	0.000	0.000	0.000

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