FMO DATABASE

FMODB ID: QY77Y

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	-1195618.210942
FMO2-HF: Nuclear repulsion	1140873.090314
FMO2-HF: Total energy	-54745.120628
FMO2-MP2: Total energy	-54904.792436

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.
-0.733	1.336	-0.04	-0.98	-1.048	0.003

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 : -0.002 / q_NPA : -0.011

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	0.021	0.020	3.762	-0.408	1.661	-0.040	-0.980	-1.048	0.003
4	D	3	VAL	0	-0.003	-0.015	6.470	-0.196	-0.196	0.000	0.000	0.000	0.000
5	D	4	PRO	0	0.003	0.003	9.742	0.037	0.037	0.000	0.000	0.000	0.000
6	D	5	GLY	0	0.042	0.023	13.265	0.078	0.078	0.000	0.000	0.000	0.000
7	D	6	GLY	0	0.008	0.001	14.572	-0.061	-0.061	0.000	0.000	0.000	0.000
8	D	7	SER	0	-0.053	-0.022	18.019	0.011	0.011	0.000	0.000	0.000	0.000
9	D	8	SER	0	0.013	0.002	19.344	-0.012	-0.012	0.000	0.000	0.000	0.000
10	D	9	PRO	0	0.072	0.017	21.086	-0.013	-0.013	0.000	0.000	0.000	0.000
11	D	10	ALA	0	0.004	0.030	23.615	-0.016	-0.016	0.000	0.000	0.000	0.000
12	D	11	TRP	0	0.066	0.036	22.701	-0.026	-0.026	0.000	0.000	0.000	0.000
13	D	12	THR	0	0.032	0.001	24.832	-0.007	-0.007	0.000	0.000	0.000	0.000
14	D	13	GLN	0	0.038	0.021	26.551	-0.014	-0.014	0.000	0.000	0.000	0.000
15	D	14	CYS	0	0.047	0.033	28.851	-0.010	-0.010	0.000	0.000	0.000	0.000
16	D	15	GLN	0	-0.024	0.019	29.184	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	16	GLN	0	0.007	0.004	30.497	-0.004	-0.004	0.000	0.000	0.000	0.000
18	D	17	LEU	0	-0.021	-0.006	33.438	-0.007	-0.007	0.000	0.000	0.000	0.000
19	D	18	SER	0	0.007	-0.026	33.920	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	19	GLN	0	0.036	0.016	35.702	-0.006	-0.006	0.000	0.000	0.000	0.000
21	D	20	LYS	1	0.947	0.967	36.788	-0.064	-0.064	0.000	0.000	0.000	0.000
22	D	21	LEU	0	0.023	0.018	38.657	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	22	CYS	0	-0.051	-0.011	39.440	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	23	THR	0	-0.031	-0.019	41.597	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	24	LEU	0	0.002	-0.005	42.745	-0.002	-0.002	0.000	0.000	0.000	0.000
26	D	25	ALA	0	0.006	0.015	45.136	-0.002	-0.002	0.000	0.000	0.000	0.000
27	D	26	TRP	0	-0.023	-0.008	45.352	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.075	-0.019	48.333	-0.002	-0.002	0.000	0.000	0.000	0.000
29	D	28	ALA	0	0.000	0.006	50.080	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	47	ASN	0	-0.043	-0.033	52.421	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	48	ASP	-1	-0.894	-0.946	51.234	0.050	0.050	0.000	0.000	0.000	0.000
32	D	49	VAL	0	-0.060	-0.020	48.508	0.002	0.002	0.000	0.000	0.000	0.000
33	D	50	PRO	0	-0.014	0.001	43.354	0.000	0.000	0.000	0.000	0.000	0.000
34	D	51	HIS	0	-0.029	-0.021	44.172	-0.001	-0.001	0.000	0.000	0.000	0.000
35	D	52	ILE	0	0.015	0.001	37.658	0.002	0.002	0.000	0.000	0.000	0.000
36	D	53	GLN	0	-0.027	-0.003	40.839	-0.002	-0.002	0.000	0.000	0.000	0.000
37	D	54	CYS	0	0.011	-0.018	39.794	0.002	0.002	0.000	0.000	0.000	0.000
38	D	55	GLY	0	0.002	0.008	38.991	0.002	0.002	0.000	0.000	0.000	0.000
39	D	56	ASP	-1	-0.809	-0.889	37.054	0.095	0.095	0.000	0.000	0.000	0.000
40	D	57	GLY	0	0.037	0.024	33.764	0.007	0.007	0.000	0.000	0.000	0.000
41	D	58	CYS	0	-0.026	0.005	31.217	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	59	ASP	-1	-0.837	-0.909	33.911	0.097	0.097	0.000	0.000	0.000	0.000
43	D	60	PRO	0	0.017	-0.020	30.915	0.007	0.007	0.000	0.000	0.000	0.000
44	D	61	GLN	0	-0.054	-0.023	28.380	0.001	0.001	0.000	0.000	0.000	0.000
45	D	62	GLY	0	0.042	0.012	29.314	0.010	0.010	0.000	0.000	0.000	0.000
46	D	63	LEU	0	-0.045	-0.022	28.115	0.013	0.013	0.000	0.000	0.000	0.000
47	D	64	ARG	1	0.906	0.958	19.296	-0.211	-0.211	0.000	0.000	0.000	0.000
48	D	65	ASP	-1	-0.880	-0.937	24.412	0.176	0.176	0.000	0.000	0.000	0.000
49	D	66	ASN	0	-0.005	-0.014	25.393	0.027	0.027	0.000	0.000	0.000	0.000
50	D	67	SER	0	0.055	0.033	25.123	-0.009	-0.009	0.000	0.000	0.000	0.000
51	D	68	GLN	0	-0.020	0.001	26.502	-0.009	-0.009	0.000	0.000	0.000	0.000
52	D	69	PHE	0	0.007	0.001	28.230	-0.009	-0.009	0.000	0.000	0.000	0.000
53	D	71	LEU	0	-0.007	-0.015	27.581	-0.009	-0.009	0.000	0.000	0.000	0.000
54	D	72	GLN	0	0.014	0.020	31.658	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	73	ARG	1	0.827	0.888	33.498	-0.093	-0.093	0.000	0.000	0.000	0.000
56	D	74	ILE	0	-0.003	-0.012	33.313	-0.008	-0.008	0.000	0.000	0.000	0.000
57	D	75	HIS	0	0.054	0.023	34.126	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	76	GLN	0	0.021	0.012	36.170	-0.009	-0.009	0.000	0.000	0.000	0.000
59	D	77	GLY	0	-0.008	-0.015	39.209	-0.006	-0.006	0.000	0.000	0.000	0.000
60	D	78	LEU	0	-0.019	-0.012	36.272	-0.006	-0.006	0.000	0.000	0.000	0.000
61	D	79	ILE	0	0.000	0.002	38.644	-0.005	-0.005	0.000	0.000	0.000	0.000
62	D	80	PHE	0	0.021	0.004	41.628	-0.004	-0.004	0.000	0.000	0.000	0.000
63	D	81	TYR	0	0.021	-0.007	43.709	-0.004	-0.004	0.000	0.000	0.000	0.000
64	D	82	GLU	-1	-0.858	-0.911	42.232	0.065	0.065	0.000	0.000	0.000	0.000
65	D	83	LYS	1	0.915	0.959	44.135	-0.074	-0.074	0.000	0.000	0.000	0.000
66	D	84	LEU	0	-0.010	-0.016	47.449	-0.003	-0.003	0.000	0.000	0.000	0.000
67	D	85	LEU	0	-0.068	-0.026	46.808	-0.003	-0.003	0.000	0.000	0.000	0.000
68	D	86	GLY	0	0.020	0.029	49.146	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	87	SER	0	-0.090	-0.056	50.300	-0.002	-0.002	0.000	0.000	0.000	0.000
70	D	88	ASP	-1	-0.849	-0.948	53.047	0.038	0.038	0.000	0.000	0.000	0.000
71	D	89	ILE	0	-0.060	-0.023	54.336	-0.002	-0.002	0.000	0.000	0.000	0.000
72	D	90	PHE	0	-0.021	-0.029	52.338	-0.002	-0.002	0.000	0.000	0.000	0.000
73	D	91	THR	0	-0.014	0.024	54.142	0.000	0.000	0.000	0.000	0.000	0.000
74	D	92	GLY	0	0.019	-0.001	56.697	0.000	0.000	0.000	0.000	0.000	0.000
75	D	93	GLU	-1	-0.908	-0.959	59.572	0.031	0.031	0.000	0.000	0.000	0.000
76	D	94	PRO	0	0.041	0.011	58.885	0.000	0.000	0.000	0.000	0.000	0.000
77	D	95	SER	0	-0.030	-0.004	60.197	0.000	0.000	0.000	0.000	0.000	0.000
78	D	96	LEU	0	-0.031	-0.029	62.068	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	97	LEU	0	-0.095	-0.041	55.073	0.001	0.001	0.000	0.000	0.000	0.000
80	D	98	PRO	0	-0.003	0.004	57.987	0.001	0.001	0.000	0.000	0.000	0.000
81	D	99	ASP	-1	-0.887	-0.932	54.312	0.029	0.029	0.000	0.000	0.000	0.000
82	D	100	SER	0	-0.017	0.003	53.570	0.001	0.001	0.000	0.000	0.000	0.000
83	D	101	PRO	0	0.042	0.015	48.092	0.001	0.001	0.000	0.000	0.000	0.000
84	D	102	VAL	0	0.024	-0.014	48.116	0.003	0.003	0.000	0.000	0.000	0.000
85	D	103	GLY	0	0.060	0.042	48.531	0.002	0.002	0.000	0.000	0.000	0.000
86	D	104	GLN	0	0.018	0.003	43.323	0.005	0.005	0.000	0.000	0.000	0.000
87	D	105	LEU	0	-0.026	-0.012	43.806	0.004	0.004	0.000	0.000	0.000	0.000
88	D	106	HIS	0	-0.037	-0.012	43.757	0.002	0.002	0.000	0.000	0.000	0.000
89	D	107	ALA	0	0.038	0.020	42.714	0.004	0.004	0.000	0.000	0.000	0.000
90	D	108	SER	0	-0.032	-0.032	39.740	0.005	0.005	0.000	0.000	0.000	0.000
91	D	109	LEU	0	-0.045	-0.016	38.788	0.006	0.006	0.000	0.000	0.000	0.000
92	D	110	LEU	0	0.038	0.031	38.896	0.006	0.006	0.000	0.000	0.000	0.000
93	D	111	GLY	0	0.022	0.017	36.743	0.006	0.006	0.000	0.000	0.000	0.000
94	D	112	LEU	0	-0.022	-0.030	33.081	0.007	0.007	0.000	0.000	0.000	0.000
95	D	113	SER	0	-0.043	-0.029	33.818	0.008	0.008	0.000	0.000	0.000	0.000
96	D	114	GLN	0	0.011	0.000	34.003	0.008	0.008	0.000	0.000	0.000	0.000
97	D	115	LEU	0	-0.039	-0.020	29.656	0.008	0.008	0.000	0.000	0.000	0.000
98	D	116	LEU	0	-0.062	-0.010	29.055	0.012	0.012	0.000	0.000	0.000	0.000
99	D	117	GLN	0	-0.040	-0.033	29.427	0.009	0.009	0.000	0.000	0.000	0.000
100	D	118	PRO	0	0.031	0.027	28.315	-0.009	-0.009	0.000	0.000	0.000	0.000
101	D	119	GLU	-1	-0.897	-0.957	30.475	0.143	0.143	0.000	0.000	0.000	0.000
102	D	120	GLY	0	-0.053	-0.030	32.675	-0.003	-0.003	0.000	0.000	0.000	0.000
103	D	121	HIS	0	-0.065	-0.027	34.601	-0.009	-0.009	0.000	0.000	0.000	0.000
104	D	122	HIS	0	-0.054	-0.003	34.395	-0.015	-0.015	0.000	0.000	0.000	0.000
105	D	137	TRP	0	0.128	0.040	60.249	0.000	0.000	0.000	0.000	0.000	0.000
106	D	138	GLN	0	-0.004	0.011	63.821	-0.001	-0.001	0.000	0.000	0.000	0.000
107	D	139	ARG	1	0.940	0.959	62.945	-0.031	-0.031	0.000	0.000	0.000	0.000
108	D	140	LEU	0	0.026	0.016	59.449	0.001	0.001	0.000	0.000	0.000	0.000
109	D	141	LEU	0	0.054	0.020	59.456	0.000	0.000	0.000	0.000	0.000	0.000
110	D	142	LEU	0	-0.042	-0.009	56.321	0.000	0.000	0.000	0.000	0.000	0.000
111	D	143	ARG	1	0.922	0.963	54.704	-0.034	-0.034	0.000	0.000	0.000	0.000
112	D	144	PHE	0	0.037	0.023	53.901	0.001	0.001	0.000	0.000	0.000	0.000
113	D	145	LYS	1	0.946	0.961	54.237	-0.037	-0.037	0.000	0.000	0.000	0.000
114	D	146	ILE	0	0.004	0.010	50.133	0.001	0.001	0.000	0.000	0.000	0.000
115	D	147	LEU	0	0.049	0.008	49.372	0.003	0.003	0.000	0.000	0.000	0.000
116	D	148	ARG	1	0.977	1.008	49.352	-0.043	-0.043	0.000	0.000	0.000	0.000
117	D	149	SER	0	-0.070	-0.032	48.472	0.001	0.001	0.000	0.000	0.000	0.000
118	D	150	LEU	0	0.016	0.018	44.134	0.003	0.003	0.000	0.000	0.000	0.000
119	D	151	GLN	0	0.033	-0.005	44.541	0.003	0.003	0.000	0.000	0.000	0.000
120	D	152	ALA	0	-0.047	-0.014	44.304	0.001	0.001	0.000	0.000	0.000	0.000
121	D	153	PHE	0	-0.014	-0.004	39.287	0.002	0.002	0.000	0.000	0.000	0.000
122	D	154	VAL	0	0.045	0.000	40.041	0.005	0.005	0.000	0.000	0.000	0.000
123	D	155	ALA	0	0.024	0.023	39.209	0.002	0.002	0.000	0.000	0.000	0.000
124	D	156	VAL	0	-0.060	-0.030	37.665	0.001	0.001	0.000	0.000	0.000	0.000
125	D	157	ALA	0	0.052	0.023	35.866	0.005	0.005	0.000	0.000	0.000	0.000
126	D	158	ALA	0	0.023	0.006	34.479	0.006	0.006	0.000	0.000	0.000	0.000
127	D	159	ARG	1	0.910	0.955	33.910	-0.060	-0.060	0.000	0.000	0.000	0.000
128	D	160	VAL	0	0.034	0.033	31.163	0.004	0.004	0.000	0.000	0.000	0.000
129	D	161	PHE	0	0.007	-0.012	29.667	0.009	0.009	0.000	0.000	0.000	0.000
130	D	162	ALA	0	-0.025	-0.008	29.073	0.004	0.004	0.000	0.000	0.000	0.000
131	D	163	HIS	0	0.031	0.012	27.978	-0.004	-0.004	0.000	0.000	0.000	0.000
132	D	164	GLY	0	0.034	0.018	25.991	0.006	0.006	0.000	0.000	0.000	0.000
133	D	165	ALA	0	-0.045	-0.041	24.470	0.012	0.012	0.000	0.000	0.000	0.000
134	D	166	ALA	0	-0.045	-0.018	23.958	0.004	0.004	0.000	0.000	0.000	0.000
135	D	167	THR	0	-0.055	-0.032	22.901	-0.002	-0.002	0.000	0.000	0.000	0.000
136	D	168	LEU	0	-0.026	-0.010	21.469	0.015	0.015	0.000	0.000	0.000	0.000
137	D	169	SER	0	-0.019	0.010	20.877	0.034	0.034	0.000	0.000	0.000	0.000
138	D	170	PRO	0	-0.010	-0.014	16.410	0.005	0.005	0.000	0.000	0.000	0.000
139	D	171	HIS	0	-0.021	-0.004	15.973	0.004	0.004	0.000	0.000	0.000	0.000
140	D	172	HIS	1	0.884	0.926	13.445	-0.245	-0.245	0.000	0.000	0.000	0.000
141	D	173	HIS	0	0.068	0.059	17.273	-0.025	-0.025	0.000	0.000	0.000	0.000

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