FMO DATABASE

FMODB ID: K9773

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	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	-1198687.551031
FMO2-HF: Nuclear repulsion	1143942.021557
FMO2-HF: Total energy	-54745.529474
FMO2-MP2: Total energy	-54905.174418

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.
-0.681	1.152	-0.021	-0.964	-0.848	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 : -0.003 / q_NPA : -0.009

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	0.017	0.015	3.873	-0.461	1.372	-0.021	-0.964	-0.848	0.003
4	D	3	VAL	0	0.001	-0.007	6.870	-0.131	-0.131	0.000	0.000	0.000	0.000
5	D	4	PRO	0	0.006	0.005	10.240	0.025	0.025	0.000	0.000	0.000	0.000
6	D	5	GLY	0	0.046	0.022	13.565	0.091	0.091	0.000	0.000	0.000	0.000
7	D	6	GLY	0	-0.007	0.007	15.209	-0.059	-0.059	0.000	0.000	0.000	0.000
8	D	7	SER	0	-0.018	-0.011	18.198	0.012	0.012	0.000	0.000	0.000	0.000
9	D	8	SER	0	-0.006	0.003	19.750	-0.005	-0.005	0.000	0.000	0.000	0.000
10	D	9	PRO	0	0.082	0.021	21.367	-0.014	-0.014	0.000	0.000	0.000	0.000
11	D	10	ALA	0	0.012	0.010	24.383	-0.014	-0.014	0.000	0.000	0.000	0.000
12	D	11	TRP	0	0.050	0.029	22.811	-0.024	-0.024	0.000	0.000	0.000	0.000
13	D	12	THR	0	0.020	-0.001	25.151	-0.006	-0.006	0.000	0.000	0.000	0.000
14	D	13	GLN	0	0.029	0.018	27.205	-0.012	-0.012	0.000	0.000	0.000	0.000
15	D	14	CYS	0	0.030	0.032	29.115	-0.008	-0.008	0.000	0.000	0.000	0.000
16	D	15	GLN	0	-0.004	0.009	29.642	-0.010	-0.010	0.000	0.000	0.000	0.000
17	D	16	GLN	0	0.010	0.011	30.982	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	17	LEU	0	-0.031	-0.008	33.989	-0.006	-0.006	0.000	0.000	0.000	0.000
19	D	18	SER	0	0.025	-0.011	34.415	-0.004	-0.004	0.000	0.000	0.000	0.000
20	D	19	GLN	0	0.063	0.036	36.267	-0.004	-0.004	0.000	0.000	0.000	0.000
21	D	20	LYS	1	0.938	0.975	36.668	-0.058	-0.058	0.000	0.000	0.000	0.000
22	D	21	LEU	0	0.021	0.017	38.706	-0.003	-0.003	0.000	0.000	0.000	0.000
23	D	22	CYS	0	-0.058	-0.028	39.688	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	23	THR	0	-0.033	-0.028	41.685	-0.003	-0.003	0.000	0.000	0.000	0.000
25	D	24	LEU	0	-0.002	-0.004	43.137	-0.002	-0.002	0.000	0.000	0.000	0.000
26	D	25	ALA	0	0.003	0.010	45.250	-0.002	-0.002	0.000	0.000	0.000	0.000
27	D	26	TRP	0	-0.036	-0.019	45.433	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.054	-0.014	48.446	-0.002	-0.002	0.000	0.000	0.000	0.000
29	D	28	ALA	0	-0.015	0.002	50.328	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	47	ASN	0	-0.039	-0.029	52.657	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	48	ASP	-1	-0.909	-0.959	51.431	0.048	0.048	0.000	0.000	0.000	0.000
32	D	49	VAL	0	-0.035	-0.009	48.680	0.002	0.002	0.000	0.000	0.000	0.000
33	D	50	PRO	0	-0.022	0.000	43.639	0.000	0.000	0.000	0.000	0.000	0.000
34	D	51	HIS	0	-0.022	-0.019	44.258	-0.002	-0.002	0.000	0.000	0.000	0.000
35	D	52	ILE	0	0.010	0.003	37.763	0.003	0.003	0.000	0.000	0.000	0.000
36	D	53	GLN	0	-0.010	-0.001	40.534	-0.002	-0.002	0.000	0.000	0.000	0.000
37	D	54	CYS	0	-0.013	-0.023	39.540	0.003	0.003	0.000	0.000	0.000	0.000
38	D	55	GLY	0	0.026	0.027	38.881	0.001	0.001	0.000	0.000	0.000	0.000
39	D	56	ASP	-1	-0.812	-0.902	36.837	0.091	0.091	0.000	0.000	0.000	0.000
40	D	57	GLY	0	0.039	0.023	33.233	0.007	0.007	0.000	0.000	0.000	0.000
41	D	58	CYS	0	-0.022	-0.001	31.708	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	59	ASP	-1	-0.796	-0.886	33.371	0.094	0.094	0.000	0.000	0.000	0.000
43	D	60	PRO	0	0.005	-0.026	30.798	0.007	0.007	0.000	0.000	0.000	0.000
44	D	61	GLN	0	-0.055	-0.022	27.475	-0.001	-0.001	0.000	0.000	0.000	0.000
45	D	62	GLY	0	0.040	0.005	28.792	0.011	0.011	0.000	0.000	0.000	0.000
46	D	63	LEU	0	-0.039	-0.021	28.409	0.013	0.013	0.000	0.000	0.000	0.000
47	D	64	ARG	1	0.887	0.938	19.441	-0.196	-0.196	0.000	0.000	0.000	0.000
48	D	65	ASP	-1	-0.852	-0.908	24.221	0.172	0.172	0.000	0.000	0.000	0.000
49	D	66	ASN	0	-0.034	-0.036	25.568	0.024	0.024	0.000	0.000	0.000	0.000
50	D	67	SER	0	0.050	0.031	25.737	-0.007	-0.007	0.000	0.000	0.000	0.000
51	D	68	GLN	0	-0.019	0.013	26.799	-0.010	-0.010	0.000	0.000	0.000	0.000
52	D	69	PHE	0	0.001	0.006	28.551	-0.008	-0.008	0.000	0.000	0.000	0.000
53	D	71	LEU	0	-0.012	-0.015	27.626	-0.008	-0.008	0.000	0.000	0.000	0.000
54	D	72	GLN	0	0.020	0.019	31.913	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	73	ARG	1	0.823	0.888	33.809	-0.088	-0.088	0.000	0.000	0.000	0.000
56	D	74	ILE	0	-0.003	-0.014	33.547	-0.008	-0.008	0.000	0.000	0.000	0.000
57	D	75	HIS	0	0.059	0.020	34.346	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	76	GLN	0	0.011	0.009	36.406	-0.008	-0.008	0.000	0.000	0.000	0.000
59	D	77	GLY	0	0.008	0.003	39.504	-0.005	-0.005	0.000	0.000	0.000	0.000
60	D	78	LEU	0	-0.038	-0.022	36.476	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	79	ILE	0	0.027	0.016	38.764	-0.005	-0.005	0.000	0.000	0.000	0.000
62	D	80	PHE	0	0.012	0.003	41.688	-0.004	-0.004	0.000	0.000	0.000	0.000
63	D	81	TYR	0	0.009	-0.037	44.062	-0.003	-0.003	0.000	0.000	0.000	0.000
64	D	82	GLU	-1	-0.850	-0.909	42.509	0.060	0.060	0.000	0.000	0.000	0.000
65	D	83	LYS	1	0.897	0.944	44.054	-0.070	-0.070	0.000	0.000	0.000	0.000
66	D	84	LEU	0	-0.038	-0.013	47.746	-0.003	-0.003	0.000	0.000	0.000	0.000
67	D	85	LEU	0	-0.043	-0.016	46.954	-0.003	-0.003	0.000	0.000	0.000	0.000
68	D	86	GLY	0	0.006	0.021	49.374	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	87	SER	0	-0.067	-0.042	50.587	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	88	ASP	-1	-0.846	-0.944	53.576	0.035	0.035	0.000	0.000	0.000	0.000
71	D	89	ILE	0	-0.057	-0.020	54.665	-0.002	-0.002	0.000	0.000	0.000	0.000
72	D	90	PHE	0	-0.010	-0.021	52.337	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	91	THR	0	-0.001	0.018	54.702	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	92	GLY	0	0.030	0.004	56.988	0.000	0.000	0.000	0.000	0.000	0.000
75	D	93	GLU	-1	-0.908	-0.958	59.858	0.028	0.028	0.000	0.000	0.000	0.000
76	D	94	PRO	0	0.054	0.021	59.290	0.000	0.000	0.000	0.000	0.000	0.000
77	D	95	SER	0	-0.025	-0.014	60.473	0.000	0.000	0.000	0.000	0.000	0.000
78	D	96	LEU	0	-0.046	-0.025	62.217	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	97	LEU	0	-0.059	-0.028	55.634	0.001	0.001	0.000	0.000	0.000	0.000
80	D	98	PRO	0	-0.011	0.010	57.012	0.001	0.001	0.000	0.000	0.000	0.000
81	D	99	ASP	-1	-0.883	-0.939	54.997	0.026	0.026	0.000	0.000	0.000	0.000
82	D	100	SER	0	-0.036	-0.004	53.600	0.001	0.001	0.000	0.000	0.000	0.000
83	D	101	PRO	0	0.032	0.006	48.451	0.001	0.001	0.000	0.000	0.000	0.000
84	D	102	VAL	0	0.000	-0.012	48.354	0.003	0.003	0.000	0.000	0.000	0.000
85	D	103	GLY	0	0.072	0.043	48.501	0.002	0.002	0.000	0.000	0.000	0.000
86	D	104	GLN	0	0.017	0.005	43.741	0.004	0.004	0.000	0.000	0.000	0.000
87	D	105	LEU	0	-0.025	-0.010	43.898	0.003	0.003	0.000	0.000	0.000	0.000
88	D	106	HIS	0	-0.030	-0.011	43.655	0.002	0.002	0.000	0.000	0.000	0.000
89	D	107	ALA	0	0.050	0.023	42.666	0.004	0.004	0.000	0.000	0.000	0.000
90	D	108	SER	0	-0.040	-0.033	39.755	0.004	0.004	0.000	0.000	0.000	0.000
91	D	109	LEU	0	-0.033	-0.019	38.853	0.005	0.005	0.000	0.000	0.000	0.000
92	D	110	LEU	0	0.048	0.036	38.947	0.005	0.005	0.000	0.000	0.000	0.000
93	D	111	GLY	0	0.025	0.024	37.052	0.005	0.005	0.000	0.000	0.000	0.000
94	D	112	LEU	0	-0.029	-0.028	33.222	0.006	0.006	0.000	0.000	0.000	0.000
95	D	113	SER	0	-0.047	-0.038	33.958	0.008	0.008	0.000	0.000	0.000	0.000
96	D	114	GLN	0	-0.002	-0.009	34.192	0.007	0.007	0.000	0.000	0.000	0.000
97	D	115	LEU	0	-0.044	-0.018	29.902	0.006	0.006	0.000	0.000	0.000	0.000
98	D	116	LEU	0	-0.065	-0.022	29.326	0.011	0.011	0.000	0.000	0.000	0.000
99	D	117	GLN	0	-0.030	-0.025	29.854	0.008	0.008	0.000	0.000	0.000	0.000
100	D	118	PRO	0	0.024	0.031	28.743	-0.008	-0.008	0.000	0.000	0.000	0.000
101	D	119	GLU	-1	-0.867	-0.939	30.864	0.128	0.128	0.000	0.000	0.000	0.000
102	D	120	GLY	0	-0.038	-0.025	32.936	-0.003	-0.003	0.000	0.000	0.000	0.000
103	D	121	HIS	0	-0.063	-0.020	34.913	-0.008	-0.008	0.000	0.000	0.000	0.000
104	D	122	HIS	0	-0.097	-0.038	34.796	-0.012	-0.012	0.000	0.000	0.000	0.000
105	D	137	TRP	0	0.136	0.041	60.055	0.000	0.000	0.000	0.000	0.000	0.000
106	D	138	GLN	0	-0.017	0.001	64.213	0.000	0.000	0.000	0.000	0.000	0.000
107	D	139	ARG	1	0.949	0.965	63.150	-0.029	-0.029	0.000	0.000	0.000	0.000
108	D	140	LEU	0	0.018	0.013	59.789	0.001	0.001	0.000	0.000	0.000	0.000
109	D	141	LEU	0	0.075	0.035	59.357	0.001	0.001	0.000	0.000	0.000	0.000
110	D	142	LEU	0	-0.059	-0.016	56.858	0.000	0.000	0.000	0.000	0.000	0.000
111	D	143	ARG	1	0.900	0.945	54.905	-0.032	-0.032	0.000	0.000	0.000	0.000
112	D	144	PHE	0	0.012	0.016	54.149	0.001	0.001	0.000	0.000	0.000	0.000
113	D	145	LYS	1	0.949	0.967	54.248	-0.035	-0.035	0.000	0.000	0.000	0.000
114	D	146	ILE	0	0.025	0.030	50.388	0.001	0.001	0.000	0.000	0.000	0.000
115	D	147	LEU	0	0.060	0.035	49.564	0.002	0.002	0.000	0.000	0.000	0.000
116	D	148	ARG	1	0.942	0.971	49.372	-0.040	-0.040	0.000	0.000	0.000	0.000
117	D	149	SER	0	-0.105	-0.035	49.008	0.001	0.001	0.000	0.000	0.000	0.000
118	D	150	LEU	0	0.039	0.021	44.108	0.002	0.002	0.000	0.000	0.000	0.000
119	D	151	GLN	0	0.020	-0.016	44.609	0.003	0.003	0.000	0.000	0.000	0.000
120	D	152	ALA	0	-0.023	-0.003	44.210	0.001	0.001	0.000	0.000	0.000	0.000
121	D	153	PHE	0	-0.001	0.007	39.423	0.002	0.002	0.000	0.000	0.000	0.000
122	D	154	VAL	0	0.033	0.008	40.183	0.004	0.004	0.000	0.000	0.000	0.000
123	D	155	ALA	0	0.046	0.020	39.217	0.003	0.003	0.000	0.000	0.000	0.000
124	D	156	VAL	0	-0.066	-0.018	37.843	0.001	0.001	0.000	0.000	0.000	0.000
125	D	157	ALA	0	0.053	0.022	35.914	0.004	0.004	0.000	0.000	0.000	0.000
126	D	158	ALA	0	0.014	0.002	34.542	0.005	0.005	0.000	0.000	0.000	0.000
127	D	159	ARG	1	0.865	0.930	34.021	-0.056	-0.056	0.000	0.000	0.000	0.000
128	D	160	VAL	0	0.036	0.024	31.109	0.003	0.003	0.000	0.000	0.000	0.000
129	D	161	PHE	0	0.016	-0.004	29.998	0.008	0.008	0.000	0.000	0.000	0.000
130	D	162	ALA	0	-0.022	-0.011	29.160	0.004	0.004	0.000	0.000	0.000	0.000
131	D	163	HIS	0	0.013	0.007	28.086	-0.005	-0.005	0.000	0.000	0.000	0.000
132	D	164	GLY	0	0.041	0.026	25.942	0.006	0.006	0.000	0.000	0.000	0.000
133	D	165	ALA	0	-0.041	-0.041	24.513	0.011	0.011	0.000	0.000	0.000	0.000
134	D	166	ALA	0	-0.039	-0.012	24.316	0.001	0.001	0.000	0.000	0.000	0.000
135	D	167	THR	0	-0.062	-0.038	22.810	0.000	0.000	0.000	0.000	0.000	0.000
136	D	168	LEU	0	-0.019	-0.003	21.221	0.015	0.015	0.000	0.000	0.000	0.000
137	D	169	SER	0	0.005	0.018	21.004	0.028	0.028	0.000	0.000	0.000	0.000
138	D	170	PRO	0	-0.012	-0.014	16.733	0.007	0.007	0.000	0.000	0.000	0.000
139	D	171	HIS	0	-0.018	-0.003	16.414	-0.006	-0.006	0.000	0.000	0.000	0.000
140	D	172	HIS	1	0.873	0.923	13.786	-0.212	-0.212	0.000	0.000	0.000	0.000
141	D	173	HIS	0	0.063	0.053	17.894	-0.019	-0.019	0.000	0.000	0.000	0.000

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