FMO DATABASE

FMODB ID: 52ZZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1214817.357754
FMO2-HF: Nuclear repulsion	1159896.699472
FMO2-HF: Total energy	-54920.658283
FMO2-MP2: Total energy	-55080.823114

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.
-1.587	0.947	-0.045	-1.292	-1.197	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 : -0.009 / 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	C	2	ALA	0	0.031	0.022	3.742	-1.897	0.637	-0.045	-1.292	-1.197	0.002
4	C	3	VAL	0	-0.016	-0.012	6.456	0.103	0.103	0.000	0.000	0.000	0.000
5	C	4	PRO	0	0.016	0.005	9.833	-0.016	-0.016	0.000	0.000	0.000	0.000
6	C	5	GLY	0	0.041	0.020	13.258	0.064	0.064	0.000	0.000	0.000	0.000
7	C	6	GLY	0	-0.002	0.010	14.806	0.016	0.016	0.000	0.000	0.000	0.000
8	C	7	SER	0	-0.020	-0.011	18.096	-0.029	-0.029	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.011	0.006	19.690	0.010	0.010	0.000	0.000	0.000	0.000
10	C	9	PRO	0	0.031	0.016	20.992	0.001	0.001	0.000	0.000	0.000	0.000
11	C	10	ALA	0	0.068	0.037	24.202	-0.012	-0.012	0.000	0.000	0.000	0.000
12	C	11	TRP	0	0.040	0.016	22.249	0.003	0.003	0.000	0.000	0.000	0.000
13	C	12	THR	0	0.056	0.023	27.106	0.005	0.005	0.000	0.000	0.000	0.000
14	C	13	GLN	0	0.037	0.017	29.530	0.006	0.006	0.000	0.000	0.000	0.000
15	C	14	CYS	0	0.015	0.019	29.662	0.005	0.005	0.000	0.000	0.000	0.000
16	C	15	GLN	0	0.015	0.020	30.856	0.001	0.001	0.000	0.000	0.000	0.000
17	C	16	GLN	0	-0.041	-0.025	32.610	0.002	0.002	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.014	-0.007	34.989	0.002	0.002	0.000	0.000	0.000	0.000
19	C	18	SER	0	-0.013	-0.018	34.280	0.002	0.002	0.000	0.000	0.000	0.000
20	C	19	GLN	0	0.043	0.025	36.778	0.004	0.004	0.000	0.000	0.000	0.000
21	C	20	LYS	1	0.863	0.931	38.661	0.011	0.011	0.000	0.000	0.000	0.000
22	C	21	LEU	0	0.004	-0.004	38.596	0.001	0.001	0.000	0.000	0.000	0.000
23	C	22	CYS	0	-0.061	-0.006	39.705	0.002	0.002	0.000	0.000	0.000	0.000
24	C	23	THR	0	-0.016	-0.013	42.653	0.000	0.000	0.000	0.000	0.000	0.000
25	C	24	LEU	0	-0.016	-0.018	43.766	0.001	0.001	0.000	0.000	0.000	0.000
26	C	25	ALA	0	-0.006	-0.004	45.006	0.001	0.001	0.000	0.000	0.000	0.000
27	C	26	TRP	0	-0.014	-0.015	45.354	0.001	0.001	0.000	0.000	0.000	0.000
28	C	27	SER	0	-0.008	0.015	48.923	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	28	ALA	0	-0.042	-0.007	50.667	0.000	0.000	0.000	0.000	0.000	0.000
30	C	29	HIS	0	-0.043	-0.015	51.724	0.001	0.001	0.000	0.000	0.000	0.000
31	C	47	ASN	0	-0.049	-0.032	49.078	-0.002	-0.002	0.000	0.000	0.000	0.000
32	C	48	ASP	-1	-0.923	-0.971	45.202	0.033	0.033	0.000	0.000	0.000	0.000
33	C	49	VAL	0	-0.048	-0.018	43.817	0.001	0.001	0.000	0.000	0.000	0.000
34	C	50	PRO	0	-0.006	0.026	38.985	0.001	0.001	0.000	0.000	0.000	0.000
35	C	51	HIS	0	-0.009	-0.016	39.731	-0.004	-0.004	0.000	0.000	0.000	0.000
36	C	52	ILE	0	0.005	-0.002	34.021	0.004	0.004	0.000	0.000	0.000	0.000
37	C	53	GLN	0	-0.065	-0.027	35.977	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	54	CYS	0	0.015	-0.019	33.492	-0.001	-0.001	0.000	0.000	0.000	0.000
39	C	55	GLY	0	-0.016	0.002	32.145	0.002	0.002	0.000	0.000	0.000	0.000
40	C	56	ASP	-1	-0.815	-0.895	30.510	0.055	0.055	0.000	0.000	0.000	0.000
41	C	57	GLY	0	0.061	0.033	27.686	0.002	0.002	0.000	0.000	0.000	0.000
42	C	58	CYS	0	-0.041	-0.007	26.709	-0.011	-0.011	0.000	0.000	0.000	0.000
43	C	59	ASP	-1	-0.843	-0.911	28.902	0.030	0.030	0.000	0.000	0.000	0.000
44	C	60	PRO	0	0.017	-0.015	28.138	0.002	0.002	0.000	0.000	0.000	0.000
45	C	61	GLN	0	-0.026	-0.016	25.200	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	62	GLY	0	0.037	0.022	24.092	0.006	0.006	0.000	0.000	0.000	0.000
47	C	63	LEU	0	-0.060	-0.025	24.419	0.007	0.007	0.000	0.000	0.000	0.000
48	C	64	ARG	1	0.886	0.942	17.677	0.024	0.024	0.000	0.000	0.000	0.000
49	C	65	ASP	-1	-0.913	-0.934	19.356	0.087	0.087	0.000	0.000	0.000	0.000
50	C	66	ASN	0	-0.005	-0.021	19.073	0.005	0.005	0.000	0.000	0.000	0.000
51	C	67	SER	0	0.061	0.040	21.388	-0.004	-0.004	0.000	0.000	0.000	0.000
52	C	68	GLN	0	-0.014	-0.006	21.616	0.006	0.006	0.000	0.000	0.000	0.000
53	C	69	PHE	0	0.033	0.019	23.013	-0.003	-0.003	0.000	0.000	0.000	0.000
54	C	71	LEU	0	0.024	-0.009	25.600	-0.005	-0.005	0.000	0.000	0.000	0.000
55	C	72	GLN	0	-0.008	0.027	28.051	0.000	0.000	0.000	0.000	0.000	0.000
56	C	73	ARG	1	0.827	0.894	29.847	-0.049	-0.049	0.000	0.000	0.000	0.000
57	C	74	ILE	0	-0.016	-0.029	31.019	-0.004	-0.004	0.000	0.000	0.000	0.000
58	C	75	HIS	0	-0.042	-0.036	32.169	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	76	GLN	0	0.057	0.029	33.977	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	77	GLY	0	0.010	0.000	36.126	-0.002	-0.002	0.000	0.000	0.000	0.000
61	C	78	LEU	0	-0.042	-0.022	35.053	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	79	ILE	0	0.018	0.012	37.046	-0.002	-0.002	0.000	0.000	0.000	0.000
63	C	80	PHE	0	0.011	0.011	39.942	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	81	TYR	0	0.031	-0.003	41.441	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	82	GLU	-1	-0.869	-0.930	41.700	0.015	0.015	0.000	0.000	0.000	0.000
66	C	83	LYS	1	1.001	1.007	44.052	-0.027	-0.027	0.000	0.000	0.000	0.000
67	C	84	LEU	0	-0.025	-0.014	45.973	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	85	LEU	0	-0.055	-0.018	46.503	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	86	GLY	0	0.025	0.026	48.245	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	87	SER	0	-0.081	-0.044	49.777	0.000	0.000	0.000	0.000	0.000	0.000
71	C	88	ASP	-1	-0.766	-0.867	51.996	0.012	0.012	0.000	0.000	0.000	0.000
72	C	89	ILE	0	-0.024	-0.018	52.396	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	90	PHE	0	0.008	-0.025	51.310	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	91	THR	0	-0.028	0.009	53.972	-0.001	-0.001	0.000	0.000	0.000	0.000
75	C	92	GLY	0	0.066	0.041	56.730	0.000	0.000	0.000	0.000	0.000	0.000
76	C	93	GLU	-1	-0.799	-0.913	60.080	0.008	0.008	0.000	0.000	0.000	0.000
77	C	94	PRO	0	-0.147	-0.131	60.705	0.000	0.000	0.000	0.000	0.000	0.000
78	C	95	SER	0	0.142	0.142	59.478	0.000	0.000	0.000	0.000	0.000	0.000
79	C	96	LEU	0	-0.013	-0.024	60.155	0.000	0.000	0.000	0.000	0.000	0.000
80	C	97	LEU	0	-0.012	0.002	62.112	0.000	0.000	0.000	0.000	0.000	0.000
81	C	98	PRO	0	-0.037	-0.016	59.658	-0.001	-0.001	0.000	0.000	0.000	0.000
82	C	99	ASP	-1	-0.839	-0.897	55.560	-0.004	-0.004	0.000	0.000	0.000	0.000
83	C	100	SER	0	-0.052	-0.053	54.376	0.001	0.001	0.000	0.000	0.000	0.000
84	C	101	PRO	0	0.032	0.024	49.766	0.000	0.000	0.000	0.000	0.000	0.000
85	C	102	VAL	0	0.009	-0.011	49.211	0.000	0.000	0.000	0.000	0.000	0.000
86	C	103	GLY	0	0.048	0.030	49.028	0.001	0.001	0.000	0.000	0.000	0.000
87	C	104	GLN	0	0.050	0.020	45.053	0.000	0.000	0.000	0.000	0.000	0.000
88	C	105	LEU	0	0.012	0.009	44.820	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	106	HIS	0	-0.045	-0.020	44.017	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	107	ALA	0	0.049	0.024	43.627	0.001	0.001	0.000	0.000	0.000	0.000
91	C	108	SER	0	-0.030	-0.028	40.972	-0.002	-0.002	0.000	0.000	0.000	0.000
92	C	109	LEU	0	-0.018	-0.008	39.484	0.000	0.000	0.000	0.000	0.000	0.000
93	C	110	LEU	0	0.034	0.021	38.730	0.002	0.002	0.000	0.000	0.000	0.000
94	C	111	GLY	0	0.001	0.017	37.800	0.001	0.001	0.000	0.000	0.000	0.000
95	C	112	LEU	0	-0.033	-0.025	32.986	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	113	SER	0	-0.033	-0.018	33.711	0.002	0.002	0.000	0.000	0.000	0.000
97	C	114	GLN	0	0.049	-0.001	33.573	0.001	0.001	0.000	0.000	0.000	0.000
98	C	115	LEU	0	-0.039	-0.014	30.843	0.000	0.000	0.000	0.000	0.000	0.000
99	C	116	LEU	0	-0.077	-0.035	29.251	-0.001	-0.001	0.000	0.000	0.000	0.000
100	C	117	GLN	0	-0.014	0.018	28.745	0.005	0.005	0.000	0.000	0.000	0.000
101	C	118	PRO	0	0.006	0.024	25.103	-0.005	-0.005	0.000	0.000	0.000	0.000
102	C	119	GLU	-1	-0.908	-0.961	25.811	0.029	0.029	0.000	0.000	0.000	0.000
103	C	120	GLY	0	-0.014	-0.013	25.647	0.008	0.008	0.000	0.000	0.000	0.000
104	C	121	HIS	0	-0.100	-0.065	23.023	0.017	0.017	0.000	0.000	0.000	0.000
105	C	122	HIS	0	-0.015	-0.004	28.138	-0.001	-0.001	0.000	0.000	0.000	0.000
106	C	123	TRP	0	0.040	0.014	26.209	-0.001	-0.001	0.000	0.000	0.000	0.000
107	C	124	GLU	-1	-0.896	-0.941	32.401	0.034	0.034	0.000	0.000	0.000	0.000
108	C	125	THR	0	-0.056	-0.017	35.942	0.004	0.004	0.000	0.000	0.000	0.000
109	C	137	TRP	0	0.028	0.016	60.650	0.000	0.000	0.000	0.000	0.000	0.000
110	C	138	GLN	0	-0.028	-0.030	60.515	0.000	0.000	0.000	0.000	0.000	0.000
111	C	139	ARG	1	0.814	0.878	58.153	-0.012	-0.012	0.000	0.000	0.000	0.000
112	C	140	LEU	0	0.031	0.016	57.760	0.000	0.000	0.000	0.000	0.000	0.000
113	C	141	LEU	0	-0.034	-0.004	58.400	0.000	0.000	0.000	0.000	0.000	0.000
114	C	142	LEU	0	0.026	-0.001	54.696	0.000	0.000	0.000	0.000	0.000	0.000
115	C	143	ARG	1	0.880	0.936	53.627	-0.007	-0.007	0.000	0.000	0.000	0.000
116	C	144	PHE	0	0.016	0.015	53.167	0.000	0.000	0.000	0.000	0.000	0.000
117	C	145	LYS	1	0.872	0.927	52.680	-0.012	-0.012	0.000	0.000	0.000	0.000
118	C	146	ILE	0	0.018	0.010	48.338	0.000	0.000	0.000	0.000	0.000	0.000
119	C	147	LEU	0	0.032	0.015	48.240	0.000	0.000	0.000	0.000	0.000	0.000
120	C	148	ARG	1	0.963	0.989	48.112	-0.011	-0.011	0.000	0.000	0.000	0.000
121	C	149	SER	0	-0.030	-0.014	45.495	0.000	0.000	0.000	0.000	0.000	0.000
122	C	150	LEU	0	0.003	0.005	42.721	0.001	0.001	0.000	0.000	0.000	0.000
123	C	151	GLN	0	-0.018	-0.014	43.153	0.000	0.000	0.000	0.000	0.000	0.000
124	C	152	ALA	0	-0.009	0.002	43.004	-0.001	-0.001	0.000	0.000	0.000	0.000
125	C	153	PHE	0	0.001	0.005	36.872	-0.001	-0.001	0.000	0.000	0.000	0.000
126	C	154	VAL	0	0.022	-0.005	38.453	0.000	0.000	0.000	0.000	0.000	0.000
127	C	155	ALA	0	0.028	0.023	38.258	-0.002	-0.002	0.000	0.000	0.000	0.000
128	C	156	VAL	0	-0.040	-0.022	34.844	-0.003	-0.003	0.000	0.000	0.000	0.000
129	C	157	ALA	0	0.041	0.023	34.015	-0.001	-0.001	0.000	0.000	0.000	0.000
130	C	158	ALA	0	0.002	-0.006	33.382	-0.002	-0.002	0.000	0.000	0.000	0.000
131	C	159	ARG	1	0.897	0.952	33.809	-0.004	-0.004	0.000	0.000	0.000	0.000
132	C	160	VAL	0	0.041	0.027	28.787	-0.004	-0.004	0.000	0.000	0.000	0.000
133	C	161	PHE	0	0.006	-0.013	29.036	-0.004	-0.004	0.000	0.000	0.000	0.000
134	C	162	ALA	0	-0.011	0.000	29.338	-0.006	-0.006	0.000	0.000	0.000	0.000
135	C	163	HIS	0	0.015	0.005	25.688	-0.004	-0.004	0.000	0.000	0.000	0.000
136	C	164	GLY	0	0.038	0.014	25.072	-0.006	-0.006	0.000	0.000	0.000	0.000
137	C	165	ALA	0	-0.015	-0.020	24.596	-0.009	-0.009	0.000	0.000	0.000	0.000
138	C	166	ALA	0	-0.044	-0.007	26.036	-0.010	-0.010	0.000	0.000	0.000	0.000
139	C	167	THR	0	-0.075	-0.046	23.766	-0.007	-0.007	0.000	0.000	0.000	0.000
140	C	168	LEU	0	-0.024	-0.003	20.273	-0.006	-0.006	0.000	0.000	0.000	0.000
141	C	169	SER	0	-0.075	-0.018	19.685	-0.015	-0.015	0.000	0.000	0.000	0.000

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