FMO DATABASE

FMODB ID: N9VJQ

Calculation Name: 4GRW-A-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: 4GRW

Chain ID: A

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	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	129
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1093080.264594
FMO2-HF: Nuclear repulsion	1042591.637032
FMO2-HF: Total energy	-50488.627562
FMO2-MP2: Total energy	-50635.612828

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(A:8:SER)

Summations of interaction energy for fragment #1(A:8:SER)

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.
-1.178	0.097999999999999	-0.011	-0.504	-0.76	0.002

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.016

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	A	10	ALA	0	0.066	0.045	3.906	-1.653	-0.506	-0.010	-0.497	-0.639	0.002
4	A	11	TRP	0	0.039	0.008	4.510	0.327	0.456	-0.001	-0.007	-0.121	0.000
5	A	12	THR	0	0.056	0.022	8.009	0.134	0.134	0.000	0.000	0.000	0.000
6	A	13	GLN	0	0.019	0.017	9.771	0.004	0.004	0.000	0.000	0.000	0.000
7	A	14	CYS	0	-0.010	0.001	9.292	0.120	0.120	0.000	0.000	0.000	0.000
8	A	15	GLN	0	0.032	0.032	11.961	0.040	0.040	0.000	0.000	0.000	0.000
9	A	16	GLN	0	-0.028	-0.015	14.024	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.002	0.003	15.219	0.021	0.021	0.000	0.000	0.000	0.000
11	A	18	SER	0	0.030	-0.008	15.051	0.022	0.022	0.000	0.000	0.000	0.000
12	A	19	GLN	0	0.055	0.036	17.363	0.007	0.007	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.889	0.957	19.616	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.004	-0.002	18.065	0.003	0.003	0.000	0.000	0.000	0.000
15	A	22	CYS	0	-0.048	-0.017	20.643	0.005	0.005	0.000	0.000	0.000	0.000
16	A	23	THR	0	-0.044	-0.025	23.399	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	24	LEU	0	-0.050	-0.030	23.615	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	25	ALA	0	0.041	0.018	25.045	0.000	0.000	0.000	0.000	0.000	0.000
19	A	26	TRP	0	-0.001	0.003	26.961	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	27	SER	0	-0.034	-0.029	29.231	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.028	-0.001	29.794	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	29	HIS	0	-0.039	-0.035	31.640	0.003	0.003	0.000	0.000	0.000	0.000
23	A	30	PRO	0	0.036	0.040	33.268	0.003	0.003	0.000	0.000	0.000	0.000
24	A	31	LEU	0	-0.043	0.000	32.391	0.001	0.001	0.000	0.000	0.000	0.000
25	A	47	ASN	0	0.037	0.009	33.900	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	48	ASP	-1	-0.983	-1.014	30.424	0.106	0.106	0.000	0.000	0.000	0.000
27	A	49	VAL	0	0.004	0.013	26.208	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	50	PRO	0	-0.016	0.018	21.791	0.000	0.000	0.000	0.000	0.000	0.000
29	A	51	HIS	0	-0.012	-0.017	23.135	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	52	ILE	0	0.005	0.001	17.273	0.015	0.015	0.000	0.000	0.000	0.000
31	A	53	GLN	0	-0.062	-0.040	20.514	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	54	CYM	-1	-0.887	-0.937	20.582	0.205	0.205	0.000	0.000	0.000	0.000
33	A	55	GLY	0	0.038	0.012	20.561	0.019	0.019	0.000	0.000	0.000	0.000
34	A	56	ASP	-1	-0.806	-0.885	16.876	0.319	0.319	0.000	0.000	0.000	0.000
35	A	57	GLY	0	0.021	0.017	15.405	0.075	0.075	0.000	0.000	0.000	0.000
36	A	58	CYS	0	-0.035	-0.016	11.939	-0.026	-0.026	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.787	-0.883	15.768	0.266	0.266	0.000	0.000	0.000	0.000
38	A	60	PRO	0	-0.008	-0.035	15.325	0.053	0.053	0.000	0.000	0.000	0.000
39	A	61	GLN	0	-0.055	-0.026	14.706	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	62	GLY	0	0.056	0.020	14.605	0.033	0.033	0.000	0.000	0.000	0.000
41	A	63	LEU	0	-0.057	-0.037	10.933	0.143	0.143	0.000	0.000	0.000	0.000
42	A	64	ARG	1	0.823	0.907	10.067	0.050	0.050	0.000	0.000	0.000	0.000
43	A	65	ASP	-1	-0.854	-0.907	10.817	0.287	0.287	0.000	0.000	0.000	0.000
44	A	66	ASN	0	-0.042	-0.044	9.270	0.272	0.272	0.000	0.000	0.000	0.000
45	A	67	SER	0	0.056	0.036	7.141	0.379	0.379	0.000	0.000	0.000	0.000
46	A	68	GLN	0	-0.001	0.003	4.989	-0.740	-0.740	0.000	0.000	0.000	0.000
47	A	69	PHE	0	0.024	0.030	8.400	-0.226	-0.226	0.000	0.000	0.000	0.000
48	A	71	LEU	0	-0.019	-0.017	6.601	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	72	GLN	0	0.006	-0.001	9.132	-0.281	-0.281	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.765	0.874	12.079	-0.411	-0.411	0.000	0.000	0.000	0.000
51	A	74	ILE	0	-0.008	-0.014	12.687	-0.084	-0.084	0.000	0.000	0.000	0.000
52	A	75	HIS	0	-0.010	0.002	12.206	-0.074	-0.074	0.000	0.000	0.000	0.000
53	A	76	GLN	0	0.036	0.016	14.287	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.010	0.000	17.404	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.038	-0.024	14.845	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	79	ILE	0	0.008	0.004	16.861	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	80	PHE	0	0.007	0.007	19.607	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	81	TYR	0	0.026	-0.015	21.735	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	82	GLU	-1	-0.847	-0.895	20.752	0.117	0.117	0.000	0.000	0.000	0.000
60	A	83	LYS	1	0.880	0.927	21.770	-0.165	-0.165	0.000	0.000	0.000	0.000
61	A	84	LEU	0	-0.017	0.003	25.871	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	85	LEU	0	-0.035	-0.010	25.757	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	86	GLY	0	0.019	0.014	27.802	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	87	SER	0	-0.035	-0.017	29.308	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	88	ASP	-1	-0.828	-0.920	31.971	0.057	0.057	0.000	0.000	0.000	0.000
66	A	89	ILE	0	-0.006	0.007	32.251	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	90	PHE	0	-0.014	-0.015	31.046	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	91	THR	0	-0.014	-0.017	32.802	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	92	GLY	0	0.010	0.017	35.495	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	93	GLU	-1	-0.940	-0.958	38.947	0.035	0.035	0.000	0.000	0.000	0.000
71	A	94	PRO	0	-0.012	-0.008	41.085	0.002	0.002	0.000	0.000	0.000	0.000
72	A	95	SER	0	0.056	0.013	39.214	0.002	0.002	0.000	0.000	0.000	0.000
73	A	96	LEU	0	-0.028	-0.009	33.197	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	97	LEU	0	0.026	0.017	37.347	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	98	PRO	0	0.004	-0.012	36.065	0.002	0.002	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.895	-0.939	34.488	0.023	0.023	0.000	0.000	0.000	0.000
77	A	100	SER	0	-0.016	0.003	33.645	0.001	0.001	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.021	0.000	29.491	0.002	0.002	0.000	0.000	0.000	0.000
79	A	102	VAL	0	0.027	0.003	28.293	0.004	0.004	0.000	0.000	0.000	0.000
80	A	103	GLY	0	0.058	0.038	27.986	0.006	0.006	0.000	0.000	0.000	0.000
81	A	104	GLN	0	0.059	0.019	24.881	0.000	0.000	0.000	0.000	0.000	0.000
82	A	105	LEU	0	-0.021	0.008	23.661	0.001	0.001	0.000	0.000	0.000	0.000
83	A	106	HIS	0	0.007	-0.008	23.079	0.002	0.002	0.000	0.000	0.000	0.000
84	A	107	ALA	0	0.013	0.003	22.483	0.011	0.011	0.000	0.000	0.000	0.000
85	A	108	SER	0	-0.039	-0.034	19.865	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	109	LEU	0	-0.022	-0.004	18.403	0.009	0.009	0.000	0.000	0.000	0.000
87	A	110	LEU	0	0.018	0.027	17.720	0.027	0.027	0.000	0.000	0.000	0.000
88	A	111	GLY	0	0.039	0.023	16.738	0.017	0.017	0.000	0.000	0.000	0.000
89	A	112	LEU	0	-0.020	-0.020	12.610	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	113	SER	0	-0.006	-0.018	12.834	0.039	0.039	0.000	0.000	0.000	0.000
91	A	114	GLN	0	0.004	-0.015	12.413	0.047	0.047	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.042	-0.024	10.110	0.012	0.012	0.000	0.000	0.000	0.000
93	A	116	LEU	0	-0.068	-0.020	8.067	-0.067	-0.067	0.000	0.000	0.000	0.000
94	A	117	GLN	0	-0.026	-0.025	7.768	0.262	0.262	0.000	0.000	0.000	0.000
95	A	118	PRO	0	-0.018	0.017	8.867	-0.090	-0.090	0.000	0.000	0.000	0.000
96	A	135	GLN	0	0.001	-0.006	38.682	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.039	0.033	43.001	0.000	0.000	0.000	0.000	0.000	0.000
98	A	137	TRP	0	0.068	0.020	43.365	0.002	0.002	0.000	0.000	0.000	0.000
99	A	138	GLN	0	0.021	0.012	43.140	0.001	0.001	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.794	0.888	38.016	-0.047	-0.047	0.000	0.000	0.000	0.000
101	A	140	LEU	0	0.010	-0.002	38.178	0.004	0.004	0.000	0.000	0.000	0.000
102	A	141	LEU	0	0.019	0.014	37.605	0.003	0.003	0.000	0.000	0.000	0.000
103	A	142	LEU	0	-0.004	0.002	33.857	0.003	0.003	0.000	0.000	0.000	0.000
104	A	143	ARG	1	0.851	0.918	33.455	-0.045	-0.045	0.000	0.000	0.000	0.000
105	A	144	PHE	0	0.012	-0.005	32.811	0.004	0.004	0.000	0.000	0.000	0.000
106	A	145	LYS	1	0.920	0.964	33.453	-0.069	-0.069	0.000	0.000	0.000	0.000
107	A	146	ILE	0	0.028	0.033	28.242	0.006	0.006	0.000	0.000	0.000	0.000
108	A	147	LEU	0	0.008	0.001	28.648	0.008	0.008	0.000	0.000	0.000	0.000
109	A	148	ARG	1	0.973	0.988	28.774	-0.060	-0.060	0.000	0.000	0.000	0.000
110	A	149	SER	0	-0.048	-0.027	27.589	0.003	0.003	0.000	0.000	0.000	0.000
111	A	150	LEU	0	0.010	0.011	22.866	0.011	0.011	0.000	0.000	0.000	0.000
112	A	151	GLN	0	-0.049	-0.041	24.038	0.009	0.009	0.000	0.000	0.000	0.000
113	A	152	ALA	0	-0.008	0.002	24.480	0.002	0.002	0.000	0.000	0.000	0.000
114	A	153	PHE	0	-0.004	0.008	17.780	0.007	0.007	0.000	0.000	0.000	0.000
115	A	154	VAL	0	0.022	-0.006	19.624	0.021	0.021	0.000	0.000	0.000	0.000
116	A	155	ALA	0	0.038	0.014	19.461	0.000	0.000	0.000	0.000	0.000	0.000
117	A	156	VAL	0	-0.049	-0.004	18.371	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	157	ALA	0	0.058	0.022	15.743	0.020	0.020	0.000	0.000	0.000	0.000
119	A	158	ALA	0	-0.006	-0.006	15.100	0.013	0.013	0.000	0.000	0.000	0.000
120	A	159	ARG	1	0.865	0.929	16.192	-0.136	-0.136	0.000	0.000	0.000	0.000
121	A	160	VAL	0	0.038	0.025	11.921	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	161	PHE	0	0.013	-0.013	9.732	0.023	0.023	0.000	0.000	0.000	0.000
123	A	162	ALA	0	-0.021	-0.005	11.896	-0.066	-0.066	0.000	0.000	0.000	0.000
124	A	163	HIS	0	0.012	0.012	12.963	-0.076	-0.076	0.000	0.000	0.000	0.000
125	A	164	GLY	0	0.037	0.019	9.546	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.033	-0.033	9.483	-0.111	-0.111	0.000	0.000	0.000	0.000
127	A	166	ALA	0	-0.039	-0.004	10.774	-0.064	-0.064	0.000	0.000	0.000	0.000
128	A	167	THR	0	-0.058	-0.023	11.762	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	168	LEU	0	-0.022	0.007	6.813	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)