FMO DATABASE

FMODB ID: 8584Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1086409.047169
FMO2-HF: Nuclear repulsion	1035920.830784
FMO2-HF: Total energy	-50488.216385
FMO2-MP2: Total energy	-50635.19294

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.
-1.362	0.148	-0.017	-0.631	-0.86	0.003

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 : -0.020 / q_NPA : -0.017

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	0.053	0.033	3.825	-1.642	-0.245	-0.016	-0.626	-0.754	0.003
4	A	11	TRP	0	0.049	0.013	4.690	-0.030	0.083	-0.001	-0.005	-0.106	0.000
5	A	12	THR	0	0.079	0.036	8.086	0.057	0.057	0.000	0.000	0.000	0.000
6	A	13	GLN	0	-0.012	0.000	10.147	-0.022	-0.022	0.000	0.000	0.000	0.000
7	A	14	CYS	0	0.003	0.001	9.207	0.085	0.085	0.000	0.000	0.000	0.000
8	A	15	GLN	0	0.025	0.034	11.898	0.012	0.012	0.000	0.000	0.000	0.000
9	A	16	GLN	0	-0.033	-0.019	13.903	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	17	LEU	0	-0.010	0.006	15.167	0.006	0.006	0.000	0.000	0.000	0.000
11	A	18	SER	0	0.013	-0.014	15.045	0.010	0.010	0.000	0.000	0.000	0.000
12	A	19	GLN	0	0.042	0.021	17.333	0.000	0.000	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.909	0.957	19.758	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.015	0.003	18.296	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	22	CYS	0	-0.042	-0.007	21.033	0.001	0.001	0.000	0.000	0.000	0.000
16	A	23	THR	0	-0.019	-0.008	23.829	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	24	LEU	0	-0.057	-0.026	23.696	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	25	ALA	0	0.055	0.017	25.339	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	26	TRP	0	0.005	0.013	27.248	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	27	SER	0	-0.051	-0.036	29.532	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.020	-0.006	30.328	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	29	HIS	0	-0.053	-0.049	31.926	0.002	0.002	0.000	0.000	0.000	0.000
23	A	30	PRO	0	0.062	0.066	33.010	0.004	0.004	0.000	0.000	0.000	0.000
24	A	31	LEU	0	-0.027	0.002	32.691	0.000	0.000	0.000	0.000	0.000	0.000
25	A	47	ASN	0	0.007	-0.045	33.535	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	48	ASP	-1	-0.983	-0.954	30.082	0.102	0.102	0.000	0.000	0.000	0.000
27	A	49	VAL	0	0.008	-0.002	26.032	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	50	PRO	0	-0.010	0.021	21.678	0.000	0.000	0.000	0.000	0.000	0.000
29	A	51	HIS	0	-0.019	-0.029	22.973	0.001	0.001	0.000	0.000	0.000	0.000
30	A	52	ILE	0	-0.008	-0.001	17.352	0.009	0.009	0.000	0.000	0.000	0.000
31	A	53	GLN	0	-0.045	-0.034	20.505	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	54	CYM	-1	-0.892	-0.951	20.687	0.200	0.200	0.000	0.000	0.000	0.000
33	A	55	GLY	0	0.018	0.010	20.870	0.014	0.014	0.000	0.000	0.000	0.000
34	A	56	ASP	-1	-0.823	-0.895	17.002	0.288	0.288	0.000	0.000	0.000	0.000
35	A	57	GLY	0	0.030	0.025	15.503	0.063	0.063	0.000	0.000	0.000	0.000
36	A	58	CYS	0	-0.045	-0.013	11.720	0.001	0.001	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.814	-0.897	15.702	0.314	0.314	0.000	0.000	0.000	0.000
38	A	60	PRO	0	-0.013	-0.036	15.215	0.054	0.054	0.000	0.000	0.000	0.000
39	A	61	GLN	0	-0.049	-0.025	14.470	0.039	0.039	0.000	0.000	0.000	0.000
40	A	62	GLY	0	0.060	0.032	14.599	0.017	0.017	0.000	0.000	0.000	0.000
41	A	63	LEU	0	-0.057	-0.041	10.581	0.127	0.127	0.000	0.000	0.000	0.000
42	A	64	ARG	1	0.874	0.943	9.771	-0.069	-0.069	0.000	0.000	0.000	0.000
43	A	65	ASP	-1	-0.871	-0.911	10.465	0.292	0.292	0.000	0.000	0.000	0.000
44	A	66	ASN	0	-0.008	-0.026	8.960	0.197	0.197	0.000	0.000	0.000	0.000
45	A	67	SER	0	0.038	0.027	6.362	0.394	0.394	0.000	0.000	0.000	0.000
46	A	68	GLN	0	-0.005	-0.006	5.058	-0.480	-0.480	0.000	0.000	0.000	0.000
47	A	69	PHE	0	0.027	0.025	8.301	-0.169	-0.169	0.000	0.000	0.000	0.000
48	A	71	LEU	0	-0.005	-0.019	6.488	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	72	GLN	0	-0.003	0.005	9.401	-0.202	-0.202	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.811	0.901	11.958	-0.355	-0.355	0.000	0.000	0.000	0.000
51	A	74	ILE	0	-0.013	-0.016	12.807	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	75	HIS	0	0.000	-0.004	11.983	-0.068	-0.068	0.000	0.000	0.000	0.000
53	A	76	GLN	0	0.035	0.015	14.060	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.002	-0.012	17.211	-0.035	-0.035	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.028	-0.019	14.645	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	79	ILE	0	0.001	0.010	16.929	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	80	PHE	0	-0.001	0.000	19.716	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	81	TYR	0	0.042	-0.003	21.779	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	82	GLU	-1	-0.848	-0.901	20.807	0.106	0.106	0.000	0.000	0.000	0.000
60	A	83	LYS	1	0.892	0.943	22.286	-0.144	-0.144	0.000	0.000	0.000	0.000
61	A	84	LEU	0	-0.001	0.003	25.769	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	85	LEU	0	-0.045	-0.020	25.703	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	86	GLY	0	0.020	0.023	27.948	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	87	SER	0	-0.044	-0.027	29.268	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	88	ASP	-1	-0.858	-0.948	31.848	0.055	0.055	0.000	0.000	0.000	0.000
66	A	89	ILE	0	-0.022	0.000	32.435	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	90	PHE	0	-0.029	-0.025	31.023	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	91	THR	0	0.007	0.000	33.062	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	92	GLY	0	-0.018	0.016	35.724	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	93	GLU	-1	-0.956	-0.959	39.039	0.034	0.034	0.000	0.000	0.000	0.000
71	A	94	PRO	0	-0.015	-0.019	41.188	0.002	0.002	0.000	0.000	0.000	0.000
72	A	95	SER	0	0.038	0.009	39.518	0.002	0.002	0.000	0.000	0.000	0.000
73	A	96	LEU	0	-0.028	-0.004	33.494	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	97	LEU	0	0.035	0.017	37.672	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	98	PRO	0	0.013	-0.012	36.382	0.002	0.002	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.913	-0.945	34.821	0.031	0.031	0.000	0.000	0.000	0.000
77	A	100	SER	0	-0.003	0.008	33.610	0.002	0.002	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.021	0.006	29.710	0.001	0.001	0.000	0.000	0.000	0.000
79	A	102	VAL	0	0.009	-0.005	28.504	0.005	0.005	0.000	0.000	0.000	0.000
80	A	103	GLY	0	0.054	0.039	28.116	0.006	0.006	0.000	0.000	0.000	0.000
81	A	104	GLN	0	0.061	0.017	25.046	0.002	0.002	0.000	0.000	0.000	0.000
82	A	105	LEU	0	-0.025	0.002	23.880	0.004	0.004	0.000	0.000	0.000	0.000
83	A	106	HIS	0	0.010	-0.004	23.283	0.004	0.004	0.000	0.000	0.000	0.000
84	A	107	ALA	0	0.005	-0.001	22.720	0.010	0.010	0.000	0.000	0.000	0.000
85	A	108	SER	0	-0.047	-0.043	20.125	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	109	LEU	0	-0.027	-0.007	18.639	0.012	0.012	0.000	0.000	0.000	0.000
87	A	110	LEU	0	0.022	0.018	17.707	0.024	0.024	0.000	0.000	0.000	0.000
88	A	111	GLY	0	0.033	0.020	16.753	0.015	0.015	0.000	0.000	0.000	0.000
89	A	112	LEU	0	-0.019	-0.013	12.703	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	113	SER	0	-0.008	-0.013	12.752	0.037	0.037	0.000	0.000	0.000	0.000
91	A	114	GLN	0	0.007	-0.011	12.675	0.034	0.034	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.030	-0.016	10.023	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	116	LEU	0	-0.071	-0.021	8.131	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	117	GLN	0	-0.048	-0.034	7.879	0.173	0.173	0.000	0.000	0.000	0.000
95	A	118	PRO	0	-0.011	0.021	9.090	-0.068	-0.068	0.000	0.000	0.000	0.000
96	A	135	GLN	0	0.013	-0.003	38.889	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.023	0.019	43.227	0.000	0.000	0.000	0.000	0.000	0.000
98	A	137	TRP	0	0.011	-0.001	43.604	0.002	0.002	0.000	0.000	0.000	0.000
99	A	138	GLN	0	0.049	0.008	43.181	0.000	0.000	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.898	0.974	38.313	-0.047	-0.047	0.000	0.000	0.000	0.000
101	A	140	LEU	0	-0.009	-0.011	38.028	0.003	0.003	0.000	0.000	0.000	0.000
102	A	141	LEU	0	0.017	0.006	37.551	0.004	0.004	0.000	0.000	0.000	0.000
103	A	142	LEU	0	0.024	0.003	33.876	0.003	0.003	0.000	0.000	0.000	0.000
104	A	143	ARG	1	0.888	0.935	33.535	-0.048	-0.048	0.000	0.000	0.000	0.000
105	A	144	PHE	0	0.004	-0.005	32.776	0.004	0.004	0.000	0.000	0.000	0.000
106	A	145	LYS	1	0.941	0.978	33.496	-0.068	-0.068	0.000	0.000	0.000	0.000
107	A	146	ILE	0	0.019	0.027	28.357	0.007	0.007	0.000	0.000	0.000	0.000
108	A	147	LEU	0	-0.002	-0.010	28.698	0.008	0.008	0.000	0.000	0.000	0.000
109	A	148	ARG	1	0.976	0.998	28.872	-0.068	-0.068	0.000	0.000	0.000	0.000
110	A	149	SER	0	-0.052	-0.035	27.706	0.005	0.005	0.000	0.000	0.000	0.000
111	A	150	LEU	0	0.012	0.010	22.887	0.012	0.012	0.000	0.000	0.000	0.000
112	A	151	GLN	0	-0.058	-0.046	24.051	0.012	0.012	0.000	0.000	0.000	0.000
113	A	152	ALA	0	-0.020	-0.001	24.877	0.005	0.005	0.000	0.000	0.000	0.000
114	A	153	PHE	0	-0.016	-0.001	17.699	0.012	0.012	0.000	0.000	0.000	0.000
115	A	154	VAL	0	0.024	-0.010	19.851	0.025	0.025	0.000	0.000	0.000	0.000
116	A	155	ALA	0	0.024	0.019	19.943	0.007	0.007	0.000	0.000	0.000	0.000
117	A	156	VAL	0	-0.047	-0.020	18.130	0.006	0.006	0.000	0.000	0.000	0.000
118	A	157	ALA	0	0.064	0.029	15.914	0.030	0.030	0.000	0.000	0.000	0.000
119	A	158	ALA	0	0.005	-0.002	15.364	0.035	0.035	0.000	0.000	0.000	0.000
120	A	159	ARG	1	0.896	0.955	16.395	-0.169	-0.169	0.000	0.000	0.000	0.000
121	A	160	VAL	0	0.033	0.025	11.967	0.004	0.004	0.000	0.000	0.000	0.000
122	A	161	PHE	0	-0.002	-0.017	9.730	0.053	0.053	0.000	0.000	0.000	0.000
123	A	162	ALA	0	-0.007	0.001	11.980	-0.028	-0.028	0.000	0.000	0.000	0.000
124	A	163	HIS	0	0.027	0.016	13.151	-0.066	-0.066	0.000	0.000	0.000	0.000
125	A	164	GLY	0	0.040	0.007	9.789	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.046	-0.038	9.599	-0.052	-0.052	0.000	0.000	0.000	0.000
127	A	166	ALA	0	-0.042	-0.003	10.752	-0.079	-0.079	0.000	0.000	0.000	0.000
128	A	167	THR	0	-0.063	-0.035	12.004	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	168	LEU	0	-0.059	-0.008	6.399	-0.010	-0.010	0.000	0.000	0.000	0.000

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