FMO DATABASE

FMODB ID: YZ6J2

Calculation Name: 4GRW-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: 4GRW

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	OptH
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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1070798.091839
FMO2-HF: Nuclear repulsion	1020723.191391
FMO2-HF: Total energy	-50074.900449
FMO2-MP2: Total energy	-50220.687652

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:9:PRO)

Summations of interaction energy for fragment #1(C:9:PRO)

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.
-2.247	4.558	3.668	-2.793	-7.682	-0.005

Interaction energy analysis for fragmet #1(C:9:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.096 / q_NPA : 0.042

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	11	TRP	0	0.039	0.013	2.527	-3.637	0.950	2.832	-2.222	-5.197	-0.003
4	C	12	THR	0	0.047	0.013	4.367	0.486	0.660	-0.001	-0.015	-0.158	0.000
5	C	13	GLN	0	0.041	0.026	7.387	0.296	0.296	0.000	0.000	0.000	0.000
6	C	14	CYS	0	0.018	0.010	4.847	0.378	0.378	0.000	0.000	0.000	0.000
7	C	15	GLN	0	0.031	0.032	6.824	0.154	0.154	0.000	0.000	0.000	0.000
8	C	16	GLN	0	-0.042	-0.018	9.009	0.165	0.165	0.000	0.000	0.000	0.000
9	C	17	LEU	0	-0.014	0.000	10.212	0.068	0.068	0.000	0.000	0.000	0.000
10	C	18	SER	0	-0.001	-0.018	9.702	0.057	0.057	0.000	0.000	0.000	0.000
11	C	19	GLN	0	0.035	0.017	11.802	0.014	0.014	0.000	0.000	0.000	0.000
12	C	20	LYS	1	0.974	0.981	14.513	0.112	0.112	0.000	0.000	0.000	0.000
13	C	21	LEU	0	0.012	0.005	12.758	0.023	0.023	0.000	0.000	0.000	0.000
14	C	22	CYS	0	-0.050	-0.008	15.440	0.016	0.016	0.000	0.000	0.000	0.000
15	C	23	THR	0	0.006	0.005	18.184	0.010	0.010	0.000	0.000	0.000	0.000
16	C	24	LEU	0	-0.020	0.004	18.418	0.009	0.009	0.000	0.000	0.000	0.000
17	C	25	ALA	0	0.050	0.018	19.782	0.010	0.010	0.000	0.000	0.000	0.000
18	C	26	TRP	0	-0.041	-0.003	21.710	0.006	0.006	0.000	0.000	0.000	0.000
19	C	27	SER	0	-0.003	-0.028	24.001	0.003	0.003	0.000	0.000	0.000	0.000
20	C	28	ALA	0	-0.039	-0.012	24.798	0.004	0.004	0.000	0.000	0.000	0.000
21	C	29	HIS	0	-0.026	-0.019	26.511	0.006	0.006	0.000	0.000	0.000	0.000
22	C	30	PRO	0	0.021	0.040	27.764	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	31	LEU	0	-0.058	-0.030	29.016	-0.001	-0.001	0.000	0.000	0.000	0.000
24	C	48	ASP	-1	-0.933	-0.977	25.378	0.086	0.086	0.000	0.000	0.000	0.000
25	C	49	VAL	0	-0.033	-0.018	21.937	0.004	0.004	0.000	0.000	0.000	0.000
26	C	50	PRO	0	-0.087	-0.022	17.314	-0.003	-0.003	0.000	0.000	0.000	0.000
27	C	51	HIS	0	0.007	-0.005	18.492	-0.014	-0.014	0.000	0.000	0.000	0.000
28	C	52	ILE	0	-0.001	-0.002	13.122	0.013	0.013	0.000	0.000	0.000	0.000
29	C	53	GLN	0	-0.005	-0.014	16.428	-0.007	-0.007	0.000	0.000	0.000	0.000
30	C	54	CYS	0	0.009	-0.025	17.014	-0.003	-0.003	0.000	0.000	0.000	0.000
31	C	55	GLY	0	-0.001	0.010	17.629	-0.012	-0.012	0.000	0.000	0.000	0.000
32	C	56	ASP	-1	-0.817	-0.907	13.416	0.105	0.105	0.000	0.000	0.000	0.000
33	C	57	GLY	0	0.009	0.020	12.174	0.015	0.015	0.000	0.000	0.000	0.000
34	C	58	CYS	0	-0.031	-0.013	8.160	-0.006	-0.006	0.000	0.000	0.000	0.000
35	C	59	ASP	-1	-0.858	-0.924	11.870	-0.162	-0.162	0.000	0.000	0.000	0.000
36	C	60	PRO	0	-0.009	-0.033	11.533	-0.019	-0.019	0.000	0.000	0.000	0.000
37	C	61	GLN	0	-0.039	-0.012	11.344	-0.048	-0.048	0.000	0.000	0.000	0.000
38	C	62	GLY	0	0.069	0.042	11.981	-0.002	-0.002	0.000	0.000	0.000	0.000
39	C	63	LEU	0	-0.049	-0.037	6.473	0.001	0.001	0.000	0.000	0.000	0.000
40	C	64	ARG	1	0.924	0.959	7.336	0.354	0.354	0.000	0.000	0.000	0.000
41	C	65	ASP	-1	-0.911	-0.935	9.678	-0.147	-0.147	0.000	0.000	0.000	0.000
42	C	66	ASN	0	-0.012	-0.024	8.079	0.068	0.068	0.000	0.000	0.000	0.000
43	C	67	SER	0	0.024	0.019	3.398	-0.048	0.250	0.010	-0.086	-0.222	0.000
44	C	68	GLN	0	0.021	0.004	4.711	0.231	0.409	-0.001	-0.006	-0.171	0.000
45	C	69	PHE	0	-0.008	0.006	6.299	0.083	0.083	0.000	0.000	0.000	0.000
46	C	71	LEU	0	0.022	-0.004	2.678	-0.815	-0.162	0.814	-0.247	-1.220	-0.001
47	C	72	GLN	0	0.034	0.027	6.840	0.191	0.191	0.000	0.000	0.000	0.000
48	C	73	ARG	1	0.841	0.944	9.461	-0.172	-0.172	0.000	0.000	0.000	0.000
49	C	74	ILE	0	-0.009	-0.019	7.991	-0.029	-0.029	0.000	0.000	0.000	0.000
50	C	75	HIS	0	0.030	0.008	8.416	-0.103	-0.103	0.000	0.000	0.000	0.000
51	C	76	GLN	0	0.039	0.020	10.143	-0.043	-0.043	0.000	0.000	0.000	0.000
52	C	77	GLY	0	0.000	-0.015	13.573	-0.027	-0.027	0.000	0.000	0.000	0.000
53	C	78	LEU	0	-0.026	-0.014	9.704	-0.034	-0.034	0.000	0.000	0.000	0.000
54	C	79	ILE	0	0.013	0.017	13.314	-0.029	-0.029	0.000	0.000	0.000	0.000
55	C	80	PHE	0	-0.027	-0.018	15.831	-0.023	-0.023	0.000	0.000	0.000	0.000
56	C	81	TYR	0	0.032	-0.007	17.086	-0.022	-0.022	0.000	0.000	0.000	0.000
57	C	82	GLU	-1	-0.920	-0.952	16.910	0.151	0.151	0.000	0.000	0.000	0.000
58	C	83	LYS	1	0.987	0.995	19.110	-0.223	-0.223	0.000	0.000	0.000	0.000
59	C	84	LEU	0	-0.005	-0.004	21.814	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	85	LEU	0	-0.060	-0.028	20.556	-0.011	-0.011	0.000	0.000	0.000	0.000
61	C	86	GLY	0	0.027	0.035	23.617	-0.008	-0.008	0.000	0.000	0.000	0.000
62	C	87	SER	0	-0.056	-0.039	25.019	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	88	ASP	-1	-0.789	-0.902	27.706	0.042	0.042	0.000	0.000	0.000	0.000
64	C	89	ILE	0	-0.036	-0.012	28.214	-0.007	-0.007	0.000	0.000	0.000	0.000
65	C	90	PHE	0	-0.015	-0.019	26.031	-0.008	-0.008	0.000	0.000	0.000	0.000
66	C	91	THR	0	0.004	0.008	28.591	-0.006	-0.006	0.000	0.000	0.000	0.000
67	C	92	GLY	0	0.049	0.049	31.102	-0.002	-0.002	0.000	0.000	0.000	0.000
68	C	93	GLU	-1	-0.868	-0.945	34.421	0.021	0.021	0.000	0.000	0.000	0.000
69	C	94	PRO	0	-0.042	-0.036	36.061	0.001	0.001	0.000	0.000	0.000	0.000
70	C	95	SER	0	0.037	0.035	34.653	0.000	0.000	0.000	0.000	0.000	0.000
71	C	96	LEU	0	-0.033	-0.011	28.362	-0.004	-0.004	0.000	0.000	0.000	0.000
72	C	97	LEU	0	0.035	0.015	31.985	0.001	0.001	0.000	0.000	0.000	0.000
73	C	98	PRO	0	0.017	-0.009	30.964	0.002	0.002	0.000	0.000	0.000	0.000
74	C	99	ASP	-1	-0.914	-0.943	29.204	-0.003	-0.003	0.000	0.000	0.000	0.000
75	C	100	SER	0	-0.001	0.006	28.057	-0.007	-0.007	0.000	0.000	0.000	0.000
76	C	101	PRO	0	0.040	0.017	24.372	0.003	0.003	0.000	0.000	0.000	0.000
77	C	102	VAL	0	0.001	-0.012	23.144	0.002	0.002	0.000	0.000	0.000	0.000
78	C	103	GLY	0	0.051	0.035	22.892	0.010	0.010	0.000	0.000	0.000	0.000
79	C	104	GLN	0	0.000	-0.010	21.179	0.002	0.002	0.000	0.000	0.000	0.000
80	C	105	LEU	0	-0.054	-0.013	18.451	0.001	0.001	0.000	0.000	0.000	0.000
81	C	106	HIS	0	0.013	-0.001	18.011	0.002	0.002	0.000	0.000	0.000	0.000
82	C	107	ALA	0	0.050	0.032	18.312	0.020	0.020	0.000	0.000	0.000	0.000
83	C	108	SER	0	-0.059	-0.049	15.308	0.008	0.008	0.000	0.000	0.000	0.000
84	C	109	LEU	0	-0.037	-0.010	13.536	0.002	0.002	0.000	0.000	0.000	0.000
85	C	110	LEU	0	0.026	0.023	12.820	0.046	0.046	0.000	0.000	0.000	0.000
86	C	111	GLY	0	0.000	0.007	12.431	0.058	0.058	0.000	0.000	0.000	0.000
87	C	112	LEU	0	-0.032	-0.024	7.512	0.030	0.030	0.000	0.000	0.000	0.000
88	C	113	SER	0	-0.002	-0.015	7.897	0.125	0.125	0.000	0.000	0.000	0.000
89	C	114	GLN	0	-0.017	-0.014	9.068	0.146	0.146	0.000	0.000	0.000	0.000
90	C	115	LEU	0	-0.068	-0.026	5.030	0.153	0.153	0.000	0.000	0.000	0.000
91	C	116	LEU	0	-0.051	-0.006	3.390	-0.122	0.582	0.016	-0.207	-0.514	-0.001
92	C	117	GLN	0	0.000	0.006	5.074	0.801	0.897	-0.001	-0.002	-0.094	0.000
93	C	135	GLN	0	0.059	0.022	37.904	-0.001	-0.001	0.000	0.000	0.000	0.000
94	C	136	PRO	0	0.020	0.006	37.844	0.000	0.000	0.000	0.000	0.000	0.000
95	C	137	TRP	0	0.072	0.024	37.634	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	138	GLN	0	0.013	-0.003	36.774	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	139	ARG	1	0.816	0.919	33.474	-0.036	-0.036	0.000	0.000	0.000	0.000
98	C	140	LEU	0	-0.005	0.008	32.784	0.000	0.000	0.000	0.000	0.000	0.000
99	C	141	LEU	0	-0.014	-0.003	32.961	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	142	LEU	0	-0.008	-0.020	30.622	-0.001	-0.001	0.000	0.000	0.000	0.000
101	C	143	ARG	1	0.811	0.885	28.646	-0.025	-0.025	0.000	0.000	0.000	0.000
102	C	144	PHE	0	0.022	0.011	28.001	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	145	LYS	1	0.931	0.974	28.388	-0.018	-0.018	0.000	0.000	0.000	0.000
104	C	146	ILE	0	0.046	0.039	23.644	-0.002	-0.002	0.000	0.000	0.000	0.000
105	C	147	LEU	0	0.039	0.021	23.590	0.000	0.000	0.000	0.000	0.000	0.000
106	C	148	ARG	1	0.893	0.944	23.471	0.021	0.021	0.000	0.000	0.000	0.000
107	C	149	SER	0	-0.032	-0.023	22.999	-0.007	-0.007	0.000	0.000	0.000	0.000
108	C	150	LEU	0	0.010	0.008	17.603	-0.003	-0.003	0.000	0.000	0.000	0.000
109	C	151	GLN	0	-0.036	-0.030	18.689	-0.010	-0.010	0.000	0.000	0.000	0.000
110	C	152	ALA	0	-0.016	0.003	19.521	-0.015	-0.015	0.000	0.000	0.000	0.000
111	C	153	PHE	0	-0.030	-0.007	12.756	-0.018	-0.018	0.000	0.000	0.000	0.000
112	C	154	VAL	0	0.030	-0.009	14.419	-0.012	-0.012	0.000	0.000	0.000	0.000
113	C	155	ALA	0	0.015	0.017	14.447	-0.036	-0.036	0.000	0.000	0.000	0.000
114	C	156	VAL	0	-0.045	-0.021	13.692	-0.036	-0.036	0.000	0.000	0.000	0.000
115	C	157	ALA	0	0.058	0.026	10.585	-0.037	-0.037	0.000	0.000	0.000	0.000
116	C	158	ALA	0	0.001	0.000	10.053	-0.076	-0.076	0.000	0.000	0.000	0.000
117	C	159	ARG	1	0.903	0.955	11.376	0.076	0.076	0.000	0.000	0.000	0.000
118	C	160	VAL	0	0.036	0.025	7.315	-0.058	-0.058	0.000	0.000	0.000	0.000
119	C	161	PHE	0	0.019	-0.009	4.465	-0.249	-0.134	-0.001	-0.008	-0.106	0.000
120	C	162	ALA	0	-0.007	0.002	7.441	-0.187	-0.187	0.000	0.000	0.000	0.000
121	C	163	HIS	0	0.023	0.010	9.926	-0.031	-0.031	0.000	0.000	0.000	0.000
122	C	164	GLY	0	0.040	0.006	6.228	-0.004	-0.004	0.000	0.000	0.000	0.000
123	C	165	ALA	0	-0.035	-0.034	7.060	-0.167	-0.167	0.000	0.000	0.000	0.000
124	C	166	ALA	0	-0.036	-0.006	8.077	0.060	0.060	0.000	0.000	0.000	0.000
125	C	167	THR	0	-0.069	-0.033	9.823	0.081	0.081	0.000	0.000	0.000	0.000
126	C	168	LEU	0	-0.048	-0.020	5.853	0.088	0.088	0.000	0.000	0.000	0.000
127	C	169	SER	0	-0.012	0.004	5.654	-0.530	-0.530	0.000	0.000	0.000	0.000
128	C	170	PRO	0	-0.022	0.004	5.559	0.222	0.222	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:9:PRO)