FMO DATABASE

FMODB ID: V58J1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1071555.495135
FMO2-HF: Nuclear repulsion	1021480.055073
FMO2-HF: Total energy	-50075.440063
FMO2-MP2: Total energy	-50221.237133

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.
-2.209	4.702	2.161	-2.495	-6.576	-0.007

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 : 0.090 / q_NPA : 0.035

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

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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	0.058	0.019	3.056	-3.403	1.456	0.670	-1.833	-3.697	-0.005
4	C	12	THR	0	0.044	0.020	4.428	0.531	0.693	-0.001	-0.013	-0.147	0.000
5	C	13	GLN	0	0.047	0.024	7.449	0.290	0.290	0.000	0.000	0.000	0.000
6	C	14	CYS	0	0.003	-0.001	4.658	0.193	0.397	0.008	-0.047	-0.166	0.000
7	C	15	GLN	0	0.037	0.039	6.951	0.136	0.136	0.000	0.000	0.000	0.000
8	C	16	GLN	0	-0.061	-0.029	9.105	0.156	0.156	0.000	0.000	0.000	0.000
9	C	17	LEU	0	-0.022	-0.004	10.069	0.065	0.065	0.000	0.000	0.000	0.000
10	C	18	SER	0	0.006	-0.017	9.704	0.046	0.046	0.000	0.000	0.000	0.000
11	C	19	GLN	0	0.047	0.021	11.858	0.008	0.008	0.000	0.000	0.000	0.000
12	C	20	LYS	1	0.972	0.986	14.617	0.091	0.091	0.000	0.000	0.000	0.000
13	C	21	LEU	0	0.008	0.003	12.529	0.023	0.023	0.000	0.000	0.000	0.000
14	C	22	CYS	0	-0.052	-0.013	15.502	0.014	0.014	0.000	0.000	0.000	0.000
15	C	23	THR	0	0.003	0.002	18.221	0.009	0.009	0.000	0.000	0.000	0.000
16	C	24	LEU	0	-0.019	0.009	18.359	0.010	0.010	0.000	0.000	0.000	0.000
17	C	25	ALA	0	0.041	0.013	19.521	0.010	0.010	0.000	0.000	0.000	0.000
18	C	26	TRP	0	-0.030	0.000	21.466	0.006	0.006	0.000	0.000	0.000	0.000
19	C	27	SER	0	-0.006	-0.033	23.921	0.003	0.003	0.000	0.000	0.000	0.000
20	C	28	ALA	0	-0.043	-0.017	24.555	0.004	0.004	0.000	0.000	0.000	0.000
21	C	29	HIS	0	-0.025	-0.017	26.261	0.005	0.005	0.000	0.000	0.000	0.000
22	C	30	PRO	0	0.030	0.048	27.555	-0.004	-0.004	0.000	0.000	0.000	0.000
23	C	31	LEU	0	-0.070	-0.038	28.932	0.001	0.001	0.000	0.000	0.000	0.000
24	C	48	ASP	-1	-0.922	-0.971	25.352	0.075	0.075	0.000	0.000	0.000	0.000
25	C	49	VAL	0	-0.050	-0.027	21.769	0.005	0.005	0.000	0.000	0.000	0.000
26	C	50	PRO	0	-0.061	-0.008	17.255	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	51	HIS	0	-0.007	-0.012	18.445	-0.016	-0.016	0.000	0.000	0.000	0.000
28	C	52	ILE	0	-0.004	-0.003	12.829	0.011	0.011	0.000	0.000	0.000	0.000
29	C	53	GLN	0	-0.006	-0.009	16.320	-0.005	-0.005	0.000	0.000	0.000	0.000
30	C	54	CYS	0	-0.001	-0.023	16.680	-0.010	-0.010	0.000	0.000	0.000	0.000
31	C	55	GLY	0	0.014	0.011	17.245	-0.015	-0.015	0.000	0.000	0.000	0.000
32	C	56	ASP	-1	-0.806	-0.893	13.248	0.061	0.061	0.000	0.000	0.000	0.000
33	C	57	GLY	0	0.014	0.024	11.970	0.002	0.002	0.000	0.000	0.000	0.000
34	C	58	CYS	0	-0.018	-0.008	7.758	-0.004	-0.004	0.000	0.000	0.000	0.000
35	C	59	ASP	-1	-0.835	-0.908	11.581	-0.256	-0.256	0.000	0.000	0.000	0.000
36	C	60	PRO	0	-0.003	-0.032	11.663	-0.033	-0.033	0.000	0.000	0.000	0.000
37	C	61	GLN	0	-0.044	-0.023	11.460	-0.073	-0.073	0.000	0.000	0.000	0.000
38	C	62	GLY	0	0.055	0.030	11.815	-0.005	-0.005	0.000	0.000	0.000	0.000
39	C	63	LEU	0	-0.057	-0.040	6.457	-0.028	-0.028	0.000	0.000	0.000	0.000
40	C	64	ARG	1	0.857	0.921	7.387	0.467	0.467	0.000	0.000	0.000	0.000
41	C	65	ASP	-1	-0.885	-0.911	9.802	-0.222	-0.222	0.000	0.000	0.000	0.000
42	C	66	ASN	0	-0.017	-0.033	8.304	0.052	0.052	0.000	0.000	0.000	0.000
43	C	67	SER	0	0.028	0.024	3.959	-0.240	-0.011	0.002	-0.061	-0.170	0.000
44	C	68	GLN	0	-0.004	-0.011	4.513	0.035	0.232	-0.001	-0.012	-0.183	0.000
45	C	69	PHE	0	0.001	0.012	6.336	0.110	0.110	0.000	0.000	0.000	0.000
46	C	71	LEU	0	0.028	0.004	2.457	-0.563	-0.265	1.464	-0.316	-1.446	-0.001
47	C	72	GLN	0	0.017	0.018	6.783	0.284	0.284	0.000	0.000	0.000	0.000
48	C	73	ARG	1	0.839	0.924	9.198	-0.113	-0.113	0.000	0.000	0.000	0.000
49	C	74	ILE	0	-0.002	-0.016	8.201	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	75	HIS	0	0.006	0.003	8.389	-0.064	-0.064	0.000	0.000	0.000	0.000
51	C	76	GLN	0	0.013	0.009	10.072	-0.045	-0.045	0.000	0.000	0.000	0.000
52	C	77	GLY	0	0.011	-0.008	13.537	-0.021	-0.021	0.000	0.000	0.000	0.000
53	C	78	LEU	0	-0.027	-0.016	9.575	-0.030	-0.030	0.000	0.000	0.000	0.000
54	C	79	ILE	0	0.015	0.014	13.293	-0.024	-0.024	0.000	0.000	0.000	0.000
55	C	80	PHE	0	-0.007	-0.008	15.696	-0.022	-0.022	0.000	0.000	0.000	0.000
56	C	81	TYR	0	0.038	-0.004	16.870	-0.020	-0.020	0.000	0.000	0.000	0.000
57	C	82	GLU	-1	-0.884	-0.934	16.632	0.170	0.170	0.000	0.000	0.000	0.000
58	C	83	LYS	1	0.969	0.991	18.827	-0.240	-0.240	0.000	0.000	0.000	0.000
59	C	84	LEU	0	-0.011	-0.003	21.647	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	85	LEU	0	-0.056	-0.028	20.377	-0.012	-0.012	0.000	0.000	0.000	0.000
61	C	86	GLY	0	0.030	0.035	23.414	-0.007	-0.007	0.000	0.000	0.000	0.000
62	C	87	SER	0	-0.045	-0.030	24.807	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	88	ASP	-1	-0.794	-0.887	27.518	0.043	0.043	0.000	0.000	0.000	0.000
64	C	89	ILE	0	-0.008	-0.001	28.094	-0.007	-0.007	0.000	0.000	0.000	0.000
65	C	90	PHE	0	-0.014	-0.020	25.811	-0.009	-0.009	0.000	0.000	0.000	0.000
66	C	91	THR	0	0.006	0.005	28.364	-0.005	-0.005	0.000	0.000	0.000	0.000
67	C	92	GLY	0	0.025	0.035	30.871	-0.002	-0.002	0.000	0.000	0.000	0.000
68	C	93	GLU	-1	-0.827	-0.892	34.188	0.023	0.023	0.000	0.000	0.000	0.000
69	C	94	PRO	0	-0.052	-0.046	35.750	0.001	0.001	0.000	0.000	0.000	0.000
70	C	95	SER	0	0.027	0.000	34.385	0.000	0.000	0.000	0.000	0.000	0.000
71	C	96	LEU	0	-0.058	-0.021	28.107	-0.005	-0.005	0.000	0.000	0.000	0.000
72	C	97	LEU	0	0.037	0.016	31.674	0.002	0.002	0.000	0.000	0.000	0.000
73	C	98	PRO	0	0.018	-0.008	30.678	0.002	0.002	0.000	0.000	0.000	0.000
74	C	99	ASP	-1	-0.900	-0.937	28.910	0.004	0.004	0.000	0.000	0.000	0.000
75	C	100	SER	0	-0.007	0.002	27.936	-0.008	-0.008	0.000	0.000	0.000	0.000
76	C	101	PRO	0	0.033	0.014	24.020	0.005	0.005	0.000	0.000	0.000	0.000
77	C	102	VAL	0	0.008	-0.008	22.859	0.002	0.002	0.000	0.000	0.000	0.000
78	C	103	GLY	0	0.048	0.035	22.623	0.010	0.010	0.000	0.000	0.000	0.000
79	C	104	GLN	0	-0.004	-0.014	21.001	0.003	0.003	0.000	0.000	0.000	0.000
80	C	105	LEU	0	-0.046	-0.003	18.024	0.003	0.003	0.000	0.000	0.000	0.000
81	C	106	HIS	0	-0.022	-0.018	17.740	0.000	0.000	0.000	0.000	0.000	0.000
82	C	107	ALA	0	0.047	0.028	18.053	0.023	0.023	0.000	0.000	0.000	0.000
83	C	108	SER	0	-0.066	-0.057	15.029	0.013	0.013	0.000	0.000	0.000	0.000
84	C	109	LEU	0	-0.030	-0.009	13.248	0.006	0.006	0.000	0.000	0.000	0.000
85	C	110	LEU	0	0.020	0.019	12.575	0.049	0.049	0.000	0.000	0.000	0.000
86	C	111	GLY	0	0.012	0.012	12.402	0.065	0.065	0.000	0.000	0.000	0.000
87	C	112	LEU	0	-0.027	-0.023	7.133	0.047	0.047	0.000	0.000	0.000	0.000
88	C	113	SER	0	-0.009	-0.019	7.644	0.139	0.139	0.000	0.000	0.000	0.000
89	C	114	GLN	0	-0.020	-0.019	8.905	0.135	0.135	0.000	0.000	0.000	0.000
90	C	115	LEU	0	-0.052	-0.017	5.109	0.169	0.169	0.000	0.000	0.000	0.000
91	C	116	LEU	0	-0.054	-0.009	3.290	0.001	0.718	0.021	-0.198	-0.539	-0.001
92	C	117	GLN	0	0.001	0.008	5.086	0.780	0.882	-0.001	-0.002	-0.099	0.000
93	C	135	GLN	0	0.072	0.024	37.803	0.000	0.000	0.000	0.000	0.000	0.000
94	C	136	PRO	0	0.022	0.014	37.653	0.000	0.000	0.000	0.000	0.000	0.000
95	C	137	TRP	0	0.071	0.018	37.426	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	138	GLN	0	-0.004	-0.005	36.789	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	139	ARG	1	0.812	0.904	33.292	-0.039	-0.039	0.000	0.000	0.000	0.000
98	C	140	LEU	0	-0.002	0.009	32.587	0.000	0.000	0.000	0.000	0.000	0.000
99	C	141	LEU	0	-0.005	-0.001	32.761	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	142	LEU	0	-0.016	-0.020	30.487	-0.002	-0.002	0.000	0.000	0.000	0.000
101	C	143	ARG	1	0.820	0.885	28.449	-0.027	-0.027	0.000	0.000	0.000	0.000
102	C	144	PHE	0	0.014	0.010	27.801	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	145	LYS	1	0.927	0.969	28.208	-0.014	-0.014	0.000	0.000	0.000	0.000
104	C	146	ILE	0	0.049	0.038	23.523	-0.003	-0.003	0.000	0.000	0.000	0.000
105	C	147	LEU	0	0.035	0.019	23.365	-0.001	-0.001	0.000	0.000	0.000	0.000
106	C	148	ARG	1	0.904	0.952	23.279	0.031	0.031	0.000	0.000	0.000	0.000
107	C	149	SER	0	-0.035	-0.025	22.857	-0.009	-0.009	0.000	0.000	0.000	0.000
108	C	150	LEU	0	0.006	0.006	17.361	-0.006	-0.006	0.000	0.000	0.000	0.000
109	C	151	GLN	0	-0.033	-0.029	18.514	-0.012	-0.012	0.000	0.000	0.000	0.000
110	C	152	ALA	0	-0.017	0.001	19.354	-0.018	-0.018	0.000	0.000	0.000	0.000
111	C	153	PHE	0	-0.025	-0.004	12.814	-0.022	-0.022	0.000	0.000	0.000	0.000
112	C	154	VAL	0	0.032	-0.005	14.244	-0.017	-0.017	0.000	0.000	0.000	0.000
113	C	155	ALA	0	0.025	0.022	14.414	-0.038	-0.038	0.000	0.000	0.000	0.000
114	C	156	VAL	0	-0.048	-0.022	13.480	-0.040	-0.040	0.000	0.000	0.000	0.000
115	C	157	ALA	0	0.062	0.026	10.431	-0.048	-0.048	0.000	0.000	0.000	0.000
116	C	158	ALA	0	0.006	0.003	10.112	-0.086	-0.086	0.000	0.000	0.000	0.000
117	C	159	ARG	1	0.894	0.952	11.433	0.111	0.111	0.000	0.000	0.000	0.000
118	C	160	VAL	0	0.028	0.020	7.256	-0.064	-0.064	0.000	0.000	0.000	0.000
119	C	161	PHE	0	0.016	-0.008	4.066	-0.308	-0.165	-0.001	-0.013	-0.129	0.000
120	C	162	ALA	0	-0.015	0.001	7.489	-0.193	-0.193	0.000	0.000	0.000	0.000
121	C	163	HIS	0	0.019	0.011	9.765	-0.018	-0.018	0.000	0.000	0.000	0.000
122	C	164	GLY	0	0.038	0.009	6.379	-0.005	-0.005	0.000	0.000	0.000	0.000
123	C	165	ALA	0	-0.034	-0.035	7.298	-0.175	-0.175	0.000	0.000	0.000	0.000
124	C	166	ALA	0	-0.033	-0.004	8.083	0.071	0.071	0.000	0.000	0.000	0.000
125	C	167	THR	0	-0.040	-0.020	10.134	0.085	0.085	0.000	0.000	0.000	0.000
126	C	168	LEU	0	-0.041	-0.011	5.890	0.110	0.110	0.000	0.000	0.000	0.000
127	C	169	SER	0	-0.017	0.003	5.730	-0.576	-0.576	0.000	0.000	0.000	0.000
128	C	170	PRO	0	-0.013	0.010	5.815	0.258	0.258	0.000	0.000	0.000	0.000

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