FMO DATABASE

FMODB ID: 85VKY

Calculation Name: 2RBL-A-Xray372

Preferred Name: Tenascin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2RBL

Chain ID: A

ChEMBL ID: CHEMBL3712856

UniProt ID: P24821

Base Structure: X-ray

Registration Date: 2023-09-19

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500487.939578
FMO2-HF: Nuclear repulsion	465576.118781
FMO2-HF: Total energy	-34911.820797
FMO2-MP2: Total energy	-35013.495621

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:803:LEU)

Summations of interaction energy for fragment #1(A:803: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.
-7.058	-2.607	0.929	-2.041	-3.339	-0.013

Interaction energy analysis for fragmet #1(A:803:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.032

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	805	ALA	0	-0.024	-0.028	3.467	-1.187	0.171	0.015	-0.583	-0.790	0.001
4	A	806	PRO	0	0.015	0.010	5.338	0.340	0.446	-0.001	-0.003	-0.102	0.000
5	A	807	SER	0	-0.003	0.003	8.220	0.081	0.081	0.000	0.000	0.000	0.000
6	A	808	GLN	0	-0.059	-0.042	10.906	0.090	0.090	0.000	0.000	0.000	0.000
7	A	809	ILE	0	0.011	0.002	10.762	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	810	GLU	-1	-0.939	-0.980	15.011	-0.284	-0.284	0.000	0.000	0.000	0.000
9	A	811	VAL	0	-0.039	-0.023	18.466	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	812	LYS	1	0.935	0.985	20.825	0.298	0.298	0.000	0.000	0.000	0.000
11	A	813	ASP	-1	-0.955	-0.989	23.559	-0.221	-0.221	0.000	0.000	0.000	0.000
12	A	814	VAL	0	-0.005	-0.005	24.854	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	815	THR	0	-0.007	0.009	27.212	0.011	0.011	0.000	0.000	0.000	0.000
14	A	816	ASP	-1	-0.931	-0.980	29.921	-0.151	-0.151	0.000	0.000	0.000	0.000
15	A	817	THR	0	-0.038	-0.012	29.613	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	818	THR	0	-0.056	-0.027	25.978	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	819	ALA	0	0.052	0.018	22.275	0.004	0.004	0.000	0.000	0.000	0.000
18	A	820	LEU	0	0.013	0.012	20.494	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	821	ILE	0	-0.024	-0.005	15.314	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	822	THR	0	-0.057	-0.033	16.212	0.014	0.014	0.000	0.000	0.000	0.000
21	A	823	TRP	0	0.054	0.038	10.325	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	824	SER	0	-0.001	0.001	12.389	0.121	0.121	0.000	0.000	0.000	0.000
23	A	825	MET	0	0.037	0.025	4.746	-0.220	-0.168	-0.001	-0.001	-0.050	0.000
24	A	826	GLN	0	-0.059	-0.034	6.321	0.031	0.031	0.000	0.000	0.000	0.000
25	A	827	LEU	0	0.077	0.011	8.420	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	828	SER	0	-0.063	-0.048	7.202	0.049	0.049	0.000	0.000	0.000	0.000
27	A	829	GLN	0	-0.002	0.002	2.691	-3.990	-1.692	0.697	-1.232	-1.763	-0.014
28	A	830	LEU	0	0.012	0.032	5.901	-0.185	-0.185	0.000	0.000	0.000	0.000
29	A	831	GLU	-1	-0.844	-0.953	5.745	0.145	0.145	0.000	0.000	0.000	0.000
30	A	832	GLY	0	0.011	0.017	9.888	-0.078	-0.078	0.000	0.000	0.000	0.000
31	A	833	ILE	0	-0.038	0.001	13.462	0.062	0.062	0.000	0.000	0.000	0.000
32	A	834	GLU	-1	-0.908	-0.946	16.435	0.092	0.092	0.000	0.000	0.000	0.000
33	A	835	LEU	0	-0.024	-0.014	19.423	0.013	0.013	0.000	0.000	0.000	0.000
34	A	836	THR	0	-0.008	-0.017	22.553	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	837	TYR	0	0.029	0.005	25.725	0.002	0.002	0.000	0.000	0.000	0.000
36	A	838	GLY	0	0.005	-0.013	29.036	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	839	ILE	0	-0.036	-0.017	32.726	0.003	0.003	0.000	0.000	0.000	0.000
38	A	840	LYS	1	0.917	0.962	33.366	-0.065	-0.065	0.000	0.000	0.000	0.000
39	A	841	ASP	-1	-0.944	-0.984	34.974	0.062	0.062	0.000	0.000	0.000	0.000
40	A	842	VAL	0	-0.034	-0.003	37.490	0.000	0.000	0.000	0.000	0.000	0.000
41	A	843	PRO	0	-0.055	-0.020	36.995	0.003	0.003	0.000	0.000	0.000	0.000
42	A	844	GLY	0	-0.003	-0.012	35.843	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	845	ASP	-1	-0.958	-0.993	34.520	0.035	0.035	0.000	0.000	0.000	0.000
44	A	846	ARG	1	0.892	0.954	29.862	-0.057	-0.057	0.000	0.000	0.000	0.000
45	A	847	THR	0	-0.034	0.006	28.374	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	848	THR	0	0.021	-0.003	23.707	0.002	0.002	0.000	0.000	0.000	0.000
47	A	849	ILE	0	-0.080	-0.039	22.667	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	850	ASP	-1	-0.885	-0.939	18.420	0.068	0.068	0.000	0.000	0.000	0.000
49	A	851	LEU	0	-0.035	-0.002	18.340	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	852	THR	0	-0.042	-0.032	14.368	0.001	0.001	0.000	0.000	0.000	0.000
51	A	853	GLU	-1	-0.975	-0.981	9.434	-0.379	-0.379	0.000	0.000	0.000	0.000
52	A	854	ASP	-1	-0.975	-0.985	13.379	-0.183	-0.183	0.000	0.000	0.000	0.000
53	A	855	GLU	-1	-0.865	-0.934	15.421	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	856	ASN	0	-0.027	-0.024	17.411	0.015	0.015	0.000	0.000	0.000	0.000
55	A	857	GLN	0	-0.050	-0.021	19.629	0.015	0.015	0.000	0.000	0.000	0.000
56	A	858	TYR	0	0.055	0.020	23.098	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	859	SER	0	-0.072	-0.030	25.164	0.008	0.008	0.000	0.000	0.000	0.000
58	A	860	ILE	0	0.052	0.032	28.765	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	861	GLY	0	0.016	-0.008	31.098	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	862	ASN	0	-0.087	-0.051	34.701	0.003	0.003	0.000	0.000	0.000	0.000
61	A	863	LEU	0	0.016	0.016	33.614	0.003	0.003	0.000	0.000	0.000	0.000
62	A	864	LYS	1	0.950	0.963	37.602	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	865	PRO	0	-0.026	-0.046	40.658	0.002	0.002	0.000	0.000	0.000	0.000
64	A	866	ASP	-1	-0.934	-0.952	42.347	0.018	0.018	0.000	0.000	0.000	0.000
65	A	867	THR	0	-0.061	-0.018	38.595	0.001	0.001	0.000	0.000	0.000	0.000
66	A	868	GLU	-1	-0.837	-0.930	36.093	0.046	0.046	0.000	0.000	0.000	0.000
67	A	869	TYR	0	-0.033	0.027	32.767	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	870	GLU	-1	-0.842	-0.943	29.603	0.078	0.078	0.000	0.000	0.000	0.000
69	A	871	VAL	0	-0.027	-0.013	25.320	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	872	SER	0	-0.004	-0.013	23.235	0.010	0.010	0.000	0.000	0.000	0.000
71	A	873	LEU	0	0.010	0.015	19.793	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	874	ILE	0	-0.044	-0.009	17.010	0.014	0.014	0.000	0.000	0.000	0.000
73	A	875	SER	0	0.064	0.027	12.473	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	876	ARG	1	0.879	0.931	13.038	-0.094	-0.094	0.000	0.000	0.000	0.000
75	A	877	ARG	1	0.980	1.000	2.933	-1.778	-1.141	0.219	-0.222	-0.634	0.000
76	A	878	GLY	0	-0.030	0.003	9.783	0.174	0.174	0.000	0.000	0.000	0.000
77	A	879	ASP	-1	-0.943	-0.986	10.806	0.277	0.277	0.000	0.000	0.000	0.000
78	A	880	MET	0	-0.113	-0.036	7.138	0.059	0.059	0.000	0.000	0.000	0.000
79	A	881	SER	0	0.011	-0.009	13.103	-0.063	-0.063	0.000	0.000	0.000	0.000
80	A	882	SER	0	-0.023	0.012	14.402	0.041	0.041	0.000	0.000	0.000	0.000
81	A	883	ASN	0	0.003	-0.006	15.947	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	884	PRO	0	0.010	-0.013	18.771	0.000	0.000	0.000	0.000	0.000	0.000
83	A	885	ALA	0	-0.030	0.010	20.991	0.005	0.005	0.000	0.000	0.000	0.000
84	A	886	LYS	1	0.932	0.945	22.511	-0.120	-0.120	0.000	0.000	0.000	0.000
85	A	887	GLU	-1	-0.915	-0.944	26.007	0.048	0.048	0.000	0.000	0.000	0.000
86	A	888	THR	0	-0.002	-0.004	28.643	0.000	0.000	0.000	0.000	0.000	0.000
87	A	889	PHE	0	-0.045	-0.021	31.237	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	890	THR	0	0.049	0.025	34.311	0.002	0.002	0.000	0.000	0.000	0.000
89	A	891	THR	0	-0.020	0.007	36.781	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:803:LEU)