FMO DATABASE

FMODB ID: 857QY

Calculation Name: 2PJY-C-Xray372

Preferred Name: Transforming growth factor beta-3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2PJY

Chain ID: C

ChEMBL ID: CHEMBL3712903

UniProt ID: P10600

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467994.810345
FMO2-HF: Nuclear repulsion	435115.518583
FMO2-HF: Total energy	-32879.291762
FMO2-MP2: Total energy	-32966.819743

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:ALA)

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

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.
-5.664	-1.505	2.504	-3.168	-3.496	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.009

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	GLN	0	-0.005	-0.006	3.817	-0.412	1.675	-0.019	-1.104	-0.964	0.005
4	C	12	CYS	0	-0.028	-0.010	6.383	0.298	0.298	0.000	0.000	0.000	0.000
5	C	13	PHE	0	-0.002	-0.007	9.665	0.125	0.125	0.000	0.000	0.000	0.000
6	C	14	CYS	0	-0.033	-0.003	12.235	0.075	0.075	0.000	0.000	0.000	0.000
7	C	15	HIS	0	0.033	0.013	14.097	0.011	0.011	0.000	0.000	0.000	0.000
8	C	16	LEU	0	0.010	0.001	16.883	0.034	0.034	0.000	0.000	0.000	0.000
9	C	18	THR	0	0.005	-0.012	15.537	-0.014	-0.014	0.000	0.000	0.000	0.000
10	C	19	LYS	1	0.926	0.958	16.972	0.040	0.040	0.000	0.000	0.000	0.000
11	C	20	ASP	-1	-0.870	-0.926	11.780	-0.135	-0.135	0.000	0.000	0.000	0.000
12	C	21	ASN	0	-0.047	-0.021	12.732	-0.031	-0.031	0.000	0.000	0.000	0.000
13	C	22	PHE	0	-0.020	-0.013	14.510	-0.039	-0.039	0.000	0.000	0.000	0.000
14	C	23	THR	0	-0.048	-0.012	9.504	-0.099	-0.099	0.000	0.000	0.000	0.000
15	C	24	CYS	0	-0.010	0.004	8.531	-0.037	-0.037	0.000	0.000	0.000	0.000
16	C	25	VAL	0	0.028	0.005	2.455	-0.642	-0.462	0.900	-0.314	-0.767	-0.001
17	C	26	THR	0	-0.030	-0.012	4.343	0.715	0.916	-0.001	-0.043	-0.157	0.000
18	C	27	ASP	-1	-0.836	-0.916	2.524	-3.025	-1.390	1.623	-1.693	-1.565	-0.018
19	C	28	GLY	0	0.014	0.014	3.898	-0.069	-0.013	0.001	-0.014	-0.043	0.000
20	C	29	LEU	0	-0.048	-0.024	6.762	-0.429	-0.429	0.000	0.000	0.000	0.000
21	C	31	PHE	0	0.017	-0.003	10.754	0.094	0.094	0.000	0.000	0.000	0.000
22	C	32	VAL	0	0.032	0.010	14.309	-0.016	-0.016	0.000	0.000	0.000	0.000
23	C	33	SER	0	-0.042	-0.010	17.791	0.028	0.028	0.000	0.000	0.000	0.000
24	C	34	VAL	0	0.028	0.018	21.236	0.000	0.000	0.000	0.000	0.000	0.000
25	C	35	THR	0	-0.029	-0.020	24.707	0.017	0.017	0.000	0.000	0.000	0.000
26	C	36	GLU	-1	-0.892	-0.951	27.936	-0.162	-0.162	0.000	0.000	0.000	0.000
27	C	37	THR	0	-0.061	-0.047	31.164	0.006	0.006	0.000	0.000	0.000	0.000
28	C	38	THR	0	-0.003	-0.013	34.594	0.002	0.002	0.000	0.000	0.000	0.000
29	C	39	ASP	-1	-0.886	-0.928	35.623	-0.095	-0.095	0.000	0.000	0.000	0.000
30	C	40	LYS	1	0.886	0.954	31.473	0.104	0.104	0.000	0.000	0.000	0.000
31	C	41	VAL	0	0.053	0.023	27.712	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	42	ILE	0	-0.079	-0.031	24.866	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	43	HIS	0	0.026	0.013	18.988	0.018	0.018	0.000	0.000	0.000	0.000
34	C	44	ASN	0	-0.061	-0.035	19.064	-0.007	-0.007	0.000	0.000	0.000	0.000
35	C	45	SER	0	0.030	0.014	15.529	0.009	0.009	0.000	0.000	0.000	0.000
36	C	46	SER	0	-0.007	-0.013	13.508	0.022	0.022	0.000	0.000	0.000	0.000
37	C	48	ILE	0	0.001	0.003	9.813	0.126	0.126	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.051	0.030	8.197	-0.116	-0.116	0.000	0.000	0.000	0.000
39	C	50	GLU	-1	-0.835	-0.928	7.954	0.468	0.468	0.000	0.000	0.000	0.000
40	C	51	ILE	0	-0.033	-0.024	9.785	-0.025	-0.025	0.000	0.000	0.000	0.000
41	C	52	ASP	-1	-0.912	-0.954	12.357	0.067	0.067	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.099	-0.026	10.344	-0.062	-0.062	0.000	0.000	0.000	0.000
43	C	54	ILE	0	0.001	0.024	14.188	0.044	0.044	0.000	0.000	0.000	0.000
44	C	55	PRO	0	-0.043	-0.040	17.521	-0.022	-0.022	0.000	0.000	0.000	0.000
45	C	56	ARG	1	0.943	0.930	11.395	-0.417	-0.417	0.000	0.000	0.000	0.000
46	C	57	ASP	-1	-0.928	-0.951	13.662	-0.015	-0.015	0.000	0.000	0.000	0.000
47	C	58	ARG	1	0.905	0.933	16.091	0.048	0.048	0.000	0.000	0.000	0.000
48	C	59	PRO	0	0.036	0.046	14.417	0.021	0.021	0.000	0.000	0.000	0.000
49	C	60	PHE	0	-0.007	-0.019	17.551	-0.029	-0.029	0.000	0.000	0.000	0.000
50	C	61	VAL	0	0.017	0.011	16.967	-0.006	-0.006	0.000	0.000	0.000	0.000
51	C	62	CYS	0	-0.025	-0.017	14.393	-0.040	-0.040	0.000	0.000	0.000	0.000
52	C	63	ALA	0	-0.056	-0.014	18.371	-0.010	-0.010	0.000	0.000	0.000	0.000
53	C	64	PRO	0	0.045	0.026	22.079	0.006	0.006	0.000	0.000	0.000	0.000
54	C	65	SER	0	0.086	0.025	23.844	0.017	0.017	0.000	0.000	0.000	0.000
55	C	66	SER	0	-0.008	-0.018	27.214	0.011	0.011	0.000	0.000	0.000	0.000
56	C	67	LYS	1	0.885	0.940	23.400	0.152	0.152	0.000	0.000	0.000	0.000
57	C	68	THR	0	-0.011	0.011	25.149	0.016	0.016	0.000	0.000	0.000	0.000
58	C	69	GLY	0	0.051	0.025	27.448	0.009	0.009	0.000	0.000	0.000	0.000
59	C	70	SER	0	-0.123	-0.055	29.813	0.005	0.005	0.000	0.000	0.000	0.000
60	C	71	VAL	0	0.009	0.026	29.377	0.001	0.001	0.000	0.000	0.000	0.000
61	C	72	THR	0	-0.012	-0.008	25.139	-0.002	-0.002	0.000	0.000	0.000	0.000
62	C	73	THR	0	-0.018	-0.005	24.467	0.004	0.004	0.000	0.000	0.000	0.000
63	C	74	THR	0	0.013	0.002	19.902	-0.013	-0.013	0.000	0.000	0.000	0.000
64	C	75	TYR	0	-0.010	-0.010	16.660	-0.004	-0.004	0.000	0.000	0.000	0.000
65	C	77	CYS	0	-0.047	0.007	12.213	0.136	0.136	0.000	0.000	0.000	0.000
66	C	78	ASN	0	0.073	0.027	8.548	0.008	0.008	0.000	0.000	0.000	0.000
67	C	79	GLN	0	-0.023	-0.019	8.256	-0.283	-0.283	0.000	0.000	0.000	0.000
68	C	80	ASP	-1	-0.748	-0.893	7.176	-2.811	-2.811	0.000	0.000	0.000	0.000
69	C	81	HIS	0	-0.128	-0.072	9.849	0.295	0.295	0.000	0.000	0.000	0.000
70	C	83	ASN	0	-0.020	-0.005	12.834	0.001	0.001	0.000	0.000	0.000	0.000
71	C	84	LYS	1	0.942	0.976	15.268	0.602	0.602	0.000	0.000	0.000	0.000
72	C	85	ILE	0	0.001	-0.010	18.235	-0.009	-0.009	0.000	0.000	0.000	0.000
73	C	86	GLU	-1	-0.902	-0.945	21.788	-0.219	-0.219	0.000	0.000	0.000	0.000
74	C	87	LEU	0	-0.054	-0.013	24.670	-0.002	-0.002	0.000	0.000	0.000	0.000

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