FMO DATABASE

FMODB ID: N98LQ

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	OptAll
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	-469326.207114
FMO2-HF: Nuclear repulsion	436446.675784
FMO2-HF: Total energy	-32879.531329
FMO2-MP2: Total energy	-32967.084933

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.
-5.815	-1.157	2.137	-3.256	-3.538	-0.016

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 : -0.005 / q_NPA : -0.001

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	GLN	0	0.016	-0.001	3.882	-0.067	1.822	-0.008	-1.004	-0.877	0.004
4	C	12	CYS	0	-0.023	0.000	6.254	0.279	0.279	0.000	0.000	0.000	0.000
5	C	13	PHE	0	0.007	-0.008	9.236	0.125	0.125	0.000	0.000	0.000	0.000
6	C	14	CYS	0	-0.036	0.003	12.355	0.067	0.067	0.000	0.000	0.000	0.000
7	C	15	HIS	0	0.045	0.027	14.191	0.006	0.006	0.000	0.000	0.000	0.000
8	C	16	LEU	0	0.023	0.003	16.816	0.033	0.033	0.000	0.000	0.000	0.000
9	C	18	THR	0	-0.001	-0.022	15.481	-0.013	-0.013	0.000	0.000	0.000	0.000
10	C	19	LYS	1	0.911	0.962	16.788	0.061	0.061	0.000	0.000	0.000	0.000
11	C	20	ASP	-1	-0.861	-0.928	12.018	-0.157	-0.157	0.000	0.000	0.000	0.000
12	C	21	ASN	0	-0.044	-0.021	12.904	-0.040	-0.040	0.000	0.000	0.000	0.000
13	C	22	PHE	0	-0.020	-0.003	15.016	-0.035	-0.035	0.000	0.000	0.000	0.000
14	C	23	THR	0	-0.064	-0.022	9.827	-0.093	-0.093	0.000	0.000	0.000	0.000
15	C	24	CYS	0	0.009	0.006	8.125	-0.031	-0.031	0.000	0.000	0.000	0.000
16	C	25	VAL	0	0.004	-0.005	2.621	-0.601	-0.395	0.691	-0.255	-0.642	0.000
17	C	26	THR	0	-0.038	-0.026	3.552	0.545	0.878	0.005	-0.110	-0.227	0.000
18	C	27	ASP	-1	-0.812	-0.904	2.598	-3.380	-1.181	1.450	-1.893	-1.755	-0.020
19	C	28	GLY	0	0.003	0.012	3.938	-0.104	-0.073	-0.001	0.006	-0.037	0.000
20	C	29	LEU	0	-0.055	-0.033	6.586	-0.362	-0.362	0.000	0.000	0.000	0.000
21	C	31	PHE	0	0.017	-0.004	10.468	0.091	0.091	0.000	0.000	0.000	0.000
22	C	32	VAL	0	0.000	-0.001	14.118	-0.022	-0.022	0.000	0.000	0.000	0.000
23	C	33	SER	0	-0.008	0.003	17.689	0.026	0.026	0.000	0.000	0.000	0.000
24	C	34	VAL	0	-0.005	-0.001	21.126	-0.004	-0.004	0.000	0.000	0.000	0.000
25	C	35	THR	0	0.001	-0.015	24.602	0.015	0.015	0.000	0.000	0.000	0.000
26	C	36	GLU	-1	-0.832	-0.916	28.029	-0.162	-0.162	0.000	0.000	0.000	0.000
27	C	37	THR	0	-0.082	-0.055	31.078	0.007	0.007	0.000	0.000	0.000	0.000
28	C	38	THR	0	0.016	0.003	34.405	0.003	0.003	0.000	0.000	0.000	0.000
29	C	39	ASP	-1	-0.894	-0.937	35.663	-0.098	-0.098	0.000	0.000	0.000	0.000
30	C	40	LYS	1	0.839	0.946	31.254	0.109	0.109	0.000	0.000	0.000	0.000
31	C	41	VAL	0	0.044	0.002	28.008	0.000	0.000	0.000	0.000	0.000	0.000
32	C	42	ILE	0	-0.036	-0.018	25.146	-0.006	-0.006	0.000	0.000	0.000	0.000
33	C	43	HIS	0	0.010	0.008	18.937	0.018	0.018	0.000	0.000	0.000	0.000
34	C	44	ASN	0	-0.057	-0.032	19.444	0.005	0.005	0.000	0.000	0.000	0.000
35	C	45	SER	0	0.011	-0.006	15.275	0.014	0.014	0.000	0.000	0.000	0.000
36	C	46	SER	0	-0.011	-0.011	13.229	0.026	0.026	0.000	0.000	0.000	0.000
37	C	48	ILE	0	0.004	0.002	9.634	0.135	0.135	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.053	0.038	8.032	-0.154	-0.154	0.000	0.000	0.000	0.000
39	C	50	GLU	-1	-0.857	-0.943	7.573	0.547	0.547	0.000	0.000	0.000	0.000
40	C	51	ILE	0	-0.024	-0.015	9.375	-0.034	-0.034	0.000	0.000	0.000	0.000
41	C	52	ASP	-1	-0.900	-0.951	12.461	0.047	0.047	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.085	-0.025	9.752	-0.058	-0.058	0.000	0.000	0.000	0.000
43	C	54	ILE	0	0.030	0.033	13.753	0.043	0.043	0.000	0.000	0.000	0.000
44	C	55	PRO	0	-0.063	-0.039	17.288	-0.024	-0.024	0.000	0.000	0.000	0.000
45	C	56	ARG	1	0.942	0.931	11.455	-0.442	-0.442	0.000	0.000	0.000	0.000
46	C	57	ASP	-1	-0.909	-0.951	13.734	0.008	0.008	0.000	0.000	0.000	0.000
47	C	58	ARG	1	0.869	0.923	16.188	0.046	0.046	0.000	0.000	0.000	0.000
48	C	59	PRO	0	0.019	0.040	13.999	0.014	0.014	0.000	0.000	0.000	0.000
49	C	60	PHE	0	0.012	-0.013	17.175	-0.032	-0.032	0.000	0.000	0.000	0.000
50	C	61	VAL	0	0.008	0.008	16.530	-0.009	-0.009	0.000	0.000	0.000	0.000
51	C	62	CYS	0	-0.032	-0.010	13.851	-0.040	-0.040	0.000	0.000	0.000	0.000
52	C	63	ALA	0	-0.020	-0.004	18.153	-0.005	-0.005	0.000	0.000	0.000	0.000
53	C	64	PRO	0	0.025	0.018	21.852	0.002	0.002	0.000	0.000	0.000	0.000
54	C	65	SER	0	0.099	0.040	23.550	0.021	0.021	0.000	0.000	0.000	0.000
55	C	66	SER	0	-0.037	-0.028	27.027	0.012	0.012	0.000	0.000	0.000	0.000
56	C	67	LYS	1	0.884	0.936	23.613	0.151	0.151	0.000	0.000	0.000	0.000
57	C	68	THR	0	-0.002	0.012	24.566	0.017	0.017	0.000	0.000	0.000	0.000
58	C	69	GLY	0	0.044	0.028	26.875	0.009	0.009	0.000	0.000	0.000	0.000
59	C	70	SER	0	-0.143	-0.077	29.494	0.006	0.006	0.000	0.000	0.000	0.000
60	C	71	VAL	0	0.011	0.018	29.694	-0.002	-0.002	0.000	0.000	0.000	0.000
61	C	72	THR	0	-0.016	0.002	25.345	-0.001	-0.001	0.000	0.000	0.000	0.000
62	C	73	THR	0	0.003	-0.006	24.280	0.005	0.005	0.000	0.000	0.000	0.000
63	C	74	THR	0	0.012	0.000	19.721	-0.010	-0.010	0.000	0.000	0.000	0.000
64	C	75	TYR	0	-0.018	-0.006	16.149	-0.005	-0.005	0.000	0.000	0.000	0.000
65	C	77	CYS	0	-0.065	-0.002	12.189	0.136	0.136	0.000	0.000	0.000	0.000
66	C	78	ASN	0	0.048	0.011	8.640	0.020	0.020	0.000	0.000	0.000	0.000
67	C	79	GLN	0	0.008	-0.007	8.382	-0.218	-0.218	0.000	0.000	0.000	0.000
68	C	80	ASP	-1	-0.758	-0.887	6.885	-3.050	-3.050	0.000	0.000	0.000	0.000
69	C	81	HIS	0	-0.111	-0.073	9.507	0.372	0.372	0.000	0.000	0.000	0.000
70	C	83	ASN	0	-0.015	0.000	12.519	-0.002	-0.002	0.000	0.000	0.000	0.000
71	C	84	LYS	1	0.925	0.968	15.043	0.659	0.659	0.000	0.000	0.000	0.000
72	C	85	ILE	0	-0.005	-0.008	17.948	-0.007	-0.007	0.000	0.000	0.000	0.000
73	C	86	GLU	-1	-0.874	-0.917	21.694	-0.224	-0.224	0.000	0.000	0.000	0.000
74	C	87	LEU	0	-0.078	-0.040	24.592	-0.003	-0.003	0.000	0.000	0.000	0.000

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