FMO DATABASE

FMODB ID: G6RV1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-467833.140924
FMO2-HF: Nuclear repulsion	434954.140411
FMO2-HF: Total energy	-32879.000513
FMO2-MP2: Total energy	-32966.531869

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.
-5.908	-1.845	2.99	-3.365	-3.689	-0.012

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 : -0.016 / q_NPA : -0.006

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	0.009	0.010	3.817	-0.479	1.679	-0.018	-1.149	-0.992	0.006
4	C	12	CYS	0	-0.009	-0.001	6.297	0.312	0.312	0.000	0.000	0.000	0.000
5	C	13	PHE	0	-0.009	-0.010	9.568	0.134	0.134	0.000	0.000	0.000	0.000
6	C	14	CYS	0	-0.017	0.009	12.225	0.074	0.074	0.000	0.000	0.000	0.000
7	C	15	HIS	0	0.022	0.014	14.000	0.013	0.013	0.000	0.000	0.000	0.000
8	C	16	LEU	0	0.013	-0.002	16.843	0.035	0.035	0.000	0.000	0.000	0.000
9	C	18	THR	0	-0.001	-0.017	15.454	-0.013	-0.013	0.000	0.000	0.000	0.000
10	C	19	LYS	1	0.923	0.952	17.087	0.041	0.041	0.000	0.000	0.000	0.000
11	C	20	ASP	-1	-0.884	-0.926	11.602	-0.135	-0.135	0.000	0.000	0.000	0.000
12	C	21	ASN	0	-0.043	-0.021	12.668	-0.034	-0.034	0.000	0.000	0.000	0.000
13	C	22	PHE	0	-0.019	-0.011	14.438	-0.036	-0.036	0.000	0.000	0.000	0.000
14	C	23	THR	0	-0.034	-0.010	9.372	-0.087	-0.087	0.000	0.000	0.000	0.000
15	C	24	CYS	0	-0.009	0.001	8.440	-0.030	-0.030	0.000	0.000	0.000	0.000
16	C	25	VAL	0	0.025	0.003	2.363	-0.600	-0.630	1.320	-0.423	-0.867	0.000
17	C	26	THR	0	-0.037	-0.015	4.314	0.743	0.954	-0.001	-0.045	-0.165	0.000
18	C	27	ASP	-1	-0.861	-0.936	2.510	-3.191	-1.529	1.688	-1.732	-1.618	-0.018
19	C	28	GLY	0	0.018	0.022	3.897	-0.077	-0.015	0.001	-0.016	-0.047	0.000
20	C	29	LEU	0	-0.050	-0.030	6.749	-0.427	-0.427	0.000	0.000	0.000	0.000
21	C	31	PHE	0	0.002	-0.012	10.734	0.099	0.099	0.000	0.000	0.000	0.000
22	C	32	VAL	0	0.028	0.001	14.289	-0.013	-0.013	0.000	0.000	0.000	0.000
23	C	33	SER	0	-0.056	-0.014	17.771	0.034	0.034	0.000	0.000	0.000	0.000
24	C	34	VAL	0	0.049	0.029	21.216	0.000	0.000	0.000	0.000	0.000	0.000
25	C	35	THR	0	-0.045	-0.031	24.687	0.017	0.017	0.000	0.000	0.000	0.000
26	C	36	GLU	-1	-0.894	-0.953	27.917	-0.168	-0.168	0.000	0.000	0.000	0.000
27	C	37	THR	0	-0.064	-0.044	31.144	0.007	0.007	0.000	0.000	0.000	0.000
28	C	38	THR	0	-0.005	-0.011	34.575	0.002	0.002	0.000	0.000	0.000	0.000
29	C	39	ASP	-1	-0.888	-0.929	35.658	-0.098	-0.098	0.000	0.000	0.000	0.000
30	C	40	LYS	1	0.884	0.953	31.099	0.111	0.111	0.000	0.000	0.000	0.000
31	C	41	VAL	0	0.058	0.025	27.679	-0.002	-0.002	0.000	0.000	0.000	0.000
32	C	42	ILE	0	-0.077	-0.035	24.813	0.000	0.000	0.000	0.000	0.000	0.000
33	C	43	HIS	0	0.044	0.025	18.883	0.016	0.016	0.000	0.000	0.000	0.000
34	C	44	ASN	0	-0.058	-0.033	19.144	-0.007	-0.007	0.000	0.000	0.000	0.000
35	C	45	SER	0	0.019	0.002	15.543	0.009	0.009	0.000	0.000	0.000	0.000
36	C	46	SER	0	-0.002	-0.008	13.489	0.023	0.023	0.000	0.000	0.000	0.000
37	C	48	ILE	0	0.015	0.013	9.796	0.132	0.132	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.063	0.029	8.192	-0.124	-0.124	0.000	0.000	0.000	0.000
39	C	50	GLU	-1	-0.870	-0.959	7.706	0.377	0.377	0.000	0.000	0.000	0.000
40	C	51	ILE	0	-0.049	-0.030	9.783	-0.015	-0.015	0.000	0.000	0.000	0.000
41	C	52	ASP	-1	-0.918	-0.954	12.351	0.035	0.035	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.106	-0.024	10.047	-0.056	-0.056	0.000	0.000	0.000	0.000
43	C	54	ILE	0	0.007	0.029	14.182	0.044	0.044	0.000	0.000	0.000	0.000
44	C	55	PRO	0	-0.036	-0.042	17.507	-0.019	-0.019	0.000	0.000	0.000	0.000
45	C	56	ARG	1	1.003	0.974	11.742	-0.327	-0.327	0.000	0.000	0.000	0.000
46	C	57	ASP	-1	-0.938	-0.951	13.648	-0.045	-0.045	0.000	0.000	0.000	0.000
47	C	58	ARG	1	0.913	0.935	16.078	0.068	0.068	0.000	0.000	0.000	0.000
48	C	59	PRO	0	0.032	0.050	14.509	0.026	0.026	0.000	0.000	0.000	0.000
49	C	60	PHE	0	-0.010	-0.025	17.543	-0.029	-0.029	0.000	0.000	0.000	0.000
50	C	61	VAL	0	0.025	0.014	16.933	-0.004	-0.004	0.000	0.000	0.000	0.000
51	C	62	CYS	0	-0.022	-0.018	14.396	-0.040	-0.040	0.000	0.000	0.000	0.000
52	C	63	ALA	0	-0.063	-0.020	18.357	-0.008	-0.008	0.000	0.000	0.000	0.000
53	C	64	PRO	0	0.049	0.032	22.065	0.006	0.006	0.000	0.000	0.000	0.000
54	C	65	SER	0	0.085	0.019	23.828	0.017	0.017	0.000	0.000	0.000	0.000
55	C	66	SER	0	-0.010	-0.015	27.197	0.011	0.011	0.000	0.000	0.000	0.000
56	C	67	LYS	1	0.889	0.943	23.127	0.164	0.164	0.000	0.000	0.000	0.000
57	C	68	THR	0	-0.020	0.009	25.333	0.016	0.016	0.000	0.000	0.000	0.000
58	C	69	GLY	0	0.059	0.025	27.434	0.010	0.010	0.000	0.000	0.000	0.000
59	C	70	SER	0	-0.128	-0.059	29.810	0.005	0.005	0.000	0.000	0.000	0.000
60	C	71	VAL	0	0.021	0.033	29.336	0.002	0.002	0.000	0.000	0.000	0.000
61	C	72	THR	0	-0.014	-0.008	24.998	-0.002	-0.002	0.000	0.000	0.000	0.000
62	C	73	THR	0	-0.025	-0.007	24.681	0.001	0.001	0.000	0.000	0.000	0.000
63	C	74	THR	0	0.007	-0.002	19.858	-0.014	-0.014	0.000	0.000	0.000	0.000
64	C	75	TYR	0	-0.008	-0.006	16.547	-0.004	-0.004	0.000	0.000	0.000	0.000
65	C	77	CYS	0	-0.052	0.016	12.215	0.139	0.139	0.000	0.000	0.000	0.000
66	C	78	ASN	0	0.073	0.028	8.507	0.019	0.019	0.000	0.000	0.000	0.000
67	C	79	GLN	0	-0.030	-0.030	8.285	-0.285	-0.285	0.000	0.000	0.000	0.000
68	C	80	ASP	-1	-0.779	-0.911	7.253	-2.853	-2.853	0.000	0.000	0.000	0.000
69	C	81	HIS	0	-0.117	-0.069	9.849	0.256	0.256	0.000	0.000	0.000	0.000
70	C	83	ASN	0	0.001	0.013	12.812	0.008	0.008	0.000	0.000	0.000	0.000
71	C	84	LYS	1	0.940	0.975	15.247	0.543	0.543	0.000	0.000	0.000	0.000
72	C	85	ILE	0	-0.003	-0.011	18.186	-0.007	-0.007	0.000	0.000	0.000	0.000
73	C	86	GLU	-1	-0.934	-0.962	21.766	-0.226	-0.226	0.000	0.000	0.000	0.000
74	C	87	LEU	0	-0.030	-0.002	24.608	-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)