FMO DATABASE

FMODB ID: R53Y8

Calculation Name: 1KTZ-B-Xray372

Preferred Name: Transforming growth factor beta-3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1KTZ

Chain ID: B

ChEMBL ID: CHEMBL3712903

UniProt ID: P10600

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	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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864661.500696
FMO2-HF: Nuclear repulsion	818450.182597
FMO2-HF: Total energy	-46211.318099
FMO2-MP2: Total energy	-46333.746634

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(B:25:PRO)

Summations of interaction energy for fragment #1(B:25: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.
-6.796	-4.354	0.773	-0.996	-2.22	0.001

Interaction energy analysis for fragmet #1(B:25:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.024

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	B	27	LEU	0	0.016	0.011	3.303	-0.623	1.085	0.013	-0.611	-1.111	0.002
4	B	28	CYS	0	-0.055	-0.030	5.982	0.548	0.548	0.000	0.000	0.000	0.000
5	B	29	LYS	1	0.852	0.935	9.410	0.963	0.963	0.000	0.000	0.000	0.000
6	B	30	PHE	0	0.025	-0.003	10.368	0.027	0.027	0.000	0.000	0.000	0.000
7	B	31	CYS	0	-0.072	0.011	13.456	0.054	0.054	0.000	0.000	0.000	0.000
8	B	32	ASP	-1	-0.807	-0.900	16.561	-0.323	-0.323	0.000	0.000	0.000	0.000
9	B	33	VAL	0	-0.031	-0.022	18.414	-0.010	-0.010	0.000	0.000	0.000	0.000
10	B	34	ARG	1	0.897	0.957	19.488	0.396	0.396	0.000	0.000	0.000	0.000
11	B	35	PHE	0	0.034	0.018	23.792	0.004	0.004	0.000	0.000	0.000	0.000
12	B	36	SER	0	-0.003	-0.005	25.067	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	37	THR	0	0.014	0.001	27.048	0.012	0.012	0.000	0.000	0.000	0.000
14	B	38	CYS	0	-0.130	-0.038	23.439	0.035	0.035	0.000	0.000	0.000	0.000
15	B	39	ASP	-1	-0.719	-0.880	28.268	-0.146	-0.146	0.000	0.000	0.000	0.000
16	B	40	ASN	0	-0.072	-0.018	31.466	0.007	0.007	0.000	0.000	0.000	0.000
17	B	41	GLN	0	0.012	0.005	27.935	0.007	0.007	0.000	0.000	0.000	0.000
18	B	42	LYS	1	0.799	0.879	26.397	0.180	0.180	0.000	0.000	0.000	0.000
19	B	43	SER	0	0.008	0.002	23.448	0.005	0.005	0.000	0.000	0.000	0.000
20	B	45	MET	0	0.027	0.034	20.080	-0.033	-0.033	0.000	0.000	0.000	0.000
21	B	46	SER	0	-0.009	-0.037	17.554	0.027	0.027	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.047	-0.020	20.047	0.020	0.020	0.000	0.000	0.000	0.000
23	B	49	SER	0	-0.022	-0.034	16.487	-0.064	-0.064	0.000	0.000	0.000	0.000
24	B	50	ILE	0	-0.002	-0.018	12.452	-0.027	-0.027	0.000	0.000	0.000	0.000
25	B	51	THR	0	-0.006	-0.032	8.113	0.090	0.090	0.000	0.000	0.000	0.000
26	B	52	SER	0	-0.033	-0.022	7.954	0.114	0.114	0.000	0.000	0.000	0.000
27	B	53	ILE	0	0.020	0.017	2.309	-1.121	-0.581	0.765	-0.358	-0.947	-0.001
28	B	54	CYS	0	-0.053	-0.006	4.634	0.399	0.515	-0.002	-0.006	-0.108	0.000
29	B	55	GLU	-1	-0.922	-0.961	5.021	-0.079	0.021	-0.001	-0.002	-0.097	0.000
30	B	56	LYS	1	0.882	0.949	7.441	0.300	0.300	0.000	0.000	0.000	0.000
31	B	57	PRO	0	0.016	-0.013	4.570	-0.241	-0.190	-0.001	-0.006	-0.044	0.000
32	B	58	GLN	0	-0.024	-0.002	5.603	0.245	0.245	0.000	0.000	0.000	0.000
33	B	59	GLU	-1	-0.955	-0.982	7.593	-0.431	-0.431	0.000	0.000	0.000	0.000
34	B	60	VAL	0	0.014	0.012	7.408	-0.109	-0.109	0.000	0.000	0.000	0.000
35	B	62	VAL	0	0.042	0.016	11.696	0.142	0.142	0.000	0.000	0.000	0.000
36	B	63	ALA	0	0.024	0.005	15.354	-0.067	-0.067	0.000	0.000	0.000	0.000
37	B	64	VAL	0	-0.022	-0.014	18.380	0.044	0.044	0.000	0.000	0.000	0.000
38	B	65	TRP	0	-0.041	-0.028	21.804	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	66	ARG	1	0.834	0.892	24.926	0.184	0.184	0.000	0.000	0.000	0.000
40	B	67	LYS	1	0.909	0.964	28.137	0.130	0.130	0.000	0.000	0.000	0.000
41	B	68	ASN	0	0.053	0.034	31.560	0.010	0.010	0.000	0.000	0.000	0.000
42	B	69	ASP	-1	-0.985	-1.001	34.343	-0.101	-0.101	0.000	0.000	0.000	0.000
43	B	70	GLU	-1	-0.920	-0.950	35.398	-0.119	-0.119	0.000	0.000	0.000	0.000
44	B	71	ASN	0	-0.105	-0.063	31.290	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	72	ILE	0	0.026	0.012	28.018	0.004	0.004	0.000	0.000	0.000	0.000
46	B	73	THR	0	-0.060	-0.029	25.552	-0.010	-0.010	0.000	0.000	0.000	0.000
47	B	74	LEU	0	-0.015	-0.022	20.497	0.005	0.005	0.000	0.000	0.000	0.000
48	B	75	GLU	-1	-0.824	-0.866	18.818	-0.279	-0.279	0.000	0.000	0.000	0.000
49	B	76	THR	0	-0.043	-0.017	15.214	-0.023	-0.023	0.000	0.000	0.000	0.000
50	B	77	VAL	0	0.028	0.019	13.693	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	79	HIS	0	0.022	-0.009	11.090	0.086	0.086	0.000	0.000	0.000	0.000
52	B	80	ASP	-1	-0.830	-0.908	11.867	0.198	0.198	0.000	0.000	0.000	0.000
53	B	81	PRO	0	0.038	0.018	11.767	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	82	LYS	1	0.832	0.920	12.985	-0.361	-0.361	0.000	0.000	0.000	0.000
55	B	83	LEU	0	-0.056	-0.031	16.063	0.009	0.009	0.000	0.000	0.000	0.000
56	B	84	PRO	0	-0.005	0.012	18.374	-0.023	-0.023	0.000	0.000	0.000	0.000
57	B	85	TYR	0	-0.013	-0.038	18.412	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	86	HIS	0	-0.092	-0.070	20.642	0.025	0.025	0.000	0.000	0.000	0.000
59	B	87	ASP	-1	-0.940	-0.973	23.978	-0.045	-0.045	0.000	0.000	0.000	0.000
60	B	88	PHE	0	-0.069	-0.027	23.324	0.014	0.014	0.000	0.000	0.000	0.000
61	B	89	ILE	0	0.016	-0.009	20.551	0.000	0.000	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.006	0.013	15.253	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	91	GLU	-1	-0.915	-0.982	17.724	-0.073	-0.073	0.000	0.000	0.000	0.000
64	B	92	ASP	-1	-0.818	-0.899	18.537	-0.162	-0.162	0.000	0.000	0.000	0.000
65	B	93	ALA	0	0.052	0.035	13.230	-0.018	-0.018	0.000	0.000	0.000	0.000
66	B	94	ALA	0	-0.017	0.006	13.032	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	95	SER	0	-0.032	-0.009	13.943	0.005	0.005	0.000	0.000	0.000	0.000
68	B	96	PRO	0	0.018	0.016	12.589	-0.072	-0.072	0.000	0.000	0.000	0.000
69	B	97	LYS	1	0.924	0.962	13.496	0.185	0.185	0.000	0.000	0.000	0.000
70	B	98	CYS	0	0.025	0.041	16.133	0.056	0.056	0.000	0.000	0.000	0.000
71	B	99	ILE	0	-0.008	0.005	17.662	0.009	0.009	0.000	0.000	0.000	0.000
72	B	100	MET	0	-0.037	-0.004	21.182	0.023	0.023	0.000	0.000	0.000	0.000
73	B	101	LYS	1	0.851	0.929	21.266	0.181	0.181	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.925	-0.965	25.562	-0.116	-0.116	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.876	0.959	23.469	0.117	0.117	0.000	0.000	0.000	0.000
76	B	104	LYS	1	0.953	0.979	28.633	0.054	0.054	0.000	0.000	0.000	0.000
77	B	105	LYS	1	0.958	0.961	28.697	0.112	0.112	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.054	-0.032	32.517	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	107	GLY	0	0.021	0.004	35.294	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	108	GLU	-1	-0.794	-0.867	29.999	-0.139	-0.139	0.000	0.000	0.000	0.000
81	B	109	THR	0	-0.033	0.009	31.083	0.007	0.007	0.000	0.000	0.000	0.000
82	B	110	PHE	0	-0.009	-0.013	24.361	-0.010	-0.010	0.000	0.000	0.000	0.000
83	B	111	PHE	0	0.042	0.011	25.356	0.012	0.012	0.000	0.000	0.000	0.000
84	B	112	MET	0	-0.037	-0.019	20.279	-0.016	-0.016	0.000	0.000	0.000	0.000
85	B	114	SER	0	0.016	-0.023	14.624	-0.023	-0.023	0.000	0.000	0.000	0.000
86	B	115	CYS	0	-0.080	-0.008	10.663	0.274	0.274	0.000	0.000	0.000	0.000
87	B	116	SER	0	0.005	-0.032	9.034	-0.055	-0.055	0.000	0.000	0.000	0.000
88	B	117	SER	0	-0.019	-0.006	7.974	0.101	0.101	0.000	0.000	0.000	0.000
89	B	118	ASP	-1	-0.833	-0.934	4.978	-5.400	-5.473	-0.001	-0.013	0.087	0.000
90	B	119	GLU	-1	-0.907	-0.925	7.734	-0.985	-0.985	0.000	0.000	0.000	0.000
91	B	121	ASN	0	-0.063	-0.042	12.739	0.026	0.026	0.000	0.000	0.000	0.000
92	B	122	ASP	-1	-0.848	-0.919	14.500	-0.607	-0.607	0.000	0.000	0.000	0.000
93	B	123	ASN	0	-0.013	-0.011	16.215	0.108	0.108	0.000	0.000	0.000	0.000
94	B	124	ILE	0	-0.041	-0.009	18.479	0.005	0.005	0.000	0.000	0.000	0.000
95	B	125	ILE	0	-0.016	-0.021	20.014	0.031	0.031	0.000	0.000	0.000	0.000
96	B	126	PHE	0	0.054	0.028	22.995	0.010	0.010	0.000	0.000	0.000	0.000
97	B	127	SER	0	0.003	-0.003	26.289	0.012	0.012	0.000	0.000	0.000	0.000
98	B	128	GLU	-1	-0.846	-0.932	24.975	-0.149	-0.149	0.000	0.000	0.000	0.000
99	B	129	GLU	-1	-0.893	-0.925	21.057	-0.247	-0.247	0.000	0.000	0.000	0.000
100	B	130	TYR	0	0.004	0.005	25.532	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:25:PRO)