FMO DATABASE

FMODB ID: Q19NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-865119.506291
FMO2-HF: Nuclear repulsion	818907.614664
FMO2-HF: Total energy	-46211.891627
FMO2-MP2: Total energy	-46334.288369

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.
-5.469	-3.289	0.984	-0.962	-2.201	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 : -0.027 / q_NPA : -0.034

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	0.013	0.009	3.558	-0.642	0.890	-0.002	-0.524	-1.006	0.002
4	B	28	CYS	0	-0.050	-0.026	6.021	0.550	0.550	0.000	0.000	0.000	0.000
5	B	29	LYS	1	0.851	0.939	9.384	0.859	0.859	0.000	0.000	0.000	0.000
6	B	30	PHE	0	0.017	-0.008	10.255	0.035	0.035	0.000	0.000	0.000	0.000
7	B	31	CYS	0	-0.048	0.026	13.447	0.038	0.038	0.000	0.000	0.000	0.000
8	B	32	ASP	-1	-0.807	-0.899	16.552	-0.310	-0.310	0.000	0.000	0.000	0.000
9	B	33	VAL	0	-0.031	-0.019	18.422	-0.006	-0.006	0.000	0.000	0.000	0.000
10	B	34	ARG	1	0.870	0.945	19.198	0.363	0.363	0.000	0.000	0.000	0.000
11	B	35	PHE	0	0.031	0.017	23.780	0.005	0.005	0.000	0.000	0.000	0.000
12	B	36	SER	0	-0.003	-0.007	24.877	-0.016	-0.016	0.000	0.000	0.000	0.000
13	B	37	THR	0	0.011	-0.001	27.022	0.011	0.011	0.000	0.000	0.000	0.000
14	B	38	CYS	0	-0.119	-0.034	23.485	0.029	0.029	0.000	0.000	0.000	0.000
15	B	39	ASP	-1	-0.674	-0.840	28.269	-0.118	-0.118	0.000	0.000	0.000	0.000
16	B	40	ASN	0	-0.099	-0.042	31.439	0.007	0.007	0.000	0.000	0.000	0.000
17	B	41	GLN	0	-0.002	0.002	27.682	0.005	0.005	0.000	0.000	0.000	0.000
18	B	42	LYS	1	0.770	0.861	25.968	0.134	0.134	0.000	0.000	0.000	0.000
19	B	43	SER	0	0.023	0.010	23.521	0.008	0.008	0.000	0.000	0.000	0.000
20	B	45	MET	0	0.015	0.025	20.049	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	46	SER	0	-0.006	-0.048	17.812	0.021	0.021	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.064	-0.031	20.248	0.014	0.014	0.000	0.000	0.000	0.000
23	B	49	SER	0	-0.034	-0.037	16.819	-0.052	-0.052	0.000	0.000	0.000	0.000
24	B	50	ILE	0	-0.009	-0.026	12.483	-0.027	-0.027	0.000	0.000	0.000	0.000
25	B	51	THR	0	-0.006	-0.024	8.558	0.076	0.076	0.000	0.000	0.000	0.000
26	B	52	SER	0	-0.036	-0.028	8.131	0.078	0.078	0.000	0.000	0.000	0.000
27	B	53	ILE	0	0.013	0.010	2.278	-1.056	-0.605	0.991	-0.412	-1.030	-0.001
28	B	54	CYS	0	-0.041	0.003	4.661	0.415	0.530	-0.002	-0.006	-0.107	0.000
29	B	55	GLU	-1	-0.838	-0.910	5.102	-0.104	0.000	-0.001	-0.002	-0.101	0.000
30	B	56	LYS	1	0.733	0.850	7.522	0.350	0.350	0.000	0.000	0.000	0.000
31	B	57	PRO	0	-0.012	-0.018	4.610	-0.195	-0.145	-0.001	-0.005	-0.043	0.000
32	B	58	GLN	0	-0.070	-0.039	5.611	0.286	0.286	0.000	0.000	0.000	0.000
33	B	59	GLU	-1	-0.879	-0.928	7.643	-0.375	-0.375	0.000	0.000	0.000	0.000
34	B	60	VAL	0	0.014	0.008	7.422	-0.051	-0.051	0.000	0.000	0.000	0.000
35	B	62	VAL	0	0.041	0.013	11.710	0.133	0.133	0.000	0.000	0.000	0.000
36	B	63	ALA	0	0.030	0.010	15.371	-0.066	-0.066	0.000	0.000	0.000	0.000
37	B	64	VAL	0	-0.029	-0.017	18.385	0.042	0.042	0.000	0.000	0.000	0.000
38	B	65	TRP	0	-0.031	-0.019	21.817	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	66	ARG	1	0.849	0.889	24.928	0.155	0.155	0.000	0.000	0.000	0.000
40	B	67	LYS	1	0.886	0.939	28.145	0.107	0.107	0.000	0.000	0.000	0.000
41	B	68	ASN	0	0.066	0.032	31.563	0.005	0.005	0.000	0.000	0.000	0.000
42	B	69	ASP	-1	-0.983	-0.996	34.353	-0.085	-0.085	0.000	0.000	0.000	0.000
43	B	70	GLU	-1	-0.925	-0.943	35.000	-0.108	-0.108	0.000	0.000	0.000	0.000
44	B	71	ASN	0	-0.098	-0.070	30.890	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	72	ILE	0	0.024	0.013	28.024	0.005	0.005	0.000	0.000	0.000	0.000
46	B	73	THR	0	-0.035	-0.022	25.549	-0.009	-0.009	0.000	0.000	0.000	0.000
47	B	74	LEU	0	-0.036	-0.020	20.741	0.007	0.007	0.000	0.000	0.000	0.000
48	B	75	GLU	-1	-0.843	-0.891	18.978	-0.237	-0.237	0.000	0.000	0.000	0.000
49	B	76	THR	0	-0.029	-0.015	15.248	-0.018	-0.018	0.000	0.000	0.000	0.000
50	B	77	VAL	0	0.016	0.014	13.707	-0.009	-0.009	0.000	0.000	0.000	0.000
51	B	79	HIS	0	0.018	-0.014	11.131	0.068	0.068	0.000	0.000	0.000	0.000
52	B	80	ASP	-1	-0.780	-0.883	11.888	0.256	0.256	0.000	0.000	0.000	0.000
53	B	81	PRO	0	0.046	0.022	11.784	-0.012	-0.012	0.000	0.000	0.000	0.000
54	B	82	LYS	1	0.815	0.921	13.316	-0.351	-0.351	0.000	0.000	0.000	0.000
55	B	83	LEU	0	-0.046	-0.024	16.387	0.001	0.001	0.000	0.000	0.000	0.000
56	B	84	PRO	0	-0.001	0.019	18.392	-0.017	-0.017	0.000	0.000	0.000	0.000
57	B	85	TYR	0	-0.012	-0.036	18.146	-0.009	-0.009	0.000	0.000	0.000	0.000
58	B	86	HIS	0	-0.077	-0.060	20.664	0.023	0.023	0.000	0.000	0.000	0.000
59	B	87	ASP	-1	-0.944	-0.966	24.027	-0.031	-0.031	0.000	0.000	0.000	0.000
60	B	88	PHE	0	-0.067	-0.032	23.302	0.013	0.013	0.000	0.000	0.000	0.000
61	B	89	ILE	0	0.008	-0.010	20.707	0.001	0.001	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.021	0.022	15.389	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	91	GLU	-1	-0.853	-0.946	17.728	-0.020	-0.020	0.000	0.000	0.000	0.000
64	B	92	ASP	-1	-0.815	-0.875	18.283	-0.093	-0.093	0.000	0.000	0.000	0.000
65	B	93	ALA	0	0.058	0.038	13.323	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	94	ALA	0	-0.016	0.008	13.026	-0.015	-0.015	0.000	0.000	0.000	0.000
67	B	95	SER	0	-0.028	-0.004	14.184	0.019	0.019	0.000	0.000	0.000	0.000
68	B	96	PRO	0	0.013	0.013	12.775	-0.051	-0.051	0.000	0.000	0.000	0.000
69	B	97	LYS	1	0.846	0.894	13.649	0.086	0.086	0.000	0.000	0.000	0.000
70	B	98	CYS	0	0.027	0.040	16.287	0.051	0.051	0.000	0.000	0.000	0.000
71	B	99	ILE	0	-0.005	0.002	17.802	0.000	0.000	0.000	0.000	0.000	0.000
72	B	100	MET	0	-0.037	0.003	21.187	0.022	0.022	0.000	0.000	0.000	0.000
73	B	101	LYS	1	0.809	0.891	21.030	0.115	0.115	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.921	-0.965	25.566	-0.088	-0.088	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.823	0.920	23.013	0.076	0.076	0.000	0.000	0.000	0.000
76	B	104	LYS	1	0.946	0.980	28.644	0.032	0.032	0.000	0.000	0.000	0.000
77	B	105	LYS	1	0.923	0.934	29.061	0.093	0.093	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.044	-0.029	32.535	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	107	GLY	0	0.017	0.001	35.328	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	108	GLU	-1	-0.784	-0.838	30.260	-0.112	-0.112	0.000	0.000	0.000	0.000
81	B	109	THR	0	-0.037	0.002	31.347	0.006	0.006	0.000	0.000	0.000	0.000
82	B	110	PHE	0	-0.018	-0.016	24.547	-0.010	-0.010	0.000	0.000	0.000	0.000
83	B	111	PHE	0	0.035	0.009	25.442	0.011	0.011	0.000	0.000	0.000	0.000
84	B	112	MET	0	-0.030	-0.018	20.259	-0.019	-0.019	0.000	0.000	0.000	0.000
85	B	114	SER	0	0.025	-0.021	14.672	-0.023	-0.023	0.000	0.000	0.000	0.000
86	B	115	CYS	0	-0.080	-0.009	10.730	0.225	0.225	0.000	0.000	0.000	0.000
87	B	116	SER	0	0.013	-0.031	8.937	-0.035	-0.035	0.000	0.000	0.000	0.000
88	B	117	SER	0	-0.025	-0.005	8.121	0.154	0.154	0.000	0.000	0.000	0.000
89	B	118	ASP	-1	-0.836	-0.930	4.981	-4.504	-4.576	-0.001	-0.013	0.086	0.000
90	B	119	GLU	-1	-0.858	-0.906	7.772	-0.846	-0.846	0.000	0.000	0.000	0.000
91	B	121	ASN	0	-0.059	-0.040	12.814	0.009	0.009	0.000	0.000	0.000	0.000
92	B	122	ASP	-1	-0.810	-0.893	14.645	-0.558	-0.558	0.000	0.000	0.000	0.000
93	B	123	ASN	0	-0.054	-0.027	16.341	0.091	0.091	0.000	0.000	0.000	0.000
94	B	124	ILE	0	-0.025	0.000	18.554	0.010	0.010	0.000	0.000	0.000	0.000
95	B	125	ILE	0	-0.009	-0.021	20.411	0.025	0.025	0.000	0.000	0.000	0.000
96	B	126	PHE	0	0.064	0.034	23.101	0.011	0.011	0.000	0.000	0.000	0.000
97	B	127	SER	0	0.011	0.010	26.408	0.009	0.009	0.000	0.000	0.000	0.000
98	B	128	GLU	-1	-0.814	-0.915	24.891	-0.094	-0.094	0.000	0.000	0.000	0.000
99	B	129	GLU	-1	-0.837	-0.872	21.463	-0.179	-0.179	0.000	0.000	0.000	0.000
100	B	130	TYR	0	0.004	0.001	25.676	0.010	0.010	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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