FMO DATABASE

FMODB ID: K3123

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

Total energy (hartree)

FMO2-HF: Electronic energy	-865515.92771
FMO2-HF: Nuclear repulsion	819303.798234
FMO2-HF: Total energy	-46212.129476
FMO2-MP2: Total energy	-46334.505105

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.
-4.428	-2.269	1.082	-0.951	-2.288	0

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 : -0.017 / q_NPA : -0.031

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	0.033	0.021	3.882	-0.650	0.608	-0.006	-0.433	-0.820	0.001
4	B	28	CYS	0	-0.019	-0.006	6.333	0.615	0.615	0.000	0.000	0.000	0.000
5	B	29	LYS	1	0.816	0.921	9.603	0.764	0.764	0.000	0.000	0.000	0.000
6	B	30	PHE	0	0.053	0.008	10.041	0.040	0.040	0.000	0.000	0.000	0.000
7	B	31	CYS	0	-0.068	0.010	13.342	0.022	0.022	0.000	0.000	0.000	0.000
8	B	32	ASP	-1	-0.825	-0.906	16.609	-0.362	-0.362	0.000	0.000	0.000	0.000
9	B	33	VAL	0	-0.035	-0.017	18.490	0.002	0.002	0.000	0.000	0.000	0.000
10	B	34	ARG	1	0.845	0.924	19.340	0.371	0.371	0.000	0.000	0.000	0.000
11	B	35	PHE	0	0.036	0.013	23.957	0.008	0.008	0.000	0.000	0.000	0.000
12	B	36	SER	0	-0.019	-0.017	25.169	-0.014	-0.014	0.000	0.000	0.000	0.000
13	B	37	THR	0	0.010	0.002	27.412	0.009	0.009	0.000	0.000	0.000	0.000
14	B	38	CYS	0	-0.102	-0.021	23.699	0.028	0.028	0.000	0.000	0.000	0.000
15	B	39	ASP	-1	-0.680	-0.838	28.516	-0.112	-0.112	0.000	0.000	0.000	0.000
16	B	40	ASN	0	-0.098	-0.046	31.627	0.007	0.007	0.000	0.000	0.000	0.000
17	B	41	GLN	0	-0.011	0.001	27.760	0.006	0.006	0.000	0.000	0.000	0.000
18	B	42	LYS	1	0.787	0.884	26.591	0.099	0.099	0.000	0.000	0.000	0.000
19	B	43	SER	0	0.010	0.003	23.625	0.007	0.007	0.000	0.000	0.000	0.000
20	B	45	MET	0	0.024	0.027	20.763	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	46	SER	0	-0.012	-0.044	18.235	0.011	0.011	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.061	-0.033	20.547	0.012	0.012	0.000	0.000	0.000	0.000
23	B	49	SER	0	0.008	-0.016	16.609	-0.061	-0.061	0.000	0.000	0.000	0.000
24	B	50	ILE	0	0.000	-0.010	13.023	-0.043	-0.043	0.000	0.000	0.000	0.000
25	B	51	THR	0	-0.006	-0.031	9.044	0.054	0.054	0.000	0.000	0.000	0.000
26	B	52	SER	0	-0.046	-0.029	8.079	0.114	0.114	0.000	0.000	0.000	0.000
27	B	53	ILE	0	-0.015	-0.008	2.407	-1.131	-0.497	1.093	-0.483	-1.243	-0.001
28	B	54	CYS	0	-0.018	0.017	4.505	0.552	0.691	-0.002	-0.010	-0.127	0.000
29	B	55	GLU	-1	-0.833	-0.904	4.582	-0.539	-0.409	-0.001	-0.008	-0.121	0.000
30	B	56	LYS	1	0.704	0.829	7.222	0.513	0.513	0.000	0.000	0.000	0.000
31	B	57	PRO	0	-0.021	-0.013	4.737	-0.191	-0.128	-0.001	-0.007	-0.054	0.000
32	B	58	GLN	0	-0.042	-0.036	5.494	0.402	0.402	0.000	0.000	0.000	0.000
33	B	59	GLU	-1	-0.865	-0.920	7.655	-0.485	-0.485	0.000	0.000	0.000	0.000
34	B	60	VAL	0	-0.004	-0.004	7.440	-0.034	-0.034	0.000	0.000	0.000	0.000
35	B	62	VAL	0	0.018	-0.002	11.554	0.147	0.147	0.000	0.000	0.000	0.000
36	B	63	ALA	0	0.018	0.005	15.306	-0.073	-0.073	0.000	0.000	0.000	0.000
37	B	64	VAL	0	-0.013	-0.010	18.329	0.043	0.043	0.000	0.000	0.000	0.000
38	B	65	TRP	0	-0.030	-0.017	21.843	-0.013	-0.013	0.000	0.000	0.000	0.000
39	B	66	ARG	1	0.857	0.896	24.960	0.165	0.165	0.000	0.000	0.000	0.000
40	B	67	LYS	1	0.872	0.925	28.155	0.101	0.101	0.000	0.000	0.000	0.000
41	B	68	ASN	0	0.014	-0.004	31.706	0.002	0.002	0.000	0.000	0.000	0.000
42	B	69	ASP	-1	-0.927	-0.955	34.784	-0.086	-0.086	0.000	0.000	0.000	0.000
43	B	70	GLU	-1	-0.953	-0.944	34.831	-0.114	-0.114	0.000	0.000	0.000	0.000
44	B	71	ASN	0	-0.064	-0.064	30.959	-0.012	-0.012	0.000	0.000	0.000	0.000
45	B	72	ILE	0	0.028	0.016	28.527	0.006	0.006	0.000	0.000	0.000	0.000
46	B	73	THR	0	-0.025	-0.020	25.898	-0.009	-0.009	0.000	0.000	0.000	0.000
47	B	74	LEU	0	-0.038	-0.014	20.929	0.010	0.010	0.000	0.000	0.000	0.000
48	B	75	GLU	-1	-0.827	-0.884	19.165	-0.250	-0.250	0.000	0.000	0.000	0.000
49	B	76	THR	0	-0.024	-0.019	15.559	-0.013	-0.013	0.000	0.000	0.000	0.000
50	B	77	VAL	0	0.024	0.024	13.566	-0.020	-0.020	0.000	0.000	0.000	0.000
51	B	79	HIS	0	0.016	-0.006	11.010	0.055	0.055	0.000	0.000	0.000	0.000
52	B	80	ASP	-1	-0.736	-0.835	11.977	0.181	0.181	0.000	0.000	0.000	0.000
53	B	81	PRO	0	0.029	0.012	11.820	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	82	LYS	1	0.762	0.866	13.327	-0.206	-0.206	0.000	0.000	0.000	0.000
55	B	83	LEU	0	-0.033	-0.010	16.565	0.004	0.004	0.000	0.000	0.000	0.000
56	B	84	PRO	0	-0.010	0.011	18.498	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	85	TYR	0	-0.018	-0.045	17.902	-0.016	-0.016	0.000	0.000	0.000	0.000
58	B	86	HIS	0	-0.064	-0.057	20.849	0.026	0.026	0.000	0.000	0.000	0.000
59	B	87	ASP	-1	-0.929	-0.958	24.064	-0.052	-0.052	0.000	0.000	0.000	0.000
60	B	88	PHE	0	-0.060	-0.020	23.712	0.018	0.018	0.000	0.000	0.000	0.000
61	B	89	ILE	0	0.007	-0.010	21.091	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.037	0.017	15.469	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	91	GLU	-1	-0.842	-0.916	18.052	-0.016	-0.016	0.000	0.000	0.000	0.000
64	B	92	ASP	-1	-0.798	-0.869	18.430	-0.077	-0.077	0.000	0.000	0.000	0.000
65	B	93	ALA	0	0.068	0.045	13.569	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	94	ALA	0	-0.025	0.000	12.960	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	95	SER	0	-0.022	-0.007	14.347	0.040	0.040	0.000	0.000	0.000	0.000
68	B	96	PRO	0	0.012	0.008	13.280	-0.037	-0.037	0.000	0.000	0.000	0.000
69	B	97	LYS	1	0.827	0.884	14.019	0.034	0.034	0.000	0.000	0.000	0.000
70	B	98	CYS	0	0.002	0.040	16.513	0.057	0.057	0.000	0.000	0.000	0.000
71	B	99	ILE	0	0.002	0.006	17.939	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	100	MET	0	-0.029	0.000	21.110	0.022	0.022	0.000	0.000	0.000	0.000
73	B	101	LYS	1	0.816	0.887	20.978	0.090	0.090	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.915	-0.958	25.358	-0.083	-0.083	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.792	0.895	22.638	0.076	0.076	0.000	0.000	0.000	0.000
76	B	104	LYS	1	0.939	0.970	28.556	0.032	0.032	0.000	0.000	0.000	0.000
77	B	105	LYS	1	0.895	0.933	28.291	0.102	0.102	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.039	-0.014	32.695	0.002	0.002	0.000	0.000	0.000	0.000
79	B	107	GLY	0	0.000	-0.011	34.811	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	108	GLU	-1	-0.778	-0.839	30.041	-0.119	-0.119	0.000	0.000	0.000	0.000
81	B	109	THR	0	-0.009	0.005	31.464	0.005	0.005	0.000	0.000	0.000	0.000
82	B	110	PHE	0	-0.015	-0.019	24.681	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	111	PHE	0	0.016	0.007	25.457	0.013	0.013	0.000	0.000	0.000	0.000
84	B	112	MET	0	-0.019	-0.013	20.352	-0.022	-0.022	0.000	0.000	0.000	0.000
85	B	114	SER	0	0.028	-0.022	14.607	-0.029	-0.029	0.000	0.000	0.000	0.000
86	B	115	CYS	0	-0.125	-0.024	11.046	0.188	0.188	0.000	0.000	0.000	0.000
87	B	116	SER	0	0.008	-0.021	8.995	-0.072	-0.072	0.000	0.000	0.000	0.000
88	B	117	SER	0	-0.034	-0.022	8.616	0.200	0.200	0.000	0.000	0.000	0.000
89	B	118	ASP	-1	-0.832	-0.921	5.129	-3.333	-3.398	-0.001	-0.010	0.077	0.000
90	B	119	GLU	-1	-0.841	-0.900	8.026	-0.813	-0.813	0.000	0.000	0.000	0.000
91	B	121	ASN	0	-0.033	-0.041	13.087	0.012	0.012	0.000	0.000	0.000	0.000
92	B	122	ASP	-1	-0.801	-0.883	14.898	-0.495	-0.495	0.000	0.000	0.000	0.000
93	B	123	ASN	0	-0.048	-0.027	16.739	0.075	0.075	0.000	0.000	0.000	0.000
94	B	124	ILE	0	0.007	0.021	18.860	0.021	0.021	0.000	0.000	0.000	0.000
95	B	125	ILE	0	-0.018	-0.026	20.887	0.018	0.018	0.000	0.000	0.000	0.000
96	B	126	PHE	0	0.048	0.026	23.510	0.010	0.010	0.000	0.000	0.000	0.000
97	B	127	SER	0	0.020	0.006	26.749	0.011	0.011	0.000	0.000	0.000	0.000
98	B	128	GLU	-1	-0.854	-0.931	24.691	-0.060	-0.060	0.000	0.000	0.000	0.000
99	B	129	GLU	-1	-0.823	-0.881	21.899	-0.121	-0.121	0.000	0.000	0.000	0.000
100	B	130	TYR	0	-0.007	0.000	26.042	0.010	0.010	0.000	0.000	0.000	0.000

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