FMO DATABASE

FMODB ID: 6646Z

Calculation Name: 3BK3-C-Xray372

Preferred Name: Bone morphogenetic protein 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BK3

Chain ID: C

ChEMBL ID: CHEMBL1926496

UniProt ID: P12643

Base Structure: X-ray

Registration Date: 2023-03-14

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-303315.667943
FMO2-HF: Nuclear repulsion	275659.078518
FMO2-HF: Total energy	-27656.589424
FMO2-MP2: Total energy	-27728.289982

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:-1:TRP)

Summations of interaction energy for fragment #1(C:-1:TRP)

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.
-5.58	-2.833	-0.006	-1.162	-1.578	0.005

Interaction energy analysis for fragmet #1(C:-1:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.016

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	2	ILE	0	0.001	0.022	3.872	-2.468	0.126	-0.005	-1.122	-1.466	0.005
4	C	3	THR	0	-0.006	-0.007	4.348	-2.197	-2.044	-0.001	-0.040	-0.112	0.000
5	C	4	GLY	0	-0.003	0.003	5.690	0.673	0.673	0.000	0.000	0.000	0.000
6	C	5	THR	0	-0.032	-0.013	8.111	0.247	0.247	0.000	0.000	0.000	0.000
7	C	6	GLU	-1	-0.870	-0.912	10.931	-0.806	-0.806	0.000	0.000	0.000	0.000
8	C	7	ALA	0	0.010	0.003	12.470	0.140	0.140	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.039	0.017	15.518	0.032	0.032	0.000	0.000	0.000	0.000
10	C	9	CYS	0	-0.152	-0.052	18.999	-0.069	-0.069	0.000	0.000	0.000	0.000
11	C	10	GLU	-1	-0.901	-0.953	22.162	-0.334	-0.334	0.000	0.000	0.000	0.000
12	C	11	ASN	0	-0.064	-0.044	25.831	0.003	0.003	0.000	0.000	0.000	0.000
13	C	12	GLU	-1	-0.761	-0.874	25.689	-0.314	-0.314	0.000	0.000	0.000	0.000
14	C	13	GLY	0	-0.044	-0.017	26.395	0.016	0.016	0.000	0.000	0.000	0.000
15	C	14	GLU	-1	-0.901	-0.926	27.258	-0.273	-0.273	0.000	0.000	0.000	0.000
16	C	15	VAL	0	-0.037	-0.030	25.550	-0.029	-0.029	0.000	0.000	0.000	0.000
17	C	16	LEU	0	-0.002	0.005	20.145	0.002	0.002	0.000	0.000	0.000	0.000
18	C	17	HIS	0	0.005	-0.016	22.891	-0.043	-0.043	0.000	0.000	0.000	0.000
19	C	18	ILE	0	0.011	0.011	17.267	0.008	0.008	0.000	0.000	0.000	0.000
20	C	19	PRO	0	0.038	0.002	20.333	-0.025	-0.025	0.000	0.000	0.000	0.000
21	C	20	ASN	0	-0.076	-0.042	17.888	-0.053	-0.053	0.000	0.000	0.000	0.000
22	C	21	ILE	0	-0.016	0.003	13.891	-0.090	-0.090	0.000	0.000	0.000	0.000
23	C	22	THR	0	-0.034	-0.026	17.366	0.014	0.014	0.000	0.000	0.000	0.000
24	C	23	ASP	-1	-0.835	-0.909	20.275	-0.599	-0.599	0.000	0.000	0.000	0.000
25	C	24	ASN	0	-0.017	0.001	19.155	0.056	0.056	0.000	0.000	0.000	0.000
26	C	25	PRO	0	0.022	-0.005	21.153	-0.004	-0.004	0.000	0.000	0.000	0.000
27	C	26	CYS	0	-0.042	-0.002	20.043	0.028	0.028	0.000	0.000	0.000	0.000
28	C	27	ILE	0	0.024	0.022	15.585	-0.008	-0.008	0.000	0.000	0.000	0.000
29	C	28	SER	0	0.009	0.005	19.486	0.039	0.039	0.000	0.000	0.000	0.000
30	C	29	CYS	0	-0.046	-0.025	15.927	-0.027	-0.027	0.000	0.000	0.000	0.000
31	C	30	VAL	0	0.018	0.005	20.765	0.049	0.049	0.000	0.000	0.000	0.000
32	C	32	LEU	0	0.020	0.001	21.332	0.053	0.053	0.000	0.000	0.000	0.000
33	C	33	ASN	0	-0.047	-0.034	21.690	0.001	0.001	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.101	-0.060	21.696	-0.017	-0.017	0.000	0.000	0.000	0.000
35	C	35	LYS	1	0.862	0.920	16.023	0.521	0.521	0.000	0.000	0.000	0.000
36	C	36	ALA	0	-0.003	-0.007	16.669	0.050	0.050	0.000	0.000	0.000	0.000
37	C	37	GLU	-1	-0.888	-0.931	16.528	-0.659	-0.659	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.801	0.914	17.144	0.468	0.468	0.000	0.000	0.000	0.000
39	C	40	GLN	0	0.033	-0.001	14.700	-0.076	-0.076	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.918	-0.952	18.181	-0.311	-0.311	0.000	0.000	0.000	0.000
41	C	42	LYS	1	0.914	0.949	20.943	0.214	0.214	0.000	0.000	0.000	0.000
42	C	43	CYS	0	0.012	-0.015	22.441	0.006	0.006	0.000	0.000	0.000	0.000
43	C	44	ALA	0	-0.009	0.003	25.476	0.011	0.011	0.000	0.000	0.000	0.000
44	C	45	PRO	0	0.022	0.007	26.949	-0.011	-0.011	0.000	0.000	0.000	0.000
45	C	46	LEU	0	-0.027	-0.022	28.797	0.004	0.004	0.000	0.000	0.000	0.000
46	C	47	ALA	0	0.016	0.011	31.994	0.005	0.005	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.934	-0.967	32.655	-0.076	-0.076	0.000	0.000	0.000	0.000
48	C	49	ASP	-1	-0.899	-0.952	34.521	-0.085	-0.085	0.000	0.000	0.000	0.000
49	C	50	CYS	0	-0.035	-0.007	32.849	-0.007	-0.007	0.000	0.000	0.000	0.000
50	C	51	ALA	0	0.007	0.005	34.915	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	52	LEU	0	-0.056	-0.033	34.940	-0.005	-0.005	0.000	0.000	0.000	0.000
52	C	53	VAL	0	0.034	0.015	29.794	0.005	0.005	0.000	0.000	0.000	0.000
53	C	54	VAL	0	-0.044	-0.030	32.515	-0.003	-0.003	0.000	0.000	0.000	0.000
54	C	55	LYS	1	0.914	0.937	24.738	0.340	0.340	0.000	0.000	0.000	0.000
55	C	56	GLN	0	-0.001	0.002	31.039	-0.004	-0.004	0.000	0.000	0.000	0.000
56	C	57	THR	0	0.047	0.029	30.832	-0.013	-0.013	0.000	0.000	0.000	0.000
57	C	58	GLY	0	0.010	0.000	28.482	0.009	0.009	0.000	0.000	0.000	0.000
58	C	59	ALA	0	-0.024	-0.003	27.983	-0.013	-0.013	0.000	0.000	0.000	0.000
59	C	62	GLU	-1	-0.912	-0.934	26.289	-0.276	-0.276	0.000	0.000	0.000	0.000
60	C	63	LYS	1	0.907	0.946	29.440	0.165	0.165	0.000	0.000	0.000	0.000
61	C	65	LYS	1	0.905	0.963	35.679	0.152	0.152	0.000	0.000	0.000	0.000
62	C	66	GLY	0	0.063	0.037	37.786	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:-1:TRP)