FMO DATABASE

FMODB ID: 22M2R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-303693.895413
FMO2-HF: Nuclear repulsion	276038.06846
FMO2-HF: Total energy	-27655.826952
FMO2-MP2: Total energy	-27727.621929

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.
-6.733	-3.844	0.022	-1.122	-1.788	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 : 0.020 / q_NPA : -0.013

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	0.009	0.025	3.545	-2.135	0.459	0.020	-1.025	-1.588	0.005
4	C	3	THR	0	-0.006	-0.004	3.894	-2.930	-2.635	0.002	-0.097	-0.200	0.000
5	C	4	GLY	0	-0.018	-0.006	5.561	0.532	0.532	0.000	0.000	0.000	0.000
6	C	5	THR	0	-0.030	-0.010	7.964	0.184	0.184	0.000	0.000	0.000	0.000
7	C	6	GLU	-1	-0.945	-0.977	10.943	-1.213	-1.213	0.000	0.000	0.000	0.000
8	C	7	ALA	0	0.001	0.002	12.260	0.175	0.175	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.018	0.007	15.292	0.014	0.014	0.000	0.000	0.000	0.000
10	C	9	CYS	0	-0.128	-0.039	18.792	-0.077	-0.077	0.000	0.000	0.000	0.000
11	C	10	GLU	-1	-0.913	-0.962	21.968	-0.370	-0.370	0.000	0.000	0.000	0.000
12	C	11	ASN	0	-0.038	-0.014	25.641	-0.005	-0.005	0.000	0.000	0.000	0.000
13	C	12	GLU	-1	-0.814	-0.911	25.507	-0.417	-0.417	0.000	0.000	0.000	0.000
14	C	13	GLY	0	-0.045	-0.017	26.341	0.021	0.021	0.000	0.000	0.000	0.000
15	C	14	GLU	-1	-0.942	-0.960	27.183	-0.317	-0.317	0.000	0.000	0.000	0.000
16	C	15	VAL	0	-0.041	-0.033	25.367	-0.035	-0.035	0.000	0.000	0.000	0.000
17	C	16	LEU	0	0.013	0.010	20.037	0.007	0.007	0.000	0.000	0.000	0.000
18	C	17	HIS	0	-0.016	-0.024	22.788	-0.048	-0.048	0.000	0.000	0.000	0.000
19	C	18	ILE	0	0.006	0.010	17.151	0.018	0.018	0.000	0.000	0.000	0.000
20	C	19	PRO	0	0.048	-0.002	20.014	-0.026	-0.026	0.000	0.000	0.000	0.000
21	C	20	ASN	0	-0.029	-0.018	17.170	-0.067	-0.067	0.000	0.000	0.000	0.000
22	C	21	ILE	0	-0.022	0.015	13.552	-0.092	-0.092	0.000	0.000	0.000	0.000
23	C	22	THR	0	-0.007	-0.022	17.095	0.004	0.004	0.000	0.000	0.000	0.000
24	C	23	ASP	-1	-0.903	-0.940	20.068	-0.619	-0.619	0.000	0.000	0.000	0.000
25	C	24	ASN	0	-0.006	0.005	19.054	0.023	0.023	0.000	0.000	0.000	0.000
26	C	25	PRO	0	0.018	-0.007	21.012	-0.009	-0.009	0.000	0.000	0.000	0.000
27	C	26	CYS	0	-0.072	-0.010	20.121	0.025	0.025	0.000	0.000	0.000	0.000
28	C	27	ILE	0	0.007	0.020	15.704	-0.018	-0.018	0.000	0.000	0.000	0.000
29	C	28	SER	0	0.000	-0.003	19.445	0.049	0.049	0.000	0.000	0.000	0.000
30	C	29	CYS	0	-0.037	-0.025	15.951	-0.016	-0.016	0.000	0.000	0.000	0.000
31	C	30	VAL	0	0.019	0.006	20.734	0.061	0.061	0.000	0.000	0.000	0.000
32	C	32	LEU	0	0.011	0.000	21.412	0.059	0.059	0.000	0.000	0.000	0.000
33	C	33	ASN	0	-0.017	-0.026	21.653	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.054	-0.017	21.610	-0.031	-0.031	0.000	0.000	0.000	0.000
35	C	35	LYS	1	0.948	0.974	16.272	0.681	0.681	0.000	0.000	0.000	0.000
36	C	36	ALA	0	0.005	0.005	16.464	0.061	0.061	0.000	0.000	0.000	0.000
37	C	37	GLU	-1	-0.878	-0.926	16.483	-0.916	-0.916	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.862	0.954	17.234	0.557	0.557	0.000	0.000	0.000	0.000
39	C	40	GLN	0	0.041	0.000	14.576	-0.036	-0.036	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.990	-1.007	18.295	-0.364	-0.364	0.000	0.000	0.000	0.000
41	C	42	LYS	1	0.970	0.983	21.111	0.312	0.312	0.000	0.000	0.000	0.000
42	C	43	CYS	0	-0.003	-0.022	22.674	0.008	0.008	0.000	0.000	0.000	0.000
43	C	44	ALA	0	-0.028	-0.017	25.708	0.006	0.006	0.000	0.000	0.000	0.000
44	C	45	PRO	0	0.006	-0.003	27.040	-0.007	-0.007	0.000	0.000	0.000	0.000
45	C	46	LEU	0	-0.013	-0.008	28.887	0.005	0.005	0.000	0.000	0.000	0.000
46	C	47	ALA	0	0.002	0.003	32.058	0.005	0.005	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.952	-0.970	33.079	-0.116	-0.116	0.000	0.000	0.000	0.000
48	C	49	ASP	-1	-0.877	-0.946	34.640	-0.118	-0.118	0.000	0.000	0.000	0.000
49	C	50	CYS	0	-0.031	-0.011	32.995	0.000	0.000	0.000	0.000	0.000	0.000
50	C	51	ALA	0	-0.006	-0.001	34.948	0.000	0.000	0.000	0.000	0.000	0.000
51	C	52	LEU	0	-0.060	-0.038	34.870	-0.003	-0.003	0.000	0.000	0.000	0.000
52	C	53	VAL	0	0.044	0.025	29.751	0.004	0.004	0.000	0.000	0.000	0.000
53	C	54	VAL	0	-0.057	-0.034	32.592	0.000	0.000	0.000	0.000	0.000	0.000
54	C	55	LYS	1	1.014	0.995	24.718	0.391	0.391	0.000	0.000	0.000	0.000
55	C	56	GLN	0	0.018	0.010	31.070	-0.005	-0.005	0.000	0.000	0.000	0.000
56	C	57	THR	0	0.045	0.027	30.799	-0.014	-0.014	0.000	0.000	0.000	0.000
57	C	58	GLY	0	0.002	-0.004	28.381	0.008	0.008	0.000	0.000	0.000	0.000
58	C	59	ALA	0	-0.026	-0.005	27.932	-0.017	-0.017	0.000	0.000	0.000	0.000
59	C	62	GLU	-1	-0.965	-0.972	27.269	-0.281	-0.281	0.000	0.000	0.000	0.000
60	C	63	LYS	1	0.938	0.972	29.554	0.199	0.199	0.000	0.000	0.000	0.000
61	C	65	LYS	1	0.873	0.947	35.715	0.174	0.174	0.000	0.000	0.000	0.000
62	C	66	GLY	0	0.053	0.032	37.717	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)