FMO DATABASE

FMODB ID: R1J98

Calculation Name: 3BK3-C-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	62
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-303516.11796
FMO2-HF: Nuclear repulsion	275860.886904
FMO2-HF: Total energy	-27655.231056
FMO2-MP2: Total energy	-27727.024545

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.
-6.994	-4.15	0.026	-1.105	-1.766	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 : 0.021 / q_NPA : -0.012

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	C	2	ILE	0	0.011	0.025	3.545	-2.236	0.314	0.023	-1.007	-1.567	0.005
4	C	3	THR	0	-0.008	-0.005	3.893	-2.970	-2.676	0.003	-0.098	-0.199	0.000
5	C	4	GLY	0	-0.017	-0.006	5.560	0.537	0.537	0.000	0.000	0.000	0.000
6	C	5	THR	0	-0.031	-0.011	7.964	0.205	0.205	0.000	0.000	0.000	0.000
7	C	6	GLU	-1	-0.945	-0.977	10.943	-1.221	-1.221	0.000	0.000	0.000	0.000
8	C	7	ALA	0	0.001	0.002	12.260	0.183	0.183	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.012	0.005	15.291	0.018	0.018	0.000	0.000	0.000	0.000
10	C	31	CYS	0	-0.120	-0.036	18.791	-0.077	-0.077	0.000	0.000	0.000	0.000
11	C	10	GLU	-1	-0.914	-0.963	21.968	-0.370	-0.370	0.000	0.000	0.000	0.000
12	C	11	ASN	0	-0.040	-0.015	25.641	-0.004	-0.004	0.000	0.000	0.000	0.000
13	C	12	GLU	-1	-0.814	-0.911	25.506	-0.421	-0.421	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	-0.320	-0.320	0.000	0.000	0.000	0.000
16	C	15	VAL	0	-0.041	-0.033	25.367	-0.036	-0.036	0.000	0.000	0.000	0.000
17	C	16	LEU	0	0.011	0.009	20.037	0.006	0.006	0.000	0.000	0.000	0.000
18	C	17	HIS	0	-0.012	-0.023	22.787	-0.050	-0.050	0.000	0.000	0.000	0.000
19	C	18	ILE	0	0.003	0.008	17.150	0.017	0.017	0.000	0.000	0.000	0.000
20	C	19	PRO	0	0.049	-0.001	20.014	-0.027	-0.027	0.000	0.000	0.000	0.000
21	C	20	ASN	0	-0.030	-0.018	17.170	-0.070	-0.070	0.000	0.000	0.000	0.000
22	C	21	ILE	0	-0.026	0.013	13.552	-0.096	-0.096	0.000	0.000	0.000	0.000
23	C	22	THR	0	-0.008	-0.023	17.095	0.006	0.006	0.000	0.000	0.000	0.000
24	C	23	ASP	-1	-0.902	-0.939	20.068	-0.626	-0.626	0.000	0.000	0.000	0.000
25	C	24	ASN	0	-0.008	0.003	19.055	0.022	0.022	0.000	0.000	0.000	0.000
26	C	25	PRO	0	0.019	-0.007	21.012	-0.009	-0.009	0.000	0.000	0.000	0.000
27	C	60	CYS	0	-0.066	-0.004	20.121	0.021	0.021	0.000	0.000	0.000	0.000
28	C	27	ILE	0	0.012	0.021	15.704	-0.024	-0.024	0.000	0.000	0.000	0.000
29	C	28	SER	0	0.019	0.009	19.445	0.047	0.047	0.000	0.000	0.000	0.000
30	C	38	CYS	0	-0.046	-0.027	15.950	-0.017	-0.017	0.000	0.000	0.000	0.000
31	C	30	VAL	0	0.019	0.005	20.733	0.064	0.064	0.000	0.000	0.000	0.000
32	C	32	LEU	0	0.010	0.001	21.412	0.061	0.061	0.000	0.000	0.000	0.000
33	C	33	ASN	0	-0.017	-0.028	21.653	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.055	-0.017	21.610	-0.032	-0.032	0.000	0.000	0.000	0.000
35	C	35	LYS	1	0.951	0.975	16.271	0.682	0.682	0.000	0.000	0.000	0.000
36	C	36	ALA	0	0.004	0.005	16.464	0.060	0.060	0.000	0.000	0.000	0.000
37	C	37	GLU	-1	-0.876	-0.926	16.482	-0.926	-0.926	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.842	0.931	17.233	0.600	0.600	0.000	0.000	0.000	0.000
39	C	40	GLN	0	0.038	0.009	14.577	-0.036	-0.036	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.985	-1.008	18.295	-0.369	-0.369	0.000	0.000	0.000	0.000
41	C	42	LYS	1	0.959	0.977	21.111	0.319	0.319	0.000	0.000	0.000	0.000
42	C	61	CYS	0	-0.006	-0.024	22.674	0.009	0.009	0.000	0.000	0.000	0.000
43	C	44	ALA	0	-0.031	-0.019	25.708	0.007	0.007	0.000	0.000	0.000	0.000
44	C	45	PRO	0	0.001	-0.005	27.040	-0.006	-0.006	0.000	0.000	0.000	0.000
45	C	46	LEU	0	-0.011	-0.007	28.887	0.006	0.006	0.000	0.000	0.000	0.000
46	C	47	ALA	0	0.003	0.003	32.058	0.006	0.006	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.964	-0.976	33.079	-0.120	-0.120	0.000	0.000	0.000	0.000
48	C	49	ASP	-1	-0.897	-0.959	34.640	-0.121	-0.121	0.000	0.000	0.000	0.000
49	C	64	CYS	0	-0.020	0.000	32.995	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	51	ALA	0	0.003	0.009	34.948	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	52	LEU	0	-0.074	-0.039	34.871	-0.006	-0.006	0.000	0.000	0.000	0.000
52	C	53	VAL	0	0.041	0.023	29.751	0.002	0.002	0.000	0.000	0.000	0.000
53	C	54	VAL	0	-0.065	-0.039	32.592	-0.001	-0.001	0.000	0.000	0.000	0.000
54	C	55	LYS	1	1.007	0.991	24.718	0.398	0.398	0.000	0.000	0.000	0.000
55	C	56	GLN	0	0.015	0.008	31.070	-0.005	-0.005	0.000	0.000	0.000	0.000
56	C	57	THR	0	0.041	0.025	30.799	-0.015	-0.015	0.000	0.000	0.000	0.000
57	C	58	GLY	0	-0.003	-0.006	28.381	0.007	0.007	0.000	0.000	0.000	0.000
58	C	59	ALA	0	-0.025	-0.004	27.932	-0.018	-0.018	0.000	0.000	0.000	0.000
59	C	62	GLU	-1	-0.964	-0.971	27.269	-0.288	-0.288	0.000	0.000	0.000	0.000
60	C	63	LYS	1	0.924	0.963	29.554	0.204	0.204	0.000	0.000	0.000	0.000
61	C	65	LYS	1	0.833	0.922	35.715	0.178	0.178	0.000	0.000	0.000	0.000
62	C	66	GLY	-1	-0.825	-0.911	37.730	-0.142	-0.142	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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