FMO DATABASE

FMODB ID: ZYZYN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-303282.77503
FMO2-HF: Nuclear repulsion	275625.893139
FMO2-HF: Total energy	-27656.881891
FMO2-MP2: Total energy	-27728.609255

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.
-6.728	-2.499	0.044	-1.866	-2.406	0.008

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 : 0.063 / q_NPA : 0.020

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	-0.014	0.008	3.182	-4.157	-0.370	0.043	-1.764	-2.066	0.008
4	C	3	THR	0	-0.006	0.001	4.044	-2.009	-1.567	0.001	-0.102	-0.340	0.000
5	C	4	GLY	0	0.025	0.006	5.626	0.431	0.431	0.000	0.000	0.000	0.000
6	C	5	THR	0	-0.075	-0.042	8.392	0.237	0.237	0.000	0.000	0.000	0.000
7	C	6	GLU	-1	-0.841	-0.893	10.957	-0.436	-0.436	0.000	0.000	0.000	0.000
8	C	7	ALA	0	0.012	0.002	12.702	0.055	0.055	0.000	0.000	0.000	0.000
9	C	8	SER	0	0.038	0.019	15.704	0.048	0.048	0.000	0.000	0.000	0.000
10	C	9	CYS	0	-0.131	-0.034	19.115	-0.046	-0.046	0.000	0.000	0.000	0.000
11	C	10	GLU	-1	-0.877	-0.939	22.256	-0.236	-0.236	0.000	0.000	0.000	0.000
12	C	11	ASN	0	-0.068	-0.049	26.028	0.008	0.008	0.000	0.000	0.000	0.000
13	C	12	GLU	-1	-0.788	-0.883	25.716	-0.172	-0.172	0.000	0.000	0.000	0.000
14	C	13	GLY	0	-0.019	-0.007	26.848	0.013	0.013	0.000	0.000	0.000	0.000
15	C	14	GLU	-1	-0.907	-0.928	27.700	-0.190	-0.190	0.000	0.000	0.000	0.000
16	C	15	VAL	0	-0.025	-0.024	25.254	-0.016	-0.016	0.000	0.000	0.000	0.000
17	C	16	LEU	0	-0.012	-0.001	20.022	-0.001	-0.001	0.000	0.000	0.000	0.000
18	C	17	HIS	0	0.029	-0.010	22.015	-0.050	-0.050	0.000	0.000	0.000	0.000
19	C	18	ILE	0	0.011	0.014	17.076	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	19	PRO	0	0.009	-0.009	20.138	-0.018	-0.018	0.000	0.000	0.000	0.000
21	C	20	ASN	0	-0.093	-0.056	17.739	-0.041	-0.041	0.000	0.000	0.000	0.000
22	C	21	ILE	0	-0.020	-0.001	13.812	-0.102	-0.102	0.000	0.000	0.000	0.000
23	C	22	THR	0	-0.036	-0.038	17.345	0.020	0.020	0.000	0.000	0.000	0.000
24	C	23	ASP	-1	-0.803	-0.886	20.391	-0.464	-0.464	0.000	0.000	0.000	0.000
25	C	24	ASN	0	-0.021	-0.008	19.042	0.060	0.060	0.000	0.000	0.000	0.000
26	C	25	PRO	0	0.029	0.002	21.144	0.002	0.002	0.000	0.000	0.000	0.000
27	C	26	CYS	0	-0.016	0.011	19.926	0.023	0.023	0.000	0.000	0.000	0.000
28	C	27	ILE	0	-0.017	-0.004	15.626	0.018	0.018	0.000	0.000	0.000	0.000
29	C	28	SER	0	0.006	0.008	19.631	0.020	0.020	0.000	0.000	0.000	0.000
30	C	29	CYS	0	-0.045	-0.018	15.820	-0.019	-0.019	0.000	0.000	0.000	0.000
31	C	30	VAL	0	-0.003	-0.005	20.555	0.029	0.029	0.000	0.000	0.000	0.000
32	C	32	LEU	0	0.023	0.001	21.850	0.035	0.035	0.000	0.000	0.000	0.000
33	C	33	ASN	0	-0.082	-0.050	22.113	0.004	0.004	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.086	-0.063	21.844	-0.006	-0.006	0.000	0.000	0.000	0.000
35	C	35	LYS	1	0.830	0.911	16.185	0.210	0.210	0.000	0.000	0.000	0.000
36	C	36	ALA	0	0.029	0.002	16.657	0.033	0.033	0.000	0.000	0.000	0.000
37	C	37	GLU	-1	-0.898	-0.930	16.550	-0.284	-0.284	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.798	0.908	16.943	0.297	0.297	0.000	0.000	0.000	0.000
39	C	40	GLN	0	0.043	0.007	14.803	-0.086	-0.086	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.907	-0.937	18.312	-0.179	-0.179	0.000	0.000	0.000	0.000
41	C	42	LYS	1	0.885	0.922	20.749	0.083	0.083	0.000	0.000	0.000	0.000
42	C	43	CYS	0	0.033	0.016	22.628	0.004	0.004	0.000	0.000	0.000	0.000
43	C	44	ALA	0	0.011	0.010	25.780	0.013	0.013	0.000	0.000	0.000	0.000
44	C	45	PRO	0	0.003	-0.005	27.554	-0.011	-0.011	0.000	0.000	0.000	0.000
45	C	46	LEU	0	-0.013	-0.013	29.242	0.001	0.001	0.000	0.000	0.000	0.000
46	C	47	ALA	0	0.010	0.004	32.281	0.005	0.005	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.922	-0.968	33.088	-0.033	-0.033	0.000	0.000	0.000	0.000
48	C	49	ASP	-1	-0.887	-0.937	34.823	-0.050	-0.050	0.000	0.000	0.000	0.000
49	C	50	CYS	0	-0.039	-0.020	32.950	-0.010	-0.010	0.000	0.000	0.000	0.000
50	C	51	ALA	0	-0.010	-0.006	34.512	-0.008	-0.008	0.000	0.000	0.000	0.000
51	C	52	LEU	0	-0.023	-0.012	35.223	-0.006	-0.006	0.000	0.000	0.000	0.000
52	C	53	VAL	0	0.010	0.020	30.180	0.005	0.005	0.000	0.000	0.000	0.000
53	C	54	VAL	0	-0.031	-0.023	32.313	-0.004	-0.004	0.000	0.000	0.000	0.000
54	C	55	LYS	1	0.890	0.931	24.948	0.242	0.242	0.000	0.000	0.000	0.000
55	C	56	GLN	0	-0.003	-0.003	31.084	-0.003	-0.003	0.000	0.000	0.000	0.000
56	C	57	THR	0	0.008	-0.002	30.783	-0.009	-0.009	0.000	0.000	0.000	0.000
57	C	58	GLY	0	0.044	0.025	28.391	0.007	0.007	0.000	0.000	0.000	0.000
58	C	59	ALA	0	-0.023	0.002	28.131	-0.004	-0.004	0.000	0.000	0.000	0.000
59	C	62	GLU	-1	-0.896	-0.925	26.289	-0.200	-0.200	0.000	0.000	0.000	0.000
60	C	63	LYS	1	0.919	0.946	29.617	0.110	0.110	0.000	0.000	0.000	0.000
61	C	65	LYS	1	0.905	0.958	35.739	0.108	0.108	0.000	0.000	0.000	0.000
62	C	66	GLY	0	0.033	0.020	37.778	0.004	0.004	0.000	0.000	0.000	0.000

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