FMO DATABASE

FMODB ID: ZY29N

Calculation Name: 4UHY-C-Xray322

Preferred Name: Bone morphogenetic protein 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UHY

Chain ID: C

ChEMBL ID: CHEMBL1926496

UniProt ID: P12643

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	69
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-388231.753967
FMO2-HF: Nuclear repulsion	359621.127719
FMO2-HF: Total energy	-28610.626247
FMO2-MP2: Total energy	-28688.817588

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:46:ACE )

Summations of interaction energy for fragment #1(C:46:ACE )

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.
4.427	5.577	0.048	-0.554	-0.644	0.001

Interaction energy analysis for fragmet #1(C:46:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.091 / q_NPA : 0.036

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	93	CYS	0	-0.013	0.049	3.190	1.502	2.440	0.027	-0.441	-0.523	0.001
4	C	49	LYS	1	0.870	0.908	4.333	1.494	1.497	0.000	-0.038	0.034	0.000
5	C	50	ILE	0	0.110	0.033	6.222	0.273	0.273	0.000	0.000	0.000	0.000
6	C	51	LEU	0	0.002	0.017	3.296	-0.055	0.154	0.021	-0.075	-0.155	0.000
7	C	52	LYS	1	0.936	0.985	7.524	0.918	0.918	0.000	0.000	0.000	0.000
8	C	85	CYS	0	0.029	0.015	9.628	0.023	0.023	0.000	0.000	0.000	0.000
9	C	54	ASN	0	0.013	0.000	11.181	0.071	0.071	0.000	0.000	0.000	0.000
10	C	55	SER	0	-0.023	-0.021	11.109	0.052	0.052	0.000	0.000	0.000	0.000
11	C	56	GLU	-1	-0.946	-0.975	13.536	-0.325	-0.325	0.000	0.000	0.000	0.000
12	C	57	PHE	0	-0.002	-0.002	15.687	0.024	0.024	0.000	0.000	0.000	0.000
13	C	58	TRP	0	-0.049	-0.014	15.697	0.021	0.021	0.000	0.000	0.000	0.000
14	C	59	SER	0	-0.051	-0.014	17.875	0.019	0.019	0.000	0.000	0.000	0.000
15	C	60	ALA	0	-0.015	-0.011	20.322	0.010	0.010	0.000	0.000	0.000	0.000
16	C	61	THR	0	-0.030	-0.014	21.520	0.009	0.009	0.000	0.000	0.000	0.000
17	C	62	SER	0	-0.030	-0.047	21.302	-0.007	-0.007	0.000	0.000	0.000	0.000
18	C	63	GLY	0	0.027	0.002	23.447	0.005	0.005	0.000	0.000	0.000	0.000
19	C	64	SER	0	-0.159	-0.048	25.469	0.001	0.001	0.000	0.000	0.000	0.000
20	C	65	HIS	0	0.094	0.041	26.468	-0.009	-0.009	0.000	0.000	0.000	0.000
21	C	66	ALA	0	-0.042	0.012	28.818	0.002	0.002	0.000	0.000	0.000	0.000
22	C	67	PRO	0	-0.077	-0.033	27.956	0.003	0.003	0.000	0.000	0.000	0.000
23	C	68	ALA	0	0.050	-0.004	27.839	-0.005	-0.005	0.000	0.000	0.000	0.000
24	C	69	SER	0	-0.037	-0.027	29.850	0.005	0.005	0.000	0.000	0.000	0.000
25	C	70	ASP	-1	-0.828	-0.925	32.667	-0.040	-0.040	0.000	0.000	0.000	0.000
26	C	71	ASP	-1	-0.906	-1.008	29.990	-0.057	-0.057	0.000	0.000	0.000	0.000
27	C	72	THR	0	-0.014	-0.026	31.199	0.003	0.003	0.000	0.000	0.000	0.000
28	C	73	PRO	0	-0.084	0.060	31.317	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	74	GLU	-1	-0.862	-0.933	29.552	-0.080	-0.080	0.000	0.000	0.000	0.000
30	C	75	PHE	0	-0.035	-0.022	28.551	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	115	CYS	0	0.068	0.039	26.550	0.002	0.002	0.000	0.000	0.000	0.000
32	C	77	ALA	0	-0.016	-0.028	25.773	-0.010	-0.010	0.000	0.000	0.000	0.000
33	C	78	ALA	0	0.045	0.035	22.261	-0.014	-0.014	0.000	0.000	0.000	0.000
34	C	79	LEU	0	0.062	0.027	20.872	-0.019	-0.019	0.000	0.000	0.000	0.000
35	C	80	ARG	1	0.941	0.964	21.589	0.097	0.097	0.000	0.000	0.000	0.000
36	C	81	SER	0	-0.008	-0.008	20.182	-0.017	-0.017	0.000	0.000	0.000	0.000
37	C	82	TYR	0	0.081	0.047	13.589	-0.055	-0.055	0.000	0.000	0.000	0.000
38	C	83	ALA	0	0.049	0.019	16.453	-0.039	-0.039	0.000	0.000	0.000	0.000
39	C	84	LEU	0	-0.078	-0.033	18.041	-0.016	-0.016	0.000	0.000	0.000	0.000
40	C	86	THR	0	0.028	0.015	13.032	-0.091	-0.091	0.000	0.000	0.000	0.000
41	C	87	ARG	1	0.961	0.961	13.908	0.152	0.152	0.000	0.000	0.000	0.000
42	C	88	ARG	1	0.923	0.985	14.322	0.351	0.351	0.000	0.000	0.000	0.000
43	C	89	THR	0	-0.026	-0.022	9.066	-0.163	-0.163	0.000	0.000	0.000	0.000
44	C	90	ALA	0	0.085	0.051	10.672	-0.086	-0.086	0.000	0.000	0.000	0.000
45	C	91	ARG	1	0.925	0.951	12.523	0.290	0.290	0.000	0.000	0.000	0.000
46	C	92	THR	0	-0.059	-0.026	7.437	0.187	0.187	0.000	0.000	0.000	0.000
47	C	94	ARG	1	0.993	0.987	9.103	0.325	0.325	0.000	0.000	0.000	0.000
48	C	95	GLY	0	0.038	0.027	10.127	0.048	0.048	0.000	0.000	0.000	0.000
49	C	96	ASP	-1	-0.855	-0.918	6.565	-0.227	-0.227	0.000	0.000	0.000	0.000
50	C	97	LEU	0	0.070	0.031	9.192	-0.026	-0.026	0.000	0.000	0.000	0.000
51	C	98	ALA	0	0.045	0.026	9.419	-0.004	-0.004	0.000	0.000	0.000	0.000
52	C	99	TYR	0	-0.025	-0.024	9.750	-0.050	-0.050	0.000	0.000	0.000	0.000
53	C	100	HIS	0	-0.051	-0.043	11.397	0.010	0.010	0.000	0.000	0.000	0.000
54	C	101	SER	0	0.009	0.018	14.168	0.015	0.015	0.000	0.000	0.000	0.000
55	C	102	ALA	0	-0.003	-0.006	13.260	0.005	0.005	0.000	0.000	0.000	0.000
56	C	103	VAL	0	-0.074	-0.050	14.892	0.014	0.014	0.000	0.000	0.000	0.000
57	C	104	HIS	0	0.000	-0.003	17.206	0.021	0.021	0.000	0.000	0.000	0.000
58	C	105	GLY	0	0.046	0.046	18.543	0.013	0.013	0.000	0.000	0.000	0.000
59	C	106	ILE	0	-0.066	-0.056	16.653	0.002	0.002	0.000	0.000	0.000	0.000
60	C	107	GLU	-1	-0.951	-0.979	20.712	-0.096	-0.096	0.000	0.000	0.000	0.000
61	C	108	ASP	-1	-0.870	-0.928	23.343	-0.062	-0.062	0.000	0.000	0.000	0.000
62	C	109	LEU	0	-0.054	-0.034	21.629	0.006	0.006	0.000	0.000	0.000	0.000
63	C	110	MET	0	-0.099	-0.047	23.383	0.003	0.003	0.000	0.000	0.000	0.000
64	C	111	SER	0	0.004	-0.001	26.746	0.004	0.004	0.000	0.000	0.000	0.000
65	C	112	GLN	0	-0.043	-0.008	27.720	0.005	0.005	0.000	0.000	0.000	0.000
66	C	113	HIS	0	-0.005	-0.001	28.415	0.002	0.002	0.000	0.000	0.000	0.000
67	C	114	ASN	0	0.004	0.009	30.826	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	116	SER	0	-0.096	-0.038	29.943	-0.006	-0.006	0.000	0.000	0.000	0.000
69	C	117	NME	0	0.017	0.010	31.629	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:46:ACE )