FMO DATABASE

FMODB ID: 9G672

Calculation Name: 4UHY-C-Xray372

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: 2023-06-20

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-383063.746301
FMO2-HF: Nuclear repulsion	354623.708097
FMO2-HF: Total energy	-28440.038204
FMO2-MP2: Total energy	-28517.632817

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:47:PRO)

Summations of interaction energy for fragment #1(C:47:PRO)

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.
-0.21	1.876	0.008	-0.702	-1.394	0.001

Interaction energy analysis for fragmet #1(C:47:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.009

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	49	LYS	1	0.862	0.919	3.536	1.398	3.051	0.000	-0.582	-1.072	0.001
4	C	50	ILE	0	0.106	0.030	6.305	-0.046	-0.046	0.000	0.000	0.000	0.000
5	C	51	LEU	0	0.008	0.019	5.623	-0.039	-0.039	0.000	0.000	0.000	0.000
6	C	52	LYS	1	0.938	0.985	7.079	-1.682	-1.682	0.000	0.000	0.000	0.000
7	C	53	CYS	0	0.024	0.013	10.660	-0.121	-0.121	0.000	0.000	0.000	0.000
8	C	54	ASN	0	0.017	0.002	12.211	-0.105	-0.105	0.000	0.000	0.000	0.000
9	C	55	SER	0	-0.022	-0.020	12.927	-0.053	-0.053	0.000	0.000	0.000	0.000
10	C	56	GLU	-1	-0.944	-0.974	13.432	0.493	0.493	0.000	0.000	0.000	0.000
11	C	57	PHE	0	-0.002	-0.002	16.739	-0.046	-0.046	0.000	0.000	0.000	0.000
12	C	58	TRP	0	-0.044	-0.014	17.545	-0.030	-0.030	0.000	0.000	0.000	0.000
13	C	59	SER	0	-0.048	-0.012	19.564	0.001	0.001	0.000	0.000	0.000	0.000
14	C	60	ALA	0	0.002	-0.003	21.823	-0.019	-0.019	0.000	0.000	0.000	0.000
15	C	61	THR	0	-0.052	-0.032	22.794	-0.024	-0.024	0.000	0.000	0.000	0.000
16	C	62	SER	0	-0.001	-0.011	22.687	0.007	0.007	0.000	0.000	0.000	0.000
17	C	63	GLY	0	0.056	0.014	25.317	0.005	0.005	0.000	0.000	0.000	0.000
18	C	64	SER	0	-0.160	-0.044	27.097	0.006	0.006	0.000	0.000	0.000	0.000
19	C	65	HIS	0	0.047	0.010	27.619	0.015	0.015	0.000	0.000	0.000	0.000
20	C	66	ALA	0	0.057	0.002	29.665	-0.003	-0.003	0.000	0.000	0.000	0.000
21	C	67	PRO	0	-0.029	-0.023	29.888	-0.006	-0.006	0.000	0.000	0.000	0.000
22	C	68	ALA	0	-0.037	-0.010	32.184	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	69	SER	0	-0.112	-0.068	35.343	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	70	ASP	-1	-0.835	-0.876	33.932	0.046	0.046	0.000	0.000	0.000	0.000
25	C	71	ASP	-1	-0.899	-0.973	31.065	0.075	0.075	0.000	0.000	0.000	0.000
26	C	72	THR	0	-0.052	-0.046	31.848	-0.007	-0.007	0.000	0.000	0.000	0.000
27	C	73	PRO	0	-0.065	0.043	30.491	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	74	GLU	-1	-0.857	-0.952	29.614	0.104	0.104	0.000	0.000	0.000	0.000
29	C	75	PHE	0	-0.035	-0.022	28.544	-0.008	-0.008	0.000	0.000	0.000	0.000
30	C	76	CYS	0	0.037	0.027	26.683	0.006	0.006	0.000	0.000	0.000	0.000
31	C	77	ALA	0	-0.014	-0.027	25.531	-0.002	-0.002	0.000	0.000	0.000	0.000
32	C	78	ALA	0	0.040	0.032	22.519	0.010	0.010	0.000	0.000	0.000	0.000
33	C	79	LEU	0	0.058	0.028	21.056	0.014	0.014	0.000	0.000	0.000	0.000
34	C	80	ARG	1	0.942	0.964	21.265	-0.067	-0.067	0.000	0.000	0.000	0.000
35	C	81	SER	0	-0.009	-0.009	19.377	-0.005	-0.005	0.000	0.000	0.000	0.000
36	C	82	TYR	0	0.085	0.049	14.100	0.024	0.024	0.000	0.000	0.000	0.000
37	C	83	ALA	0	0.048	0.019	15.901	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	84	LEU	0	-0.076	-0.033	16.718	-0.030	-0.030	0.000	0.000	0.000	0.000
39	C	86	THR	0	0.027	0.015	11.802	-0.009	-0.009	0.000	0.000	0.000	0.000
40	C	87	ARG	1	0.963	0.961	12.001	-0.084	-0.084	0.000	0.000	0.000	0.000
41	C	88	ARG	1	0.928	0.988	11.499	-0.168	-0.168	0.000	0.000	0.000	0.000
42	C	89	THR	0	-0.026	-0.016	6.798	-0.052	-0.052	0.000	0.000	0.000	0.000
43	C	90	ALA	0	0.105	0.053	8.017	-0.276	-0.276	0.000	0.000	0.000	0.000
44	C	91	ARG	1	0.932	0.955	8.968	0.144	0.144	0.000	0.000	0.000	0.000
45	C	92	THR	0	-0.103	-0.046	3.574	-0.261	0.172	0.008	-0.120	-0.322	0.000
46	C	94	ARG	1	0.996	0.990	7.086	0.601	0.601	0.000	0.000	0.000	0.000
47	C	95	GLY	0	0.043	0.029	8.295	0.133	0.133	0.000	0.000	0.000	0.000
48	C	96	ASP	-1	-0.852	-0.915	6.769	-0.421	-0.421	0.000	0.000	0.000	0.000
49	C	97	LEU	0	0.073	0.033	8.968	0.099	0.099	0.000	0.000	0.000	0.000
50	C	98	ALA	0	0.046	0.027	10.217	0.050	0.050	0.000	0.000	0.000	0.000
51	C	99	TYR	0	-0.028	-0.025	9.043	0.047	0.047	0.000	0.000	0.000	0.000
52	C	100	HIS	0	-0.050	-0.044	11.036	0.047	0.047	0.000	0.000	0.000	0.000
53	C	101	SER	0	0.011	0.019	14.140	0.026	0.026	0.000	0.000	0.000	0.000
54	C	102	ALA	0	-0.004	-0.006	13.532	0.020	0.020	0.000	0.000	0.000	0.000
55	C	103	VAL	0	-0.071	-0.050	14.155	0.009	0.009	0.000	0.000	0.000	0.000
56	C	104	HIS	0	-0.001	-0.004	16.682	0.005	0.005	0.000	0.000	0.000	0.000
57	C	105	GLY	0	0.045	0.046	18.589	0.005	0.005	0.000	0.000	0.000	0.000
58	C	106	ILE	0	-0.059	-0.053	16.609	0.009	0.009	0.000	0.000	0.000	0.000
59	C	107	GLU	-1	-0.954	-0.979	20.736	-0.042	-0.042	0.000	0.000	0.000	0.000
60	C	108	ASP	-1	-0.886	-0.937	23.166	-0.007	-0.007	0.000	0.000	0.000	0.000
61	C	109	LEU	0	-0.033	-0.025	22.365	0.005	0.005	0.000	0.000	0.000	0.000
62	C	110	MET	0	-0.098	-0.051	23.112	0.005	0.005	0.000	0.000	0.000	0.000
63	C	111	SER	0	0.001	-0.003	26.662	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	112	GLN	0	-0.030	0.001	28.023	0.006	0.006	0.000	0.000	0.000	0.000
65	C	113	HIS	0	-0.031	-0.013	27.323	0.005	0.005	0.000	0.000	0.000	0.000
66	C	114	ASN	0	0.009	0.011	31.141	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	116	SER	0	-0.029	-0.008	29.072	-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:47:PRO)