FMO DATABASE

FMODB ID: M378Z

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	OptHSide
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	-383807.164864
FMO2-HF: Nuclear repulsion	355366.794544
FMO2-HF: Total energy	-28440.37032
FMO2-MP2: Total energy	-28517.948204

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.
-0.373	1.77	-0.004	-0.754	-1.385	0.002

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 : 0.055 / q_NPA : 0.008

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	49	LYS	1	0.866	0.916	3.617	0.961	2.692	-0.008	-0.642	-1.081	0.002
4	C	50	ILE	0	0.097	0.030	6.260	-0.154	-0.154	0.000	0.000	0.000	0.000
5	C	51	LEU	0	0.017	0.024	6.236	-0.128	-0.128	0.000	0.000	0.000	0.000
6	C	52	LYS	1	0.930	0.985	7.427	-1.422	-1.422	0.000	0.000	0.000	0.000
7	C	53	CYS	0	0.005	0.013	10.595	-0.132	-0.132	0.000	0.000	0.000	0.000
8	C	54	ASN	0	0.028	0.017	12.476	-0.133	-0.133	0.000	0.000	0.000	0.000
9	C	55	SER	0	-0.013	-0.023	12.958	-0.068	-0.068	0.000	0.000	0.000	0.000
10	C	56	GLU	-1	-0.933	-0.971	12.965	0.536	0.536	0.000	0.000	0.000	0.000
11	C	57	PHE	0	0.006	0.000	16.675	-0.052	-0.052	0.000	0.000	0.000	0.000
12	C	58	TRP	0	-0.031	-0.011	17.884	-0.035	-0.035	0.000	0.000	0.000	0.000
13	C	59	SER	0	-0.049	-0.011	19.571	-0.006	-0.006	0.000	0.000	0.000	0.000
14	C	60	ALA	0	-0.004	-0.006	21.759	-0.020	-0.020	0.000	0.000	0.000	0.000
15	C	61	THR	0	-0.043	-0.025	22.913	-0.026	-0.026	0.000	0.000	0.000	0.000
16	C	62	SER	0	-0.010	-0.016	22.950	0.012	0.012	0.000	0.000	0.000	0.000
17	C	63	GLY	0	0.047	0.009	25.536	0.006	0.006	0.000	0.000	0.000	0.000
18	C	64	SER	0	-0.167	-0.042	27.236	0.004	0.004	0.000	0.000	0.000	0.000
19	C	65	HIS	0	0.034	-0.006	27.798	0.014	0.014	0.000	0.000	0.000	0.000
20	C	66	ALA	0	0.052	-0.001	29.806	-0.004	-0.004	0.000	0.000	0.000	0.000
21	C	67	PRO	0	-0.026	-0.024	30.085	-0.005	-0.005	0.000	0.000	0.000	0.000
22	C	68	ALA	0	-0.038	-0.010	32.201	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	69	SER	0	-0.110	-0.066	35.385	-0.005	-0.005	0.000	0.000	0.000	0.000
24	C	70	ASP	-1	-0.828	-0.871	34.010	0.066	0.066	0.000	0.000	0.000	0.000
25	C	71	ASP	-1	-0.872	-0.954	30.406	0.101	0.101	0.000	0.000	0.000	0.000
26	C	72	THR	0	-0.054	-0.044	31.612	-0.007	-0.007	0.000	0.000	0.000	0.000
27	C	73	PRO	0	-0.074	0.033	30.470	-0.005	-0.005	0.000	0.000	0.000	0.000
28	C	74	GLU	-1	-0.836	-0.943	29.466	0.119	0.119	0.000	0.000	0.000	0.000
29	C	75	PHE	0	-0.050	-0.034	28.654	-0.008	-0.008	0.000	0.000	0.000	0.000
30	C	76	CYS	0	0.079	0.063	26.699	0.004	0.004	0.000	0.000	0.000	0.000
31	C	77	ALA	0	0.000	-0.015	25.506	0.000	0.000	0.000	0.000	0.000	0.000
32	C	78	ALA	0	0.060	0.055	22.470	0.011	0.011	0.000	0.000	0.000	0.000
33	C	79	LEU	0	0.060	0.026	21.008	0.019	0.019	0.000	0.000	0.000	0.000
34	C	80	ARG	1	0.935	0.962	21.265	-0.084	-0.084	0.000	0.000	0.000	0.000
35	C	81	SER	0	-0.019	-0.030	19.297	0.000	0.000	0.000	0.000	0.000	0.000
36	C	82	TYR	0	0.047	0.020	14.134	0.028	0.028	0.000	0.000	0.000	0.000
37	C	83	ALA	0	0.066	0.028	15.901	0.010	0.010	0.000	0.000	0.000	0.000
38	C	84	LEU	0	-0.072	-0.025	16.718	-0.025	-0.025	0.000	0.000	0.000	0.000
39	C	86	THR	0	0.038	0.018	11.800	0.007	0.007	0.000	0.000	0.000	0.000
40	C	87	ARG	1	0.944	0.944	12.001	-0.119	-0.119	0.000	0.000	0.000	0.000
41	C	88	ARG	1	0.926	0.988	11.290	-0.188	-0.188	0.000	0.000	0.000	0.000
42	C	89	THR	0	-0.025	-0.027	6.839	-0.055	-0.055	0.000	0.000	0.000	0.000
43	C	90	ALA	0	0.084	0.044	8.039	-0.197	-0.197	0.000	0.000	0.000	0.000
44	C	91	ARG	1	0.931	0.957	9.072	0.113	0.113	0.000	0.000	0.000	0.000
45	C	92	THR	0	-0.078	-0.037	3.686	-0.294	0.118	0.004	-0.112	-0.304	0.000
46	C	94	ARG	1	0.984	0.986	7.180	0.467	0.467	0.000	0.000	0.000	0.000
47	C	95	GLY	0	0.043	0.030	8.405	0.101	0.101	0.000	0.000	0.000	0.000
48	C	96	ASP	-1	-0.865	-0.920	6.829	0.085	0.085	0.000	0.000	0.000	0.000
49	C	97	LEU	0	0.078	0.033	9.049	0.061	0.061	0.000	0.000	0.000	0.000
50	C	98	ALA	0	0.053	0.028	10.352	0.020	0.020	0.000	0.000	0.000	0.000
51	C	99	TYR	0	-0.021	-0.026	9.259	0.022	0.022	0.000	0.000	0.000	0.000
52	C	100	HIS	0	-0.034	-0.025	11.224	0.009	0.009	0.000	0.000	0.000	0.000
53	C	101	SER	0	0.039	0.030	14.307	0.001	0.001	0.000	0.000	0.000	0.000
54	C	102	ALA	0	-0.031	-0.017	13.699	0.005	0.005	0.000	0.000	0.000	0.000
55	C	103	VAL	0	-0.063	-0.042	14.419	-0.006	-0.006	0.000	0.000	0.000	0.000
56	C	104	HIS	0	-0.020	-0.017	16.881	-0.013	-0.013	0.000	0.000	0.000	0.000
57	C	105	GLY	0	0.027	0.032	18.791	-0.003	-0.003	0.000	0.000	0.000	0.000
58	C	106	ILE	0	-0.050	-0.046	16.886	0.000	0.000	0.000	0.000	0.000	0.000
59	C	107	GLU	-1	-0.956	-0.974	20.965	0.011	0.011	0.000	0.000	0.000	0.000
60	C	108	ASP	-1	-0.851	-0.926	23.376	0.041	0.041	0.000	0.000	0.000	0.000
61	C	109	LEU	0	-0.052	-0.027	22.721	0.000	0.000	0.000	0.000	0.000	0.000
62	C	110	MET	0	-0.100	-0.051	22.671	0.001	0.001	0.000	0.000	0.000	0.000
63	C	111	SER	0	0.011	0.005	26.860	-0.004	-0.004	0.000	0.000	0.000	0.000
64	C	112	GLN	0	-0.042	-0.012	28.083	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	113	HIS	0	-0.014	-0.009	27.585	0.004	0.004	0.000	0.000	0.000	0.000
66	C	114	ASN	0	-0.029	-0.004	31.385	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	116	SER	0	-0.064	-0.035	29.140	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:47:PRO)