FMO DATABASE

FMODB ID: 7GRNK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-385643.363026
FMO2-HF: Nuclear repulsion	357202.618959
FMO2-HF: Total energy	-28440.744067
FMO2-MP2: Total energy	-28518.249626

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.
1.377	3.38	-0.005	-0.753	-1.245	0.003

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 : 0.058 / 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

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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	0.878	0.912	3.615	1.434	3.119	-0.009	-0.686	-0.990	0.003
4	C	50	ILE	0	0.071	0.016	6.126	-0.019	-0.019	0.000	0.000	0.000	0.000
5	C	51	LEU	0	0.010	0.018	6.627	-0.140	-0.140	0.000	0.000	0.000	0.000
6	C	52	LYS	1	0.929	0.991	7.730	-0.739	-0.739	0.000	0.000	0.000	0.000
7	C	53	CYS	0	-0.027	0.002	10.557	-0.106	-0.106	0.000	0.000	0.000	0.000
8	C	54	ASN	0	0.059	0.038	12.472	-0.122	-0.122	0.000	0.000	0.000	0.000
9	C	55	SER	0	-0.003	-0.007	12.848	-0.063	-0.063	0.000	0.000	0.000	0.000
10	C	56	GLU	-1	-0.906	-0.968	13.081	0.324	0.324	0.000	0.000	0.000	0.000
11	C	57	PHE	0	-0.007	-0.005	16.375	-0.041	-0.041	0.000	0.000	0.000	0.000
12	C	58	TRP	0	0.017	0.003	18.069	-0.030	-0.030	0.000	0.000	0.000	0.000
13	C	59	SER	0	-0.073	-0.029	18.806	-0.016	-0.016	0.000	0.000	0.000	0.000
14	C	60	ALA	0	-0.027	-0.008	21.239	-0.019	-0.019	0.000	0.000	0.000	0.000
15	C	61	THR	0	-0.089	-0.050	22.488	-0.024	-0.024	0.000	0.000	0.000	0.000
16	C	62	SER	0	0.010	-0.012	22.739	0.014	0.014	0.000	0.000	0.000	0.000
17	C	63	GLY	0	0.029	-0.001	25.278	0.009	0.009	0.000	0.000	0.000	0.000
18	C	64	SER	0	-0.117	-0.026	26.955	0.005	0.005	0.000	0.000	0.000	0.000
19	C	65	HIS	0	0.018	0.009	27.485	0.008	0.008	0.000	0.000	0.000	0.000
20	C	66	ALA	0	0.047	0.002	29.481	-0.005	-0.005	0.000	0.000	0.000	0.000
21	C	67	PRO	0	-0.024	-0.027	29.569	-0.003	-0.003	0.000	0.000	0.000	0.000
22	C	68	ALA	0	-0.029	-0.006	31.770	0.001	0.001	0.000	0.000	0.000	0.000
23	C	69	SER	0	-0.112	-0.067	35.082	-0.005	-0.005	0.000	0.000	0.000	0.000
24	C	70	ASP	-1	-0.838	-0.878	33.902	0.068	0.068	0.000	0.000	0.000	0.000
25	C	71	ASP	-1	-0.864	-0.941	30.458	0.093	0.093	0.000	0.000	0.000	0.000
26	C	72	THR	0	-0.041	-0.026	31.164	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	73	PRO	0	-0.106	-0.017	29.967	-0.004	-0.004	0.000	0.000	0.000	0.000
28	C	74	GLU	-1	-0.826	-0.931	29.462	0.088	0.088	0.000	0.000	0.000	0.000
29	C	75	PHE	0	-0.037	-0.024	28.675	-0.006	-0.006	0.000	0.000	0.000	0.000
30	C	76	CYS	0	0.051	0.037	26.704	0.003	0.003	0.000	0.000	0.000	0.000
31	C	77	ALA	0	0.005	-0.003	25.421	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	78	ALA	0	0.081	0.056	22.015	0.002	0.002	0.000	0.000	0.000	0.000
33	C	79	LEU	0	0.058	0.031	20.748	0.011	0.011	0.000	0.000	0.000	0.000
34	C	80	ARG	1	0.947	0.969	20.904	-0.052	-0.052	0.000	0.000	0.000	0.000
35	C	81	SER	0	-0.022	-0.024	19.061	-0.003	-0.003	0.000	0.000	0.000	0.000
36	C	82	TYR	0	0.037	0.007	13.994	0.015	0.015	0.000	0.000	0.000	0.000
37	C	83	ALA	0	0.072	0.033	15.961	0.003	0.003	0.000	0.000	0.000	0.000
38	C	84	LEU	0	-0.073	-0.018	17.008	-0.027	-0.027	0.000	0.000	0.000	0.000
39	C	86	THR	0	0.041	0.014	11.963	-0.034	-0.034	0.000	0.000	0.000	0.000
40	C	87	ARG	1	0.924	0.932	12.027	-0.083	-0.083	0.000	0.000	0.000	0.000
41	C	88	ARG	1	0.922	0.974	11.554	-0.034	-0.034	0.000	0.000	0.000	0.000
42	C	89	THR	0	0.005	-0.013	6.994	-0.100	-0.100	0.000	0.000	0.000	0.000
43	C	90	ALA	0	0.080	0.055	7.821	-0.209	-0.209	0.000	0.000	0.000	0.000
44	C	91	ARG	1	0.929	0.953	9.105	0.182	0.182	0.000	0.000	0.000	0.000
45	C	92	THR	0	-0.083	-0.041	3.570	-0.298	0.020	0.004	-0.067	-0.255	0.000
46	C	94	ARG	1	0.970	0.983	7.308	0.460	0.460	0.000	0.000	0.000	0.000
47	C	95	GLY	0	0.048	0.033	8.379	0.051	0.051	0.000	0.000	0.000	0.000
48	C	96	ASP	-1	-0.872	-0.925	6.435	1.008	1.008	0.000	0.000	0.000	0.000
49	C	97	LEU	0	0.060	0.024	8.394	-0.019	-0.019	0.000	0.000	0.000	0.000
50	C	98	ALA	0	0.040	0.025	10.129	-0.039	-0.039	0.000	0.000	0.000	0.000
51	C	99	TYR	0	-0.008	-0.029	9.372	-0.057	-0.057	0.000	0.000	0.000	0.000
52	C	100	HIS	0	-0.040	-0.029	11.235	-0.068	-0.068	0.000	0.000	0.000	0.000
53	C	101	SER	0	0.025	0.024	14.075	-0.021	-0.021	0.000	0.000	0.000	0.000
54	C	102	ALA	0	-0.014	0.000	13.852	-0.014	-0.014	0.000	0.000	0.000	0.000
55	C	103	VAL	0	-0.051	-0.031	14.470	-0.021	-0.021	0.000	0.000	0.000	0.000
56	C	104	HIS	0	0.001	-0.012	16.985	-0.022	-0.022	0.000	0.000	0.000	0.000
57	C	105	GLY	0	0.047	0.033	19.038	-0.007	-0.007	0.000	0.000	0.000	0.000
58	C	106	ILE	0	-0.044	-0.034	16.764	-0.006	-0.006	0.000	0.000	0.000	0.000
59	C	107	GLU	-1	-0.970	-0.976	20.971	0.023	0.023	0.000	0.000	0.000	0.000
60	C	108	ASP	-1	-0.843	-0.919	23.287	0.069	0.069	0.000	0.000	0.000	0.000
61	C	109	LEU	0	-0.042	-0.015	22.609	-0.004	-0.004	0.000	0.000	0.000	0.000
62	C	110	MET	0	-0.085	-0.052	22.532	-0.006	-0.006	0.000	0.000	0.000	0.000
63	C	111	SER	0	-0.012	-0.008	26.515	-0.008	-0.008	0.000	0.000	0.000	0.000
64	C	112	GLN	0	-0.029	-0.010	27.623	-0.003	-0.003	0.000	0.000	0.000	0.000
65	C	113	HIS	0	-0.030	-0.020	27.264	0.003	0.003	0.000	0.000	0.000	0.000
66	C	114	ASN	0	-0.034	-0.011	30.906	-0.006	-0.006	0.000	0.000	0.000	0.000
67	C	116	SER	0	-0.080	-0.036	29.102	-0.008	-0.008	0.000	0.000	0.000	0.000

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