FMO DATABASE

FMODB ID: 85J1Y

Calculation Name: 2DSR-I-Xray372

Preferred Name: Insulin-like growth factor binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DSR

Chain ID: I

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

Base Structure: X-ray

Registration Date: 2023-06-21

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-340621.686203
FMO2-HF: Nuclear repulsion	314507.913351
FMO2-HF: Total energy	-26113.772853
FMO2-MP2: Total energy	-26184.871428

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(I:2:PRO)

Summations of interaction energy for fragment #1(I:2: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.
-1.537	1.158	-0.04	-1.333	-1.322	0.002

Interaction energy analysis for fragmet #1(I:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.013

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	I	4	THR	0	-0.029	-0.009	3.794	-0.345	2.230	-0.038	-1.307	-1.229	0.002
4	I	5	LEU	0	0.074	0.022	7.016	-0.130	-0.130	0.000	0.000	0.000	0.000
5	I	6	CYS	0	-0.043	0.001	9.227	0.003	0.003	0.000	0.000	0.000	0.000
6	I	7	GLY	0	0.029	0.002	13.838	-0.024	-0.024	0.000	0.000	0.000	0.000
7	I	8	ALA	0	0.018	-0.006	17.492	0.011	0.011	0.000	0.000	0.000	0.000
8	I	9	GLU	-1	-0.855	-0.920	14.251	-0.685	-0.685	0.000	0.000	0.000	0.000
9	I	10	LEU	0	-0.038	-0.007	12.318	0.009	0.009	0.000	0.000	0.000	0.000
10	I	11	VAL	0	-0.030	-0.023	14.670	0.045	0.045	0.000	0.000	0.000	0.000
11	I	12	ASP	-1	-0.882	-0.943	18.012	-0.264	-0.264	0.000	0.000	0.000	0.000
12	I	13	ALA	0	-0.027	-0.012	13.463	0.018	0.018	0.000	0.000	0.000	0.000
13	I	14	LEU	0	-0.038	-0.026	15.388	0.039	0.039	0.000	0.000	0.000	0.000
14	I	15	GLN	0	-0.010	-0.004	16.977	0.019	0.019	0.000	0.000	0.000	0.000
15	I	16	PHE	0	-0.013	-0.001	15.333	0.018	0.018	0.000	0.000	0.000	0.000
16	I	17	VAL	0	-0.028	-0.017	13.768	0.021	0.021	0.000	0.000	0.000	0.000
17	I	18	CYS	0	-0.120	-0.021	17.144	0.015	0.015	0.000	0.000	0.000	0.000
18	I	19	GLY	0	0.046	0.024	20.162	0.020	0.020	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.930	-0.991	23.034	-0.081	-0.081	0.000	0.000	0.000	0.000
20	I	21	ARG	1	0.807	0.920	20.539	0.025	0.025	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.045	0.041	23.779	0.008	0.008	0.000	0.000	0.000	0.000
22	I	23	PHE	0	-0.009	-0.022	19.862	0.008	0.008	0.000	0.000	0.000	0.000
23	I	24	TYR	0	-0.019	0.003	21.207	0.001	0.001	0.000	0.000	0.000	0.000
24	I	25	PHE	0	0.040	0.004	19.219	0.003	0.003	0.000	0.000	0.000	0.000
25	I	26	ASN	0	-0.039	-0.024	19.627	0.019	0.019	0.000	0.000	0.000	0.000
26	I	27	LYS	1	0.933	0.988	17.276	-0.221	-0.221	0.000	0.000	0.000	0.000
27	I	28	PRO	0	0.035	0.081	21.959	0.017	0.017	0.000	0.000	0.000	0.000
28	I	29	THR	0	0.032	0.077	21.627	0.030	0.030	0.000	0.000	0.000	0.000
29	I	30	GLY	0	0.021	0.016	23.490	-0.011	-0.011	0.000	0.000	0.000	0.000
30	I	31	TYR	0	0.042	0.021	26.186	-0.009	-0.009	0.000	0.000	0.000	0.000
31	I	32	GLY	0	0.032	0.016	28.996	-0.009	-0.009	0.000	0.000	0.000	0.000
32	I	33	SER	0	-0.167	0.068	24.812	-0.004	-0.004	0.000	0.000	0.000	0.000
33	I	34	SER	0	0.023	-0.036	21.545	0.004	0.004	0.000	0.000	0.000	0.000
34	I	35	SER	0	0.317	0.233	20.914	0.017	0.017	0.000	0.000	0.000	0.000
35	I	36	ARG	1	1.020	0.880	22.702	-0.127	-0.127	0.000	0.000	0.000	0.000
36	I	37	ARG	0	-0.285	-0.261	26.907	-0.001	-0.001	0.000	0.000	0.000	0.000
37	I	38	ALA	0	-0.011	-0.018	28.121	-0.001	-0.001	0.000	0.000	0.000	0.000
38	I	39	PRO	0	-0.074	-0.087	25.055	-0.006	-0.006	0.000	0.000	0.000	0.000
39	I	40	GLN	0	0.031	-0.005	22.632	0.003	0.003	0.000	0.000	0.000	0.000
40	I	41	THR	0	-0.043	-0.009	17.032	0.020	0.020	0.000	0.000	0.000	0.000
41	I	42	GLY	0	0.105	0.045	17.606	-0.019	-0.019	0.000	0.000	0.000	0.000
42	I	43	ILE	0	-0.005	0.000	12.551	0.024	0.024	0.000	0.000	0.000	0.000
43	I	44	VAL	0	0.035	0.008	13.666	-0.031	-0.031	0.000	0.000	0.000	0.000
44	I	45	ASP	-1	-0.900	-0.952	13.961	-0.017	-0.017	0.000	0.000	0.000	0.000
45	I	46	GLU	-1	-0.926	-0.982	11.275	0.288	0.288	0.000	0.000	0.000	0.000
46	I	47	CYS	0	-0.047	-0.013	5.639	0.323	0.323	0.000	0.000	0.000	0.000
47	I	49	PHE	0	-0.010	-0.011	10.469	-0.086	-0.086	0.000	0.000	0.000	0.000
48	I	50	ARG	1	0.851	0.945	8.523	-0.158	-0.158	0.000	0.000	0.000	0.000
49	I	51	SER	0	0.031	0.006	4.341	-0.198	-0.094	-0.001	-0.020	-0.084	0.000
50	I	53	ASP	-1	-0.807	-0.909	5.154	0.476	0.492	-0.001	-0.006	-0.009	0.000
51	I	54	LEU	0	0.075	0.019	7.124	0.105	0.105	0.000	0.000	0.000	0.000
52	I	55	ARG	1	0.906	0.967	9.833	-0.195	-0.195	0.000	0.000	0.000	0.000
53	I	56	ARG	1	0.826	0.911	8.397	-0.572	-0.572	0.000	0.000	0.000	0.000
54	I	57	LEU	0	0.042	0.004	10.789	-0.008	-0.008	0.000	0.000	0.000	0.000
55	I	58	GLU	-1	-0.860	-0.940	13.397	0.035	0.035	0.000	0.000	0.000	0.000
56	I	59	MET	0	-0.166	-0.064	13.434	0.019	0.019	0.000	0.000	0.000	0.000
57	I	60	TYR	0	-0.038	-0.011	15.146	0.006	0.006	0.000	0.000	0.000	0.000
58	I	62	ALA	0	0.005	0.008	20.515	0.023	0.023	0.000	0.000	0.000	0.000
59	I	63	PRO	0	-0.040	-0.022	24.287	-0.003	-0.003	0.000	0.000	0.000	0.000
60	I	64	LEU	0	0.027	0.019	25.689	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(I:2:PRO)