FMO DATABASE

FMODB ID: N93RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-340769.848414
FMO2-HF: Nuclear repulsion	314655.540473
FMO2-HF: Total energy	-26114.307941
FMO2-MP2: Total energy	-26185.361146

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.
-1.809	0.934	-0.04	-1.355	-1.347	0.001

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 : -0.029 / q_NPA : -0.014

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	I	4	THR	0	-0.026	-0.006	3.794	-0.433	2.190	-0.038	-1.328	-1.257	0.001
4	I	5	LEU	0	0.068	0.017	6.986	-0.112	-0.112	0.000	0.000	0.000	0.000
5	I	6	CYS	0	-0.048	-0.003	9.190	-0.006	-0.006	0.000	0.000	0.000	0.000
6	I	7	GLY	0	0.040	0.009	13.804	-0.020	-0.020	0.000	0.000	0.000	0.000
7	I	8	ALA	0	0.018	-0.008	17.486	0.010	0.010	0.000	0.000	0.000	0.000
8	I	9	GLU	-1	-0.859	-0.921	14.399	-0.721	-0.721	0.000	0.000	0.000	0.000
9	I	10	LEU	0	-0.028	-0.001	12.216	0.011	0.011	0.000	0.000	0.000	0.000
10	I	11	VAL	0	-0.026	-0.023	14.665	0.047	0.047	0.000	0.000	0.000	0.000
11	I	12	ASP	-1	-0.885	-0.939	17.952	-0.282	-0.282	0.000	0.000	0.000	0.000
12	I	13	ALA	0	-0.032	-0.015	13.448	0.022	0.022	0.000	0.000	0.000	0.000
13	I	14	LEU	0	-0.040	-0.024	15.397	0.041	0.041	0.000	0.000	0.000	0.000
14	I	15	GLN	0	-0.014	-0.010	16.971	0.025	0.025	0.000	0.000	0.000	0.000
15	I	16	PHE	0	-0.023	-0.001	15.524	0.021	0.021	0.000	0.000	0.000	0.000
16	I	17	VAL	0	-0.027	-0.017	13.772	0.023	0.023	0.000	0.000	0.000	0.000
17	I	18	CYS	0	-0.122	-0.021	17.145	0.017	0.017	0.000	0.000	0.000	0.000
18	I	19	GLY	0	0.056	0.028	20.159	0.022	0.022	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.923	-0.985	23.034	-0.091	-0.091	0.000	0.000	0.000	0.000
20	I	21	ARG	1	0.789	0.906	20.714	0.032	0.032	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.049	0.041	23.771	0.007	0.007	0.000	0.000	0.000	0.000
22	I	23	PHE	0	-0.009	-0.022	19.856	0.008	0.008	0.000	0.000	0.000	0.000
23	I	24	TYR	0	-0.017	0.000	21.200	0.002	0.002	0.000	0.000	0.000	0.000
24	I	25	PHE	0	0.045	0.007	19.258	0.001	0.001	0.000	0.000	0.000	0.000
25	I	26	ASN	0	-0.043	-0.032	19.603	0.014	0.014	0.000	0.000	0.000	0.000
26	I	27	LYS	1	0.907	0.974	17.139	-0.185	-0.185	0.000	0.000	0.000	0.000
27	I	28	PRO	0	0.011	0.062	21.905	0.016	0.016	0.000	0.000	0.000	0.000
28	I	29	THR	0	0.037	0.062	21.550	0.023	0.023	0.000	0.000	0.000	0.000
29	I	30	GLY	0	0.013	0.011	23.442	-0.009	-0.009	0.000	0.000	0.000	0.000
30	I	31	TYR	0	0.032	0.035	26.138	-0.007	-0.007	0.000	0.000	0.000	0.000
31	I	32	GLY	0	0.014	0.009	28.967	-0.009	-0.009	0.000	0.000	0.000	0.000
32	I	33	SER	0	-0.203	-0.006	24.999	-0.002	-0.002	0.000	0.000	0.000	0.000
33	I	34	SER	0	0.048	-0.018	21.561	0.008	0.008	0.000	0.000	0.000	0.000
34	I	35	SER	0	0.291	0.165	20.896	0.019	0.019	0.000	0.000	0.000	0.000
35	I	36	ARG	1	0.883	0.782	23.065	-0.108	-0.108	0.000	0.000	0.000	0.000
36	I	37	ARG	0	-0.109	-0.049	27.027	0.006	0.006	0.000	0.000	0.000	0.000
37	I	38	ALA	0	0.075	0.154	27.244	0.006	0.006	0.000	0.000	0.000	0.000
38	I	39	PRO	0	-0.059	-0.172	24.845	-0.014	-0.014	0.000	0.000	0.000	0.000
39	I	40	GLN	0	0.018	-0.037	22.680	0.004	0.004	0.000	0.000	0.000	0.000
40	I	41	THR	0	-0.058	-0.015	17.023	0.023	0.023	0.000	0.000	0.000	0.000
41	I	42	GLY	0	0.102	0.043	17.556	-0.015	-0.015	0.000	0.000	0.000	0.000
42	I	43	ILE	0	0.017	0.013	12.541	0.017	0.017	0.000	0.000	0.000	0.000
43	I	44	VAL	0	0.030	0.006	13.613	-0.041	-0.041	0.000	0.000	0.000	0.000
44	I	45	ASP	-1	-0.910	-0.956	13.924	-0.059	-0.059	0.000	0.000	0.000	0.000
45	I	46	GLU	-1	-0.890	-0.927	11.197	0.238	0.238	0.000	0.000	0.000	0.000
46	I	47	CYS	0	-0.051	-0.015	5.601	0.398	0.398	0.000	0.000	0.000	0.000
47	I	49	PHE	0	-0.013	-0.014	10.457	-0.088	-0.088	0.000	0.000	0.000	0.000
48	I	50	ARG	1	0.853	0.942	8.510	-0.067	-0.067	0.000	0.000	0.000	0.000
49	I	51	SER	0	0.030	0.012	4.237	-0.193	-0.082	-0.001	-0.021	-0.088	0.000
50	I	53	ASP	-1	-0.794	-0.891	5.139	0.056	0.065	-0.001	-0.006	-0.002	0.000
51	I	54	LEU	0	0.076	0.015	7.113	0.115	0.115	0.000	0.000	0.000	0.000
52	I	55	ARG	1	0.851	0.918	9.803	-0.165	-0.165	0.000	0.000	0.000	0.000
53	I	56	ARG	1	0.796	0.882	7.920	-0.520	-0.520	0.000	0.000	0.000	0.000
54	I	57	LEU	0	0.036	0.000	10.758	-0.004	-0.004	0.000	0.000	0.000	0.000
55	I	58	GLU	-1	-0.796	-0.886	13.383	0.060	0.060	0.000	0.000	0.000	0.000
56	I	59	MET	0	-0.159	-0.066	13.610	0.021	0.021	0.000	0.000	0.000	0.000
57	I	60	TYR	0	-0.048	-0.040	15.112	0.012	0.012	0.000	0.000	0.000	0.000
58	I	62	ALA	0	0.003	0.011	20.502	0.023	0.023	0.000	0.000	0.000	0.000
59	I	63	PRO	0	-0.037	-0.017	24.273	-0.002	-0.002	0.000	0.000	0.000	0.000
60	I	64	LEU	0	0.028	0.019	25.379	-0.004	-0.004	0.000	0.000	0.000	0.000

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