FMO DATABASE

FMODB ID: JLM89

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

Total energy (hartree)

FMO2-HF: Electronic energy	-341775.287744
FMO2-HF: Nuclear repulsion	315658.919325
FMO2-HF: Total energy	-26116.368419
FMO2-MP2: Total energy	-26187.172584

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.
-0.819	1.415	-0.022	-1.125	-1.086	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 : -0.022 / q_NPA : -0.012

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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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	-0.025	-0.015	3.865	0.005	2.146	-0.021	-1.113	-1.007	0.002
4	I	5	LEU	0	0.064	0.020	7.111	-0.102	-0.102	0.000	0.000	0.000	0.000
5	I	6	CYS	0	-0.042	-0.004	9.458	-0.016	-0.016	0.000	0.000	0.000	0.000
6	I	7	GLY	0	0.051	0.010	14.080	-0.008	-0.008	0.000	0.000	0.000	0.000
7	I	8	ALA	0	0.008	-0.006	17.873	0.011	0.011	0.000	0.000	0.000	0.000
8	I	9	GLU	-1	-0.857	-0.923	14.987	-0.680	-0.680	0.000	0.000	0.000	0.000
9	I	10	LEU	0	-0.031	0.000	12.532	-0.011	-0.011	0.000	0.000	0.000	0.000
10	I	11	VAL	0	-0.030	-0.022	15.176	0.049	0.049	0.000	0.000	0.000	0.000
11	I	12	ASP	-1	-0.886	-0.940	17.958	-0.297	-0.297	0.000	0.000	0.000	0.000
12	I	13	ALA	0	-0.022	-0.012	13.424	0.024	0.024	0.000	0.000	0.000	0.000
13	I	14	LEU	0	-0.035	-0.022	15.563	0.039	0.039	0.000	0.000	0.000	0.000
14	I	15	GLN	0	-0.029	-0.018	17.124	0.025	0.025	0.000	0.000	0.000	0.000
15	I	16	PHE	0	-0.032	-0.008	15.660	0.022	0.022	0.000	0.000	0.000	0.000
16	I	17	VAL	0	-0.025	-0.016	13.693	0.022	0.022	0.000	0.000	0.000	0.000
17	I	18	CYS	0	-0.116	-0.017	17.097	0.021	0.021	0.000	0.000	0.000	0.000
18	I	19	GLY	0	0.065	0.029	20.282	0.023	0.023	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.929	-0.987	23.127	-0.095	-0.095	0.000	0.000	0.000	0.000
20	I	21	ARG	1	0.786	0.906	20.382	0.037	0.037	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.035	0.034	24.001	0.008	0.008	0.000	0.000	0.000	0.000
22	I	23	PHE	0	-0.015	-0.030	20.093	0.006	0.006	0.000	0.000	0.000	0.000
23	I	24	TYR	0	-0.016	0.000	21.291	0.003	0.003	0.000	0.000	0.000	0.000
24	I	25	PHE	0	0.041	0.008	19.426	0.002	0.002	0.000	0.000	0.000	0.000
25	I	26	ASN	0	-0.046	-0.031	19.392	0.008	0.008	0.000	0.000	0.000	0.000
26	I	27	LYS	1	0.916	0.976	17.031	-0.165	-0.165	0.000	0.000	0.000	0.000
27	I	28	PRO	0	0.018	0.022	21.374	0.014	0.014	0.000	0.000	0.000	0.000
28	I	29	THR	0	-0.060	-0.025	21.097	0.027	0.027	0.000	0.000	0.000	0.000
29	I	30	GLY	0	0.088	0.049	23.363	-0.003	-0.003	0.000	0.000	0.000	0.000
30	I	31	TYR	0	-0.057	-0.053	26.179	-0.004	-0.004	0.000	0.000	0.000	0.000
31	I	32	GLY	0	0.031	0.022	29.348	-0.007	-0.007	0.000	0.000	0.000	0.000
32	I	33	SER	0	-0.071	-0.041	26.020	-0.009	-0.009	0.000	0.000	0.000	0.000
33	I	34	SER	0	0.102	0.055	21.108	0.011	0.011	0.000	0.000	0.000	0.000
34	I	35	SER	0	0.002	-0.028	21.274	0.014	0.014	0.000	0.000	0.000	0.000
35	I	36	ARG	1	0.889	0.938	23.558	-0.091	-0.091	0.000	0.000	0.000	0.000
36	I	37	ARG	0	0.046	0.041	27.001	0.011	0.011	0.000	0.000	0.000	0.000
37	I	38	ALA	0	-0.008	-0.010	25.980	-0.007	-0.007	0.000	0.000	0.000	0.000
38	I	39	PRO	0	0.025	0.032	24.634	-0.007	-0.007	0.000	0.000	0.000	0.000
39	I	40	GLN	0	-0.002	-0.024	22.059	0.002	0.002	0.000	0.000	0.000	0.000
40	I	41	THR	0	0.000	0.013	16.599	0.027	0.027	0.000	0.000	0.000	0.000
41	I	42	GLY	0	0.100	0.039	17.123	-0.013	-0.013	0.000	0.000	0.000	0.000
42	I	43	ILE	0	0.008	0.020	12.508	0.004	0.004	0.000	0.000	0.000	0.000
43	I	44	VAL	0	0.039	0.008	13.605	-0.054	-0.054	0.000	0.000	0.000	0.000
44	I	45	ASP	-1	-0.803	-0.886	14.100	-0.078	-0.078	0.000	0.000	0.000	0.000
45	I	46	GLU	-1	-0.878	-0.908	10.965	0.217	0.217	0.000	0.000	0.000	0.000
46	I	47	CYS	0	-0.093	-0.008	5.710	0.312	0.312	0.000	0.000	0.000	0.000
47	I	49	PHE	0	-0.025	-0.014	11.153	-0.075	-0.075	0.000	0.000	0.000	0.000
48	I	50	ARG	1	0.752	0.863	8.853	0.009	0.009	0.000	0.000	0.000	0.000
49	I	51	SER	0	0.021	-0.010	4.513	0.345	0.438	-0.001	-0.012	-0.079	0.000
50	I	53	ASP	-1	-0.750	-0.872	5.239	-0.012	-0.012	0.000	0.000	0.000	0.000
51	I	54	LEU	0	0.059	0.016	7.073	0.145	0.145	0.000	0.000	0.000	0.000
52	I	55	ARG	1	0.844	0.902	9.759	-0.136	-0.136	0.000	0.000	0.000	0.000
53	I	56	ARG	1	0.771	0.857	7.325	-0.527	-0.527	0.000	0.000	0.000	0.000
54	I	57	LEU	0	0.038	0.010	11.258	0.003	0.003	0.000	0.000	0.000	0.000
55	I	58	GLU	-1	-0.766	-0.872	13.560	0.079	0.079	0.000	0.000	0.000	0.000
56	I	59	MET	0	-0.150	-0.063	13.405	0.022	0.022	0.000	0.000	0.000	0.000
57	I	60	TYR	0	-0.035	-0.036	15.015	0.012	0.012	0.000	0.000	0.000	0.000
58	I	62	ALA	0	0.009	0.014	20.396	0.024	0.024	0.000	0.000	0.000	0.000
59	I	63	PRO	0	-0.028	-0.014	24.066	0.001	0.001	0.000	0.000	0.000	0.000
60	I	64	LEU	0	0.016	0.016	25.301	-0.006	-0.006	0.000	0.000	0.000	0.000

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