FMO DATABASE

FMODB ID: VRN91

Calculation Name: 2DSQ-H-Xray372

Preferred Name: Insulin-like growth factor binding protein 1

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 2DSQ

Chain ID: H

ChEMBL ID: CHEMBL4178

UniProt ID: P08833

Base Structure: X-ray

Registration Date: 2023-03-13

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-328090.546569
FMO2-HF: Nuclear repulsion	302993.282358
FMO2-HF: Total energy	-25097.264211
FMO2-MP2: Total energy	-25166.510293

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(H:148:LYS)

Summations of interaction energy for fragment #1(H:148:LYS)

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.
70.648	76.512	0.617	-2.141	-4.337	-0.004

Interaction energy analysis for fragmet #1(H:148:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.979 / q_NPA : 0.997

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	H	150	PRO	0	-0.022	-0.007	2.852	-6.636	-2.896	0.177	-1.406	-2.511	0.001
4	H	151	CYS	0	0.036	0.034	4.124	2.406	2.625	0.001	-0.029	-0.190	0.000
5	H	152	ARG	1	0.866	0.912	5.579	36.571	36.571	0.000	0.000	0.000	0.000
6	H	153	ILE	0	-0.078	-0.037	2.585	-1.668	-0.687	0.241	-0.327	-0.894	-0.004
7	H	154	GLU	-1	-0.852	-0.908	6.068	-22.882	-22.882	0.000	0.000	0.000	0.000
8	H	155	LEU	0	0.013	-0.002	9.038	2.880	2.880	0.000	0.000	0.000	0.000
9	H	156	TYR	0	-0.016	-0.002	8.148	1.127	1.127	0.000	0.000	0.000	0.000
10	H	157	ARG	1	0.997	0.995	6.382	36.150	36.150	0.000	0.000	0.000	0.000
11	H	158	VAL	0	-0.005	0.011	11.412	1.878	1.878	0.000	0.000	0.000	0.000
12	H	159	VAL	0	-0.015	-0.019	14.158	1.481	1.481	0.000	0.000	0.000	0.000
13	H	160	GLU	-1	-0.984	-0.994	12.384	-22.501	-22.501	0.000	0.000	0.000	0.000
14	H	161	SER	0	-0.071	-0.025	15.306	1.037	1.037	0.000	0.000	0.000	0.000
15	H	162	LEU	0	-0.066	-0.011	17.619	1.255	1.255	0.000	0.000	0.000	0.000
16	H	176	PHE	0	0.005	-0.013	20.812	-0.091	-0.091	0.000	0.000	0.000	0.000
17	H	177	TYR	0	-0.043	-0.027	15.047	0.192	0.192	0.000	0.000	0.000	0.000
18	H	178	LEU	0	0.023	0.016	16.244	-0.705	-0.705	0.000	0.000	0.000	0.000
19	H	179	PRO	0	0.026	0.020	12.572	0.776	0.776	0.000	0.000	0.000	0.000
20	H	180	ASN	0	-0.013	-0.012	14.742	0.264	0.264	0.000	0.000	0.000	0.000
21	H	182	ASN	0	-0.017	-0.013	10.673	1.165	1.165	0.000	0.000	0.000	0.000
22	H	183	LYS	1	1.005	0.989	11.040	17.183	17.183	0.000	0.000	0.000	0.000
23	H	184	ASN	0	-0.038	-0.021	6.912	-0.453	-0.453	0.000	0.000	0.000	0.000
24	H	185	GLY	0	0.083	0.033	6.364	-3.537	-3.537	0.000	0.000	0.000	0.000
25	H	186	PHE	0	-0.079	-0.037	2.564	-4.988	-4.064	0.198	-0.379	-0.742	-0.001
26	H	187	TYR	0	-0.008	-0.033	7.810	0.695	0.695	0.000	0.000	0.000	0.000
27	H	188	HIS	0	-0.017	-0.007	11.006	0.394	0.394	0.000	0.000	0.000	0.000
28	H	189	SER	0	0.018	-0.006	14.523	-0.455	-0.455	0.000	0.000	0.000	0.000
29	H	190	ARG	1	0.892	0.930	16.368	13.056	13.056	0.000	0.000	0.000	0.000
30	H	191	GLN	0	0.106	0.040	13.816	-1.039	-1.039	0.000	0.000	0.000	0.000
31	H	192	CYS	0	0.011	0.039	18.748	0.738	0.738	0.000	0.000	0.000	0.000
32	H	201	GLY	0	0.041	0.017	27.726	0.082	0.082	0.000	0.000	0.000	0.000
33	H	202	LEU	0	0.010	-0.019	24.415	0.381	0.381	0.000	0.000	0.000	0.000
34	H	203	CYS	0	-0.035	0.007	22.453	-0.595	-0.595	0.000	0.000	0.000	0.000
35	H	204	TRP	0	0.035	0.018	16.868	0.773	0.773	0.000	0.000	0.000	0.000
36	H	226	CYS	0	-0.025	0.002	19.044	-0.290	-0.290	0.000	0.000	0.000	0.000
37	H	206	VAL	0	-0.047	-0.001	13.845	-0.076	-0.076	0.000	0.000	0.000	0.000
38	H	207	TYR	0	0.035	0.001	12.367	0.730	0.730	0.000	0.000	0.000	0.000
39	H	208	PRO	0	0.024	0.007	10.609	-1.647	-1.647	0.000	0.000	0.000	0.000
40	H	209	TRP	0	0.049	0.017	7.152	-2.426	-2.426	0.000	0.000	0.000	0.000
41	H	210	ASN	0	0.006	-0.019	6.344	-3.033	-3.033	0.000	0.000	0.000	0.000
42	H	211	GLY	0	0.074	0.051	8.655	-0.907	-0.907	0.000	0.000	0.000	0.000
43	H	212	LYS	1	0.912	0.951	11.472	22.678	22.678	0.000	0.000	0.000	0.000
44	H	213	ARG	1	0.856	0.914	14.163	14.924	14.924	0.000	0.000	0.000	0.000
45	H	214	ILE	0	-0.030	-0.005	17.117	0.061	0.061	0.000	0.000	0.000	0.000
46	H	215	PRO	0	0.033	0.006	18.990	0.504	0.504	0.000	0.000	0.000	0.000
47	H	216	GLY	0	0.006	0.003	22.198	0.077	0.077	0.000	0.000	0.000	0.000
48	H	217	SER	0	-0.040	-0.007	21.772	0.190	0.190	0.000	0.000	0.000	0.000
49	H	218	PRO	0	0.015	0.013	23.879	-0.203	-0.203	0.000	0.000	0.000	0.000
50	H	219	GLU	-1	-0.866	-0.934	23.207	-13.861	-13.861	0.000	0.000	0.000	0.000
51	H	220	ILE	0	0.002	0.005	25.588	0.431	0.431	0.000	0.000	0.000	0.000
52	H	221	ARG	1	0.890	0.946	27.184	10.012	10.012	0.000	0.000	0.000	0.000
53	H	222	GLY	0	0.005	-0.010	27.970	0.468	0.468	0.000	0.000	0.000	0.000
54	H	223	ASP	-1	-0.851	-0.927	26.094	-12.113	-12.113	0.000	0.000	0.000	0.000
55	H	224	PRO	0	-0.041	0.008	23.070	0.254	0.254	0.000	0.000	0.000	0.000
56	H	225	ASN	0	0.054	0.019	24.815	-0.059	-0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:148:LYS)