FMO DATABASE

FMODB ID: N18KQ

Calculation Name: 2DSQ-G-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: G

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	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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-473148.007583
FMO2-HF: Nuclear repulsion	441410.883148
FMO2-HF: Total energy	-31737.124435
FMO2-MP2: Total energy	-31825.03541

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(G:149:GLU)

Summations of interaction energy for fragment #1(G:149:GLU)

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.
-165.759	-167.999	37.02	-16.527	-18.252	0.122

Interaction energy analysis for fragmet #1(G:149:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.861 / q_NPA : -0.908

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	G	151	CYS	0	0.020	0.035	3.852	-4.847	-3.127	-0.013	-0.706	-1.002	0.001
4	G	152	ARG	1	0.890	0.927	1.700	-130.226	-140.105	30.742	-11.796	-9.068	0.133
5	G	153	ILE	0	-0.038	-0.021	3.060	-5.800	-5.036	0.051	-0.202	-0.613	-0.001
6	G	154	GLU	-1	-0.886	-0.924	6.058	20.802	20.802	0.000	0.000	0.000	0.000
7	G	155	LEU	0	0.007	-0.003	7.448	-2.238	-2.238	0.000	0.000	0.000	0.000
8	G	156	TYR	0	0.028	-0.004	6.674	0.960	0.960	0.000	0.000	0.000	0.000
9	G	157	ARG	1	0.920	0.968	9.230	-25.754	-25.754	0.000	0.000	0.000	0.000
10	G	158	VAL	0	-0.009	0.001	12.338	-1.531	-1.531	0.000	0.000	0.000	0.000
11	G	159	VAL	0	0.019	0.007	13.196	-1.410	-1.410	0.000	0.000	0.000	0.000
12	G	160	GLU	-1	-0.929	-0.948	14.081	18.574	18.574	0.000	0.000	0.000	0.000
13	G	161	SER	0	-0.043	-0.035	16.153	-1.373	-1.373	0.000	0.000	0.000	0.000
14	G	162	LEU	0	-0.020	-0.012	17.713	-0.904	-0.904	0.000	0.000	0.000	0.000
15	G	163	ALA	0	-0.040	-0.025	19.114	-0.744	-0.744	0.000	0.000	0.000	0.000
16	G	164	LYS	1	0.900	0.968	20.848	-13.465	-13.465	0.000	0.000	0.000	0.000
17	G	165	ALA	0	0.008	0.017	22.708	-0.606	-0.606	0.000	0.000	0.000	0.000
18	G	174	SER	0	-0.063	-0.054	23.518	-0.012	-0.012	0.000	0.000	0.000	0.000
19	G	175	LYS	1	0.812	0.887	24.118	-11.995	-11.995	0.000	0.000	0.000	0.000
20	G	176	PHE	0	0.013	0.023	18.408	0.005	0.005	0.000	0.000	0.000	0.000
21	G	177	TYR	0	-0.007	-0.026	13.091	-0.242	-0.242	0.000	0.000	0.000	0.000
22	G	178	LEU	0	0.018	0.011	12.957	0.649	0.649	0.000	0.000	0.000	0.000
23	G	179	PRO	0	0.027	0.025	9.581	-0.224	-0.224	0.000	0.000	0.000	0.000
24	G	180	ASN	0	-0.008	-0.007	10.982	0.564	0.564	0.000	0.000	0.000	0.000
25	G	182	ASN	0	-0.022	-0.019	6.605	1.972	1.972	0.000	0.000	0.000	0.000
26	G	183	LYS	1	0.991	0.975	6.758	-24.231	-24.231	0.000	0.000	0.000	0.000
27	G	184	ASN	0	-0.031	-0.029	4.564	4.269	4.490	-0.001	-0.019	-0.200	0.000
28	G	185	GLY	0	0.081	0.066	2.241	11.547	14.116	4.342	-3.001	-3.909	0.006
29	G	186	PHE	0	-0.065	-0.030	2.680	-8.746	-6.444	1.900	-0.795	-3.406	-0.017
30	G	187	TYR	0	0.000	-0.025	4.724	0.252	0.315	-0.001	-0.008	-0.054	0.000
31	G	188	HIS	0	-0.020	-0.012	8.118	-0.926	-0.926	0.000	0.000	0.000	0.000
32	G	189	SER	0	0.009	-0.002	11.512	-0.464	-0.464	0.000	0.000	0.000	0.000
33	G	190	ARG	1	0.925	0.957	14.223	-15.849	-15.849	0.000	0.000	0.000	0.000
34	G	191	GLN	0	0.003	0.035	11.200	1.022	1.022	0.000	0.000	0.000	0.000
35	G	192	CYS	0	0.047	0.031	15.743	-0.323	-0.323	0.000	0.000	0.000	0.000
36	G	193	GLU	-1	-0.799	-0.892	17.717	12.936	12.936	0.000	0.000	0.000	0.000
37	G	194	THR	0	-0.031	-0.009	19.741	-0.124	-0.124	0.000	0.000	0.000	0.000
38	G	195	SER	0	-0.050	-0.043	21.762	0.048	0.048	0.000	0.000	0.000	0.000
39	G	196	MET	0	-0.161	-0.030	25.436	0.027	0.027	0.000	0.000	0.000	0.000
40	G	197	ASP	-1	-0.639	-0.846	27.554	9.599	9.599	0.000	0.000	0.000	0.000
41	G	198	GLY	0	-0.063	-0.043	27.904	0.056	0.056	0.000	0.000	0.000	0.000
42	G	199	GLU	-1	-0.852	-0.911	22.100	13.921	13.921	0.000	0.000	0.000	0.000
43	G	200	ALA	0	-0.064	-0.019	25.051	-0.420	-0.420	0.000	0.000	0.000	0.000
44	G	201	GLY	0	0.005	0.002	24.273	-0.464	-0.464	0.000	0.000	0.000	0.000
45	G	202	LEU	0	-0.027	-0.031	23.016	-0.179	-0.179	0.000	0.000	0.000	0.000
46	G	204	TRP	0	0.005	-0.009	15.508	-0.830	-0.830	0.000	0.000	0.000	0.000
47	G	205	CYS	0	-0.044	0.000	17.003	0.689	0.689	0.000	0.000	0.000	0.000
48	G	206	VAL	0	-0.039	-0.017	11.611	-0.490	-0.490	0.000	0.000	0.000	0.000
49	G	207	TYR	0	0.014	-0.011	11.964	-0.285	-0.285	0.000	0.000	0.000	0.000
50	G	208	PRO	0	0.027	0.011	9.491	0.979	0.979	0.000	0.000	0.000	0.000
51	G	209	TRP	0	0.016	-0.002	6.651	2.581	2.581	0.000	0.000	0.000	0.000
52	G	210	ASN	0	0.025	-0.018	6.088	2.175	2.175	0.000	0.000	0.000	0.000
53	G	211	GLY	0	0.099	0.074	8.499	0.513	0.513	0.000	0.000	0.000	0.000
54	G	212	LYS	1	0.864	0.932	10.193	-16.727	-16.727	0.000	0.000	0.000	0.000
55	G	213	ARG	1	0.842	0.902	13.450	-12.792	-12.792	0.000	0.000	0.000	0.000
56	G	214	ILE	0	0.010	0.015	16.212	-0.341	-0.341	0.000	0.000	0.000	0.000
57	G	215	PRO	0	-0.017	-0.002	18.070	-0.432	-0.432	0.000	0.000	0.000	0.000
58	G	216	GLY	0	0.035	0.019	21.475	-0.062	-0.062	0.000	0.000	0.000	0.000
59	G	217	SER	0	-0.046	-0.020	20.229	-0.168	-0.168	0.000	0.000	0.000	0.000
60	G	218	PRO	0	0.055	0.013	22.626	-0.022	-0.022	0.000	0.000	0.000	0.000
61	G	219	GLU	-1	-0.894	-0.929	22.688	12.952	12.952	0.000	0.000	0.000	0.000
62	G	220	ILE	0	-0.029	-0.014	24.051	-0.519	-0.519	0.000	0.000	0.000	0.000
63	G	221	ARG	1	0.927	0.970	24.995	-10.050	-10.050	0.000	0.000	0.000	0.000
64	G	222	GLY	0	0.052	0.018	25.253	-0.459	-0.459	0.000	0.000	0.000	0.000
65	G	223	ASP	-1	-0.850	-0.928	23.204	13.329	13.329	0.000	0.000	0.000	0.000
66	G	224	PRO	0	-0.039	-0.027	20.897	-0.377	-0.377	0.000	0.000	0.000	0.000
67	G	225	ASN	0	-0.056	-0.023	22.846	-0.205	-0.205	0.000	0.000	0.000	0.000
68	G	227	GLN	0	0.051	0.018	19.987	0.446	0.446	0.000	0.000	0.000	0.000
69	G	228	ILE	0	-0.041	-0.022	14.459	0.184	0.184	0.000	0.000	0.000	0.000
70	G	229	TYR	0	0.003	-0.001	18.186	-0.209	-0.209	0.000	0.000	0.000	0.000
71	G	230	PHE	0	0.000	0.014	10.485	0.510	0.510	0.000	0.000	0.000	0.000
72	G	231	ASN	0	0.007	0.007	15.287	-0.255	-0.255	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:149:GLU)