FMO DATABASE

FMODB ID: J3YN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-475330.218812
FMO2-HF: Nuclear repulsion	443592.258515
FMO2-HF: Total energy	-31737.960297
FMO2-MP2: Total energy	-31825.802691

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.
-179.234	-182.545	41.066	-18.093	-19.661	0.142

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 : -0.828 / q_NPA : -0.882

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	0.001	0.018	3.886	-4.821	-3.305	-0.010	-0.624	-0.882	0.001
4	G	152	ARG	1	0.830	0.885	1.671	-135.361	-144.624	33.910	-13.817	-10.829	0.148
5	G	153	ILE	0	-0.019	-0.016	2.943	-4.960	-4.205	0.082	-0.183	-0.654	0.000
6	G	154	GLU	-1	-0.866	-0.907	5.942	20.441	20.441	0.000	0.000	0.000	0.000
7	G	155	LEU	0	0.029	0.000	7.292	-2.028	-2.028	0.000	0.000	0.000	0.000
8	G	156	TYR	0	0.005	-0.006	6.463	1.781	1.781	0.000	0.000	0.000	0.000
9	G	157	ARG	1	0.980	0.989	9.544	-26.093	-26.093	0.000	0.000	0.000	0.000
10	G	158	VAL	0	-0.017	0.006	11.771	-1.787	-1.787	0.000	0.000	0.000	0.000
11	G	159	VAL	0	-0.015	-0.011	12.905	-1.443	-1.443	0.000	0.000	0.000	0.000
12	G	160	GLU	-1	-0.953	-0.971	14.198	18.476	18.476	0.000	0.000	0.000	0.000
13	G	161	SER	0	-0.034	-0.023	16.026	-1.462	-1.462	0.000	0.000	0.000	0.000
14	G	162	LEU	0	-0.022	-0.017	17.435	-0.908	-0.908	0.000	0.000	0.000	0.000
15	G	163	ALA	0	-0.018	-0.009	18.692	-0.770	-0.770	0.000	0.000	0.000	0.000
16	G	164	LYS	1	0.895	0.968	20.404	-13.639	-13.639	0.000	0.000	0.000	0.000
17	G	165	ALA	0	-0.017	0.000	22.208	-0.824	-0.824	0.000	0.000	0.000	0.000
18	G	174	SER	0	-0.035	-0.026	23.476	-0.047	-0.047	0.000	0.000	0.000	0.000
19	G	175	LYS	1	0.819	0.908	24.404	-11.778	-11.778	0.000	0.000	0.000	0.000
20	G	176	PHE	0	0.010	-0.003	18.268	0.080	0.080	0.000	0.000	0.000	0.000
21	G	177	TYR	0	-0.019	-0.030	13.062	-0.158	-0.158	0.000	0.000	0.000	0.000
22	G	178	LEU	0	0.035	0.002	13.031	0.321	0.321	0.000	0.000	0.000	0.000
23	G	179	PRO	0	-0.004	0.019	9.506	0.061	0.061	0.000	0.000	0.000	0.000
24	G	180	ASN	0	0.061	0.030	10.700	0.776	0.776	0.000	0.000	0.000	0.000
25	G	182	ASN	0	-0.031	-0.017	6.983	2.066	2.066	0.000	0.000	0.000	0.000
26	G	183	LYS	1	0.974	0.965	6.368	-25.550	-25.550	0.000	0.000	0.000	0.000
27	G	184	ASN	0	-0.040	-0.016	4.126	3.758	4.080	0.002	-0.069	-0.254	0.000
28	G	185	GLY	0	0.087	0.047	2.190	6.232	8.677	5.833	-3.993	-4.285	0.009
29	G	186	PHE	0	-0.059	-0.018	2.825	-10.801	-9.956	1.250	0.603	-2.699	-0.016
30	G	187	TYR	0	0.019	-0.019	4.526	0.287	0.356	-0.001	-0.010	-0.058	0.000
31	G	188	HIS	0	-0.010	-0.002	8.098	-0.464	-0.464	0.000	0.000	0.000	0.000
32	G	189	SER	0	0.013	0.004	11.464	-0.372	-0.372	0.000	0.000	0.000	0.000
33	G	190	ARG	1	0.938	0.961	14.044	-15.998	-15.998	0.000	0.000	0.000	0.000
34	G	191	GLN	0	-0.041	-0.008	11.336	1.176	1.176	0.000	0.000	0.000	0.000
35	G	192	CYS	0	0.014	0.019	15.723	-0.242	-0.242	0.000	0.000	0.000	0.000
36	G	193	GLU	-1	-0.779	-0.890	17.871	12.807	12.807	0.000	0.000	0.000	0.000
37	G	194	THR	0	-0.025	-0.004	19.659	-0.200	-0.200	0.000	0.000	0.000	0.000
38	G	195	SER	0	-0.053	-0.053	21.740	0.041	0.041	0.000	0.000	0.000	0.000
39	G	196	MET	0	-0.041	-0.005	25.272	0.092	0.092	0.000	0.000	0.000	0.000
40	G	197	ASP	-1	-0.833	-0.921	26.954	9.734	9.734	0.000	0.000	0.000	0.000
41	G	198	GLY	0	-0.038	-0.007	28.172	0.120	0.120	0.000	0.000	0.000	0.000
42	G	199	GLU	-1	-0.818	-0.899	22.374	13.975	13.975	0.000	0.000	0.000	0.000
43	G	200	ALA	0	-0.037	-0.013	25.223	-0.458	-0.458	0.000	0.000	0.000	0.000
44	G	201	GLY	0	0.018	0.006	24.372	-0.459	-0.459	0.000	0.000	0.000	0.000
45	G	202	LEU	0	-0.055	-0.038	23.147	-0.197	-0.197	0.000	0.000	0.000	0.000
46	G	204	TRP	0	0.034	0.007	15.589	-0.871	-0.871	0.000	0.000	0.000	0.000
47	G	205	CYS	0	-0.048	-0.011	16.987	0.508	0.508	0.000	0.000	0.000	0.000
48	G	206	VAL	0	-0.012	-0.004	11.786	-0.490	-0.490	0.000	0.000	0.000	0.000
49	G	207	TYR	0	0.042	0.007	12.064	-0.266	-0.266	0.000	0.000	0.000	0.000
50	G	208	PRO	0	0.011	0.004	9.555	1.089	1.089	0.000	0.000	0.000	0.000
51	G	209	TRP	0	0.031	0.003	6.810	2.892	2.892	0.000	0.000	0.000	0.000
52	G	210	ASN	0	-0.010	-0.028	6.630	1.547	1.547	0.000	0.000	0.000	0.000
53	G	211	GLY	0	0.076	0.057	8.530	-0.298	-0.298	0.000	0.000	0.000	0.000
54	G	212	LYS	1	0.875	0.936	10.405	-16.657	-16.657	0.000	0.000	0.000	0.000
55	G	213	ARG	1	0.833	0.904	13.696	-12.813	-12.813	0.000	0.000	0.000	0.000
56	G	214	ILE	0	-0.001	0.012	16.544	-0.279	-0.279	0.000	0.000	0.000	0.000
57	G	215	PRO	0	-0.007	-0.005	18.358	-0.435	-0.435	0.000	0.000	0.000	0.000
58	G	216	GLY	0	0.032	0.017	21.832	-0.008	-0.008	0.000	0.000	0.000	0.000
59	G	217	SER	0	-0.037	-0.013	20.444	-0.151	-0.151	0.000	0.000	0.000	0.000
60	G	218	PRO	0	0.040	0.007	22.594	-0.072	-0.072	0.000	0.000	0.000	0.000
61	G	219	GLU	-1	-0.893	-0.933	22.579	12.940	12.940	0.000	0.000	0.000	0.000
62	G	220	ILE	0	-0.041	-0.014	24.039	-0.556	-0.556	0.000	0.000	0.000	0.000
63	G	221	ARG	1	0.923	0.972	24.952	-10.170	-10.170	0.000	0.000	0.000	0.000
64	G	222	GLY	0	0.057	0.019	25.469	-0.405	-0.405	0.000	0.000	0.000	0.000
65	G	223	ASP	-1	-0.829	-0.920	22.701	13.560	13.560	0.000	0.000	0.000	0.000
66	G	224	PRO	0	-0.037	-0.023	20.920	-0.403	-0.403	0.000	0.000	0.000	0.000
67	G	225	ASN	0	-0.078	-0.033	22.818	-0.226	-0.226	0.000	0.000	0.000	0.000
68	G	227	GLN	0	0.097	0.044	20.090	0.725	0.725	0.000	0.000	0.000	0.000
69	G	228	ILE	0	-0.082	-0.049	14.848	0.263	0.263	0.000	0.000	0.000	0.000
70	G	229	TYR	0	0.014	0.006	18.368	-0.016	-0.016	0.000	0.000	0.000	0.000
71	G	230	PHE	0	0.006	0.019	10.528	0.166	0.166	0.000	0.000	0.000	0.000
72	G	231	ASN	0	-0.030	-0.008	15.203	-0.212	-0.212	0.000	0.000	0.000	0.000

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