FMO DATABASE

FMODB ID: 14YMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-327869.609078
FMO2-HF: Nuclear repulsion	302771.98242
FMO2-HF: Total energy	-25097.626658
FMO2-MP2: Total energy	-25166.838481

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.
69.832	76.238	0.732	-2.646	-4.491	-0.003

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 : 0.973 / q_NPA : 0.989

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	-0.020	-0.006	3.019	-6.262	-2.007	0.097	-1.872	-2.480	0.000
4	H	151	CYS	0	0.041	0.043	4.189	2.295	2.500	0.001	-0.031	-0.174	0.000
5	H	152	ARG	1	0.886	0.922	5.705	35.553	35.553	0.000	0.000	0.000	0.000
6	H	153	ILE	0	-0.068	-0.035	2.654	-0.779	0.076	0.321	-0.268	-0.909	-0.003
7	H	154	GLU	-1	-0.804	-0.884	5.787	-22.551	-22.551	0.000	0.000	0.000	0.000
8	H	155	LEU	0	0.022	-0.003	8.866	2.723	2.723	0.000	0.000	0.000	0.000
9	H	156	TYR	0	-0.018	-0.007	8.525	1.144	1.144	0.000	0.000	0.000	0.000
10	H	157	ARG	1	1.014	1.012	6.908	34.639	34.639	0.000	0.000	0.000	0.000
11	H	158	VAL	0	-0.008	0.011	11.817	1.837	1.837	0.000	0.000	0.000	0.000
12	H	159	VAL	0	-0.020	-0.023	14.047	1.440	1.440	0.000	0.000	0.000	0.000
13	H	160	GLU	-1	-0.982	-0.988	12.570	-22.644	-22.644	0.000	0.000	0.000	0.000
14	H	161	SER	0	-0.073	-0.036	15.685	0.959	0.959	0.000	0.000	0.000	0.000
15	H	162	LEU	0	-0.065	-0.008	18.066	1.222	1.222	0.000	0.000	0.000	0.000
16	H	176	PHE	0	-0.006	-0.015	20.856	-0.119	-0.119	0.000	0.000	0.000	0.000
17	H	177	TYR	0	-0.050	-0.037	14.095	0.872	0.872	0.000	0.000	0.000	0.000
18	H	178	LEU	0	0.017	0.020	15.664	-0.704	-0.704	0.000	0.000	0.000	0.000
19	H	179	PRO	0	0.013	0.018	12.169	0.752	0.752	0.000	0.000	0.000	0.000
20	H	180	ASN	0	-0.044	-0.044	14.708	0.695	0.695	0.000	0.000	0.000	0.000
21	H	182	ASN	0	-0.014	-0.010	10.322	1.126	1.126	0.000	0.000	0.000	0.000
22	H	183	LYS	1	1.013	0.992	11.016	16.979	16.979	0.000	0.000	0.000	0.000
23	H	184	ASN	0	-0.047	-0.028	6.904	-0.169	-0.169	0.000	0.000	0.000	0.000
24	H	185	GLY	0	0.091	0.049	6.344	-3.448	-3.448	0.000	0.000	0.000	0.000
25	H	186	PHE	0	-0.095	-0.045	2.449	-4.900	-3.809	0.313	-0.475	-0.928	0.000
26	H	187	TYR	0	-0.002	-0.025	7.723	0.582	0.582	0.000	0.000	0.000	0.000
27	H	188	HIS	0	-0.016	-0.005	11.195	0.213	0.213	0.000	0.000	0.000	0.000
28	H	189	SER	0	0.002	-0.006	14.620	-0.373	-0.373	0.000	0.000	0.000	0.000
29	H	190	ARG	1	0.888	0.915	16.558	12.872	12.872	0.000	0.000	0.000	0.000
30	H	191	GLN	0	0.108	0.049	13.858	-1.278	-1.278	0.000	0.000	0.000	0.000
31	H	192	CYS	0	0.008	0.047	18.736	0.733	0.733	0.000	0.000	0.000	0.000
32	H	201	GLY	0	0.046	0.018	27.772	0.084	0.084	0.000	0.000	0.000	0.000
33	H	202	LEU	0	0.005	-0.018	24.362	0.378	0.378	0.000	0.000	0.000	0.000
34	H	203	CYS	0	-0.072	-0.015	22.473	-0.461	-0.461	0.000	0.000	0.000	0.000
35	H	204	TRP	0	0.048	0.019	16.794	0.743	0.743	0.000	0.000	0.000	0.000
36	H	226	CYS	0	0.000	0.009	19.232	-0.297	-0.297	0.000	0.000	0.000	0.000
37	H	206	VAL	0	-0.041	-0.009	13.663	-0.063	-0.063	0.000	0.000	0.000	0.000
38	H	207	TYR	0	0.028	0.005	12.440	0.692	0.692	0.000	0.000	0.000	0.000
39	H	208	PRO	0	0.025	0.005	10.672	-1.597	-1.597	0.000	0.000	0.000	0.000
40	H	209	TRP	0	0.044	0.017	7.284	-2.271	-2.271	0.000	0.000	0.000	0.000
41	H	210	ASN	0	0.008	-0.027	6.485	-2.782	-2.782	0.000	0.000	0.000	0.000
42	H	211	GLY	0	0.067	0.051	8.780	-0.840	-0.840	0.000	0.000	0.000	0.000
43	H	212	LYS	1	0.908	0.954	11.430	22.171	22.171	0.000	0.000	0.000	0.000
44	H	213	ARG	1	0.828	0.882	14.146	14.617	14.617	0.000	0.000	0.000	0.000
45	H	214	ILE	0	-0.028	-0.005	17.221	0.046	0.046	0.000	0.000	0.000	0.000
46	H	215	PRO	0	0.022	0.003	19.117	0.514	0.514	0.000	0.000	0.000	0.000
47	H	216	GLY	0	0.003	0.001	22.307	0.074	0.074	0.000	0.000	0.000	0.000
48	H	217	SER	0	0.017	0.012	21.992	0.323	0.323	0.000	0.000	0.000	0.000
49	H	218	PRO	0	-0.034	-0.001	24.026	-0.228	-0.228	0.000	0.000	0.000	0.000
50	H	219	GLU	-1	-0.832	-0.899	23.305	-13.752	-13.752	0.000	0.000	0.000	0.000
51	H	220	ILE	0	-0.001	0.004	25.502	0.411	0.411	0.000	0.000	0.000	0.000
52	H	221	ARG	1	0.879	0.940	27.174	9.952	9.952	0.000	0.000	0.000	0.000
53	H	222	GLY	0	0.015	-0.005	27.974	0.466	0.466	0.000	0.000	0.000	0.000
54	H	223	ASP	-1	-0.837	-0.909	26.577	-11.853	-11.853	0.000	0.000	0.000	0.000
55	H	224	PRO	0	-0.037	0.001	23.136	0.252	0.252	0.000	0.000	0.000	0.000
56	H	225	ASN	0	0.044	0.024	24.702	-0.156	-0.156	0.000	0.000	0.000	0.000

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