FMO DATABASE

FMODB ID: GNRJ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-328083.872961
FMO2-HF: Nuclear repulsion	302985.942145
FMO2-HF: Total energy	-25097.930816
FMO2-MP2: Total energy	-25167.116539

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.
62.914	68.951	0.43	-2.563	-3.904	-0.013

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 : 0.976 / q_NPA : 0.992

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	-0.032	-0.007	2.993	-10.724	-6.335	0.163	-2.111	-2.441	-0.009
4	H	151	CYS	0	0.027	0.027	4.307	1.597	1.772	-0.001	-0.018	-0.155	0.000
5	H	152	ARG	1	0.862	0.903	5.459	36.240	36.240	0.000	0.000	0.000	0.000
6	H	153	ILE	0	-0.046	-0.019	2.891	-1.515	-0.469	0.261	-0.311	-0.997	-0.004
7	H	154	GLU	-1	-0.779	-0.850	5.911	-22.134	-22.134	0.000	0.000	0.000	0.000
8	H	155	LEU	0	0.026	-0.003	9.003	2.548	2.548	0.000	0.000	0.000	0.000
9	H	156	TYR	0	-0.005	-0.006	8.463	1.268	1.268	0.000	0.000	0.000	0.000
10	H	157	ARG	1	0.917	0.949	8.292	32.540	32.540	0.000	0.000	0.000	0.000
11	H	158	VAL	0	-0.022	0.001	11.455	1.898	1.898	0.000	0.000	0.000	0.000
12	H	159	VAL	0	-0.012	-0.012	13.901	1.418	1.418	0.000	0.000	0.000	0.000
13	H	160	GLU	-1	-0.888	-0.935	11.235	-25.344	-25.344	0.000	0.000	0.000	0.000
14	H	161	SER	0	-0.070	-0.034	15.090	1.030	1.030	0.000	0.000	0.000	0.000
15	H	162	LEU	0	-0.074	-0.018	17.468	1.331	1.331	0.000	0.000	0.000	0.000
16	H	176	PHE	0	0.032	0.015	20.965	0.109	0.109	0.000	0.000	0.000	0.000
17	H	177	TYR	0	-0.093	-0.085	13.998	0.861	0.861	0.000	0.000	0.000	0.000
18	H	178	LEU	0	0.025	0.021	15.523	-0.429	-0.429	0.000	0.000	0.000	0.000
19	H	179	PRO	0	0.003	0.040	11.812	0.730	0.730	0.000	0.000	0.000	0.000
20	H	180	ASN	0	-0.035	-0.046	14.378	1.011	1.011	0.000	0.000	0.000	0.000
21	H	182	ASN	0	-0.022	-0.013	10.616	1.239	1.239	0.000	0.000	0.000	0.000
22	H	183	LYS	1	1.010	0.983	11.852	16.822	16.822	0.000	0.000	0.000	0.000
23	H	184	ASN	0	-0.044	-0.018	7.537	0.323	0.323	0.000	0.000	0.000	0.000
24	H	185	GLY	0	0.083	0.040	6.973	-3.559	-3.559	0.000	0.000	0.000	0.000
25	H	186	PHE	0	-0.057	-0.020	3.291	-4.600	-4.173	0.007	-0.123	-0.311	0.000
26	H	187	TYR	0	-0.009	-0.029	7.958	0.635	0.635	0.000	0.000	0.000	0.000
27	H	188	HIS	0	-0.004	0.000	11.305	0.209	0.209	0.000	0.000	0.000	0.000
28	H	189	SER	0	0.001	-0.001	14.819	-0.370	-0.370	0.000	0.000	0.000	0.000
29	H	190	ARG	1	0.895	0.927	16.728	12.908	12.908	0.000	0.000	0.000	0.000
30	H	191	GLN	0	0.089	0.050	13.709	-1.145	-1.145	0.000	0.000	0.000	0.000
31	H	192	CYS	0	-0.013	0.000	17.796	0.890	0.890	0.000	0.000	0.000	0.000
32	H	201	GLY	0	0.047	0.029	27.821	0.111	0.111	0.000	0.000	0.000	0.000
33	H	202	LEU	0	0.019	-0.008	24.164	0.278	0.278	0.000	0.000	0.000	0.000
34	H	203	CYS	0	-0.076	-0.015	22.741	-0.438	-0.438	0.000	0.000	0.000	0.000
35	H	204	TRP	0	0.052	0.029	17.212	0.814	0.814	0.000	0.000	0.000	0.000
36	H	226	CYS	0	-0.012	-0.004	19.459	-0.299	-0.299	0.000	0.000	0.000	0.000
37	H	206	VAL	0	-0.030	-0.016	13.912	0.036	0.036	0.000	0.000	0.000	0.000
38	H	207	TYR	0	0.053	0.015	12.871	0.607	0.607	0.000	0.000	0.000	0.000
39	H	208	PRO	0	0.002	-0.004	11.618	-1.725	-1.725	0.000	0.000	0.000	0.000
40	H	209	TRP	0	0.041	0.008	8.068	-2.120	-2.120	0.000	0.000	0.000	0.000
41	H	210	ASN	0	-0.012	-0.030	7.030	-2.454	-2.454	0.000	0.000	0.000	0.000
42	H	211	GLY	0	0.069	0.048	9.047	-0.574	-0.574	0.000	0.000	0.000	0.000
43	H	212	LYS	1	0.909	0.957	11.532	22.314	22.314	0.000	0.000	0.000	0.000
44	H	213	ARG	1	0.820	0.882	14.165	14.559	14.559	0.000	0.000	0.000	0.000
45	H	214	ILE	0	-0.017	0.002	17.582	-0.041	-0.041	0.000	0.000	0.000	0.000
46	H	215	PRO	0	-0.006	-0.015	19.248	0.562	0.562	0.000	0.000	0.000	0.000
47	H	216	GLY	0	0.026	0.015	22.426	0.124	0.124	0.000	0.000	0.000	0.000
48	H	217	SER	0	-0.029	-0.007	22.223	0.204	0.204	0.000	0.000	0.000	0.000
49	H	218	PRO	0	-0.007	0.012	24.225	-0.033	-0.033	0.000	0.000	0.000	0.000
50	H	219	GLU	-1	-0.816	-0.891	23.735	-13.890	-13.890	0.000	0.000	0.000	0.000
51	H	220	ILE	0	-0.009	-0.001	25.845	0.483	0.483	0.000	0.000	0.000	0.000
52	H	221	ARG	1	0.858	0.910	27.171	9.977	9.977	0.000	0.000	0.000	0.000
53	H	222	GLY	0	0.036	0.007	28.427	0.451	0.451	0.000	0.000	0.000	0.000
54	H	223	ASP	-1	-0.796	-0.879	27.290	-11.768	-11.768	0.000	0.000	0.000	0.000
55	H	224	PRO	0	-0.049	-0.005	23.472	0.220	0.220	0.000	0.000	0.000	0.000
56	H	225	ASN	0	0.020	0.008	25.050	-0.271	-0.271	0.000	0.000	0.000	0.000

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