FMO DATABASE

FMODB ID: 3N5VL

Calculation Name: 2DSQ-H-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	62
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-340094.028221
FMO2-HF: Nuclear repulsion	314484.036409
FMO2-HF: Total energy	-25609.991812
FMO2-MP2: Total energy	-25680.87944

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:147:ACE )

Summations of interaction energy for fragment #1(H:147:ACE )

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.
0.386	1.36	-0.005	-0.45	-0.52	0

Interaction energy analysis for fragmet #1(H:147:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.010

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].
3	H	149	GLU	-1	-0.803	-0.867	3.854	0.053	0.957	-0.006	-0.428	-0.470
4	H	150	PRO	0	-0.016	-0.003	6.681	0.135	0.135	0.000	0.000	0.000
5	H	181	CYS	0	0.030	0.029	9.650	0.091	0.091	0.000	0.000	0.000
6	H	152	ARG	1	0.861	0.909	10.005	0.392	0.392	0.000	0.000	0.000
7	H	153	ILE	0	-0.070	-0.033	10.641	0.026	0.026	0.000	0.000	0.000
8	H	154	GLU	-1	-0.852	-0.907	13.379	-0.153	-0.153	0.000	0.000	0.000
9	H	155	LEU	0	0.005	-0.005	15.563	0.035	0.035	0.000	0.000	0.000
10	H	156	TYR	0	-0.012	-0.001	14.116	0.007	0.007	0.000	0.000	0.000
11	H	157	ARG	1	0.996	0.995	16.028	0.327	0.327	0.000	0.000	0.000
12	H	158	VAL	0	-0.003	0.011	19.744	0.021	0.021	0.000	0.000	0.000
13	H	159	VAL	0	-0.017	-0.022	21.182	0.017	0.017	0.000	0.000	0.000
14	H	160	GLU	-1	-0.983	-0.993	20.648	-0.187	-0.187	0.000	0.000	0.000
15	H	161	SER	0	-0.071	-0.026	23.772	0.010	0.010	0.000	0.000	0.000
16	H	162	LEU	0	-0.080	-0.024	25.701	0.012	0.012	0.000	0.000	0.000
17	H	163	NME	0	0.013	0.015	27.959	0.000	0.000	0.000	0.000	0.000
18	H	175	ACE	0	0.005	-0.008	31.102	0.001	0.001	0.000	0.000	0.000
19	H	176	PHE	0	0.007	-0.010	26.088	-0.002	-0.002	0.000	0.000	0.000
20	H	177	TYR	0	-0.036	-0.025	19.527	0.002	0.002	0.000	0.000	0.000
21	H	178	LEU	0	0.024	0.017	21.160	-0.011	-0.011	0.000	0.000	0.000
22	H	179	PRO	0	0.039	0.022	17.078	0.014	0.014	0.000	0.000	0.000
23	H	180	ASN	0	-0.014	-0.013	18.408	-0.006	-0.006	0.000	0.000	0.000
24	H	182	ASN	0	-0.029	-0.017	11.859	0.050	0.050	0.000	0.000	0.000
25	H	183	LYS	1	1.018	0.994	12.016	-0.139	-0.139	0.000	0.000	0.000
26	H	184	ASN	0	-0.041	-0.022	7.797	-0.009	-0.009	0.000	0.000	0.000
27	H	185	GLY	0	0.083	0.032	7.847	-0.102	-0.102	0.000	0.000	0.000
28	H	186	PHE	0	-0.081	-0.036	3.937	-0.198	-0.128	0.001	-0.022	-0.050
29	H	187	TYR	0	-0.014	-0.037	9.779	0.000	0.000	0.000	0.000	0.000
30	H	188	HIS	0	-0.015	-0.008	13.159	0.063	0.063	0.000	0.000	0.000
31	H	189	SER	0	0.016	-0.008	16.094	-0.018	-0.018	0.000	0.000	0.000
32	H	190	ARG	1	0.903	0.936	18.092	-0.012	-0.012	0.000	0.000	0.000
33	H	191	GLN	0	0.115	0.008	17.667	-0.015	-0.015	0.000	0.000	0.000
34	H	192	CYS	0	-0.052	-0.030	21.903	0.006	0.006	0.000	0.000	0.000
35	H	193	NME	0	0.017	0.089	21.123	-0.003	-0.003	0.000	0.000	0.000
36	H	200	ACE	0	0.006	-0.007	35.892	0.000	0.000	0.000	0.000	0.000
37	H	201	GLY	0	0.019	0.007	31.811	0.000	0.000	0.000	0.000	0.000
38	H	202	LEU	0	-0.015	-0.022	28.510	0.002	0.002	0.000	0.000	0.000
39	H	203	CYS	0	-0.027	0.021	25.794	-0.004	-0.004	0.000	0.000	0.000
40	H	204	TRP	0	0.031	0.015	20.609	0.006	0.006	0.000	0.000	0.000
41	H	226	CYS	0	-0.049	-0.017	21.047	-0.001	-0.001	0.000	0.000	0.000
42	H	206	VAL	0	-0.045	0.000	16.319	-0.006	-0.006	0.000	0.000	0.000
43	H	207	TYR	0	0.031	-0.001	13.706	0.023	0.023	0.000	0.000	0.000
44	H	208	PRO	0	0.022	0.006	11.377	-0.035	-0.035	0.000	0.000	0.000
45	H	209	TRP	0	0.055	0.020	8.492	-0.032	-0.032	0.000	0.000	0.000
46	H	210	ASN	0	0.003	-0.020	8.921	-0.124	-0.124	0.000	0.000	0.000
47	H	211	GLY	0	0.069	0.049	11.492	-0.030	-0.030	0.000	0.000	0.000
48	H	212	LYS	1	0.918	0.953	14.535	0.128	0.128	0.000	0.000	0.000
49	H	213	ARG	1	0.857	0.915	17.166	0.062	0.062	0.000	0.000	0.000
50	H	214	ILE	0	-0.031	-0.006	18.523	0.002	0.002	0.000	0.000	0.000
51	H	215	PRO	0	0.035	0.007	20.963	-0.002	-0.002	0.000	0.000	0.000
52	H	216	GLY	0	0.006	0.003	24.135	0.007	0.007	0.000	0.000	0.000
53	H	217	SER	0	-0.041	-0.006	23.770	0.001	0.001	0.000	0.000	0.000
54	H	218	PRO	0	0.014	0.012	25.782	-0.006	-0.006	0.000	0.000	0.000
55	H	219	GLU	-1	-0.860	-0.931	26.932	-0.045	-0.045	0.000	0.000	0.000
56	H	220	ILE	0	-0.008	-0.001	28.443	-0.001	-0.001	0.000	0.000	0.000
57	H	221	ARG	1	0.934	0.971	30.149	0.021	0.021	0.000	0.000	0.000
58	H	222	GLY	0	0.010	-0.008	30.821	0.002	0.002	0.000	0.000	0.000
59	H	223	ASP	-1	-0.850	-0.927	27.674	0.008	0.008	0.000	0.000	0.000
60	H	224	PRO	0	-0.049	0.004	25.155	0.002	0.002	0.000	0.000	0.000
61	H	225	ASN	0	0.061	0.021	25.929	-0.002	-0.002	0.000	0.000	0.000
62	H	227	NME	0	0.023	0.020	20.581	0.003	0.003	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:147:ACE )