FMO DATABASE

FMODB ID: 827RY

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	OptH
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	-472887.417544
FMO2-HF: Nuclear repulsion	441150.66013
FMO2-HF: Total energy	-31736.757414
FMO2-MP2: Total energy	-31824.678031

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.
-141.941	-137.191	22.186	-12.086	-14.851	0.073

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 : -0.910 / q_NPA : -0.942

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	0.024	0.026	3.852	-5.045	-3.254	-0.014	-0.742	-1.035	0.002
4	G	152	ARG	1	0.929	0.955	1.660	-108.678	-111.452	16.649	-7.612	-6.264	0.087
5	G	153	ILE	0	-0.030	-0.015	3.316	-5.841	-5.144	0.035	-0.177	-0.556	0.000
6	G	154	GLU	-1	-0.885	-0.922	6.077	20.489	20.489	0.000	0.000	0.000	0.000
7	G	155	LEU	0	0.006	-0.003	7.569	-2.261	-2.261	0.000	0.000	0.000	0.000
8	G	156	TYR	0	0.030	0.003	6.342	0.866	0.866	0.000	0.000	0.000	0.000
9	G	157	ARG	1	0.918	0.963	8.886	-26.085	-26.085	0.000	0.000	0.000	0.000
10	G	158	VAL	0	0.004	0.009	12.348	-1.487	-1.487	0.000	0.000	0.000	0.000
11	G	159	VAL	0	0.023	0.009	13.178	-1.375	-1.375	0.000	0.000	0.000	0.000
12	G	160	GLU	-1	-0.957	-0.960	14.083	18.757	18.757	0.000	0.000	0.000	0.000
13	G	161	SER	0	-0.054	-0.037	16.154	-1.335	-1.335	0.000	0.000	0.000	0.000
14	G	162	LEU	0	-0.006	-0.015	17.734	-0.899	-0.899	0.000	0.000	0.000	0.000
15	G	163	ALA	0	-0.040	-0.019	19.142	-0.729	-0.729	0.000	0.000	0.000	0.000
16	G	164	LYS	1	0.904	0.972	20.850	-13.339	-13.339	0.000	0.000	0.000	0.000
17	G	165	ALA	0	-0.002	0.009	22.708	-0.600	-0.600	0.000	0.000	0.000	0.000
18	G	174	SER	0	-0.059	-0.058	23.430	0.000	0.000	0.000	0.000	0.000	0.000
19	G	175	LYS	1	0.842	0.915	23.722	-12.215	-12.215	0.000	0.000	0.000	0.000
20	G	176	PHE	0	0.024	0.021	18.330	0.017	0.017	0.000	0.000	0.000	0.000
21	G	177	TYR	0	-0.002	-0.031	13.184	-0.108	-0.108	0.000	0.000	0.000	0.000
22	G	178	LEU	0	0.020	0.012	12.778	0.602	0.602	0.000	0.000	0.000	0.000
23	G	179	PRO	0	0.030	0.028	9.516	-0.226	-0.226	0.000	0.000	0.000	0.000
24	G	180	ASN	0	0.006	-0.003	10.925	0.863	0.863	0.000	0.000	0.000	0.000
25	G	182	ASN	0	-0.023	-0.020	6.472	1.915	1.915	0.000	0.000	0.000	0.000
26	G	183	LYS	1	0.994	0.972	6.678	-23.951	-23.951	0.000	0.000	0.000	0.000
27	G	184	ASN	0	-0.029	-0.025	4.484	4.648	4.897	-0.001	-0.018	-0.230	0.000
28	G	185	GLY	0	0.072	0.063	2.183	10.873	13.669	3.741	-2.852	-3.684	0.003
29	G	186	PHE	0	-0.051	-0.028	2.575	-6.544	-4.623	1.777	-0.676	-3.022	-0.019
30	G	187	TYR	0	-0.011	-0.030	4.716	0.080	0.150	-0.001	-0.009	-0.060	0.000
31	G	188	HIS	0	-0.025	-0.015	8.108	-0.945	-0.945	0.000	0.000	0.000	0.000
32	G	189	SER	0	0.001	-0.007	11.442	-0.486	-0.486	0.000	0.000	0.000	0.000
33	G	190	ARG	1	0.980	0.982	14.214	-16.171	-16.171	0.000	0.000	0.000	0.000
34	G	191	GLN	0	-0.002	0.049	11.262	1.031	1.031	0.000	0.000	0.000	0.000
35	G	192	CYS	0	0.061	0.042	15.653	-0.309	-0.309	0.000	0.000	0.000	0.000
36	G	193	GLU	-1	-0.845	-0.917	17.650	13.335	13.335	0.000	0.000	0.000	0.000
37	G	194	THR	0	-0.029	-0.004	19.703	-0.137	-0.137	0.000	0.000	0.000	0.000
38	G	195	SER	0	-0.089	-0.067	21.711	0.008	0.008	0.000	0.000	0.000	0.000
39	G	196	MET	0	-0.108	0.005	25.128	0.054	0.054	0.000	0.000	0.000	0.000
40	G	197	ASP	-1	-0.674	-0.868	27.510	9.511	9.511	0.000	0.000	0.000	0.000
41	G	198	GLY	0	-0.058	-0.037	27.901	0.035	0.035	0.000	0.000	0.000	0.000
42	G	199	GLU	-1	-0.946	-0.973	22.053	13.863	13.863	0.000	0.000	0.000	0.000
43	G	200	ALA	0	-0.051	-0.003	25.003	-0.388	-0.388	0.000	0.000	0.000	0.000
44	G	201	GLY	0	-0.003	-0.005	24.202	-0.437	-0.437	0.000	0.000	0.000	0.000
45	G	202	LEU	0	-0.019	-0.026	22.944	-0.186	-0.186	0.000	0.000	0.000	0.000
46	G	204	TRP	0	0.020	-0.003	15.470	-0.807	-0.807	0.000	0.000	0.000	0.000
47	G	205	CYS	0	-0.044	0.001	16.995	0.700	0.700	0.000	0.000	0.000	0.000
48	G	206	VAL	0	-0.037	-0.013	11.699	-0.485	-0.485	0.000	0.000	0.000	0.000
49	G	207	TYR	0	0.016	-0.016	11.918	-0.308	-0.308	0.000	0.000	0.000	0.000
50	G	208	PRO	0	0.029	0.011	9.516	0.986	0.986	0.000	0.000	0.000	0.000
51	G	209	TRP	0	0.018	-0.001	6.644	2.562	2.562	0.000	0.000	0.000	0.000
52	G	210	ASN	0	0.025	0.001	6.082	2.448	2.448	0.000	0.000	0.000	0.000
53	G	211	GLY	0	0.117	0.078	8.491	0.551	0.551	0.000	0.000	0.000	0.000
54	G	212	LYS	1	0.853	0.920	10.181	-16.737	-16.737	0.000	0.000	0.000	0.000
55	G	213	ARG	1	0.855	0.900	13.440	-12.761	-12.761	0.000	0.000	0.000	0.000
56	G	214	ILE	0	-0.007	0.008	16.229	-0.338	-0.338	0.000	0.000	0.000	0.000
57	G	215	PRO	0	-0.019	-0.013	18.062	-0.428	-0.428	0.000	0.000	0.000	0.000
58	G	216	GLY	0	0.036	0.018	21.467	-0.057	-0.057	0.000	0.000	0.000	0.000
59	G	217	SER	0	-0.061	-0.012	20.229	-0.185	-0.185	0.000	0.000	0.000	0.000
60	G	218	PRO	0	0.069	0.029	22.617	-0.057	-0.057	0.000	0.000	0.000	0.000
61	G	219	GLU	-1	-0.887	-0.932	22.551	13.007	13.007	0.000	0.000	0.000	0.000
62	G	220	ILE	0	-0.023	-0.011	24.039	-0.527	-0.527	0.000	0.000	0.000	0.000
63	G	221	ARG	1	0.929	0.966	24.906	-9.983	-9.983	0.000	0.000	0.000	0.000
64	G	222	GLY	0	0.047	0.017	25.167	-0.459	-0.459	0.000	0.000	0.000	0.000
65	G	223	ASP	-1	-0.864	-0.941	22.957	13.390	13.390	0.000	0.000	0.000	0.000
66	G	224	PRO	0	-0.045	-0.025	20.681	-0.375	-0.375	0.000	0.000	0.000	0.000
67	G	225	ASN	0	-0.014	-0.005	22.844	0.090	0.090	0.000	0.000	0.000	0.000
68	G	227	GLN	0	0.045	0.017	19.980	0.101	0.101	0.000	0.000	0.000	0.000
69	G	228	ILE	0	-0.047	-0.027	14.691	0.199	0.199	0.000	0.000	0.000	0.000
70	G	229	TYR	0	0.002	0.001	18.182	-0.202	-0.202	0.000	0.000	0.000	0.000
71	G	230	PHE	0	0.005	0.013	10.561	0.604	0.604	0.000	0.000	0.000	0.000
72	G	231	ASN	0	0.003	0.006	15.261	-0.040	-0.040	0.000	0.000	0.000	0.000

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