FMO DATABASE

FMODB ID: YY142

Calculation Name: 2DSR-G-Xray372

Preferred Name: Insulin-like growth factor binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DSR

Chain ID: G

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-472888.735391
FMO2-HF: Nuclear repulsion	440927.483577
FMO2-HF: Total energy	-31961.251814
FMO2-MP2: Total energy	-32050.598334

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:151:GLY)

Summations of interaction energy for fragment #1(G:151:GLY)

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.
-0.209	4.694	2.575	-3.324	-4.153	-0.019

Interaction energy analysis for fragmet #1(G:151:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.039

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	G	153	CYS	0	-0.033	0.012	3.754	-0.259	1.366	-0.003	-0.855	-0.767	0.003
4	G	154	GLN	0	0.039	0.012	2.892	-0.222	0.838	0.111	-0.429	-0.741	0.000
5	G	155	SER	0	-0.028	-0.012	3.787	1.963	2.232	-0.001	-0.090	-0.177	0.000
6	G	156	GLU	-1	-0.841	-0.915	6.054	-0.489	-0.489	0.000	0.000	0.000	0.000
7	G	157	LEU	0	-0.003	0.000	7.846	0.454	0.454	0.000	0.000	0.000	0.000
8	G	158	HIS	0	-0.004	0.001	8.509	0.288	0.288	0.000	0.000	0.000	0.000
9	G	159	ARG	1	0.848	0.900	10.185	1.407	1.407	0.000	0.000	0.000	0.000
10	G	160	ALA	0	-0.010	0.004	12.239	0.173	0.173	0.000	0.000	0.000	0.000
11	G	161	LEU	0	-0.001	-0.007	12.089	0.141	0.141	0.000	0.000	0.000	0.000
12	G	162	GLU	-1	-0.831	-0.904	14.146	-0.681	-0.681	0.000	0.000	0.000	0.000
13	G	163	ARG	1	0.830	0.903	15.972	0.729	0.729	0.000	0.000	0.000	0.000
14	G	164	LEU	0	-0.014	0.000	16.746	0.069	0.069	0.000	0.000	0.000	0.000
15	G	165	ALA	0	0.021	0.009	18.954	0.053	0.053	0.000	0.000	0.000	0.000
16	G	166	ALA	0	-0.041	-0.014	20.693	0.039	0.039	0.000	0.000	0.000	0.000
17	G	167	SER	0	-0.040	-0.010	22.494	0.019	0.019	0.000	0.000	0.000	0.000
18	G	168	GLN	0	-0.020	0.000	24.821	0.003	0.003	0.000	0.000	0.000	0.000
19	G	169	SER	0	-0.003	-0.001	27.328	0.010	0.010	0.000	0.000	0.000	0.000
20	G	170	ARG	1	0.812	0.886	22.364	0.346	0.346	0.000	0.000	0.000	0.000
21	G	171	THR	0	0.014	-0.017	25.338	0.015	0.015	0.000	0.000	0.000	0.000
22	G	172	HIS	0	0.039	-0.013	23.890	-0.039	-0.039	0.000	0.000	0.000	0.000
23	G	173	GLU	-1	-0.881	-0.929	24.017	-0.221	-0.221	0.000	0.000	0.000	0.000
24	G	174	ASP	-1	-0.809	-0.876	22.807	-0.308	-0.308	0.000	0.000	0.000	0.000
25	G	175	LEU	0	-0.027	-0.014	18.690	-0.043	-0.043	0.000	0.000	0.000	0.000
26	G	176	TYR	0	-0.033	-0.020	19.636	-0.035	-0.035	0.000	0.000	0.000	0.000
27	G	177	ILE	0	-0.033	-0.015	20.957	-0.020	-0.020	0.000	0.000	0.000	0.000
28	G	178	ILE	0	-0.065	-0.027	17.025	-0.031	-0.031	0.000	0.000	0.000	0.000
29	G	179	PRO	0	-0.012	0.009	15.833	-0.021	-0.021	0.000	0.000	0.000	0.000
30	G	180	ILE	0	0.014	-0.001	12.518	-0.122	-0.122	0.000	0.000	0.000	0.000
31	G	181	PRO	0	-0.029	-0.001	9.431	0.093	0.093	0.000	0.000	0.000	0.000
32	G	182	ASN	0	0.014	-0.007	11.008	-0.035	-0.035	0.000	0.000	0.000	0.000
33	G	184	ASP	-1	-0.805	-0.906	6.163	0.887	0.887	0.000	0.000	0.000	0.000
34	G	185	ARG	1	0.940	0.966	6.736	-0.684	-0.684	0.000	0.000	0.000	0.000
35	G	186	ASN	0	-0.078	-0.049	5.629	0.008	0.008	0.000	0.000	0.000	0.000
36	G	187	GLY	0	0.053	0.034	2.126	2.783	3.466	1.166	-0.909	-0.940	-0.005
37	G	188	ASN	0	-0.072	-0.032	2.793	-5.346	-4.100	1.300	-1.022	-1.524	-0.017
38	G	189	PHE	0	0.037	0.021	3.998	-0.285	-0.265	0.002	-0.019	-0.004	0.000
39	G	190	HIS	0	-0.024	-0.006	7.569	0.373	0.373	0.000	0.000	0.000	0.000
40	G	191	PRO	0	-0.014	-0.014	10.870	-0.072	-0.072	0.000	0.000	0.000	0.000
41	G	192	LYS	1	0.837	0.910	13.300	0.113	0.113	0.000	0.000	0.000	0.000
42	G	193	GLN	0	-0.037	-0.013	10.902	-0.095	-0.095	0.000	0.000	0.000	0.000
43	G	194	CYS	0	-0.062	-0.047	15.329	0.042	0.042	0.000	0.000	0.000	0.000
44	G	195	HIS	0	0.059	0.048	17.914	-0.030	-0.030	0.000	0.000	0.000	0.000
45	G	196	PRO	0	0.005	0.006	19.697	0.019	0.019	0.000	0.000	0.000	0.000
46	G	197	ALA	0	-0.055	-0.036	21.630	0.016	0.016	0.000	0.000	0.000	0.000
47	G	198	LEU	0	0.031	0.019	25.261	-0.012	-0.012	0.000	0.000	0.000	0.000
48	G	199	ASP	-1	-0.870	-0.928	28.157	-0.149	-0.149	0.000	0.000	0.000	0.000
49	G	200	GLY	0	-0.015	-0.004	31.280	0.009	0.009	0.000	0.000	0.000	0.000
50	G	201	GLN	0	-0.067	-0.032	30.024	0.011	0.011	0.000	0.000	0.000	0.000
51	G	202	ARG	1	0.935	0.958	21.654	0.157	0.157	0.000	0.000	0.000	0.000
52	G	203	GLY	0	0.057	0.040	23.242	0.008	0.008	0.000	0.000	0.000	0.000
53	G	204	LYS	1	0.828	0.910	23.520	0.140	0.140	0.000	0.000	0.000	0.000
54	G	206	TRP	0	0.039	0.000	15.418	0.049	0.049	0.000	0.000	0.000	0.000
55	G	207	CYS	0	-0.066	-0.034	16.565	-0.042	-0.042	0.000	0.000	0.000	0.000
56	G	208	VAL	0	-0.005	-0.004	11.353	-0.021	-0.021	0.000	0.000	0.000	0.000
57	G	209	ASP	-1	-0.783	-0.891	9.895	-0.010	-0.010	0.000	0.000	0.000	0.000
58	G	210	ARG	1	0.929	0.961	8.660	-0.324	-0.324	0.000	0.000	0.000	0.000
59	G	211	LYS	1	0.976	1.002	5.684	-0.687	-0.687	0.000	0.000	0.000	0.000
60	G	212	THR	0	-0.041	-0.040	5.696	-0.510	-0.510	0.000	0.000	0.000	0.000
61	G	213	GLY	0	0.027	0.027	8.347	-0.079	-0.079	0.000	0.000	0.000	0.000
62	G	214	VAL	0	-0.006	-0.008	10.145	0.060	0.060	0.000	0.000	0.000	0.000
63	G	215	LYS	1	0.822	0.917	13.571	0.247	0.247	0.000	0.000	0.000	0.000
64	G	216	LEU	0	-0.004	0.003	15.238	0.027	0.027	0.000	0.000	0.000	0.000
65	G	217	PRO	0	-0.019	-0.014	18.031	-0.011	-0.011	0.000	0.000	0.000	0.000
66	G	218	GLY	0	0.058	0.018	21.896	0.016	0.016	0.000	0.000	0.000	0.000
67	G	219	GLY	0	0.024	0.028	23.710	-0.015	-0.015	0.000	0.000	0.000	0.000
68	G	220	LEU	0	-0.020	-0.014	22.166	-0.022	-0.022	0.000	0.000	0.000	0.000
69	G	221	GLU	-1	-0.781	-0.891	23.584	-0.112	-0.112	0.000	0.000	0.000	0.000
70	G	222	PRO	0	0.051	0.029	23.637	-0.022	-0.022	0.000	0.000	0.000	0.000
71	G	223	LYS	1	0.980	0.974	20.021	0.120	0.120	0.000	0.000	0.000	0.000
72	G	224	GLY	0	-0.083	-0.050	22.606	0.007	0.007	0.000	0.000	0.000	0.000
73	G	225	GLU	-1	-0.872	-0.923	25.435	-0.077	-0.077	0.000	0.000	0.000	0.000
74	G	226	LEU	0	-0.012	0.008	20.122	0.007	0.007	0.000	0.000	0.000	0.000
75	G	227	ASP	-1	-0.826	-0.910	20.844	-0.015	-0.015	0.000	0.000	0.000	0.000
76	G	229	HIS	0	0.020	0.023	16.687	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:151:GLY)