FMO DATABASE

FMODB ID: 2N5VR

Calculation Name: 2DSP-B-Xray372

Preferred Name: Insulin-like growth factor binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DSP

Chain ID: B

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

Base Structure: X-ray

Registration Date: 2023-09-23

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533337.734111
FMO2-HF: Nuclear repulsion	495351.569299
FMO2-HF: Total energy	-37986.164811
FMO2-MP2: Total energy	-38083.940896

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(B:1:ASP)

Summations of interaction energy for fragment #1(B:1:ASP)

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.
3.738	-1.742	0.166	6.111	-0.798	-0.001

Interaction energy analysis for fragmet #1(B:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.986 / q_NPA : -0.987

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	B	3	ALA	0	0.032	-0.018	2.843	2.507	-3.058	0.167	6.138	-0.740	-0.001
4	B	4	ILE	0	-0.100	-0.028	4.810	-6.376	-6.291	-0.001	-0.027	-0.058	0.000
5	B	5	HIS	0	0.050	0.032	7.550	-2.296	-2.296	0.000	0.000	0.000	0.000
6	B	6	CYS	0	-0.063	-0.051	11.081	-0.303	-0.303	0.000	0.000	0.000	0.000
7	B	7	PRO	0	0.028	0.012	14.608	0.325	0.325	0.000	0.000	0.000	0.000
8	B	8	PRO	0	0.012	0.014	16.415	-0.297	-0.297	0.000	0.000	0.000	0.000
9	B	9	CYS	0	-0.039	-0.045	18.732	-0.115	-0.115	0.000	0.000	0.000	0.000
10	B	10	SER	0	0.029	0.016	22.238	-0.088	-0.088	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.847	-0.936	25.029	10.211	10.211	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.849	-0.892	28.518	9.112	9.112	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.895	0.936	25.293	-11.316	-11.316	0.000	0.000	0.000	0.000
14	B	14	LEU	0	0.034	-0.013	25.556	-0.231	-0.231	0.000	0.000	0.000	0.000
15	B	15	ALA	0	0.019	0.024	29.058	-0.210	-0.210	0.000	0.000	0.000	0.000
16	B	16	ARG	1	0.787	0.873	31.397	-9.524	-9.524	0.000	0.000	0.000	0.000
17	B	17	CYS	0	-0.158	-0.031	24.188	-0.256	-0.256	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.999	0.997	32.049	-8.453	-8.453	0.000	0.000	0.000	0.000
19	B	19	PRO	0	-0.014	-0.012	34.195	0.179	0.179	0.000	0.000	0.000	0.000
20	B	20	PRO	0	-0.005	0.014	32.621	-0.253	-0.253	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.008	-0.017	35.709	-0.101	-0.101	0.000	0.000	0.000	0.000
22	B	22	GLY	0	-0.002	-0.005	38.568	0.053	0.053	0.000	0.000	0.000	0.000
23	B	23	CYS	0	-0.066	-0.027	30.774	0.044	0.044	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.891	-0.942	36.867	8.157	8.157	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.877	-0.942	30.423	10.506	10.506	0.000	0.000	0.000	0.000
26	B	26	LEU	0	-0.041	-0.029	30.868	0.008	0.008	0.000	0.000	0.000	0.000
27	B	27	VAL	0	0.020	0.031	26.155	0.348	0.348	0.000	0.000	0.000	0.000
28	B	28	ARG	1	0.872	0.908	18.655	-15.080	-15.080	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.826	-0.926	24.957	11.283	11.283	0.000	0.000	0.000	0.000
30	B	30	PRO	0	0.020	0.032	22.670	0.747	0.747	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.028	0.021	18.681	-0.044	-0.044	0.000	0.000	0.000	0.000
32	B	33	GLY	0	0.041	0.045	19.150	-0.263	-0.263	0.000	0.000	0.000	0.000
33	B	36	ALA	0	0.049	0.022	26.561	0.432	0.432	0.000	0.000	0.000	0.000
34	B	37	THR	0	-0.017	-0.010	28.969	-0.177	-0.177	0.000	0.000	0.000	0.000
35	B	39	ALA	0	-0.002	0.010	29.942	0.274	0.274	0.000	0.000	0.000	0.000
36	B	40	LEU	0	-0.033	-0.015	29.020	-0.371	-0.371	0.000	0.000	0.000	0.000
37	B	41	GLY	0	0.056	-0.014	30.981	0.208	0.208	0.000	0.000	0.000	0.000
38	B	42	LEU	0	0.007	-0.020	32.500	0.199	0.199	0.000	0.000	0.000	0.000
39	B	43	GLY	0	-0.011	-0.007	32.725	-0.290	-0.290	0.000	0.000	0.000	0.000
40	B	44	MET	0	-0.021	0.037	32.698	-0.072	-0.072	0.000	0.000	0.000	0.000
41	B	45	PRO	0	0.027	0.003	31.302	0.332	0.332	0.000	0.000	0.000	0.000
42	B	46	CYS	0	-0.038	0.004	23.464	-0.350	-0.350	0.000	0.000	0.000	0.000
43	B	47	GLY	0	0.027	-0.009	24.473	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	48	VAL	0	-0.053	-0.028	19.691	0.083	0.083	0.000	0.000	0.000	0.000
45	B	49	TYR	0	-0.025	-0.019	20.287	0.314	0.314	0.000	0.000	0.000	0.000
46	B	50	THR	0	0.000	0.016	24.492	-0.378	-0.378	0.000	0.000	0.000	0.000
47	B	51	PRO	0	0.004	-0.007	25.733	0.418	0.418	0.000	0.000	0.000	0.000
48	B	52	ARG	1	0.831	0.903	19.426	-14.167	-14.167	0.000	0.000	0.000	0.000
49	B	53	CYS	0	-0.061	-0.012	25.804	0.099	0.099	0.000	0.000	0.000	0.000
50	B	54	GLY	0	0.039	0.027	26.773	0.341	0.341	0.000	0.000	0.000	0.000
51	B	55	SER	0	-0.052	-0.026	26.739	0.352	0.352	0.000	0.000	0.000	0.000
52	B	56	GLY	0	0.030	0.007	26.748	-0.326	-0.326	0.000	0.000	0.000	0.000
53	B	57	LEU	0	-0.006	0.009	27.309	-0.259	-0.259	0.000	0.000	0.000	0.000
54	B	58	ARG	1	0.933	0.976	18.886	-15.383	-15.383	0.000	0.000	0.000	0.000
55	B	60	TYR	0	0.012	-0.012	21.840	1.111	1.111	0.000	0.000	0.000	0.000
56	B	61	PRO	0	0.006	0.013	23.976	-0.533	-0.533	0.000	0.000	0.000	0.000
57	B	62	PRO	0	0.038	0.003	26.975	0.060	0.060	0.000	0.000	0.000	0.000
58	B	63	ARG	1	0.823	0.863	29.583	-9.752	-9.752	0.000	0.000	0.000	0.000
59	B	64	GLY	0	0.012	0.027	30.027	-0.153	-0.153	0.000	0.000	0.000	0.000
60	B	65	VAL	0	-0.039	-0.009	28.190	-0.163	-0.163	0.000	0.000	0.000	0.000
61	B	66	GLU	-1	-0.884	-0.931	29.358	10.291	10.291	0.000	0.000	0.000	0.000
62	B	67	LYS	1	0.927	0.955	26.185	-11.025	-11.025	0.000	0.000	0.000	0.000
63	B	68	PRO	0	0.078	0.032	23.316	0.052	0.052	0.000	0.000	0.000	0.000
64	B	69	LEU	0	0.053	0.019	18.420	-0.010	-0.010	0.000	0.000	0.000	0.000
65	B	70	HIS	0	0.019	-0.007	21.935	-0.161	-0.161	0.000	0.000	0.000	0.000
66	B	71	THR	0	-0.003	0.017	24.403	-0.345	-0.345	0.000	0.000	0.000	0.000
67	B	72	LEU	0	0.055	0.023	21.057	-0.193	-0.193	0.000	0.000	0.000	0.000
68	B	73	MET	0	-0.072	-0.023	19.788	0.230	0.230	0.000	0.000	0.000	0.000
69	B	74	HIS	0	-0.034	-0.023	23.465	-0.049	-0.049	0.000	0.000	0.000	0.000
70	B	75	GLY	0	-0.018	0.000	26.345	-0.421	-0.421	0.000	0.000	0.000	0.000
71	B	76	GLN	0	-0.071	-0.033	28.036	-0.192	-0.192	0.000	0.000	0.000	0.000
72	B	77	GLY	0	0.016	0.014	27.136	-0.054	-0.054	0.000	0.000	0.000	0.000
73	B	78	VAL	0	0.028	0.006	28.155	-0.390	-0.390	0.000	0.000	0.000	0.000
74	B	80	MET	0	0.004	0.024	27.765	-0.352	-0.352	0.000	0.000	0.000	0.000
75	B	81	GLU	-1	-0.815	-0.894	28.025	11.305	11.305	0.000	0.000	0.000	0.000
76	B	82	LEU	0	-0.008	-0.047	23.720	0.223	0.223	0.000	0.000	0.000	0.000
77	B	83	ALA	0	0.030	0.015	26.744	0.193	0.193	0.000	0.000	0.000	0.000
78	B	84	GLU	-1	-0.809	-0.884	29.299	10.112	10.112	0.000	0.000	0.000	0.000
79	B	85	ILE	0	-0.014	-0.016	23.297	0.135	0.135	0.000	0.000	0.000	0.000
80	B	86	GLU	-1	-0.930	-0.961	24.835	12.662	12.662	0.000	0.000	0.000	0.000
81	B	87	ALA	0	0.023	0.013	25.981	-0.013	-0.013	0.000	0.000	0.000	0.000
82	B	88	ILE	0	-0.067	-0.034	26.927	-0.159	-0.159	0.000	0.000	0.000	0.000
83	B	89	GLN	0	-0.078	-0.044	20.764	0.067	0.067	0.000	0.000	0.000	0.000
84	B	90	GLU	-1	-0.923	-0.959	24.803	12.113	12.113	0.000	0.000	0.000	0.000
85	B	91	SER	0	-0.110	-0.037	26.619	-0.429	-0.429	0.000	0.000	0.000	0.000
86	B	92	LEU	0	-0.072	-0.028	24.694	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ASP)