FMO DATABASE

FMODB ID: ZVG4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-534462.36788
FMO2-HF: Nuclear repulsion	496475.648303
FMO2-HF: Total energy	-37986.719578
FMO2-MP2: Total energy	-38084.45439

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.
-3.026	-6.789	0.063	4.52	-0.818	0.003

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 : -0.964 / q_NPA : -0.975

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	0.017	-0.015	3.005	-2.153	-6.086	0.062	4.584	-0.712	0.003
4	B	4	ILE	0	-0.099	-0.029	4.535	-8.038	-7.868	0.001	-0.064	-0.106	0.000
5	B	5	HIS	0	0.044	0.026	7.216	-2.541	-2.541	0.000	0.000	0.000	0.000
6	B	6	CYS	0	-0.080	-0.043	10.629	-0.203	-0.203	0.000	0.000	0.000	0.000
7	B	7	PRO	0	0.026	0.016	14.295	0.313	0.313	0.000	0.000	0.000	0.000
8	B	8	PRO	0	0.004	0.005	16.293	-0.316	-0.316	0.000	0.000	0.000	0.000
9	B	9	CYS	0	-0.045	-0.056	18.617	0.130	0.130	0.000	0.000	0.000	0.000
10	B	10	SER	0	0.037	0.021	21.990	-0.228	-0.228	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.839	-0.932	24.661	10.288	10.288	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.846	-0.889	28.157	9.296	9.296	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.804	0.874	25.010	-11.797	-11.797	0.000	0.000	0.000	0.000
14	B	14	LEU	0	0.024	-0.008	25.258	-0.208	-0.208	0.000	0.000	0.000	0.000
15	B	15	ALA	0	0.015	0.007	28.812	-0.244	-0.244	0.000	0.000	0.000	0.000
16	B	16	ARG	1	0.780	0.877	31.360	-9.754	-9.754	0.000	0.000	0.000	0.000
17	B	17	CYS	0	-0.107	-0.016	23.849	-0.217	-0.217	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.967	0.985	31.846	-8.633	-8.633	0.000	0.000	0.000	0.000
19	B	19	PRO	0	0.007	0.002	33.811	0.207	0.207	0.000	0.000	0.000	0.000
20	B	20	PRO	0	-0.016	0.011	32.379	-0.233	-0.233	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.002	-0.016	35.305	-0.134	-0.134	0.000	0.000	0.000	0.000
22	B	22	GLY	0	0.012	-0.003	38.117	0.062	0.062	0.000	0.000	0.000	0.000
23	B	23	CYS	0	-0.057	-0.022	30.475	0.065	0.065	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.895	-0.936	36.178	8.328	8.328	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.829	-0.896	30.028	10.707	10.707	0.000	0.000	0.000	0.000
26	B	26	LEU	0	-0.035	-0.029	30.537	-0.037	-0.037	0.000	0.000	0.000	0.000
27	B	27	VAL	0	0.006	0.017	25.696	0.378	0.378	0.000	0.000	0.000	0.000
28	B	28	ARG	1	0.865	0.917	17.809	-16.034	-16.034	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.724	-0.843	24.463	11.914	11.914	0.000	0.000	0.000	0.000
30	B	30	PRO	0	0.053	0.038	22.604	0.722	0.722	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.040	0.021	18.430	0.074	0.074	0.000	0.000	0.000	0.000
32	B	33	GLY	0	0.035	0.037	18.719	-0.272	-0.272	0.000	0.000	0.000	0.000
33	B	36	ALA	0	0.021	0.002	26.288	0.475	0.475	0.000	0.000	0.000	0.000
34	B	37	THR	0	-0.046	-0.036	28.406	-0.218	-0.218	0.000	0.000	0.000	0.000
35	B	39	ALA	0	0.011	0.021	29.509	0.296	0.296	0.000	0.000	0.000	0.000
36	B	40	LEU	0	-0.043	-0.016	28.291	-0.382	-0.382	0.000	0.000	0.000	0.000
37	B	41	GLY	0	0.073	-0.010	30.541	0.242	0.242	0.000	0.000	0.000	0.000
38	B	42	LEU	0	0.018	-0.008	32.187	0.177	0.177	0.000	0.000	0.000	0.000
39	B	43	GLY	0	-0.022	-0.005	32.197	-0.312	-0.312	0.000	0.000	0.000	0.000
40	B	44	MET	0	-0.028	0.025	32.105	-0.061	-0.061	0.000	0.000	0.000	0.000
41	B	45	PRO	0	0.022	0.002	30.863	0.379	0.379	0.000	0.000	0.000	0.000
42	B	46	CYS	0	-0.048	0.003	22.938	-0.361	-0.361	0.000	0.000	0.000	0.000
43	B	47	GLY	0	0.028	-0.010	24.176	-0.011	-0.011	0.000	0.000	0.000	0.000
44	B	48	VAL	0	-0.055	-0.027	19.040	0.062	0.062	0.000	0.000	0.000	0.000
45	B	49	TYR	0	-0.026	-0.017	20.605	0.339	0.339	0.000	0.000	0.000	0.000
46	B	50	THR	0	-0.001	0.014	24.198	-0.421	-0.421	0.000	0.000	0.000	0.000
47	B	51	PRO	0	-0.002	-0.009	25.424	0.432	0.432	0.000	0.000	0.000	0.000
48	B	52	ARG	1	0.827	0.910	19.095	-14.722	-14.722	0.000	0.000	0.000	0.000
49	B	53	CYS	0	-0.024	-0.009	25.418	0.172	0.172	0.000	0.000	0.000	0.000
50	B	54	GLY	0	0.046	0.030	26.430	0.300	0.300	0.000	0.000	0.000	0.000
51	B	55	SER	0	-0.049	-0.052	26.611	0.370	0.370	0.000	0.000	0.000	0.000
52	B	56	GLY	0	0.003	0.001	26.450	-0.348	-0.348	0.000	0.000	0.000	0.000
53	B	57	LEU	0	-0.031	-0.001	27.201	-0.085	-0.085	0.000	0.000	0.000	0.000
54	B	58	ARG	1	0.932	0.968	19.065	-15.523	-15.523	0.000	0.000	0.000	0.000
55	B	60	TYR	0	0.007	-0.014	21.215	1.214	1.214	0.000	0.000	0.000	0.000
56	B	61	PRO	0	0.016	0.015	23.360	-0.574	-0.574	0.000	0.000	0.000	0.000
57	B	62	PRO	0	0.034	0.001	26.342	-0.011	-0.011	0.000	0.000	0.000	0.000
58	B	63	ARG	1	0.869	0.901	28.987	-9.839	-9.839	0.000	0.000	0.000	0.000
59	B	64	GLY	0	-0.012	0.001	30.013	-0.084	-0.084	0.000	0.000	0.000	0.000
60	B	65	VAL	0	-0.050	-0.007	27.312	-0.298	-0.298	0.000	0.000	0.000	0.000
61	B	66	GLU	-1	-0.873	-0.938	28.167	10.713	10.713	0.000	0.000	0.000	0.000
62	B	67	LYS	1	0.864	0.928	25.607	-11.913	-11.913	0.000	0.000	0.000	0.000
63	B	68	PRO	0	0.075	0.037	22.638	0.222	0.222	0.000	0.000	0.000	0.000
64	B	69	LEU	0	0.053	0.025	17.951	0.017	0.017	0.000	0.000	0.000	0.000
65	B	70	HIS	0	0.030	0.004	21.453	-0.350	-0.350	0.000	0.000	0.000	0.000
66	B	71	THR	0	0.034	0.018	24.168	-0.291	-0.291	0.000	0.000	0.000	0.000
67	B	72	LEU	0	0.018	0.012	20.484	-0.207	-0.207	0.000	0.000	0.000	0.000
68	B	73	MET	0	-0.064	-0.022	19.558	0.270	0.270	0.000	0.000	0.000	0.000
69	B	74	HIS	0	-0.024	-0.019	23.259	-0.090	-0.090	0.000	0.000	0.000	0.000
70	B	75	GLY	0	-0.032	0.000	26.167	-0.444	-0.444	0.000	0.000	0.000	0.000
71	B	76	GLN	0	-0.040	-0.025	27.554	-0.229	-0.229	0.000	0.000	0.000	0.000
72	B	77	GLY	0	0.020	0.016	26.561	-0.024	-0.024	0.000	0.000	0.000	0.000
73	B	78	VAL	0	0.006	-0.017	27.582	-0.400	-0.400	0.000	0.000	0.000	0.000
74	B	80	MET	0	-0.011	0.025	27.315	-0.384	-0.384	0.000	0.000	0.000	0.000
75	B	81	GLU	-1	-0.809	-0.909	27.818	11.403	11.403	0.000	0.000	0.000	0.000
76	B	82	LEU	0	0.007	-0.015	23.498	0.288	0.288	0.000	0.000	0.000	0.000
77	B	83	ALA	0	0.067	0.029	26.230	0.254	0.254	0.000	0.000	0.000	0.000
78	B	84	GLU	-1	-0.850	-0.898	28.821	10.172	10.172	0.000	0.000	0.000	0.000
79	B	85	ILE	0	-0.036	-0.034	22.808	0.135	0.135	0.000	0.000	0.000	0.000
80	B	86	GLU	-1	-0.957	-0.965	24.538	13.037	13.037	0.000	0.000	0.000	0.000
81	B	87	ALA	0	0.064	0.030	25.563	0.083	0.083	0.000	0.000	0.000	0.000
82	B	88	ILE	0	-0.063	-0.028	26.125	-0.157	-0.157	0.000	0.000	0.000	0.000
83	B	89	GLN	0	-0.048	-0.029	19.817	0.084	0.084	0.000	0.000	0.000	0.000
84	B	90	GLU	-1	-0.943	-0.960	24.155	12.165	12.165	0.000	0.000	0.000	0.000
85	B	91	SER	0	-0.111	-0.050	26.328	-0.325	-0.325	0.000	0.000	0.000	0.000
86	B	92	LEU	0	-0.089	-0.045	24.028	0.295	0.295	0.000	0.000	0.000	0.000

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