FMO DATABASE

FMODB ID: VK451

Calculation Name: 2DSR-I-Xray540

Preferred Name: Insulin-like growth factor binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DSR

Chain ID: I

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-340757.32351
FMO2-HF: Nuclear repulsion	314655.540473
FMO2-HF: Total energy	-26101.783036
FMO2-MP2: Total energy	-26172.570326

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(I:2:PRO)

Summations of interaction energy for fragment #1(I:2:PRO)

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.
-6.662	-2.645	-0.006	-1.853	-2.158	-0.003

Interaction energy analysis for fragmet #1(I:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.027

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	I	3	GLU	-1	-1.006	-0.827	3.241	-4.351	-3.195	0.039	-0.412	-0.783	-0.002
4	I	4	THR	0	-0.015	-0.086	3.794	-0.746	2.042	-0.040	-1.410	-1.337	-0.001
5	I	4	THR	0	-0.036	0.073	5.793	-0.113	-0.113	0.000	0.000	0.000	0.000
6	I	5	LEU	0	0.100	-0.106	6.986	-0.186	-0.186	0.000	0.000	0.000	0.000
7	I	5	LEU	0	-0.060	0.126	9.026	0.045	0.045	0.000	0.000	0.000	0.000
8	I	6	CYS	0	0.131	-0.103	10.296	0.171	0.171	0.000	0.000	0.000	0.000
9	I	6	CYS	0	-0.227	0.181	12.665	0.044	0.044	0.000	0.000	0.000	0.000
10	I	7	GLY	0	0.027	-0.118	13.804	-0.016	-0.016	0.000	0.000	0.000	0.000
11	I	8	ALA	0	0.131	0.005	17.486	0.009	0.009	0.000	0.000	0.000	0.000
12	I	8	ALA	0	-0.057	0.114	19.517	0.005	0.005	0.000	0.000	0.000	0.000
13	I	9	GLU	0	0.117	-0.091	15.070	0.073	0.073	0.000	0.000	0.000	0.000
14	I	9	GLU	-1	-0.995	-0.857	14.399	-0.824	-0.824	0.000	0.000	0.000	0.000
15	I	10	LEU	0	0.104	-0.077	13.792	-0.016	-0.016	0.000	0.000	0.000	0.000
16	I	10	LEU	0	-0.118	0.085	12.216	0.008	0.008	0.000	0.000	0.000	0.000
17	I	11	VAL	0	0.037	-0.098	14.665	0.029	0.029	0.000	0.000	0.000	0.000
18	I	11	VAL	0	-0.082	0.077	18.731	0.009	0.009	0.000	0.000	0.000	0.000
19	I	12	ASP	0	0.121	-0.128	18.163	0.047	0.047	0.000	0.000	0.000	0.000
20	I	12	ASP	-1	-1.015	-0.835	17.952	-0.341	-0.341	0.000	0.000	0.000	0.000
21	I	13	ALA	0	0.096	-0.099	14.112	0.056	0.056	0.000	0.000	0.000	0.000
22	I	13	ALA	0	-0.081	0.102	13.448	-0.025	-0.025	0.000	0.000	0.000	0.000
23	I	14	LEU	0	0.056	-0.109	15.566	0.025	0.025	0.000	0.000	0.000	0.000
24	I	14	LEU	0	-0.131	0.074	15.397	0.010	0.010	0.000	0.000	0.000	0.000
25	I	15	GLN	0	0.100	-0.083	16.971	0.041	0.041	0.000	0.000	0.000	0.000
26	I	15	GLN	0	-0.062	0.097	20.908	-0.013	-0.013	0.000	0.000	0.000	0.000
27	I	16	PHE	0	0.063	-0.071	18.134	0.043	0.043	0.000	0.000	0.000	0.000
28	I	16	PHE	0	-0.122	0.057	15.524	-0.010	-0.010	0.000	0.000	0.000	0.000
29	I	17	VAL	0	0.038	-0.095	15.908	0.023	0.023	0.000	0.000	0.000	0.000
30	I	17	VAL	0	-0.117	0.067	13.772	-0.002	-0.002	0.000	0.000	0.000	0.000
31	I	18	CYS	0	0.055	-0.127	17.145	0.033	0.033	0.000	0.000	0.000	0.000
32	I	18	CYS	0	-0.287	0.190	18.761	0.001	0.001	0.000	0.000	0.000	0.000
33	I	19	GLY	0	0.058	-0.070	20.159	0.025	0.025	0.000	0.000	0.000	0.000
34	I	20	ASP	0	0.072	-0.027	23.034	-0.005	-0.005	0.000	0.000	0.000	0.000
35	I	20	ASP	-1	-0.972	-0.852	27.518	-0.095	-0.095	0.000	0.000	0.000	0.000
36	I	21	ARG	0	-0.004	-0.124	24.695	0.004	0.004	0.000	0.000	0.000	0.000
37	I	21	ARG	1	0.797	1.020	20.714	0.031	0.031	0.000	0.000	0.000	0.000
38	I	22	GLY	0	0.017	-0.049	23.771	0.007	0.007	0.000	0.000	0.000	0.000
39	I	23	PHE	0	0.035	-0.005	20.555	0.016	0.016	0.000	0.000	0.000	0.000
40	I	23	PHE	0	-0.037	0.096	19.856	-0.006	-0.006	0.000	0.000	0.000	0.000
41	I	24	TYR	0	0.033	-0.129	21.200	-0.007	-0.007	0.000	0.000	0.000	0.000
42	I	24	TYR	0	-0.069	0.106	22.063	0.005	0.005	0.000	0.000	0.000	0.000
43	I	25	PHE	0	0.146	-0.080	19.820	-0.005	-0.005	0.000	0.000	0.000	0.000
44	I	25	PHE	0	-0.087	0.109	19.258	0.004	0.004	0.000	0.000	0.000	0.000
45	I	26	ASN	0	0.065	-0.076	19.603	-0.001	-0.001	0.000	0.000	0.000	0.000
46	I	26	ASN	0	-0.112	0.041	21.285	0.005	0.005	0.000	0.000	0.000	0.000
47	I	27	LYS	0	0.103	-0.096	20.943	-0.012	-0.012	0.000	0.000	0.000	0.000
48	I	27	LYS	1	0.828	1.072	17.139	-0.155	-0.155	0.000	0.000	0.000	0.000
49	I	28	PRO	0	0.018	-0.023	21.905	0.014	0.014	0.000	0.000	0.000	0.000
50	I	29	THR	0	0.026	0.053	22.651	0.010	0.010	0.000	0.000	0.000	0.000
51	I	29	THR	0	-0.011	0.112	21.550	0.009	0.009	0.000	0.000	0.000	0.000
52	I	30	GLY	0	-0.012	-0.100	23.442	-0.009	-0.009	0.000	0.000	0.000	0.000
53	I	31	TYR	0	0.081	0.045	26.138	-0.002	-0.002	0.000	0.000	0.000	0.000
54	I	31	TYR	0	-0.098	0.126	28.994	-0.003	-0.003	0.000	0.000	0.000	0.000
55	I	32	GLY	0	0.091	-0.109	28.967	-0.009	-0.009	0.000	0.000	0.000	0.000
56	I	33	SER	0	0.181	-0.142	25.703	-0.013	-0.013	0.000	0.000	0.000	0.000
57	I	33	SER	0	-0.404	0.111	24.999	0.007	0.007	0.000	0.000	0.000	0.000
58	I	34	SER	0	0.008	-0.131	22.257	0.010	0.010	0.000	0.000	0.000	0.000
59	I	34	SER	0	-0.013	0.054	21.561	-0.004	-0.004	0.000	0.000	0.000	0.000
60	I	35	SER	0	0.323	0.075	21.456	0.028	0.028	0.000	0.000	0.000	0.000
61	I	35	SER	0	0.083	0.066	20.896	-0.003	-0.003	0.000	0.000	0.000	0.000
62	I	36	ARG	0	-0.146	-0.096	23.065	-0.019	-0.019	0.000	0.000	0.000	0.000
63	I	36	ARG	1	0.970	0.982	27.677	-0.074	-0.074	0.000	0.000	0.000	0.000
64	I	37	ARG	0	-0.102	-0.105	27.027	0.007	0.007	0.000	0.000	0.000	0.000
65	I	37	ARG	0	0.030	0.038	30.089	0.002	0.002	0.000	0.000	0.000	0.000
66	I	38	ALA	0	0.251	-0.194	28.072	0.007	0.007	0.000	0.000	0.000	0.000
67	I	38	ALA	0	0.189	0.201	27.244	0.000	0.000	0.000	0.000	0.000	0.000
68	I	39	PRO	0	-0.441	-0.028	24.845	-0.015	-0.015	0.000	0.000	0.000	0.000
69	I	40	GLN	0	0.078	-0.043	22.756	0.006	0.006	0.000	0.000	0.000	0.000
70	I	40	GLN	0	-0.042	0.110	22.680	0.003	0.003	0.000	0.000	0.000	0.000
71	I	41	THR	0	-0.048	-0.100	18.027	0.004	0.004	0.000	0.000	0.000	0.000
72	I	41	THR	0	-0.031	0.071	17.023	0.016	0.016	0.000	0.000	0.000	0.000
73	I	42	GLY	0	0.099	-0.052	17.556	-0.009	-0.009	0.000	0.000	0.000	0.000
74	I	43	ILE	0	0.077	-0.008	14.736	0.023	0.023	0.000	0.000	0.000	0.000
75	I	43	ILE	0	-0.043	0.127	12.541	0.002	0.002	0.000	0.000	0.000	0.000
76	I	44	VAL	0	0.096	-0.095	13.613	-0.054	-0.054	0.000	0.000	0.000	0.000
77	I	44	VAL	0	-0.037	0.097	16.391	0.002	0.002	0.000	0.000	0.000	0.000
78	I	45	ASP	0	0.103	-0.083	13.924	-0.080	-0.080	0.000	0.000	0.000	0.000
79	I	45	ASP	-1	-1.014	-0.888	15.482	-0.055	-0.055	0.000	0.000	0.000	0.000
80	I	46	GLU	0	-0.017	-0.107	11.629	-0.027	-0.027	0.000	0.000	0.000	0.000
81	I	46	GLU	-1	-0.866	-0.806	11.197	0.202	0.202	0.000	0.000	0.000	0.000
82	I	47	CYS	0	0.083	-0.112	9.255	0.045	0.045	0.000	0.000	0.000	0.000
83	I	47	CYS	0	-0.231	0.249	7.090	0.110	0.110	0.000	0.000	0.000	0.000
84	I	48	CYS	0	0.111	-0.076	9.190	-0.286	-0.286	0.000	0.000	0.000	0.000
85	I	49	PHE	0	0.068	-0.062	10.457	-0.155	-0.155	0.000	0.000	0.000	0.000
86	I	49	PHE	0	-0.109	0.073	12.452	0.007	0.007	0.000	0.000	0.000	0.000
87	I	50	ARG	0	0.143	-0.020	8.510	0.051	0.051	0.000	0.000	0.000	0.000
88	I	50	ARG	1	0.724	0.967	9.014	-0.065	-0.065	0.000	0.000	0.000	0.000
89	I	51	SER	0	0.075	-0.062	4.981	-0.181	-0.151	-0.002	-0.004	-0.024	0.000
90	I	51	SER	0	-0.018	0.058	4.237	-0.034	0.051	-0.001	-0.023	-0.062	0.000
91	I	52	CYS	0	0.047	-0.133	5.601	0.498	0.498	0.000	0.000	0.000	0.000
92	I	53	ASP	0	0.061	-0.068	5.139	-0.722	-0.764	-0.002	-0.004	0.048	0.000
93	I	53	ASP	-1	-0.881	-0.835	5.525	0.672	0.672	0.000	0.000	0.000	0.000
94	I	54	LEU	0	0.125	-0.117	7.113	0.076	0.076	0.000	0.000	0.000	0.000
95	I	54	LEU	0	-0.033	0.131	9.373	0.007	0.007	0.000	0.000	0.000	0.000
96	I	55	ARG	0	0.142	-0.062	9.803	-0.028	-0.028	0.000	0.000	0.000	0.000
97	I	55	ARG	1	0.732	1.002	10.591	-0.183	-0.183	0.000	0.000	0.000	0.000
98	I	56	ARG	0	0.052	-0.121	10.266	0.015	0.015	0.000	0.000	0.000	0.000
99	I	56	ARG	1	0.748	0.993	7.920	-0.422	-0.422	0.000	0.000	0.000	0.000
100	I	57	LEU	0	0.043	-0.111	11.457	0.032	0.032	0.000	0.000	0.000	0.000
101	I	57	LEU	0	-0.041	0.108	10.758	-0.006	-0.006	0.000	0.000	0.000	0.000
102	I	58	GLU	0	0.134	-0.116	13.383	-0.012	-0.012	0.000	0.000	0.000	0.000
103	I	58	GLU	-1	-0.896	-0.785	14.517	0.066	0.066	0.000	0.000	0.000	0.000
104	I	59	MET	0	-0.022	-0.104	15.219	-0.003	-0.003	0.000	0.000	0.000	0.000
105	I	59	MET	0	-0.140	0.059	13.610	0.017	0.017	0.000	0.000	0.000	0.000
106	I	60	TYR	0	0.011	-0.106	16.878	0.023	0.023	0.000	0.000	0.000	0.000
107	I	60	TYR	0	-0.128	0.069	15.112	0.003	0.003	0.000	0.000	0.000	0.000
108	I	61	CYS	0	0.137	-0.117	18.616	-0.021	-0.021	0.000	0.000	0.000	0.000
109	I	62	ALA	0	0.080	-0.107	20.502	0.025	0.025	0.000	0.000	0.000	0.000
110	I	62	ALA	0	-0.041	0.141	24.797	-0.001	-0.001	0.000	0.000	0.000	0.000
111	I	63	PRO	0	-0.082	-0.131	24.273	-0.001	-0.001	0.000	0.000	0.000	0.000
112	I	64	LEU	0	-0.023	-0.018	26.621	-0.006	-0.006	0.000	0.000	0.000	0.000
113	I	64	LEU	0	0.048	0.043	25.379	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:2:PRO)