FMO DATABASE

FMODB ID: GYM61

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	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	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-340609.60865
FMO2-HF: Nuclear repulsion	314507.913351
FMO2-HF: Total energy	-26101.6953
FMO2-MP2: Total energy	-26172.53092

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.
-6.479	-2.493	-0.002	-1.854	-2.13	-0.002

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 : -0.026 / q_NPA : -0.026

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	-1.008	-0.810	2.990	-4.523	-3.297	0.043	-0.461	-0.808	-0.002
4	I	4	THR	0	-0.023	-0.082	3.794	-0.590	2.102	-0.040	-1.363	-1.289	0.000
5	I	4	THR	0	-0.028	0.071	5.774	-0.119	-0.119	0.000	0.000	0.000	0.000
6	I	5	LEU	0	0.091	-0.125	7.016	-0.199	-0.199	0.000	0.000	0.000	0.000
7	I	5	LEU	0	-0.050	0.147	9.071	0.044	0.044	0.000	0.000	0.000	0.000
8	I	6	CYS	0	0.113	-0.106	10.303	0.165	0.165	0.000	0.000	0.000	0.000
9	I	6	CYS	0	-0.217	0.192	12.773	0.038	0.038	0.000	0.000	0.000	0.000
10	I	7	GLY	0	0.018	-0.117	13.838	-0.020	-0.020	0.000	0.000	0.000	0.000
11	I	8	ALA	0	0.125	-0.006	17.492	0.011	0.011	0.000	0.000	0.000	0.000
12	I	8	ALA	0	-0.051	0.120	19.494	0.004	0.004	0.000	0.000	0.000	0.000
13	I	9	GLU	0	0.119	-0.090	15.057	0.068	0.068	0.000	0.000	0.000	0.000
14	I	9	GLU	-1	-0.999	-0.849	14.251	-0.784	-0.784	0.000	0.000	0.000	0.000
15	I	10	LEU	0	0.095	-0.087	13.849	-0.019	-0.019	0.000	0.000	0.000	0.000
16	I	10	LEU	0	-0.124	0.084	12.318	0.011	0.011	0.000	0.000	0.000	0.000
17	I	11	VAL	0	0.002	-0.092	14.670	0.028	0.028	0.000	0.000	0.000	0.000
18	I	11	VAL	0	-0.068	0.068	18.914	0.009	0.009	0.000	0.000	0.000	0.000
19	I	12	ASP	0	0.133	-0.125	18.177	0.044	0.044	0.000	0.000	0.000	0.000
20	I	12	ASP	-1	-1.004	-0.830	18.012	-0.322	-0.322	0.000	0.000	0.000	0.000
21	I	13	ALA	0	0.097	-0.108	14.109	0.050	0.050	0.000	0.000	0.000	0.000
22	I	13	ALA	0	-0.077	0.107	13.463	-0.023	-0.023	0.000	0.000	0.000	0.000
23	I	14	LEU	0	0.037	-0.114	15.564	0.021	0.021	0.000	0.000	0.000	0.000
24	I	14	LEU	0	-0.117	0.081	15.388	0.011	0.011	0.000	0.000	0.000	0.000
25	I	15	GLN	0	0.094	-0.088	16.977	0.039	0.039	0.000	0.000	0.000	0.000
26	I	15	GLN	0	-0.049	0.101	20.802	-0.015	-0.015	0.000	0.000	0.000	0.000
27	I	16	PHE	0	0.064	-0.069	18.145	0.040	0.040	0.000	0.000	0.000	0.000
28	I	16	PHE	0	-0.122	0.057	15.333	-0.011	-0.011	0.000	0.000	0.000	0.000
29	I	17	VAL	0	0.023	-0.090	15.908	0.019	0.019	0.000	0.000	0.000	0.000
30	I	17	VAL	0	-0.099	0.059	13.768	-0.002	-0.002	0.000	0.000	0.000	0.000
31	I	18	CYS	0	0.056	-0.125	17.144	0.031	0.031	0.000	0.000	0.000	0.000
32	I	18	CYS	0	-0.261	0.198	18.845	0.002	0.002	0.000	0.000	0.000	0.000
33	I	19	GLY	0	0.045	-0.072	20.162	0.023	0.023	0.000	0.000	0.000	0.000
34	I	20	ASP	0	0.067	-0.021	23.034	-0.003	-0.003	0.000	0.000	0.000	0.000
35	I	20	ASP	-1	-1.012	-0.862	27.589	-0.088	-0.088	0.000	0.000	0.000	0.000
36	I	21	ARG	0	0.017	-0.129	24.798	0.004	0.004	0.000	0.000	0.000	0.000
37	I	21	ARG	1	0.831	1.030	20.539	0.026	0.026	0.000	0.000	0.000	0.000
38	I	22	GLY	0	0.012	-0.046	23.779	0.008	0.008	0.000	0.000	0.000	0.000
39	I	23	PHE	0	0.020	-0.007	20.559	0.014	0.014	0.000	0.000	0.000	0.000
40	I	23	PHE	0	-0.023	0.091	19.862	-0.006	-0.006	0.000	0.000	0.000	0.000
41	I	24	TYR	0	0.048	-0.129	21.207	-0.008	-0.008	0.000	0.000	0.000	0.000
42	I	24	TYR	0	-0.078	0.107	22.074	0.004	0.004	0.000	0.000	0.000	0.000
43	I	25	PHE	0	0.133	-0.083	19.840	-0.002	-0.002	0.000	0.000	0.000	0.000
44	I	25	PHE	0	-0.087	0.111	19.219	0.004	0.004	0.000	0.000	0.000	0.000
45	I	26	ASN	0	0.062	-0.087	19.627	0.002	0.002	0.000	0.000	0.000	0.000
46	I	26	ASN	0	-0.092	0.051	21.441	0.006	0.006	0.000	0.000	0.000	0.000
47	I	27	LYS	0	0.092	-0.077	20.963	-0.014	-0.014	0.000	0.000	0.000	0.000
48	I	27	LYS	1	0.857	1.061	17.276	-0.188	-0.188	0.000	0.000	0.000	0.000
49	I	28	PRO	0	-0.032	-0.002	21.959	0.014	0.014	0.000	0.000	0.000	0.000
50	I	29	THR	0	0.028	0.066	22.706	0.015	0.015	0.000	0.000	0.000	0.000
51	I	29	THR	0	0.023	0.114	21.627	0.011	0.011	0.000	0.000	0.000	0.000
52	I	30	GLY	0	0.015	-0.076	23.490	-0.010	-0.010	0.000	0.000	0.000	0.000
53	I	31	TYR	0	0.050	-0.004	26.186	-0.003	-0.003	0.000	0.000	0.000	0.000
54	I	31	TYR	0	-0.086	0.133	28.780	-0.004	-0.004	0.000	0.000	0.000	0.000
55	I	32	GLY	0	0.084	-0.086	28.996	-0.009	-0.009	0.000	0.000	0.000	0.000
56	I	33	SER	0	-0.142	-0.050	25.441	-0.012	-0.012	0.000	0.000	0.000	0.000
57	I	33	SER	0	-0.023	0.066	24.812	0.005	0.005	0.000	0.000	0.000	0.000
58	I	34	SER	0	0.013	-0.130	22.328	0.010	0.010	0.000	0.000	0.000	0.000
59	I	34	SER	0	0.009	0.081	21.545	-0.008	-0.008	0.000	0.000	0.000	0.000
60	I	35	SER	0	0.165	0.036	21.483	0.028	0.028	0.000	0.000	0.000	0.000
61	I	35	SER	0	0.009	0.026	20.914	-0.001	-0.001	0.000	0.000	0.000	0.000
62	I	36	ARG	0	0.178	0.005	22.702	-0.025	-0.025	0.000	0.000	0.000	0.000
63	I	36	ARG	1	1.005	0.986	27.658	-0.084	-0.084	0.000	0.000	0.000	0.000
64	I	37	ARG	0	-0.070	-0.182	26.907	0.004	0.004	0.000	0.000	0.000	0.000
65	I	37	ARG	0	-0.124	0.040	30.452	0.002	0.002	0.000	0.000	0.000	0.000
66	I	38	ALA	0	-0.290	-0.222	28.758	0.001	0.001	0.000	0.000	0.000	0.000
67	I	38	ALA	0	0.014	0.146	28.121	-0.001	-0.001	0.000	0.000	0.000	0.000
68	I	39	PRO	0	0.141	-0.048	25.055	-0.010	-0.010	0.000	0.000	0.000	0.000
69	I	40	GLN	0	0.073	-0.046	22.800	0.004	0.004	0.000	0.000	0.000	0.000
70	I	40	GLN	0	-0.010	0.131	22.632	0.002	0.002	0.000	0.000	0.000	0.000
71	I	41	THR	0	-0.040	-0.083	18.018	0.003	0.003	0.000	0.000	0.000	0.000
72	I	41	THR	0	-0.024	0.082	17.032	0.014	0.014	0.000	0.000	0.000	0.000
73	I	42	GLY	0	0.096	-0.053	17.606	-0.013	-0.013	0.000	0.000	0.000	0.000
74	I	43	ILE	0	0.040	-0.011	14.786	0.029	0.029	0.000	0.000	0.000	0.000
75	I	43	ILE	0	-0.027	0.113	12.551	0.003	0.003	0.000	0.000	0.000	0.000
76	I	44	VAL	0	0.093	-0.082	13.666	-0.043	-0.043	0.000	0.000	0.000	0.000
77	I	44	VAL	0	-0.034	0.094	16.389	0.000	0.000	0.000	0.000	0.000	0.000
78	I	45	ASP	0	0.094	-0.074	13.961	-0.073	-0.073	0.000	0.000	0.000	0.000
79	I	45	ASP	-1	-0.994	-0.905	15.646	-0.022	-0.022	0.000	0.000	0.000	0.000
80	I	46	GLU	0	-0.012	-0.104	11.668	-0.025	-0.025	0.000	0.000	0.000	0.000
81	I	46	GLU	-1	-0.902	-0.850	11.275	0.241	0.241	0.000	0.000	0.000	0.000
82	I	47	CYS	0	0.071	-0.125	9.304	0.066	0.066	0.000	0.000	0.000	0.000
83	I	47	CYS	0	-0.214	0.245	7.162	0.093	0.093	0.000	0.000	0.000	0.000
84	I	48	CYS	0	0.127	-0.069	9.227	-0.266	-0.266	0.000	0.000	0.000	0.000
85	I	49	PHE	0	0.050	-0.076	10.469	-0.148	-0.148	0.000	0.000	0.000	0.000
86	I	49	PHE	0	-0.104	0.076	12.442	0.003	0.003	0.000	0.000	0.000	0.000
87	I	50	ARG	0	0.114	-0.037	8.523	0.042	0.042	0.000	0.000	0.000	0.000
88	I	50	ARG	1	0.738	0.964	8.887	-0.146	-0.146	0.000	0.000	0.000	0.000
89	I	51	SER	0	0.094	-0.037	5.008	-0.198	-0.166	-0.002	-0.004	-0.026	0.000
90	I	51	SER	0	-0.024	0.061	4.341	-0.040	0.038	-0.001	-0.022	-0.055	0.000
91	I	52	CYS	0	0.046	-0.136	5.639	0.430	0.430	0.000	0.000	0.000	0.000
92	I	53	ASP	0	0.083	-0.077	5.154	-0.622	-0.664	-0.002	-0.004	0.048	0.000
93	I	53	ASP	-1	-0.919	-0.838	5.406	1.009	1.009	0.000	0.000	0.000	0.000
94	I	54	LEU	0	0.122	-0.123	7.124	0.077	0.077	0.000	0.000	0.000	0.000
95	I	54	LEU	0	-0.031	0.138	9.582	0.005	0.005	0.000	0.000	0.000	0.000
96	I	55	ARG	0	0.131	-0.077	9.833	-0.026	-0.026	0.000	0.000	0.000	0.000
97	I	55	ARG	1	0.811	1.057	10.417	-0.214	-0.214	0.000	0.000	0.000	0.000
98	I	56	ARG	0	0.074	-0.111	10.277	0.005	0.005	0.000	0.000	0.000	0.000
99	I	56	ARG	1	0.754	1.023	8.397	-0.461	-0.461	0.000	0.000	0.000	0.000
100	I	57	LEU	0	0.030	-0.121	11.470	0.029	0.029	0.000	0.000	0.000	0.000
101	I	57	LEU	0	-0.022	0.112	10.789	-0.005	-0.005	0.000	0.000	0.000	0.000
102	I	58	GLU	0	0.133	-0.102	13.397	-0.012	-0.012	0.000	0.000	0.000	0.000
103	I	58	GLU	-1	-0.986	-0.838	14.632	0.041	0.041	0.000	0.000	0.000	0.000
104	I	59	MET	0	0.000	-0.104	15.238	-0.006	-0.006	0.000	0.000	0.000	0.000
105	I	59	MET	0	-0.155	0.054	13.434	0.017	0.017	0.000	0.000	0.000	0.000
106	I	60	TYR	0	-0.003	-0.108	16.901	0.020	0.020	0.000	0.000	0.000	0.000
107	I	60	TYR	0	-0.101	0.094	15.146	-0.001	-0.001	0.000	0.000	0.000	0.000
108	I	61	CYS	0	0.129	-0.117	18.635	-0.022	-0.022	0.000	0.000	0.000	0.000
109	I	62	ALA	0	0.068	-0.112	20.515	0.025	0.025	0.000	0.000	0.000	0.000
110	I	62	ALA	0	-0.030	0.146	24.924	-0.001	-0.001	0.000	0.000	0.000	0.000
111	I	63	PRO	0	-0.088	-0.129	24.287	-0.002	-0.002	0.000	0.000	0.000	0.000
112	I	64	LEU	0	-0.022	-0.022	26.633	-0.005	-0.005	0.000	0.000	0.000	0.000
113	I	64	LEU	0	0.049	0.047	25.689	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)