FMO DATABASE

FMODB ID: 4LYKN

Calculation Name: 2DSR-G-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: G

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

Base Structure: X-ray

Registration Date: 2025-07-08

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-471634.126469
FMO2-HF: Nuclear repulsion	439687.88311
FMO2-HF: Total energy	-31946.243359
FMO2-MP2: Total energy	-32035.19539

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.
-5.591	0.634	3.199	-4.224	-5.204	-0.031

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 : 0.031 / q_NPA : 0.002

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	G	152	SER	0	0.010	0.106	4.715	0.234	0.450	-0.001	-0.081	-0.133	0.000
4	G	153	CYS	0	0.178	-0.105	3.440	0.239	1.655	0.001	-0.673	-0.744	0.000
5	G	153	CYS	0	-0.222	0.225	4.796	0.221	0.272	-0.002	-0.006	-0.044	0.000
6	G	154	GLN	0	0.134	-0.078	3.275	1.403	1.641	0.006	-0.041	-0.203	0.000
7	G	154	GLN	0	-0.067	0.107	2.882	-0.869	-0.391	0.087	-0.190	-0.375	0.000
8	G	155	SER	0	-0.013	-0.106	4.500	1.164	1.300	-0.001	-0.026	-0.109	0.000
9	G	155	SER	0	-0.055	0.073	4.742	0.555	0.609	-0.001	-0.018	-0.035	0.000
10	G	156	GLU	0	0.057	-0.129	6.450	0.595	0.595	0.000	0.000	0.000	0.000
11	G	156	GLU	-1	-1.005	-0.847	8.142	-1.369	-1.369	0.000	0.000	0.000	0.000
12	G	157	LEU	0	0.098	-0.111	7.711	0.385	0.385	0.000	0.000	0.000	0.000
13	G	157	LEU	0	-0.093	0.100	7.764	-0.023	-0.023	0.000	0.000	0.000	0.000
14	G	158	HIS	0	0.062	-0.092	8.465	0.179	0.179	0.000	0.000	0.000	0.000
15	G	158	HIS	0	-0.077	0.093	8.859	0.011	0.011	0.000	0.000	0.000	0.000
16	G	159	ARG	0	0.178	-0.058	10.303	0.148	0.148	0.000	0.000	0.000	0.000
17	G	159	ARG	1	0.822	1.046	11.506	0.619	0.619	0.000	0.000	0.000	0.000
18	G	160	ALA	0	0.051	-0.129	12.182	0.122	0.122	0.000	0.000	0.000	0.000
19	G	160	ALA	0	-0.046	0.131	13.125	-0.013	-0.013	0.000	0.000	0.000	0.000
20	G	161	LEU	0	0.023	-0.116	13.405	0.066	0.066	0.000	0.000	0.000	0.000
21	G	161	LEU	0	-0.051	0.101	12.259	0.005	0.005	0.000	0.000	0.000	0.000
22	G	162	GLU	0	0.146	-0.093	14.652	0.052	0.052	0.000	0.000	0.000	0.000
23	G	162	GLU	-1	-1.058	-0.857	14.860	-0.191	-0.191	0.000	0.000	0.000	0.000
24	G	163	ARG	0	0.049	-0.106	16.468	0.046	0.046	0.000	0.000	0.000	0.000
25	G	163	ARG	1	0.853	1.054	16.494	0.307	0.307	0.000	0.000	0.000	0.000
26	G	164	LEU	0	0.054	-0.121	17.930	0.037	0.037	0.000	0.000	0.000	0.000
27	G	164	LEU	0	-0.097	0.112	16.880	0.002	0.002	0.000	0.000	0.000	0.000
28	G	165	ALA	0	0.134	-0.073	19.253	0.018	0.018	0.000	0.000	0.000	0.000
29	G	165	ALA	0	-0.061	0.114	19.724	0.002	0.002	0.000	0.000	0.000	0.000
30	G	166	ALA	0	0.045	-0.112	21.140	0.024	0.024	0.000	0.000	0.000	0.000
31	G	166	ALA	0	-0.079	0.109	21.637	-0.001	-0.001	0.000	0.000	0.000	0.000
32	G	167	SER	0	-0.066	-0.110	23.033	0.015	0.015	0.000	0.000	0.000	0.000
33	G	167	SER	0	-0.043	0.061	24.989	-0.001	-0.001	0.000	0.000	0.000	0.000
34	G	168	GLN	0	0.041	-0.110	25.054	-0.016	-0.016	0.000	0.000	0.000	0.000
35	G	168	GLN	0	-0.030	0.120	25.685	0.009	0.009	0.000	0.000	0.000	0.000
36	G	169	SER	0	0.064	-0.055	27.214	0.006	0.006	0.000	0.000	0.000	0.000
37	G	169	SER	0	-0.067	0.052	28.390	-0.001	-0.001	0.000	0.000	0.000	0.000
38	G	170	ARG	0	0.044	-0.103	24.078	0.010	0.010	0.000	0.000	0.000	0.000
39	G	170	ARG	1	0.758	1.011	22.544	0.185	0.185	0.000	0.000	0.000	0.000
40	G	171	THR	0	0.020	-0.087	25.605	0.004	0.004	0.000	0.000	0.000	0.000
41	G	171	THR	0	-0.003	0.073	27.601	-0.001	-0.001	0.000	0.000	0.000	0.000
42	G	172	HIS	0	0.101	-0.084	23.994	-0.016	-0.016	0.000	0.000	0.000	0.000
43	G	172	HIS	0	-0.070	0.093	23.750	-0.008	-0.008	0.000	0.000	0.000	0.000
44	G	173	GLU	0	0.095	-0.127	23.976	-0.025	-0.025	0.000	0.000	0.000	0.000
45	G	173	GLU	-1	-0.970	-0.822	27.246	-0.153	-0.153	0.000	0.000	0.000	0.000
46	G	174	ASP	0	0.063	-0.092	23.665	-0.014	-0.014	0.000	0.000	0.000	0.000
47	G	174	ASP	-1	-0.869	-0.824	23.112	-0.182	-0.182	0.000	0.000	0.000	0.000
48	G	175	LEU	0	0.023	-0.129	19.908	-0.019	-0.019	0.000	0.000	0.000	0.000
49	G	175	LEU	0	-0.076	0.119	18.589	-0.003	-0.003	0.000	0.000	0.000	0.000
50	G	176	TYR	0	0.104	-0.100	19.415	-0.053	-0.053	0.000	0.000	0.000	0.000
51	G	176	TYR	0	-0.079	0.101	23.102	0.003	0.003	0.000	0.000	0.000	0.000
52	G	177	ILE	0	-0.030	-0.111	20.724	-0.027	-0.027	0.000	0.000	0.000	0.000
53	G	177	ILE	0	-0.062	0.094	22.246	0.003	0.003	0.000	0.000	0.000	0.000
54	G	178	ILE	0	-0.002	-0.117	18.284	-0.019	-0.019	0.000	0.000	0.000	0.000
55	G	178	ILE	0	-0.090	0.081	17.093	0.001	0.001	0.000	0.000	0.000	0.000
56	G	179	PRO	0	0.015	-0.080	15.624	-0.005	-0.005	0.000	0.000	0.000	0.000
57	G	180	ILE	0	0.094	-0.030	13.176	-0.075	-0.075	0.000	0.000	0.000	0.000
58	G	180	ILE	0	-0.084	0.115	12.283	0.005	0.005	0.000	0.000	0.000	0.000
59	G	181	PRO	0	-0.046	-0.097	9.117	0.047	0.047	0.000	0.000	0.000	0.000
60	G	182	ASN	0	0.183	0.046	10.923	-0.046	-0.046	0.000	0.000	0.000	0.000
61	G	182	ASN	0	-0.185	0.040	12.522	0.013	0.013	0.000	0.000	0.000	0.000
62	G	183	CYS	0	0.085	-0.132	7.064	0.078	0.078	0.000	0.000	0.000	0.000
63	G	184	ASP	0	0.058	-0.079	7.241	0.337	0.337	0.000	0.000	0.000	0.000
64	G	184	ASP	-1	-0.922	-0.847	6.433	-1.512	-1.512	0.000	0.000	0.000	0.000
65	G	185	ARG	0	0.142	-0.076	6.893	-0.346	-0.346	0.000	0.000	0.000	0.000
66	G	185	ARG	1	0.859	1.053	9.597	0.223	0.223	0.000	0.000	0.000	0.000
67	G	186	ASN	0	0.022	-0.099	5.444	0.205	0.205	0.000	0.000	0.000	0.000
68	G	186	ASN	0	-0.147	0.054	5.030	0.212	0.212	0.000	0.000	0.000	0.000
69	G	187	GLY	0	0.059	-0.066	2.580	-1.539	-0.423	0.380	-0.672	-0.824	-0.004
70	G	188	ASN	0	0.062	0.021	2.540	-5.416	-4.173	1.577	-1.475	-1.346	-0.017
71	G	188	ASN	0	-0.117	0.052	2.542	-1.195	0.055	1.153	-1.022	-1.382	-0.010
72	G	189	PHE	0	0.107	-0.086	4.007	0.101	0.130	0.002	-0.018	-0.014	0.000
73	G	189	PHE	0	-0.039	0.134	5.805	-0.032	-0.032	0.000	0.000	0.000	0.000
74	G	190	HIS	0	0.034	-0.111	7.260	0.197	0.197	0.000	0.000	0.000	0.000
75	G	190	HIS	0	-0.088	0.098	11.382	0.056	0.056	0.000	0.000	0.000	0.000
76	G	191	PRO	0	-0.012	-0.098	10.569	-0.010	-0.010	0.000	0.000	0.000	0.000
77	G	192	LYS	0	0.201	0.065	12.799	0.013	0.013	0.000	0.000	0.000	0.000
78	G	192	LYS	1	0.631	0.952	16.288	0.304	0.304	0.000	0.000	0.000	0.000
79	G	193	GLN	0	0.037	-0.155	14.288	-0.047	-0.047	0.000	0.000	0.000	0.000
80	G	193	GLN	0	-0.058	0.124	10.653	0.000	0.000	0.000	0.000	0.000	0.000
81	G	194	CYS	0	0.033	-0.103	15.033	0.049	0.049	0.000	0.000	0.000	0.000
82	G	194	CYS	0	-0.203	0.156	18.760	0.008	0.008	0.000	0.000	0.000	0.000
83	G	195	HIS	0	0.155	-0.061	17.739	-0.053	-0.053	0.000	0.000	0.000	0.000
84	G	195	HIS	0	-0.052	0.106	20.166	0.016	0.016	0.000	0.000	0.000	0.000
85	G	196	PRO	0	-0.040	-0.085	19.158	0.008	0.008	0.000	0.000	0.000	0.000
86	G	197	ALA	0	0.149	0.015	21.222	0.008	0.008	0.000	0.000	0.000	0.000
87	G	197	ALA	0	-0.112	0.079	25.001	0.002	0.002	0.000	0.000	0.000	0.000
88	G	198	LEU	0	-0.026	-0.155	24.889	-0.005	-0.005	0.000	0.000	0.000	0.000
89	G	198	LEU	0	-0.016	0.142	25.495	0.000	0.000	0.000	0.000	0.000	0.000
90	G	199	ASP	0	0.047	-0.115	27.732	0.000	0.000	0.000	0.000	0.000	0.000
91	G	199	ASP	-1	-0.970	-0.821	31.531	-0.141	-0.141	0.000	0.000	0.000	0.000
92	G	200	GLY	0	0.020	-0.105	30.497	0.008	0.008	0.000	0.000	0.000	0.000
93	G	201	GLN	0	0.002	-0.039	29.769	0.005	0.005	0.000	0.000	0.000	0.000
94	G	201	GLN	0	-0.044	0.126	29.718	-0.003	-0.003	0.000	0.000	0.000	0.000
95	G	202	ARG	0	0.145	-0.072	25.929	-0.012	-0.012	0.000	0.000	0.000	0.000
96	G	202	ARG	1	0.844	1.041	21.807	0.245	0.245	0.000	0.000	0.000	0.000
97	G	203	GLY	0	-0.014	-0.076	23.092	0.010	0.010	0.000	0.000	0.000	0.000
98	G	204	LYS	0	0.053	-0.006	23.292	-0.006	-0.006	0.000	0.000	0.000	0.000
99	G	204	LYS	1	0.894	1.074	24.007	0.181	0.181	0.000	0.000	0.000	0.000
100	G	205	CYS	0	0.046	-0.108	19.658	-0.024	-0.024	0.000	0.000	0.000	0.000
101	G	206	TRP	0	0.140	-0.065	18.191	0.044	0.044	0.000	0.000	0.000	0.000
102	G	206	TRP	0	-0.070	0.098	15.073	0.021	0.021	0.000	0.000	0.000	0.000
103	G	207	CYS	0	0.097	-0.112	15.943	-0.045	-0.045	0.000	0.000	0.000	0.000
104	G	207	CYS	0	-0.221	0.166	16.481	-0.001	-0.001	0.000	0.000	0.000	0.000
105	G	208	VAL	0	-0.008	-0.089	12.271	0.070	0.070	0.000	0.000	0.000	0.000
106	G	208	VAL	0	-0.023	0.097	10.569	-0.014	-0.014	0.000	0.000	0.000	0.000
107	G	209	ASP	0	0.141	-0.100	11.067	0.012	0.012	0.000	0.000	0.000	0.000
108	G	209	ASP	-1	-0.896	-0.808	9.353	-0.383	-0.383	0.000	0.000	0.000	0.000
109	G	210	ARG	0	0.061	-0.082	8.324	-0.158	-0.158	0.000	0.000	0.000	0.000
110	G	210	ARG	1	0.876	1.054	7.878	0.489	0.489	0.000	0.000	0.000	0.000
111	G	211	LYS	0	0.141	-0.043	5.087	-0.432	-0.432	0.000	0.000	0.000	0.000
112	G	211	LYS	1	0.842	1.048	5.436	-0.302	-0.302	0.000	0.000	0.000	0.000
113	G	212	THR	0	0.003	-0.107	5.083	-0.502	-0.504	-0.002	-0.002	0.005	0.000
114	G	212	THR	0	-0.103	0.057	9.014	0.090	0.090	0.000	0.000	0.000	0.000
115	G	213	GLY	0	0.057	-0.072	7.772	-0.092	-0.092	0.000	0.000	0.000	0.000
116	G	214	VAL	0	0.058	-0.022	9.308	0.036	0.036	0.000	0.000	0.000	0.000
117	G	214	VAL	0	-0.066	0.113	11.368	0.011	0.011	0.000	0.000	0.000	0.000
118	G	215	LYS	0	0.131	-0.085	12.701	0.007	0.007	0.000	0.000	0.000	0.000
119	G	215	LYS	1	0.812	1.047	16.409	0.271	0.271	0.000	0.000	0.000	0.000
120	G	216	LEU	0	0.004	-0.140	15.687	0.027	0.027	0.000	0.000	0.000	0.000
121	G	216	LEU	0	-0.051	0.130	14.789	0.008	0.008	0.000	0.000	0.000	0.000
122	G	217	PRO	0	-0.034	-0.116	17.567	-0.002	-0.002	0.000	0.000	0.000	0.000
123	G	218	GLY	0	0.047	0.023	21.412	0.000	0.000	0.000	0.000	0.000	0.000
124	G	219	GLY	0	-0.011	-0.009	22.976	-0.012	-0.012	0.000	0.000	0.000	0.000
125	G	220	LEU	0	0.098	0.005	22.904	-0.013	-0.013	0.000	0.000	0.000	0.000
126	G	220	LEU	0	-0.105	0.080	21.677	-0.001	-0.001	0.000	0.000	0.000	0.000
127	G	221	GLU	0	0.085	-0.135	23.218	0.018	0.018	0.000	0.000	0.000	0.000
128	G	221	GLU	-1	-0.967	-0.787	24.115	-0.171	-0.171	0.000	0.000	0.000	0.000
129	G	222	PRO	0	0.008	-0.105	23.558	-0.027	-0.027	0.000	0.000	0.000	0.000
130	G	223	LYS	0	0.183	0.045	22.084	0.000	0.000	0.000	0.000	0.000	0.000
131	G	223	LYS	1	0.813	1.022	19.791	0.289	0.289	0.000	0.000	0.000	0.000
132	G	224	GLY	0	-0.071	-0.150	22.877	-0.010	-0.010	0.000	0.000	0.000	0.000
133	G	225	GLU	0	0.092	0.006	25.322	0.006	0.006	0.000	0.000	0.000	0.000
134	G	225	GLU	-1	-0.956	-0.819	26.929	-0.150	-0.150	0.000	0.000	0.000	0.000
135	G	226	LEU	0	0.152	-0.073	22.179	0.015	0.015	0.000	0.000	0.000	0.000
136	G	226	LEU	0	-0.156	0.074	19.130	-0.007	-0.007	0.000	0.000	0.000	0.000
137	G	227	ASP	0	0.096	-0.126	21.641	-0.020	-0.020	0.000	0.000	0.000	0.000
138	G	227	ASP	-1	-0.979	-0.810	22.339	-0.179	-0.179	0.000	0.000	0.000	0.000
139	G	228	CYS	0	-0.010	-0.113	17.424	0.015	0.015	0.000	0.000	0.000	0.000
140	G	229	HIS	0	0.036	-0.087	17.308	-0.012	-0.012	0.000	0.000	0.000	0.000
141	G	229	HIS	0	0.053	0.021	16.031	-0.017	-0.017	0.000	0.000	0.000	0.000

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