FMO DATABASE

FMODB ID: 53YVZ

Calculation Name: 2DSR-G-Xray372

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: 2023-03-13

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-472116.856864
FMO2-HF: Nuclear repulsion	440155.858684
FMO2-HF: Total energy	-31960.99818
FMO2-MP2: Total energy	-32050.352615

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.
-2.851	3.32	2.858	-4.085	-4.944	-0.027

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 : 0.050 / q_NPA : 0.034

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	153	CYS	0	-0.045	0.000	3.455	-0.665	1.731	-0.003	-1.301	-1.091	0.005
4	G	154	GLN	0	0.054	0.022	3.298	0.381	1.102	0.040	-0.230	-0.532	0.000
5	G	155	SER	0	-0.026	-0.011	4.260	1.950	2.130	-0.001	-0.039	-0.140	0.000
6	G	156	GLU	-1	-0.848	-0.918	6.437	-0.543	-0.543	0.000	0.000	0.000	0.000
7	G	157	LEU	0	-0.010	-0.010	7.996	0.470	0.470	0.000	0.000	0.000	0.000
8	G	158	HIS	0	-0.008	-0.001	8.819	0.265	0.265	0.000	0.000	0.000	0.000
9	G	159	ARG	1	0.870	0.915	10.521	1.400	1.400	0.000	0.000	0.000	0.000
10	G	160	ALA	0	-0.026	-0.003	12.527	0.181	0.181	0.000	0.000	0.000	0.000
11	G	161	LEU	0	0.019	-0.001	12.652	0.136	0.136	0.000	0.000	0.000	0.000
12	G	162	GLU	-1	-0.924	-0.955	14.789	-0.675	-0.675	0.000	0.000	0.000	0.000
13	G	163	ARG	1	0.939	0.962	16.614	0.705	0.705	0.000	0.000	0.000	0.000
14	G	164	LEU	0	-0.029	-0.009	17.127	0.071	0.071	0.000	0.000	0.000	0.000
15	G	165	ALA	0	0.017	0.014	19.566	0.054	0.054	0.000	0.000	0.000	0.000
16	G	166	ALA	0	-0.044	-0.011	21.385	0.037	0.037	0.000	0.000	0.000	0.000
17	G	167	SER	0	-0.042	-0.020	23.200	0.031	0.031	0.000	0.000	0.000	0.000
18	G	168	GLN	0	-0.031	0.013	25.398	0.001	0.001	0.000	0.000	0.000	0.000
19	G	169	SER	0	0.013	-0.018	27.530	0.003	0.003	0.000	0.000	0.000	0.000
20	G	170	ARG	1	0.800	0.890	22.719	0.359	0.359	0.000	0.000	0.000	0.000
21	G	171	THR	0	0.028	0.001	25.871	0.013	0.013	0.000	0.000	0.000	0.000
22	G	172	HIS	0	0.029	-0.025	23.894	-0.037	-0.037	0.000	0.000	0.000	0.000
23	G	173	GLU	-1	-0.882	-0.930	24.114	-0.223	-0.223	0.000	0.000	0.000	0.000
24	G	174	ASP	-1	-0.797	-0.880	23.324	-0.307	-0.307	0.000	0.000	0.000	0.000
25	G	175	LEU	0	-0.033	-0.012	19.020	-0.042	-0.042	0.000	0.000	0.000	0.000
26	G	176	TYR	0	-0.030	-0.017	19.559	-0.040	-0.040	0.000	0.000	0.000	0.000
27	G	177	ILE	0	-0.033	-0.008	20.814	-0.019	-0.019	0.000	0.000	0.000	0.000
28	G	178	ILE	0	-0.077	-0.038	17.332	-0.034	-0.034	0.000	0.000	0.000	0.000
29	G	179	PRO	0	-0.002	0.013	15.666	-0.019	-0.019	0.000	0.000	0.000	0.000
30	G	180	ILE	0	-0.010	-0.013	12.461	-0.117	-0.117	0.000	0.000	0.000	0.000
31	G	181	PRO	0	-0.018	0.005	9.258	0.100	0.100	0.000	0.000	0.000	0.000
32	G	182	ASN	0	0.000	-0.021	10.942	-0.043	-0.043	0.000	0.000	0.000	0.000
33	G	184	ASP	-1	-0.821	-0.913	6.123	0.793	0.793	0.000	0.000	0.000	0.000
34	G	185	ARG	1	0.958	0.962	6.647	-0.586	-0.586	0.000	0.000	0.000	0.000
35	G	186	ASN	0	-0.089	-0.052	5.589	-0.140	-0.140	0.000	0.000	0.000	0.000
36	G	187	GLY	0	0.051	0.045	2.429	2.281	2.950	0.480	-0.388	-0.761	-0.003
37	G	188	ASN	0	-0.053	-0.032	2.376	-7.016	-4.867	2.342	-2.103	-2.388	-0.029
38	G	189	PHE	0	0.026	0.035	4.027	-0.347	-0.302	0.001	-0.022	-0.024	0.000
39	G	190	HIS	0	-0.021	-0.007	7.283	0.457	0.457	0.000	0.000	0.000	0.000
40	G	191	PRO	0	0.002	0.003	10.589	-0.075	-0.075	0.000	0.000	0.000	0.000
41	G	192	LYS	1	0.820	0.901	12.813	0.070	0.070	0.000	0.000	0.000	0.000
42	G	193	GLN	0	-0.030	-0.008	10.640	-0.120	-0.120	0.000	0.000	0.000	0.000
43	G	194	CYS	0	-0.070	-0.046	15.061	0.039	0.039	0.000	0.000	0.000	0.000
44	G	195	HIS	0	0.063	0.046	17.772	-0.032	-0.032	0.000	0.000	0.000	0.000
45	G	196	PRO	0	-0.002	0.010	19.271	0.022	0.022	0.000	0.000	0.000	0.000
46	G	197	ALA	0	-0.045	-0.038	21.236	0.016	0.016	0.000	0.000	0.000	0.000
47	G	198	LEU	0	0.036	0.020	24.887	-0.013	-0.013	0.000	0.000	0.000	0.000
48	G	199	ASP	-1	-0.885	-0.937	27.772	-0.152	-0.152	0.000	0.000	0.000	0.000
49	G	200	GLY	0	-0.023	-0.008	30.508	0.011	0.011	0.000	0.000	0.000	0.000
50	G	201	GLN	0	-0.045	-0.017	29.718	0.012	0.012	0.000	0.000	0.000	0.000
51	G	202	ARG	1	0.937	0.957	21.586	0.150	0.150	0.000	0.000	0.000	0.000
52	G	203	GLY	0	0.050	0.042	23.125	0.007	0.007	0.000	0.000	0.000	0.000
53	G	204	LYS	1	0.795	0.896	23.323	0.131	0.131	0.000	0.000	0.000	0.000
54	G	206	TRP	0	0.042	0.006	15.026	0.053	0.053	0.000	0.000	0.000	0.000
55	G	207	CYS	0	-0.072	-0.032	15.957	-0.036	-0.036	0.000	0.000	0.000	0.000
56	G	208	VAL	0	-0.015	-0.002	10.604	-0.015	-0.015	0.000	0.000	0.000	0.000
57	G	209	ASP	-1	-0.807	-0.895	9.272	0.209	0.209	0.000	0.000	0.000	0.000
58	G	210	ARG	1	0.941	0.959	7.936	-0.445	-0.445	0.000	0.000	0.000	0.000
59	G	211	LYS	1	0.975	1.003	5.079	-1.051	-1.051	0.000	0.000	0.000	0.000
60	G	212	THR	0	-0.046	-0.052	5.083	-0.555	-0.544	-0.001	-0.002	-0.008	0.000
61	G	213	GLY	0	0.042	0.025	7.773	-0.221	-0.221	0.000	0.000	0.000	0.000
62	G	214	VAL	0	-0.020	-0.012	9.324	0.019	0.019	0.000	0.000	0.000	0.000
63	G	215	LYS	1	0.846	0.925	12.712	0.251	0.251	0.000	0.000	0.000	0.000
64	G	216	LEU	0	0.004	0.004	14.756	0.027	0.027	0.000	0.000	0.000	0.000
65	G	217	PRO	0	-0.013	-0.014	17.573	-0.016	-0.016	0.000	0.000	0.000	0.000
66	G	218	GLY	0	0.068	0.030	21.419	0.013	0.013	0.000	0.000	0.000	0.000
67	G	219	GLY	0	-0.006	0.006	22.991	-0.021	-0.021	0.000	0.000	0.000	0.000
68	G	220	LEU	0	-0.005	-0.007	21.613	-0.003	-0.003	0.000	0.000	0.000	0.000
69	G	221	GLU	-1	-0.748	-0.890	23.242	-0.082	-0.082	0.000	0.000	0.000	0.000
70	G	222	PRO	0	0.025	0.026	23.582	-0.025	-0.025	0.000	0.000	0.000	0.000
71	G	223	LYS	1	0.996	0.981	20.014	0.123	0.123	0.000	0.000	0.000	0.000
72	G	224	GLY	0	-0.085	-0.054	22.899	0.009	0.009	0.000	0.000	0.000	0.000
73	G	225	GLU	-1	-0.858	-0.921	25.344	-0.064	-0.064	0.000	0.000	0.000	0.000
74	G	226	LEU	0	-0.044	0.002	19.705	0.006	0.006	0.000	0.000	0.000	0.000
75	G	227	ASP	-1	-0.845	-0.929	21.595	0.020	0.020	0.000	0.000	0.000	0.000
76	G	229	HIS	0	0.058	0.040	16.105	0.052	0.052	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:151:GLY)