FMO DATABASE

FMODB ID: 436VN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-471648.538222
FMO2-HF: Nuclear repulsion	439687.88311
FMO2-HF: Total energy	-31960.655112
FMO2-MP2: Total energy	-32049.976548

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.
-5.477	0.512	3.128	-4.014	-5.102	-0.03

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 : 0.032 / q_NPA : 0.011

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	G	153	CYS	0	-0.016	0.010	3.440	0.397	1.859	-0.001	-0.685	-0.777	0.000
4	G	154	GLN	0	0.056	0.023	2.882	0.504	1.257	0.080	-0.227	-0.605	-0.001
5	G	155	SER	0	-0.026	-0.014	4.500	1.659	1.842	-0.001	-0.037	-0.145	0.000
6	G	156	GLU	-1	-0.962	-0.992	6.450	-0.740	-0.740	0.000	0.000	0.000	0.000
7	G	157	LEU	0	-0.004	-0.009	7.711	0.348	0.348	0.000	0.000	0.000	0.000
8	G	158	HIS	0	-0.013	-0.003	8.465	0.206	0.206	0.000	0.000	0.000	0.000
9	G	159	ARG	1	0.986	0.992	10.303	0.709	0.709	0.000	0.000	0.000	0.000
10	G	160	ALA	0	-0.012	0.000	12.182	0.098	0.098	0.000	0.000	0.000	0.000
11	G	161	LEU	0	0.020	-0.003	12.259	0.078	0.078	0.000	0.000	0.000	0.000
12	G	162	GLU	-1	-0.949	-0.959	14.652	-0.122	-0.122	0.000	0.000	0.000	0.000
13	G	163	ARG	1	0.938	0.960	16.468	0.323	0.323	0.000	0.000	0.000	0.000
14	G	164	LEU	0	-0.026	-0.010	16.880	0.034	0.034	0.000	0.000	0.000	0.000
15	G	165	ALA	0	0.021	0.020	19.253	0.024	0.024	0.000	0.000	0.000	0.000
16	G	166	ALA	0	-0.044	-0.010	21.140	0.021	0.021	0.000	0.000	0.000	0.000
17	G	167	SER	0	-0.046	-0.031	23.033	0.013	0.013	0.000	0.000	0.000	0.000
18	G	168	GLN	0	-0.012	0.020	25.054	-0.005	-0.005	0.000	0.000	0.000	0.000
19	G	169	SER	0	0.015	-0.022	27.214	0.004	0.004	0.000	0.000	0.000	0.000
20	G	170	ARG	1	0.813	0.925	22.544	0.182	0.182	0.000	0.000	0.000	0.000
21	G	171	THR	0	0.031	0.012	25.605	0.002	0.002	0.000	0.000	0.000	0.000
22	G	172	HIS	0	0.016	-0.028	23.750	-0.024	-0.024	0.000	0.000	0.000	0.000
23	G	173	GLU	-1	-0.889	-0.932	23.976	-0.170	-0.170	0.000	0.000	0.000	0.000
24	G	174	ASP	-1	-0.813	-0.914	23.112	-0.190	-0.190	0.000	0.000	0.000	0.000
25	G	175	LEU	0	-0.033	-0.016	18.589	-0.025	-0.025	0.000	0.000	0.000	0.000
26	G	176	TYR	0	-0.026	-0.011	19.415	-0.044	-0.044	0.000	0.000	0.000	0.000
27	G	177	ILE	0	-0.032	-0.006	20.724	-0.020	-0.020	0.000	0.000	0.000	0.000
28	G	178	ILE	0	-0.076	-0.037	17.093	-0.017	-0.017	0.000	0.000	0.000	0.000
29	G	179	PRO	0	-0.001	0.013	15.624	-0.006	-0.006	0.000	0.000	0.000	0.000
30	G	180	ILE	0	-0.012	-0.017	12.283	-0.066	-0.066	0.000	0.000	0.000	0.000
31	G	181	PRO	0	-0.010	0.012	9.117	0.050	0.050	0.000	0.000	0.000	0.000
32	G	182	ASN	0	-0.009	-0.020	10.923	-0.040	-0.040	0.000	0.000	0.000	0.000
33	G	184	ASP	-1	-0.854	-0.935	6.433	-1.217	-1.217	0.000	0.000	0.000	0.000
34	G	185	ARG	1	0.956	0.953	6.893	-0.058	-0.058	0.000	0.000	0.000	0.000
35	G	186	ASN	0	-0.053	-0.026	5.030	0.374	0.374	0.000	0.000	0.000	0.000
36	G	187	GLY	0	0.047	0.043	2.580	-1.783	-0.631	0.370	-0.691	-0.831	-0.004
37	G	188	ASN	0	-0.057	-0.027	2.540	-5.916	-3.522	2.679	-2.352	-2.721	-0.025
38	G	189	PHE	0	0.023	0.034	4.007	0.154	0.194	0.002	-0.020	-0.021	0.000
39	G	190	HIS	0	-0.020	-0.007	7.260	0.278	0.278	0.000	0.000	0.000	0.000
40	G	191	PRO	0	0.001	0.001	10.569	-0.006	-0.006	0.000	0.000	0.000	0.000
41	G	192	LYS	1	0.822	0.913	12.799	0.318	0.318	0.000	0.000	0.000	0.000
42	G	193	GLN	0	-0.022	-0.005	10.653	-0.051	-0.051	0.000	0.000	0.000	0.000
43	G	194	CYS	0	-0.066	-0.040	15.033	0.041	0.041	0.000	0.000	0.000	0.000
44	G	195	HIS	0	0.056	0.041	17.739	-0.026	-0.026	0.000	0.000	0.000	0.000
45	G	196	PRO	0	0.005	0.013	19.158	0.006	0.006	0.000	0.000	0.000	0.000
46	G	197	ALA	0	-0.046	-0.036	21.222	0.015	0.015	0.000	0.000	0.000	0.000
47	G	198	LEU	0	0.037	0.015	24.889	-0.003	-0.003	0.000	0.000	0.000	0.000
48	G	199	ASP	-1	-0.891	-0.937	27.732	-0.134	-0.134	0.000	0.000	0.000	0.000
49	G	200	GLY	0	-0.022	-0.005	30.497	0.007	0.007	0.000	0.000	0.000	0.000
50	G	201	GLN	0	-0.037	-0.016	29.718	0.000	0.000	0.000	0.000	0.000	0.000
51	G	202	ARG	1	0.939	0.962	21.807	0.227	0.227	0.000	0.000	0.000	0.000
52	G	203	GLY	0	0.043	0.037	23.092	0.009	0.009	0.000	0.000	0.000	0.000
53	G	204	LYS	1	0.939	0.962	23.292	0.169	0.169	0.000	0.000	0.000	0.000
54	G	206	TRP	0	0.036	0.012	15.073	0.057	0.057	0.000	0.000	0.000	0.000
55	G	207	CYS	0	-0.075	-0.034	15.943	-0.040	-0.040	0.000	0.000	0.000	0.000
56	G	208	VAL	0	-0.021	-0.003	10.569	0.025	0.025	0.000	0.000	0.000	0.000
57	G	209	ASP	-1	-0.820	-0.905	9.353	-0.350	-0.350	0.000	0.000	0.000	0.000
58	G	210	ARG	1	0.967	0.970	7.878	0.336	0.336	0.000	0.000	0.000	0.000
59	G	211	LYS	1	0.952	0.990	5.087	-0.717	-0.717	0.000	0.000	0.000	0.000
60	G	212	THR	0	-0.061	-0.042	5.083	-0.384	-0.379	-0.001	-0.002	-0.002	0.000
61	G	213	GLY	0	0.063	0.033	7.772	-0.097	-0.097	0.000	0.000	0.000	0.000
62	G	214	VAL	0	-0.018	-0.016	9.308	0.080	0.080	0.000	0.000	0.000	0.000
63	G	215	LYS	1	0.873	0.941	12.701	0.276	0.276	0.000	0.000	0.000	0.000
64	G	216	LEU	0	0.005	0.002	14.789	0.038	0.038	0.000	0.000	0.000	0.000
65	G	217	PRO	0	-0.008	-0.014	17.567	-0.003	-0.003	0.000	0.000	0.000	0.000
66	G	218	GLY	0	0.056	0.028	21.412	0.000	0.000	0.000	0.000	0.000	0.000
67	G	219	GLY	0	-0.022	-0.008	22.976	-0.011	-0.011	0.000	0.000	0.000	0.000
68	G	220	LEU	0	-0.041	-0.026	21.677	-0.015	-0.015	0.000	0.000	0.000	0.000
69	G	221	GLU	-1	-0.851	-0.926	23.218	-0.148	-0.148	0.000	0.000	0.000	0.000
70	G	222	PRO	0	0.020	0.010	23.558	-0.028	-0.028	0.000	0.000	0.000	0.000
71	G	223	LYS	1	0.987	0.966	19.791	0.285	0.285	0.000	0.000	0.000	0.000
72	G	224	GLY	0	-0.069	-0.047	22.877	-0.009	-0.009	0.000	0.000	0.000	0.000
73	G	225	GLU	-1	-0.864	-0.915	25.322	-0.139	-0.139	0.000	0.000	0.000	0.000
74	G	226	LEU	0	-0.031	0.001	19.130	0.001	0.001	0.000	0.000	0.000	0.000
75	G	227	ASP	-1	-0.872	-0.944	21.641	-0.194	-0.194	0.000	0.000	0.000	0.000
76	G	229	HIS	0	0.041	0.025	16.031	-0.027	-0.027	0.000	0.000	0.000	0.000

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