FMO DATABASE

FMODB ID: 6YR1Z

Calculation Name: 2DSP-B-Xray372

Preferred Name: Insulin-like growth factor binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DSP

Chain ID: B

ChEMBL ID: CHEMBL2310

UniProt ID: P22692

Base Structure: X-ray

Registration Date: 2023-09-23

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533311.724566
FMO2-HF: Nuclear repulsion	495325.286134
FMO2-HF: Total energy	-37986.438431
FMO2-MP2: Total energy	-38084.207294

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(B:1:ASP)

Summations of interaction energy for fragment #1(B:1:ASP)

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.
2.536	-3.066	0.184	6.205	-0.787	0

Interaction energy analysis for fragmet #1(B:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.984 / q_NPA : -0.980

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].
3	B	3	ALA	0	0.040	-0.017	2.813	3.685	-2.007	0.185	6.233	-0.726
4	B	4	ILE	0	-0.102	-0.030	4.810	-7.086	-6.996	-0.001	-0.028	-0.061
5	B	5	HIS	0	0.041	0.029	7.550	-2.752	-2.752	0.000	0.000	0.000
6	B	6	CYS	0	-0.071	-0.052	11.081	-0.276	-0.276	0.000	0.000	0.000
7	B	7	PRO	0	0.031	0.019	14.608	0.293	0.293	0.000	0.000	0.000
8	B	8	PRO	0	0.009	0.009	16.438	-0.313	-0.313	0.000	0.000	0.000
9	B	9	CYS	0	-0.033	-0.042	18.732	-0.053	-0.053	0.000	0.000	0.000
10	B	10	SER	0	0.031	0.013	22.238	-0.111	-0.111	0.000	0.000	0.000
11	B	11	GLU	-1	-0.852	-0.936	25.029	10.228	10.228	0.000	0.000	0.000
12	B	12	GLU	-1	-0.851	-0.897	28.493	9.226	9.226	0.000	0.000	0.000
13	B	13	LYS	1	0.863	0.924	25.305	-11.641	-11.641	0.000	0.000	0.000
14	B	14	LEU	0	0.029	-0.012	25.591	-0.226	-0.226	0.000	0.000	0.000
15	B	15	ALA	0	0.018	0.022	29.058	-0.212	-0.212	0.000	0.000	0.000
16	B	16	ARG	1	0.792	0.877	31.381	-9.667	-9.667	0.000	0.000	0.000
17	B	17	CYS	0	-0.159	-0.043	24.188	-0.264	-0.264	0.000	0.000	0.000
18	B	18	ARG	1	1.002	0.999	32.049	-8.618	-8.618	0.000	0.000	0.000
19	B	19	PRO	0	-0.010	-0.011	34.195	0.181	0.181	0.000	0.000	0.000
20	B	20	PRO	0	-0.019	0.011	32.734	-0.256	-0.256	0.000	0.000	0.000
21	B	21	VAL	0	0.005	-0.012	35.715	-0.106	-0.106	0.000	0.000	0.000
22	B	22	GLY	0	-0.001	-0.004	38.573	0.060	0.060	0.000	0.000	0.000
23	B	23	CYS	0	-0.073	-0.032	30.779	0.050	0.050	0.000	0.000	0.000
24	B	24	GLU	-1	-0.885	-0.934	36.709	8.231	8.231	0.000	0.000	0.000
25	B	25	GLU	-1	-0.864	-0.931	30.254	10.594	10.594	0.000	0.000	0.000
26	B	26	LEU	0	-0.037	-0.026	30.924	0.021	0.021	0.000	0.000	0.000
27	B	27	VAL	0	0.016	0.026	26.184	0.340	0.340	0.000	0.000	0.000
28	B	28	ARG	1	0.862	0.900	18.415	-15.495	-15.495	0.000	0.000	0.000
29	B	29	GLU	-1	-0.787	-0.898	24.775	11.672	11.672	0.000	0.000	0.000
30	B	30	PRO	0	0.038	0.033	22.669	0.734	0.734	0.000	0.000	0.000
31	B	31	GLY	0	0.025	0.016	18.698	-0.045	-0.045	0.000	0.000	0.000
32	B	33	GLY	0	0.027	0.038	19.150	-0.281	-0.281	0.000	0.000	0.000
33	B	36	ALA	0	0.048	0.021	26.561	0.439	0.439	0.000	0.000	0.000
34	B	37	THR	0	-0.028	-0.020	28.616	-0.164	-0.164	0.000	0.000	0.000
35	B	39	ALA	0	0.008	0.018	29.924	0.299	0.299	0.000	0.000	0.000
36	B	40	LEU	0	-0.024	-0.012	28.733	-0.379	-0.379	0.000	0.000	0.000
37	B	41	GLY	0	0.078	-0.002	30.975	0.216	0.216	0.000	0.000	0.000
38	B	42	LEU	0	0.000	-0.022	32.494	0.213	0.213	0.000	0.000	0.000
39	B	43	GLY	0	-0.010	-0.004	32.629	-0.298	-0.298	0.000	0.000	0.000
40	B	44	MET	0	-0.038	0.025	32.462	-0.086	-0.086	0.000	0.000	0.000
41	B	45	PRO	0	0.032	0.003	31.303	0.339	0.339	0.000	0.000	0.000
42	B	46	CYS	0	-0.056	-0.002	23.448	-0.348	-0.348	0.000	0.000	0.000
43	B	47	GLY	0	0.026	-0.010	24.483	0.000	0.000	0.000	0.000	0.000
44	B	48	VAL	0	-0.057	-0.031	19.577	0.082	0.082	0.000	0.000	0.000
45	B	49	TYR	0	-0.022	-0.017	20.532	0.308	0.308	0.000	0.000	0.000
46	B	50	THR	0	0.005	0.023	24.513	-0.401	-0.401	0.000	0.000	0.000
47	B	51	PRO	0	-0.003	-0.011	25.746	0.427	0.427	0.000	0.000	0.000
48	B	52	ARG	1	0.852	0.923	19.406	-14.571	-14.571	0.000	0.000	0.000
49	B	53	CYS	0	-0.059	-0.010	25.810	0.102	0.102	0.000	0.000	0.000
50	B	54	GLY	0	0.031	0.025	26.764	0.336	0.336	0.000	0.000	0.000
51	B	55	SER	0	-0.045	-0.032	26.704	0.339	0.339	0.000	0.000	0.000
52	B	56	GLY	0	0.020	0.005	26.764	-0.327	-0.327	0.000	0.000	0.000
53	B	57	LEU	0	-0.016	0.005	27.200	-0.264	-0.264	0.000	0.000	0.000
54	B	58	ARG	1	0.950	0.980	18.848	-15.601	-15.601	0.000	0.000	0.000
55	B	60	TYR	0	0.010	-0.017	21.460	1.175	1.175	0.000	0.000	0.000
56	B	61	PRO	0	0.011	0.016	23.746	-0.551	-0.551	0.000	0.000	0.000
57	B	62	PRO	0	0.031	0.000	26.713	0.052	0.052	0.000	0.000	0.000
58	B	63	ARG	1	0.819	0.859	29.164	-9.824	-9.824	0.000	0.000	0.000
59	B	64	GLY	0	0.011	0.030	29.438	-0.145	-0.145	0.000	0.000	0.000
60	B	65	VAL	0	-0.039	-0.008	27.803	-0.176	-0.176	0.000	0.000	0.000
61	B	66	GLU	-1	-0.879	-0.932	28.883	10.549	10.549	0.000	0.000	0.000
62	B	67	LYS	1	0.897	0.944	25.929	-11.621	-11.621	0.000	0.000	0.000
63	B	68	PRO	0	0.092	0.040	22.995	0.127	0.127	0.000	0.000	0.000
64	B	69	LEU	0	0.051	0.022	18.401	0.003	0.003	0.000	0.000	0.000
65	B	70	HIS	0	0.022	-0.006	21.904	-0.302	-0.302	0.000	0.000	0.000
66	B	71	THR	0	0.029	0.025	24.425	-0.345	-0.345	0.000	0.000	0.000
67	B	72	LEU	0	0.020	0.010	21.053	-0.226	-0.226	0.000	0.000	0.000
68	B	73	MET	0	-0.069	-0.023	19.836	0.253	0.253	0.000	0.000	0.000
69	B	74	HIS	0	-0.034	-0.021	23.487	-0.070	-0.070	0.000	0.000	0.000
70	B	75	GLY	0	-0.020	0.000	26.365	-0.450	-0.450	0.000	0.000	0.000
71	B	76	GLN	0	-0.053	-0.028	28.052	-0.166	-0.166	0.000	0.000	0.000
72	B	77	GLY	0	0.008	0.009	27.141	-0.059	-0.059	0.000	0.000	0.000
73	B	78	VAL	0	0.024	-0.002	28.160	-0.400	-0.400	0.000	0.000	0.000
74	B	80	MET	0	0.010	0.026	27.493	-0.366	-0.366	0.000	0.000	0.000
75	B	81	GLU	-1	-0.822	-0.900	27.819	11.331	11.331	0.000	0.000	0.000
76	B	82	LEU	0	0.005	-0.035	23.799	0.246	0.246	0.000	0.000	0.000
77	B	83	ALA	0	0.035	0.018	26.731	0.207	0.207	0.000	0.000	0.000
78	B	84	GLU	-1	-0.818	-0.885	29.334	10.151	10.151	0.000	0.000	0.000
79	B	85	ILE	0	-0.036	-0.028	23.135	0.128	0.128	0.000	0.000	0.000
80	B	86	GLU	-1	-0.942	-0.964	24.944	12.872	12.872	0.000	0.000	0.000
81	B	87	ALA	0	0.036	0.016	25.953	-0.001	-0.001	0.000	0.000	0.000
82	B	88	ILE	0	-0.057	-0.022	26.462	-0.131	-0.131	0.000	0.000	0.000
83	B	89	GLN	0	-0.055	-0.023	20.058	-0.118	-0.118	0.000	0.000	0.000
84	B	90	GLU	-1	-0.939	-0.962	24.599	12.206	12.206	0.000	0.000	0.000
85	B	91	SER	0	-0.118	-0.062	26.548	-0.433	-0.433	0.000	0.000	0.000
86	B	92	LEU	0	-0.070	-0.026	24.638	0.046	0.046	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ASP)