FMO DATABASE

FMODB ID: VR1L1

Calculation Name: 5DOL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DOL

Chain ID: A

ChEMBL ID:

UniProt ID: P37542

Base Structure: X-ray

Registration Date: 2023-06-20

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-275149.724778
FMO2-HF: Nuclear repulsion	249558.504666
FMO2-HF: Total energy	-25591.220113
FMO2-MP2: Total energy	-25666.787681

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(A:2:ASP)

Summations of interaction energy for fragment #1(A:2: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.
31.382	32.662	10.75	-5.82	-6.21	0.02

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.844 / q_NPA : -0.946

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	A	4	LYS	1	0.834	0.891	2.788	-40.494	-37.704	0.217	-1.258	-1.749	0.005
4	A	5	GLU	-1	-0.924	-0.942	1.574	40.664	38.473	10.530	-4.461	-3.878	0.015
5	A	6	LEU	0	0.074	0.073	3.308	-6.346	-5.770	0.004	-0.094	-0.487	0.000
6	A	7	PHE	0	-0.014	-0.033	4.860	-4.302	-4.197	-0.001	-0.007	-0.096	0.000
7	A	8	ASP	-1	-0.778	-0.887	7.106	27.191	27.191	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.002	-0.011	6.312	-2.832	-2.832	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.026	-0.020	8.963	-2.193	-2.193	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.018	0.017	11.095	-1.309	-1.309	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.010	0.025	11.926	-2.067	-2.067	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.012	-0.009	12.835	-1.351	-1.351	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.943	-0.969	15.102	15.387	15.387	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.929	-0.970	16.663	15.903	15.903	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.082	-0.053	15.449	-1.544	-1.544	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.005	0.007	19.044	-0.902	-0.902	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.011	0.003	21.068	-0.682	-0.682	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.053	-0.046	22.291	-0.831	-0.831	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.020	0.001	22.345	-0.533	-0.533	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.033	-0.004	25.285	-0.568	-0.568	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.962	0.984	24.182	-11.680	-11.680	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.007	0.003	25.794	-0.568	-0.568	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.016	0.005	29.522	-0.351	-0.351	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.027	-0.015	31.308	-0.333	-0.333	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.867	-0.939	32.480	8.835	8.835	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.015	-0.009	33.661	-0.301	-0.301	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.934	0.965	35.383	-8.530	-8.530	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.019	-0.008	37.312	-0.225	-0.225	0.000	0.000	0.000	0.000
29	A	30	HIS	0	0.017	0.006	38.043	-0.245	-0.245	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.034	-0.010	37.782	-0.191	-0.191	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.011	-0.007	41.318	-0.180	-0.180	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.889	-0.949	43.343	6.910	6.910	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.026	0.015	43.742	-0.151	-0.151	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.059	-0.024	43.734	-0.172	-0.172	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.966	-0.993	47.208	6.221	6.221	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.935	-0.957	48.842	6.074	6.074	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.030	-0.022	49.699	-0.134	-0.134	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.058	-0.029	51.470	-0.136	-0.136	0.000	0.000	0.000	0.000
39	A	40	HIS	0	0.045	0.005	52.220	-0.223	-0.223	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.068	0.046	52.973	-0.147	-0.147	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.056	-0.024	53.966	-0.070	-0.070	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.069	-0.036	57.475	-0.138	-0.138	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.881	-0.936	59.289	5.089	5.089	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.027	-0.017	59.968	-0.134	-0.134	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.935	0.958	59.310	-5.275	-5.275	0.000	0.000	0.000	0.000
46	A	47	HIS	0	0.019	0.012	63.608	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.004	0.001	63.332	-0.107	-0.107	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.926	0.967	62.741	-4.934	-4.934	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.929	0.976	67.555	-4.386	-4.386	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.941	0.983	69.426	-4.349	-4.349	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.036	-0.007	69.366	-0.072	-0.072	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.887	-0.915	71.787	4.269	4.269	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.907	-0.956	73.636	4.186	4.186	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.040	-0.023	74.427	-0.073	-0.073	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.036	-0.040	74.929	-0.057	-0.057	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.013	0.006	77.605	-0.062	-0.062	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.101	-0.058	79.025	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.019	-0.021	79.387	-0.055	-0.055	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.981	-0.978	81.692	3.808	3.808	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.869	0.960	83.492	-3.757	-3.757	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.021	-0.003	84.787	-0.049	-0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)