FMO DATABASE

FMODB ID: 6YRZZ

Calculation Name: 1RMR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RMR

Chain ID: A

ChEMBL ID:

UniProt ID: P83658

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-319605.806711
FMO2-HF: Nuclear repulsion	292176.059317
FMO2-HF: Total energy	-27429.747394
FMO2-MP2: Total energy	-27500.746225

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:1:ASN)

Summations of interaction energy for fragment #1(A:1:ASN)

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.
-3.927	-0.161	-0.047	-2.146	-1.574	-0.002

Interaction energy analysis for fragmet #1(A:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.031

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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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	3	DVA	0	0.032	0.017	3.566	-2.091	1.675	-0.047	-2.146	-1.574	-0.002
4	A	4	HIS	0	0.054	0.033	5.640	-1.132	-1.132	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.014	-0.001	7.008	0.192	0.192	0.000	0.000	0.000	0.000
6	A	6	CYS	0	0.029	0.031	9.597	0.189	0.189	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.067	-0.024	10.613	0.250	0.250	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.823	-0.921	12.353	-1.007	-1.007	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.084	-0.048	11.730	0.092	0.092	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.045	-0.023	13.794	0.087	0.087	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.006	0.006	17.150	0.080	0.080	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.120	-0.061	15.043	0.050	0.050	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.898	-0.936	16.097	-0.319	-0.319	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.009	-0.022	15.712	-0.119	-0.119	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.924	0.971	12.547	1.310	1.310	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.886	-0.957	17.304	-0.363	-0.363	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.018	0.010	20.941	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.917	-0.940	16.617	-0.693	-0.693	0.000	0.000	0.000	0.000
19	A	19	HIS	0	-0.020	-0.020	19.692	0.039	0.039	0.000	0.000	0.000	0.000
20	A	20	CYS	0	-0.118	-0.032	17.197	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.016	0.017	11.950	-0.077	-0.077	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.007	-0.017	12.476	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.028	0.008	14.594	0.057	0.057	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.050	-0.029	17.449	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.009	0.002	20.095	0.014	0.014	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.918	-0.965	16.917	-0.352	-0.352	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.052	-0.028	15.007	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	30	TYR	0	0.016	0.010	16.546	0.060	0.060	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.009	-0.017	20.213	0.004	0.004	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.011	-0.003	21.695	0.016	0.016	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.040	0.009	24.169	0.011	0.011	0.000	0.000	0.000	0.000
32	A	34	SER	0	0.036	0.031	27.934	0.009	0.009	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.024	-0.005	29.928	0.006	0.006	0.000	0.000	0.000	0.000
34	A	36	THR	0	-0.058	-0.042	25.774	0.014	0.014	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.030	-0.014	28.287	0.003	0.003	0.000	0.000	0.000	0.000
36	A	38	CYS	0	-0.026	-0.014	22.193	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.889	0.932	25.094	0.013	0.013	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.928	0.962	27.622	0.028	0.028	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.008	0.007	30.743	0.010	0.010	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.909	0.933	30.601	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.047	0.019	35.221	0.002	0.002	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.789	-0.873	37.726	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.027	-0.006	37.632	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.072	-0.042	36.654	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.083	-0.026	32.227	0.009	0.009	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.763	-0.868	28.698	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.025	-0.008	29.505	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.030	-0.011	27.130	0.003	0.003	0.000	0.000	0.000	0.000
49	A	52	GLY	0	-0.009	0.001	27.162	0.008	0.008	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.027	-0.014	26.705	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	54	THR	0	-0.036	-0.013	24.005	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.049	0.033	19.062	0.006	0.006	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.873	-0.928	20.687	-0.131	-0.131	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.016	0.026	24.765	0.022	0.022	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.936	0.960	27.878	0.007	0.007	0.000	0.000	0.000	0.000
56	A	60	ASN	0	0.021	-0.007	30.357	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.895	0.928	30.112	0.066	0.066	0.000	0.000	0.000	0.000
58	A	62	TYR	0	0.015	0.019	36.042	0.002	0.002	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.072	-0.021	33.795	0.009	0.009	0.000	0.000	0.000	0.000
60	A	64	VAL	0	0.015	0.015	37.343	-0.001	-0.001	0.000	0.000	0.000	0.000

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