FMO DATABASE

FMODB ID: 2N54R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-319329.40721
FMO2-HF: Nuclear repulsion	291900.10729
FMO2-HF: Total energy	-27429.29992
FMO2-MP2: Total energy	-27500.314337

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.
-3.716	-0.113	-0.052	-2.044	-1.507	-0.004

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 : -0.012 / q_NPA : -0.024

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	3	DVA	0	0.016	0.023	3.676	-2.692	0.911	-0.052	-2.044	-1.507	-0.004
4	A	4	HIS	0	0.072	0.044	6.531	-0.585	-0.585	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.024	0.005	7.766	0.218	0.218	0.000	0.000	0.000	0.000
6	A	6	CYS	0	0.017	0.028	10.575	0.154	0.154	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.092	-0.038	10.813	0.197	0.197	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.807	-0.910	12.808	-0.571	-0.571	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.057	-0.033	11.704	0.063	0.063	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.062	-0.028	13.736	0.071	0.071	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.018	0.000	17.126	0.053	0.053	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.130	-0.066	14.773	0.023	0.023	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.858	-0.924	16.087	-0.240	-0.240	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.038	-0.032	16.015	-0.075	-0.075	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.924	0.968	14.614	0.844	0.844	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.888	-0.953	17.942	-0.272	-0.272	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.037	-0.004	21.742	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.939	-0.972	17.744	-0.584	-0.584	0.000	0.000	0.000	0.000
19	A	19	HIS	0	-0.004	-0.008	20.235	0.026	0.026	0.000	0.000	0.000	0.000
20	A	20	CYS	0	-0.109	-0.030	16.946	0.037	0.037	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.015	0.015	12.030	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.017	-0.025	12.303	-0.112	-0.112	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.036	0.008	14.422	0.086	0.086	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.054	-0.028	17.125	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.013	-0.001	19.450	0.012	0.012	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.942	-0.974	16.734	-0.531	-0.531	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.029	-0.017	15.216	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	30	TYR	0	0.052	0.035	16.926	0.073	0.073	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.007	-0.014	20.281	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	32	LEU	0	0.002	0.001	21.553	0.020	0.020	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.020	0.000	24.021	0.026	0.026	0.000	0.000	0.000	0.000
32	A	34	SER	0	0.044	0.026	27.809	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.022	-0.002	29.720	0.010	0.010	0.000	0.000	0.000	0.000
34	A	36	THR	0	-0.052	-0.031	25.375	0.009	0.009	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.038	-0.020	27.740	0.003	0.003	0.000	0.000	0.000	0.000
36	A	38	CYS	0	-0.008	0.000	22.129	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.960	0.974	24.252	0.127	0.127	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.969	0.971	26.795	0.163	0.163	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.002	0.010	29.910	0.002	0.002	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.916	0.934	29.700	0.078	0.078	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.033	0.019	34.416	0.002	0.002	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.827	-0.911	37.173	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.036	-0.007	36.742	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.028	-0.004	36.051	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.110	-0.036	31.352	0.006	0.006	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.804	-0.894	28.195	-0.130	-0.130	0.000	0.000	0.000	0.000
47	A	49	TYR	0	-0.004	-0.021	28.797	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.034	-0.020	26.925	0.009	0.009	0.000	0.000	0.000	0.000
49	A	52	GLY	0	-0.009	0.006	26.997	0.014	0.014	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.023	-0.009	26.869	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	54	THR	0	-0.025	0.001	23.993	0.006	0.006	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.056	0.035	18.976	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.896	-0.948	20.422	-0.237	-0.237	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.005	0.011	24.478	0.021	0.021	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.955	0.977	27.788	0.086	0.086	0.000	0.000	0.000	0.000
56	A	60	ASN	0	0.006	-0.018	30.244	0.009	0.009	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.909	0.943	30.252	0.125	0.125	0.000	0.000	0.000	0.000
58	A	62	TYR	0	0.004	0.015	35.981	0.006	0.006	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.054	-0.021	33.306	0.008	0.008	0.000	0.000	0.000	0.000
60	A	64	VAL	0	0.001	0.008	37.213	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)