FMO DATABASE

FMODB ID: 82VLY

Calculation Name: 1RP3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RP3

Chain ID: B

ChEMBL ID:

UniProt ID: O67268

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	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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-392613.663328
FMO2-HF: Nuclear repulsion	362243.415886
FMO2-HF: Total energy	-30370.247441
FMO2-MP2: Total energy	-30461.074326

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:2:VAL)

Summations of interaction energy for fragment #1(B:2:VAL)

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.
-21.493	-15.782	16.294	-10.202	-11.802	-0.002

Interaction energy analysis for fragmet #1(B:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.001

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	B	4	ARG	1	0.934	0.939	3.326	-5.834	-1.075	-0.023	-2.434	-2.302	0.008
4	B	5	ILE	0	0.007	0.002	2.618	-4.456	-2.588	1.709	-1.318	-2.259	0.014
5	B	6	GLU	-1	-0.751	-0.838	1.990	-5.303	-6.891	10.335	-5.176	-3.571	-0.003
6	B	7	LEU	0	0.014	0.014	3.164	-0.614	-0.846	0.069	0.487	-0.324	-0.001
7	B	8	SER	0	-0.017	-0.011	5.983	-0.321	-0.321	0.000	0.000	0.000	0.000
8	B	9	ARG	1	0.830	0.897	6.378	-0.513	-0.513	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.047	-0.025	6.288	-0.264	-0.264	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.020	0.001	9.013	-0.092	-0.092	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.008	0.010	10.975	-0.069	-0.069	0.000	0.000	0.000	0.000
12	B	13	LEU	0	-0.021	-0.016	10.995	-0.067	-0.067	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.022	-0.015	13.454	-0.045	-0.045	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.045	-0.037	15.299	-0.020	-0.020	0.000	0.000	0.000	0.000
15	B	16	GLU	-1	-0.942	-0.939	16.846	0.219	0.219	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.109	-0.031	18.391	-0.033	-0.033	0.000	0.000	0.000	0.000
17	B	28	SER	0	-0.007	-0.026	23.704	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	29	GLY	0	0.087	0.061	21.440	0.009	0.009	0.000	0.000	0.000	0.000
19	B	30	THR	0	-0.104	-0.052	22.104	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	31	ASN	0	0.056	0.004	21.426	-0.015	-0.015	0.000	0.000	0.000	0.000
21	B	32	LYS	1	0.967	0.993	20.809	0.038	0.038	0.000	0.000	0.000	0.000
22	B	33	ILE	0	-0.010	-0.003	20.829	-0.016	-0.016	0.000	0.000	0.000	0.000
23	B	34	GLU	-1	-0.846	-0.924	17.765	-0.039	-0.039	0.000	0.000	0.000	0.000
24	B	35	ASP	-1	-0.810	-0.922	16.319	-0.014	-0.014	0.000	0.000	0.000	0.000
25	B	36	LYS	1	0.882	0.959	15.966	0.190	0.190	0.000	0.000	0.000	0.000
26	B	37	VAL	0	0.011	-0.008	13.072	-0.047	-0.047	0.000	0.000	0.000	0.000
27	B	38	THR	0	0.024	0.014	11.577	-0.094	-0.094	0.000	0.000	0.000	0.000
28	B	39	LEU	0	0.009	-0.007	11.211	-0.056	-0.056	0.000	0.000	0.000	0.000
29	B	40	SER	0	-0.073	-0.034	12.236	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	41	LYS	1	0.947	0.978	7.771	0.415	0.415	0.000	0.000	0.000	0.000
31	B	42	ILE	0	0.013	0.006	7.415	-0.250	-0.250	0.000	0.000	0.000	0.000
32	B	43	ALA	0	0.016	0.005	8.559	-0.091	-0.091	0.000	0.000	0.000	0.000
33	B	44	GLN	0	-0.002	0.000	8.039	0.083	0.083	0.000	0.000	0.000	0.000
34	B	45	GLU	-1	-0.884	-0.932	2.488	-6.156	-5.760	3.626	-1.536	-2.485	-0.022
35	B	46	LEU	0	-0.055	-0.031	5.432	0.002	0.002	0.000	0.000	0.000	0.000
36	B	47	SER	0	-0.019	0.009	8.092	0.095	0.095	0.000	0.000	0.000	0.000
37	B	48	LYS	1	0.794	0.894	2.650	2.341	2.849	0.578	-0.225	-0.861	0.002
38	B	49	ASN	0	-0.071	-0.048	5.982	-0.048	-0.048	0.000	0.000	0.000	0.000
39	B	50	ASP	-1	-0.840	-0.920	9.503	-0.325	-0.325	0.000	0.000	0.000	0.000
40	B	51	VAL	0	-0.041	-0.030	12.653	0.004	0.004	0.000	0.000	0.000	0.000
41	B	52	GLU	-1	-0.917	-0.972	15.933	-0.123	-0.123	0.000	0.000	0.000	0.000
42	B	53	GLU	-1	-0.879	-0.923	17.784	-0.155	-0.155	0.000	0.000	0.000	0.000
43	B	54	LYS	1	0.818	0.921	16.417	0.158	0.158	0.000	0.000	0.000	0.000
44	B	55	ASP	-1	-0.861	-0.958	21.416	-0.073	-0.073	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.016	0.014	24.207	0.011	0.011	0.000	0.000	0.000	0.000
46	B	57	GLU	-1	-0.738	-0.888	26.063	-0.092	-0.092	0.000	0.000	0.000	0.000
47	B	58	LYS	1	0.808	0.909	24.922	0.100	0.100	0.000	0.000	0.000	0.000
48	B	59	LYS	1	0.975	0.994	27.785	0.058	0.058	0.000	0.000	0.000	0.000
49	B	60	VAL	0	0.020	0.013	29.878	0.006	0.006	0.000	0.000	0.000	0.000
50	B	61	LYS	1	0.848	0.919	32.168	0.055	0.055	0.000	0.000	0.000	0.000
51	B	62	GLU	-1	-0.884	-0.958	33.421	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	63	LEU	0	-0.014	-0.016	32.595	0.004	0.004	0.000	0.000	0.000	0.000
53	B	64	LYS	1	0.793	0.888	35.855	0.049	0.049	0.000	0.000	0.000	0.000
54	B	65	GLU	-1	-0.809	-0.879	38.003	-0.040	-0.040	0.000	0.000	0.000	0.000
55	B	66	LYS	1	0.917	0.957	37.737	0.026	0.026	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.025	-0.002	38.083	0.003	0.003	0.000	0.000	0.000	0.000
57	B	68	GLU	-1	-0.869	-0.923	41.736	-0.040	-0.040	0.000	0.000	0.000	0.000
58	B	69	LYS	1	0.777	0.882	42.396	0.034	0.034	0.000	0.000	0.000	0.000
59	B	70	GLY	0	0.014	0.014	45.017	0.002	0.002	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.959	-0.968	42.733	-0.019	-0.019	0.000	0.000	0.000	0.000
61	B	72	TYR	0	-0.017	-0.030	36.206	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	73	GLU	-1	-0.913	-0.948	41.080	-0.010	-0.010	0.000	0.000	0.000	0.000
63	B	74	VAL	0	-0.003	0.007	40.420	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	75	SER	0	0.059	0.016	40.822	0.001	0.001	0.000	0.000	0.000	0.000
65	B	76	ASP	-1	-0.859	-0.940	40.766	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	77	GLU	-1	-0.954	-0.985	38.256	0.001	0.001	0.000	0.000	0.000	0.000
67	B	78	LYS	1	0.916	0.966	36.599	0.013	0.013	0.000	0.000	0.000	0.000
68	B	79	VAL	0	-0.014	0.000	35.701	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	80	VAL	0	0.001	0.005	36.356	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.844	0.909	30.251	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	82	GLY	0	-0.005	-0.007	31.901	0.000	0.000	0.000	0.000	0.000	0.000
72	B	83	LEU	0	-0.010	-0.012	31.466	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	84	ILE	0	0.010	0.004	32.432	0.000	0.000	0.000	0.000	0.000	0.000
74	B	85	GLU	-1	-0.865	-0.905	27.712	0.008	0.008	0.000	0.000	0.000	0.000
75	B	86	PHE	0	-0.060	-0.018	26.497	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	87	PHE	0	-0.038	-0.027	27.892	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	88	THR	0	-0.100	-0.044	28.254	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:VAL)