FMO DATABASE

FMODB ID: R9NQ8

Calculation Name: 3R84-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R84

Chain ID: B

ChEMBL ID:

UniProt ID: Q99278

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptAll
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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-441008.583517
FMO2-HF: Nuclear repulsion	408993.735114
FMO2-HF: Total energy	-32014.848403
FMO2-MP2: Total energy	-32107.533565

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:SER)

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

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.
-23.507	-23.086	7.034	-3.351	-4.105	0.033

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.017

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	GLN	0	-0.026	-0.008	3.097	-2.880	-0.636	0.001	-1.042	-1.203	0.001
4	B	5	ALA	0	0.079	0.037	4.039	0.522	0.789	0.000	-0.052	-0.215	0.000
5	B	6	LEU	0	-0.047	-0.019	4.905	0.524	0.723	-0.001	-0.025	-0.173	0.000
6	B	7	TYR	0	0.003	0.007	7.409	0.203	0.203	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.791	-0.881	7.921	-1.656	-1.656	0.000	0.000	0.000	0.000
8	B	9	LYS	1	0.809	0.892	9.423	0.332	0.332	0.000	0.000	0.000	0.000
9	B	10	LEU	0	0.003	0.016	11.232	0.072	0.072	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.916	-0.959	13.212	-0.140	-0.140	0.000	0.000	0.000	0.000
11	B	12	GLN	0	0.026	0.029	14.015	0.059	0.059	0.000	0.000	0.000	0.000
12	B	13	THR	0	-0.017	-0.029	14.600	0.016	0.016	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.963	0.983	17.109	-0.058	-0.058	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.010	-0.008	18.392	0.013	0.013	0.000	0.000	0.000	0.000
15	B	16	ILE	0	0.005	0.009	18.334	0.010	0.010	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.020	-0.010	20.222	0.011	0.011	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.048	-0.032	23.063	0.005	0.005	0.000	0.000	0.000	0.000
18	B	19	VAL	0	0.035	0.018	24.415	0.004	0.004	0.000	0.000	0.000	0.000
19	B	20	LYS	1	0.790	0.886	24.629	0.103	0.103	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.038	0.022	27.201	0.005	0.005	0.000	0.000	0.000	0.000
21	B	22	ALA	0	0.006	0.005	28.815	0.004	0.004	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.781	-0.869	28.502	-0.088	-0.088	0.000	0.000	0.000	0.000
23	B	24	LEU	0	-0.032	-0.015	31.249	0.002	0.002	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.032	-0.023	32.277	0.003	0.003	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.061	-0.033	34.264	0.001	0.001	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.067	-0.012	34.851	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	28	THR	0	-0.003	-0.005	38.384	0.006	0.006	0.000	0.000	0.000	0.000
28	B	29	THR	0	0.013	-0.006	40.768	0.000	0.000	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.059	-0.018	43.315	0.003	0.003	0.000	0.000	0.000	0.000
30	B	31	ALA	0	-0.013	-0.003	46.801	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	32	ASP	-1	-0.924	-0.962	48.850	-0.014	-0.014	0.000	0.000	0.000	0.000
32	B	41	PHE	0	0.045	0.011	57.018	0.001	0.001	0.000	0.000	0.000	0.000
33	B	42	ALA	0	-0.006	0.006	56.593	0.000	0.000	0.000	0.000	0.000	0.000
34	B	43	GLN	0	-0.049	-0.032	54.730	0.001	0.001	0.000	0.000	0.000	0.000
35	B	44	GLU	-1	-0.868	-0.945	52.691	-0.032	-0.032	0.000	0.000	0.000	0.000
36	B	45	ASN	0	-0.028	-0.031	51.746	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	46	SER	0	-0.037	-0.019	51.091	0.001	0.001	0.000	0.000	0.000	0.000
38	B	47	GLU	-1	-0.940	-0.947	49.905	-0.040	-0.040	0.000	0.000	0.000	0.000
39	B	48	LEU	0	0.000	-0.007	47.264	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	49	ALA	0	-0.005	0.002	46.259	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	50	VAL	0	0.037	0.016	45.457	0.001	0.001	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.065	0.049	44.491	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	52	THR	0	0.040	0.021	43.488	0.002	0.002	0.000	0.000	0.000	0.000
44	B	53	THR	0	-0.001	0.003	41.075	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.020	-0.022	39.935	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	55	VAL	0	0.043	0.014	38.993	0.001	0.001	0.000	0.000	0.000	0.000
47	B	56	MET	0	-0.012	-0.003	37.727	0.002	0.002	0.000	0.000	0.000	0.000
48	B	57	MET	0	-0.006	0.003	35.478	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.053	0.024	34.158	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	59	ASN	0	-0.037	-0.017	33.387	0.006	0.006	0.000	0.000	0.000	0.000
51	B	60	ASN	0	0.008	0.010	30.839	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	61	GLN	0	-0.067	-0.042	29.618	-0.011	-0.011	0.000	0.000	0.000	0.000
53	B	62	THR	0	-0.002	-0.015	28.468	0.004	0.004	0.000	0.000	0.000	0.000
54	B	63	MET	0	-0.009	-0.001	27.172	0.004	0.004	0.000	0.000	0.000	0.000
55	B	64	GLN	0	-0.011	-0.024	24.968	-0.014	-0.014	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.008	0.007	23.663	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	66	ILE	0	0.027	0.012	23.371	0.014	0.014	0.000	0.000	0.000	0.000
58	B	67	LYS	1	0.858	0.925	17.499	0.169	0.169	0.000	0.000	0.000	0.000
59	B	68	ASN	0	-0.017	-0.035	19.058	-0.016	-0.016	0.000	0.000	0.000	0.000
60	B	69	VAL	0	0.041	0.017	18.616	0.025	0.025	0.000	0.000	0.000	0.000
61	B	70	GLN	0	-0.012	-0.010	19.009	0.027	0.027	0.000	0.000	0.000	0.000
62	B	71	ASP	-1	-0.784	-0.862	15.127	-0.105	-0.105	0.000	0.000	0.000	0.000
63	B	72	LEU	0	0.019	0.012	14.126	0.053	0.053	0.000	0.000	0.000	0.000
64	B	73	LEU	0	-0.006	0.018	15.051	0.103	0.103	0.000	0.000	0.000	0.000
65	B	74	ILE	0	-0.035	-0.028	11.426	0.090	0.090	0.000	0.000	0.000	0.000
66	B	75	LEU	0	0.011	0.017	9.261	0.131	0.131	0.000	0.000	0.000	0.000
67	B	76	THR	0	0.013	-0.003	10.669	0.289	0.289	0.000	0.000	0.000	0.000
68	B	77	ARG	1	0.924	0.959	12.904	-0.183	-0.183	0.000	0.000	0.000	0.000
69	B	78	SER	0	-0.026	-0.019	7.358	0.215	0.215	0.000	0.000	0.000	0.000
70	B	79	ILE	0	0.010	0.004	8.488	0.480	0.480	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.804	0.888	9.891	-0.597	-0.597	0.000	0.000	0.000	0.000
72	B	81	GLU	-1	-0.768	-0.883	10.743	0.733	0.733	0.000	0.000	0.000	0.000
73	B	82	LYS	1	0.900	0.953	1.911	-21.998	-24.287	7.034	-2.232	-2.514	0.032
74	B	83	TRP	0	-0.025	-0.008	8.831	-0.078	-0.078	0.000	0.000	0.000	0.000
75	B	84	LEU	0	-0.017	-0.020	12.098	-0.117	-0.117	0.000	0.000	0.000	0.000
76	B	85	LEU	0	-0.032	0.002	10.624	-0.145	-0.145	0.000	0.000	0.000	0.000
77	B	86	ASN	0	-0.082	-0.052	7.893	0.524	0.524	0.000	0.000	0.000	0.000
78	B	87	GLN	0	-0.012	0.019	11.224	0.013	0.013	0.000	0.000	0.000	0.000
79	B	88	ILE	0	0.008	0.001	14.026	-0.058	-0.058	0.000	0.000	0.000	0.000
80	B	89	PRO	0	-0.011	0.002	16.333	-0.042	-0.042	0.000	0.000	0.000	0.000

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