FMO DATABASE

FMODB ID: 6NLZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-438980.222563
FMO2-HF: Nuclear repulsion	406965.996997
FMO2-HF: Total energy	-32014.225566
FMO2-MP2: Total energy	-32106.946585

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.
-4.87	-1.086	0.154	-1.544	-2.394	0.004

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 : 0.039 / q_NPA : 0.007

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	-0.019	-0.018	2.953	-3.524	-0.876	0.060	-1.242	-1.466	0.004
4	B	5	ALA	0	0.043	0.020	3.208	-0.038	0.595	0.094	-0.167	-0.560	-0.001
5	B	6	LEU	0	-0.035	-0.018	4.031	0.947	1.183	-0.001	-0.039	-0.196	0.000
6	B	7	TYR	0	-0.003	0.000	6.378	0.649	0.649	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.799	-0.885	7.981	-1.307	-1.307	0.000	0.000	0.000	0.000
8	B	9	LYS	1	0.940	0.981	8.648	0.868	0.868	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.023	-0.017	10.445	0.230	0.230	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.916	-0.956	12.457	-0.506	-0.506	0.000	0.000	0.000	0.000
11	B	12	GLN	0	0.011	0.028	13.388	0.033	0.033	0.000	0.000	0.000	0.000
12	B	13	THR	0	-0.022	-0.018	13.909	0.092	0.092	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.956	0.977	16.396	0.285	0.285	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.014	-0.017	17.672	0.051	0.051	0.000	0.000	0.000	0.000
15	B	16	ILE	0	-0.008	-0.004	17.874	0.037	0.037	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.011	-0.004	19.375	0.031	0.031	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.056	-0.025	22.451	0.024	0.024	0.000	0.000	0.000	0.000
18	B	19	VAL	0	0.041	0.022	23.849	0.017	0.017	0.000	0.000	0.000	0.000
19	B	20	LYS	1	0.848	0.916	24.380	0.186	0.186	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.014	0.006	26.564	0.014	0.014	0.000	0.000	0.000	0.000
21	B	22	ALA	0	0.019	0.004	28.404	0.012	0.012	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.867	-0.936	28.754	-0.138	-0.138	0.000	0.000	0.000	0.000
23	B	24	LEU	0	-0.028	-0.017	30.894	0.008	0.008	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.044	-0.027	31.855	0.007	0.007	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.051	-0.021	33.469	0.010	0.010	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.063	-0.005	34.347	0.003	0.003	0.000	0.000	0.000	0.000
27	B	28	THR	0	0.000	-0.001	37.999	0.003	0.003	0.000	0.000	0.000	0.000
28	B	29	THR	0	0.012	-0.004	40.152	0.001	0.001	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.050	-0.017	42.591	0.003	0.003	0.000	0.000	0.000	0.000
30	B	31	ALA	0	-0.025	-0.007	46.257	0.000	0.000	0.000	0.000	0.000	0.000
31	B	32	ASP	-1	-0.930	-0.966	48.051	-0.036	-0.036	0.000	0.000	0.000	0.000
32	B	41	PHE	0	0.039	0.003	56.808	0.001	0.001	0.000	0.000	0.000	0.000
33	B	42	ALA	0	0.004	0.002	56.405	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	43	GLN	0	-0.003	-0.010	55.016	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	44	GLU	-1	-0.862	-0.923	52.050	-0.042	-0.042	0.000	0.000	0.000	0.000
36	B	45	ASN	0	-0.010	-0.009	51.572	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	46	SER	0	-0.082	-0.040	50.819	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	47	GLU	-1	-0.954	-0.968	49.126	-0.043	-0.043	0.000	0.000	0.000	0.000
39	B	48	LEU	0	-0.020	-0.018	46.774	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	49	ALA	0	0.026	0.028	45.890	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	50	VAL	0	0.038	0.021	45.016	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.058	0.035	44.012	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	52	THR	0	0.040	0.019	42.870	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	53	THR	0	-0.007	-0.016	40.296	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.038	-0.024	39.330	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	55	VAL	0	0.049	0.024	38.417	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	56	MET	0	-0.025	-0.016	37.213	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	57	MET	0	0.000	0.002	35.005	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.062	0.029	33.569	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	59	ASN	0	-0.034	-0.031	32.652	-0.004	-0.004	0.000	0.000	0.000	0.000
51	B	60	ASN	0	0.018	0.020	30.413	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	61	GLN	0	-0.092	-0.044	29.026	-0.006	-0.006	0.000	0.000	0.000	0.000
53	B	62	THR	0	0.019	0.006	27.789	-0.010	-0.010	0.000	0.000	0.000	0.000
54	B	63	MET	0	-0.012	0.002	27.083	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	64	GLN	0	0.031	0.014	24.471	-0.022	-0.022	0.000	0.000	0.000	0.000
56	B	65	LEU	0	0.002	0.010	23.193	-0.021	-0.021	0.000	0.000	0.000	0.000
57	B	66	ILE	0	0.017	0.010	23.002	-0.009	-0.009	0.000	0.000	0.000	0.000
58	B	67	LYS	1	0.871	0.932	17.453	0.245	0.245	0.000	0.000	0.000	0.000
59	B	68	ASN	0	-0.033	-0.050	18.663	-0.042	-0.042	0.000	0.000	0.000	0.000
60	B	69	VAL	0	0.039	0.023	18.011	-0.029	-0.029	0.000	0.000	0.000	0.000
61	B	70	GLN	0	-0.010	-0.008	18.274	-0.010	-0.010	0.000	0.000	0.000	0.000
62	B	71	ASP	-1	-0.834	-0.904	14.391	-0.274	-0.274	0.000	0.000	0.000	0.000
63	B	72	LEU	0	0.002	0.003	13.634	-0.054	-0.054	0.000	0.000	0.000	0.000
64	B	73	LEU	0	-0.021	0.007	14.443	0.009	0.009	0.000	0.000	0.000	0.000
65	B	74	ILE	0	-0.022	-0.020	11.002	0.051	0.051	0.000	0.000	0.000	0.000
66	B	75	LEU	0	0.017	0.020	8.537	0.043	0.043	0.000	0.000	0.000	0.000
67	B	76	THR	0	0.021	0.006	10.220	0.037	0.037	0.000	0.000	0.000	0.000
68	B	77	ARG	1	0.912	0.950	12.651	0.037	0.037	0.000	0.000	0.000	0.000
69	B	78	SER	0	-0.023	-0.009	7.500	0.002	0.002	0.000	0.000	0.000	0.000
70	B	79	ILE	0	0.009	-0.002	8.641	0.199	0.199	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.934	0.961	9.770	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	81	GLU	-1	-0.887	-0.958	10.640	0.423	0.423	0.000	0.000	0.000	0.000
73	B	82	LYS	1	0.933	0.981	3.763	-3.385	-3.118	0.001	-0.096	-0.172	0.001
74	B	83	TRP	0	-0.042	-0.014	9.658	0.050	0.050	0.000	0.000	0.000	0.000
75	B	84	LEU	0	-0.028	-0.012	12.962	-0.019	-0.019	0.000	0.000	0.000	0.000
76	B	85	LEU	0	-0.007	0.007	10.968	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	86	ASN	0	-0.078	-0.043	9.122	0.165	0.165	0.000	0.000	0.000	0.000
78	B	87	GLN	0	-0.003	0.017	11.992	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	88	ILE	0	0.009	-0.009	14.802	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	89	PRO	0	-0.015	0.005	16.910	-0.043	-0.043	0.000	0.000	0.000	0.000

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