FMO DATABASE

FMODB ID: Z6R7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-439530.720392
FMO2-HF: Nuclear repulsion	407515.951132
FMO2-HF: Total energy	-32014.76926
FMO2-MP2: Total energy	-32107.464489

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.
-15.088	-10.321	0.389	-2.14	-3.016	0.009

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 : 0.036 / q_NPA : 0.012

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	-0.027	-0.016	2.772	-3.963	-1.287	0.081	-1.249	-1.508	0.002
4	B	5	ALA	0	0.060	0.028	3.194	-0.120	0.479	0.097	-0.164	-0.532	-0.001
5	B	6	LEU	0	-0.039	-0.018	4.695	0.542	0.772	-0.001	-0.041	-0.188	0.000
6	B	7	TYR	0	0.002	0.000	6.858	0.220	0.220	0.000	0.000	0.000	0.000
7	B	8	GLU	-1	-0.802	-0.886	7.869	-1.526	-1.526	0.000	0.000	0.000	0.000
8	B	9	LYS	1	0.820	0.907	8.678	0.507	0.507	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.016	-0.003	10.476	0.107	0.107	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.912	-0.956	12.493	-0.208	-0.208	0.000	0.000	0.000	0.000
11	B	12	GLN	0	0.022	0.031	13.421	0.042	0.042	0.000	0.000	0.000	0.000
12	B	13	THR	0	-0.006	-0.023	14.099	0.027	0.027	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.967	0.986	16.584	0.021	0.021	0.000	0.000	0.000	0.000
14	B	15	THR	0	-0.013	-0.015	17.752	0.022	0.022	0.000	0.000	0.000	0.000
15	B	16	ILE	0	0.002	0.002	17.838	0.016	0.016	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.014	-0.006	19.997	0.017	0.017	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.051	-0.023	22.563	0.012	0.012	0.000	0.000	0.000	0.000
18	B	19	VAL	0	0.037	0.018	23.909	0.008	0.008	0.000	0.000	0.000	0.000
19	B	20	LYS	1	0.812	0.890	24.567	0.140	0.140	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.011	0.007	26.756	0.008	0.008	0.000	0.000	0.000	0.000
21	B	22	ALA	0	0.023	0.009	28.447	0.006	0.006	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.797	-0.869	28.457	-0.114	-0.114	0.000	0.000	0.000	0.000
23	B	24	LEU	0	-0.025	-0.015	31.051	0.004	0.004	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.039	-0.023	31.901	0.005	0.005	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.075	-0.043	33.728	0.005	0.005	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.059	-0.003	34.582	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	28	THR	0	0.006	0.000	38.116	0.005	0.005	0.000	0.000	0.000	0.000
28	B	29	THR	0	0.014	-0.003	40.501	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.061	-0.021	42.944	0.003	0.003	0.000	0.000	0.000	0.000
30	B	31	ALA	0	-0.022	-0.004	46.595	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	32	ASP	-1	-0.915	-0.962	48.468	-0.025	-0.025	0.000	0.000	0.000	0.000
32	B	41	PHE	0	0.038	0.005	56.830	0.001	0.001	0.000	0.000	0.000	0.000
33	B	42	ALA	0	-0.002	-0.002	56.451	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	43	GLN	0	-0.030	-0.018	54.358	0.001	0.001	0.000	0.000	0.000	0.000
35	B	44	GLU	-1	-0.873	-0.936	52.245	-0.041	-0.041	0.000	0.000	0.000	0.000
36	B	45	ASN	0	-0.012	-0.012	51.595	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	46	SER	0	-0.032	-0.015	51.000	0.000	0.000	0.000	0.000	0.000	0.000
38	B	47	GLU	-1	-0.971	-0.979	49.388	-0.049	-0.049	0.000	0.000	0.000	0.000
39	B	48	LEU	0	-0.016	-0.009	46.953	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	49	ALA	0	0.016	0.018	45.995	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	50	VAL	0	0.037	0.010	45.149	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.053	0.039	44.240	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	52	THR	0	0.039	0.013	43.242	0.001	0.001	0.000	0.000	0.000	0.000
44	B	53	THR	0	0.015	0.008	40.383	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.039	-0.020	39.616	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	55	VAL	0	0.048	0.023	38.808	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	56	MET	0	-0.020	-0.007	37.628	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	57	MET	0	0.002	0.003	35.266	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.060	0.028	33.925	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	59	ASN	0	-0.037	-0.033	33.196	0.002	0.002	0.000	0.000	0.000	0.000
51	B	60	ASN	0	0.015	0.020	30.497	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	61	GLN	0	-0.077	-0.041	29.096	-0.014	-0.014	0.000	0.000	0.000	0.000
53	B	62	THR	0	0.008	-0.007	28.338	0.000	0.000	0.000	0.000	0.000	0.000
54	B	63	MET	0	-0.009	0.003	27.321	0.000	0.000	0.000	0.000	0.000	0.000
55	B	64	GLN	0	-0.004	-0.017	24.889	-0.020	-0.020	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.001	0.007	23.713	-0.008	-0.008	0.000	0.000	0.000	0.000
57	B	66	ILE	0	0.012	0.005	23.612	0.008	0.008	0.000	0.000	0.000	0.000
58	B	67	LYS	1	0.864	0.930	17.374	0.240	0.240	0.000	0.000	0.000	0.000
59	B	68	ASN	0	-0.031	-0.046	19.188	-0.032	-0.032	0.000	0.000	0.000	0.000
60	B	69	VAL	0	0.044	0.023	18.645	0.008	0.008	0.000	0.000	0.000	0.000
61	B	70	GLN	0	0.000	-0.005	18.907	0.013	0.013	0.000	0.000	0.000	0.000
62	B	71	ASP	-1	-0.799	-0.870	14.949	-0.219	-0.219	0.000	0.000	0.000	0.000
63	B	72	LEU	0	0.009	0.007	14.230	0.021	0.021	0.000	0.000	0.000	0.000
64	B	73	LEU	0	-0.014	0.009	15.191	0.079	0.079	0.000	0.000	0.000	0.000
65	B	74	ILE	0	-0.022	-0.021	11.384	0.079	0.079	0.000	0.000	0.000	0.000
66	B	75	LEU	0	0.025	0.022	9.385	0.094	0.094	0.000	0.000	0.000	0.000
67	B	76	THR	0	0.023	0.005	10.939	0.221	0.221	0.000	0.000	0.000	0.000
68	B	77	ARG	1	0.933	0.960	13.184	-0.058	-0.058	0.000	0.000	0.000	0.000
69	B	78	SER	0	-0.026	-0.010	7.836	0.146	0.146	0.000	0.000	0.000	0.000
70	B	79	ILE	0	0.004	-0.004	9.039	0.349	0.349	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.853	0.917	10.174	-0.397	-0.397	0.000	0.000	0.000	0.000
72	B	81	GLU	-1	-0.829	-0.920	10.635	0.574	0.574	0.000	0.000	0.000	0.000
73	B	82	LYS	1	0.923	0.974	2.836	-11.825	-10.563	0.212	-0.686	-0.788	0.008
74	B	83	TRP	0	-0.039	-0.013	9.488	-0.014	-0.014	0.000	0.000	0.000	0.000
75	B	84	LEU	0	-0.031	-0.015	12.808	-0.090	-0.090	0.000	0.000	0.000	0.000
76	B	85	LEU	0	-0.029	-0.005	10.664	-0.093	-0.093	0.000	0.000	0.000	0.000
77	B	86	ASN	0	-0.073	-0.043	8.760	0.272	0.272	0.000	0.000	0.000	0.000
78	B	87	GLN	0	-0.006	0.022	12.014	0.025	0.025	0.000	0.000	0.000	0.000
79	B	88	ILE	0	0.010	-0.007	14.811	-0.045	-0.045	0.000	0.000	0.000	0.000
80	B	89	PRO	0	-0.011	0.006	16.902	-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)