FMO DATABASE

FMODB ID: NNVKQ

Calculation Name: 2OO2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OO2

Chain ID: A

ChEMBL ID:

UniProt ID: O28492

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-527371.363214
FMO2-HF: Nuclear repulsion	495482.384486
FMO2-HF: Total energy	-31888.978727
FMO2-MP2: Total energy	-31983.052874

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-8.547	-4.571	4.958	-4.171	-4.762	0.017

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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	A	2	GLU	-1	-0.947	-0.974	2.978	-0.528	2.484	0.449	-1.517	-1.943	0.009
4	A	3	GLU	-1	-0.928	-0.955	2.004	-4.342	-3.989	4.502	-2.383	-2.473	0.007
5	A	4	GLU	-1	-0.933	-0.959	3.618	0.016	0.627	0.007	-0.271	-0.346	0.001
6	A	5	LEU	0	0.033	0.002	5.517	-0.461	-0.461	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.974	1.003	5.414	-2.590	-2.590	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.835	0.913	5.767	-1.400	-1.400	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.818	-0.899	9.394	0.480	0.480	0.000	0.000	0.000	0.000
10	A	9	THR	0	0.024	-0.012	11.400	-0.177	-0.177	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.013	0.001	11.628	-0.090	-0.090	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.821	0.934	12.841	-0.651	-0.651	0.000	0.000	0.000	0.000
13	A	12	TRP	0	-0.005	-0.031	14.838	-0.103	-0.103	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.037	0.024	16.997	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.908	-0.958	17.265	0.366	0.366	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.840	0.935	18.012	-0.355	-0.355	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.013	0.006	21.428	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	17	GLU	-1	-0.847	-0.905	22.089	0.291	0.291	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.940	-0.971	24.529	0.169	0.169	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.828	0.901	25.614	-0.177	-0.177	0.000	0.000	0.000	0.000
21	A	20	VAL	0	-0.022	-0.023	27.278	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.915	0.948	29.168	-0.166	-0.166	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.930	-0.949	29.538	0.146	0.146	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.050	-0.011	30.943	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.947	-0.967	33.866	0.099	0.099	0.000	0.000	0.000	0.000
26	A	25	GLY	0	0.018	-0.011	36.667	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.901	-0.954	37.310	0.110	0.110	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.830	-0.934	36.547	0.122	0.122	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.034	-0.002	36.209	0.007	0.007	0.000	0.000	0.000	0.000
30	A	29	PHE	0	-0.029	-0.016	32.548	0.008	0.008	0.000	0.000	0.000	0.000
31	A	30	MET	0	0.046	0.027	31.888	0.015	0.015	0.000	0.000	0.000	0.000
32	A	31	ARG	1	0.823	0.915	31.814	-0.120	-0.120	0.000	0.000	0.000	0.000
33	A	32	ASN	0	0.005	0.003	29.923	0.010	0.010	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.012	0.020	26.757	0.019	0.019	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.895	-0.945	26.616	0.242	0.242	0.000	0.000	0.000	0.000
36	A	35	ALA	0	-0.007	0.017	27.303	0.014	0.014	0.000	0.000	0.000	0.000
37	A	36	TYR	0	-0.006	-0.017	23.551	0.009	0.009	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.032	0.008	22.809	0.044	0.044	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.001	-0.001	22.638	0.028	0.028	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.921	-0.960	22.601	0.296	0.296	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.105	-0.058	17.771	0.041	0.041	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.861	0.906	18.124	-0.215	-0.215	0.000	0.000	0.000	0.000
43	A	42	TYR	0	-0.014	0.004	19.176	0.030	0.030	0.000	0.000	0.000	0.000
44	A	43	PHE	0	-0.026	-0.040	17.026	0.008	0.008	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.018	-0.011	12.711	0.100	0.100	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.976	-0.971	14.718	0.447	0.447	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.862	0.945	16.493	-0.397	-0.397	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.014	-0.007	12.804	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.935	-0.965	12.726	0.657	0.657	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.029	-0.008	8.066	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	50	VAL	0	0.018	0.020	11.971	-0.053	-0.053	0.000	0.000	0.000	0.000
52	A	51	ARG	1	0.942	0.985	13.552	-0.469	-0.469	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.024	0.014	14.249	-0.051	-0.051	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.010	-0.001	12.980	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.955	-0.983	15.081	0.292	0.292	0.000	0.000	0.000	0.000
56	A	55	CYS	0	-0.012	-0.007	17.953	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	56	VAL	0	0.043	0.025	16.445	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	57	VAL	0	-0.029	0.003	17.424	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	58	TRP	0	-0.020	-0.006	20.086	-0.050	-0.050	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.010	-0.012	22.694	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.010	-0.034	20.320	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	61	ALA	0	-0.026	0.014	23.881	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	62	TRP	0	-0.035	-0.022	25.811	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	63	LEU	0	0.011	0.002	26.496	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.903	-0.979	25.718	0.165	0.165	0.000	0.000	0.000	0.000
66	A	65	ILE	0	-0.011	-0.003	28.131	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.017	-0.004	30.962	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.014	-0.003	30.249	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.971	-0.971	32.316	0.102	0.102	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.119	-0.062	34.219	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.002	0.013	36.708	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.846	0.916	36.179	-0.105	-0.105	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.083	-0.025	31.963	0.001	0.001	0.000	0.000	0.000	0.000
74	A	73	HIS	0	0.027	0.012	36.016	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.838	-0.896	32.260	0.134	0.134	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.061	-0.025	35.744	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)