FMO DATABASE

FMODB ID: 3J3LL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-529870.304974
FMO2-HF: Nuclear repulsion	497980.040113
FMO2-HF: Total energy	-31890.264861
FMO2-MP2: Total energy	-31984.134828

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.
-7.355	-2.616	1.41	-2.698	-3.452	0.002

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 : 0.037 / q_NPA : 0.013

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

Sort

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	-0.810	-0.895	3.352	-0.290	2.165	0.051	-1.197	-1.310	0.005
4	A	3	GLU	-1	-0.854	-0.912	2.426	-3.989	-2.257	1.359	-1.268	-1.823	-0.004
5	A	4	GLU	-1	-0.946	-0.968	3.943	-3.266	-2.769	0.001	-0.232	-0.266	0.001
6	A	5	LEU	0	0.032	0.013	5.886	0.657	0.657	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.841	0.916	6.178	-1.051	-1.051	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.856	0.910	4.663	0.463	0.518	-0.001	-0.001	-0.053	0.000
9	A	8	GLU	-1	-0.796	-0.876	9.601	-0.375	-0.375	0.000	0.000	0.000	0.000
10	A	9	THR	0	0.004	-0.024	11.649	0.076	0.076	0.000	0.000	0.000	0.000
11	A	10	LEU	0	-0.011	0.007	11.526	0.033	0.033	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.815	0.897	11.974	0.370	0.370	0.000	0.000	0.000	0.000
13	A	12	TRP	0	-0.031	-0.041	14.373	0.051	0.051	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.058	0.044	17.151	0.014	0.014	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.909	-0.968	16.621	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.849	0.933	18.267	0.141	0.141	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.007	0.011	21.465	0.008	0.008	0.000	0.000	0.000	0.000
18	A	17	GLU	-1	-0.828	-0.912	22.812	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.834	-0.894	24.727	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.732	0.858	25.640	0.066	0.066	0.000	0.000	0.000	0.000
21	A	20	VAL	0	-0.011	-0.016	27.385	0.003	0.003	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.734	0.846	27.973	0.034	0.034	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.925	-0.945	29.526	-0.047	-0.047	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.019	-0.005	30.475	0.000	0.000	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.877	-0.909	34.231	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	25	GLY	0	0.033	-0.003	36.917	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.860	-0.921	37.178	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.727	-0.842	36.655	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.025	-0.002	36.364	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	PHE	0	0.006	-0.010	32.722	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	30	MET	0	0.039	0.030	32.048	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	31	ARG	1	0.713	0.823	31.862	0.026	0.026	0.000	0.000	0.000	0.000
33	A	32	ASN	0	-0.024	-0.015	30.325	0.003	0.003	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.011	0.012	27.102	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.788	-0.891	26.917	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	35	ALA	0	-0.040	-0.010	27.470	0.003	0.003	0.000	0.000	0.000	0.000
37	A	36	TYR	0	0.010	-0.001	23.660	0.002	0.002	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.018	0.013	22.894	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.013	-0.009	22.757	0.005	0.005	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.914	-0.959	22.920	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.090	-0.054	18.146	0.007	0.007	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.806	0.880	18.600	0.034	0.034	0.000	0.000	0.000	0.000
43	A	42	TYR	0	-0.014	-0.001	19.598	0.018	0.018	0.000	0.000	0.000	0.000
44	A	43	PHE	0	-0.021	-0.035	17.513	0.018	0.018	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.013	-0.007	12.904	0.029	0.029	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.933	-0.949	15.224	0.088	0.088	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.730	0.860	17.294	-0.056	-0.056	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.010	-0.002	13.296	0.011	0.011	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.873	-0.922	12.651	0.106	0.106	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.011	-0.014	8.239	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	50	VAL	0	0.006	0.004	12.100	-0.081	-0.081	0.000	0.000	0.000	0.000
52	A	51	ARG	1	0.823	0.896	13.824	0.044	0.044	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.057	0.029	14.621	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.028	0.022	13.118	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.816	-0.883	15.275	-0.116	-0.116	0.000	0.000	0.000	0.000
56	A	55	CYS	0	-0.051	-0.018	18.140	0.009	0.009	0.000	0.000	0.000	0.000
57	A	56	VAL	0	0.043	0.026	16.552	0.004	0.004	0.000	0.000	0.000	0.000
58	A	57	VAL	0	-0.024	-0.008	17.012	0.002	0.002	0.000	0.000	0.000	0.000
59	A	58	TRP	0	-0.045	-0.018	19.873	0.011	0.011	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.008	0.009	22.922	0.009	0.009	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.022	-0.033	20.235	0.007	0.007	0.000	0.000	0.000	0.000
62	A	61	ALA	0	-0.041	-0.005	23.688	0.006	0.006	0.000	0.000	0.000	0.000
63	A	62	TRP	0	-0.022	-0.028	25.327	0.010	0.010	0.000	0.000	0.000	0.000
64	A	63	LEU	0	0.006	0.011	26.538	0.006	0.006	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.787	-0.916	25.255	-0.073	-0.073	0.000	0.000	0.000	0.000
66	A	65	ILE	0	-0.026	-0.011	27.061	0.004	0.004	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.007	-0.006	30.100	0.005	0.005	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.022	-0.001	29.869	0.005	0.005	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.939	-0.952	31.405	-0.055	-0.055	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.115	-0.065	33.423	0.004	0.004	0.000	0.000	0.000	0.000
71	A	70	GLY	0	-0.001	0.009	36.114	0.003	0.003	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.785	0.887	35.742	0.038	0.038	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.081	-0.029	32.011	0.002	0.002	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.009	-0.008	35.865	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.820	-0.899	31.687	-0.049	-0.049	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.123	-0.073	35.763	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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