FMO DATABASE

FMODB ID: R5VR8

Calculation Name: 2H4O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H4O

Chain ID: A

ChEMBL ID:

UniProt ID: O31947

Base Structure: X-ray

Registration Date: 2023-06-19

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-295704.516759
FMO2-HF: Nuclear repulsion	270547.456506
FMO2-HF: Total energy	-25157.060253
FMO2-MP2: Total energy	-25229.808172

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-0.063	1.095	-0.005	-0.5	-0.653	0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.003

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	4	LYS	1	0.960	0.974	3.775	0.045	1.203	-0.005	-0.500	-0.653	0.002
4	A	5	LYS	1	0.970	0.990	6.224	0.454	0.454	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.019	-0.008	9.733	-0.073	-0.073	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.052	-0.044	11.232	0.041	0.041	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.059	-0.044	14.942	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.060	0.039	16.874	0.018	0.018	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.046	-0.008	19.580	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	11	VAL	0	0.066	0.017	22.405	0.007	0.007	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.878	0.939	26.099	0.088	0.088	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.036	0.005	28.396	0.004	0.004	0.000	0.000	0.000	0.000
13	A	14	PHE	0	-0.031	-0.010	32.092	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	15	PHE	0	-0.029	-0.027	31.498	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.814	-0.892	33.924	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	17	MET	0	-0.022	-0.026	33.218	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.963	-0.973	35.134	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.029	-0.014	38.146	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	MET	0	-0.094	-0.041	30.012	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.932	-0.968	32.923	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.051	-0.022	29.505	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.020	0.008	32.677	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.893	-0.915	30.693	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.003	-0.002	34.136	0.003	0.003	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.018	0.010	33.762	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.871	0.933	35.929	0.046	0.046	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.904	-0.942	35.900	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.004	-0.003	37.968	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.946	-0.973	37.894	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.079	-0.042	33.920	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.044	0.021	34.998	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.108	-0.072	30.103	0.000	0.000	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.749	-0.878	31.928	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	35	PHE	0	0.011	-0.011	25.816	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.856	0.925	28.217	0.065	0.065	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.808	-0.896	28.804	-0.083	-0.083	0.000	0.000	0.000	0.000
37	A	38	ILE	0	-0.002	0.011	24.292	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.029	-0.027	24.409	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.088	-0.043	24.299	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.866	-0.900	21.716	-0.148	-0.148	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.054	-0.045	17.090	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.027	-0.010	20.836	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.006	0.008	22.023	0.006	0.006	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.818	0.903	16.627	0.176	0.176	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.014	-0.005	13.597	0.032	0.032	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.036	0.023	15.092	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.069	-0.041	14.248	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.045	0.025	16.326	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.037	-0.019	19.124	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.032	0.021	21.381	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.792	0.890	24.670	0.111	0.111	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.842	-0.914	26.635	-0.075	-0.075	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.855	-0.909	28.455	-0.096	-0.096	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.039	-0.040	31.491	0.002	0.002	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.904	-0.946	34.854	-0.054	-0.054	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.035	-0.019	35.559	0.000	0.000	0.000	0.000	0.000	0.000
57	A	58	PRO	0	-0.013	0.001	38.897	0.002	0.002	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.022	0.010	42.485	0.001	0.001	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.940	0.947	44.602	0.032	0.032	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.025	-0.029	47.385	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.010	0.029	46.738	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.960	-0.974	48.626	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)