FMO DATABASE

FMODB ID: ZY13N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-295449.433331
FMO2-HF: Nuclear repulsion	270293.035676
FMO2-HF: Total energy	-25156.397654
FMO2-MP2: Total energy	-25229.177495

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.
0.042	1.214	-0.005	-0.509	-0.659	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 : 0.037 / q_NPA : 0.005

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	0.956	0.976	3.775	0.049	1.221	-0.005	-0.509	-0.659	0.002
4	A	5	LYS	1	0.974	0.993	6.224	0.508	0.508	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.016	-0.009	9.836	-0.070	-0.070	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.023	-0.010	11.218	0.040	0.040	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.035	-0.030	14.962	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.064	0.047	16.857	0.016	0.016	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.071	-0.027	19.364	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	VAL	0	0.071	0.019	22.346	0.006	0.006	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.944	0.974	26.041	0.082	0.082	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.035	0.006	28.342	0.004	0.004	0.000	0.000	0.000	0.000
13	A	14	PHE	0	-0.030	-0.010	32.038	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	15	PHE	0	-0.018	-0.022	31.466	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.783	-0.884	33.907	-0.055	-0.055	0.000	0.000	0.000	0.000
16	A	17	MET	0	-0.039	-0.031	33.229	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.952	-0.968	35.141	-0.058	-0.058	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.050	-0.019	38.134	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	MET	0	-0.119	-0.050	30.014	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.937	-0.972	32.915	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.045	-0.012	29.405	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.016	0.013	32.660	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.895	-0.940	30.358	-0.078	-0.078	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.009	0.002	34.079	0.002	0.002	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.010	0.014	33.748	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.844	0.913	35.871	0.045	0.045	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.926	-0.983	35.571	-0.042	-0.042	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.014	-0.006	37.882	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.952	-0.972	37.852	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.038	-0.005	33.829	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.051	0.016	35.016	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.097	-0.044	30.073	0.000	0.000	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.745	-0.887	31.926	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	35	PHE	0	0.007	-0.012	25.569	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.966	0.987	28.205	0.066	0.066	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.901	-0.931	28.795	-0.086	-0.086	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.009	0.021	24.331	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.054	-0.042	24.063	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.096	-0.064	24.292	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.911	-0.935	21.641	-0.145	-0.145	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.080	-0.059	17.388	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.022	-0.015	20.832	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.009	-0.003	22.024	0.005	0.005	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.889	0.949	17.138	0.191	0.191	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.029	-0.010	13.732	0.032	0.032	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.040	0.023	15.088	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.060	-0.042	13.986	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.030	0.022	16.315	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.017	-0.012	19.243	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.024	0.019	21.365	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.889	0.949	23.900	0.113	0.113	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.855	-0.934	26.595	-0.072	-0.072	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-1.003	-0.996	28.308	-0.082	-0.082	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.050	-0.029	31.454	0.002	0.002	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.890	-0.942	34.820	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.036	-0.019	36.132	0.000	0.000	0.000	0.000	0.000	0.000
57	A	58	PRO	0	-0.030	-0.001	38.869	0.002	0.002	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.031	0.014	42.457	0.001	0.001	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.946	0.946	44.576	0.028	0.028	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.031	-0.033	47.363	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.008	0.033	46.799	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.960	-0.975	48.595	-0.022	-0.022	0.000	0.000	0.000	0.000

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