FMO DATABASE

FMODB ID: 59KYZ

Calculation Name: 1H3O-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H3O

Chain ID: A

ChEMBL ID:

UniProt ID: Q16514

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	50
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-226301.979874
FMO2-HF: Nuclear repulsion	206696.145356
FMO2-HF: Total energy	-19605.834518
FMO2-MP2: Total energy	-19663.931754

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:869:MET )

Summations of interaction energy for fragment #1(A:869:MET )

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.
-15.046	-8.38	12.725	-4.242	-15.149	-0.028

Interaction energy analysis for fragmet #1(A:869:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.020

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	871	LEU	0	0.003	0.013	2.196	-0.401	1.854	1.164	-1.127	-2.292	-0.003
4	A	872	LEU	0	0.035	0.005	2.547	-3.025	-1.522	1.935	-1.430	-2.007	-0.019
5	A	873	GLN	0	0.111	0.035	2.574	-3.171	-1.139	4.484	-2.359	-4.157	-0.004
6	A	874	ALA	0	0.014	0.008	3.819	0.283	-1.563	0.049	2.116	-0.319	0.002
7	A	875	PRO	0	-0.025	-0.026	7.292	-0.085	-0.085	0.000	0.000	0.000	0.000
8	A	876	LEU	0	0.014	0.036	3.353	-1.021	-0.483	0.487	-0.202	-0.823	0.002
9	A	877	GLN	0	0.051	0.020	5.877	-0.411	-0.411	0.000	0.000	0.000	0.000
10	A	878	ARG	1	0.964	0.972	7.248	-0.803	-0.803	0.000	0.000	0.000	0.000
11	A	879	ARG	1	0.998	1.005	10.167	-0.645	-0.645	0.000	0.000	0.000	0.000
12	A	880	ILE	0	0.011	0.011	7.255	-0.135	-0.135	0.000	0.000	0.000	0.000
13	A	881	LEU	0	0.012	-0.007	10.550	-0.169	-0.169	0.000	0.000	0.000	0.000
14	A	882	GLU	-1	-1.020	-0.996	12.777	0.255	0.255	0.000	0.000	0.000	0.000
15	A	883	ILE	0	0.068	0.016	13.589	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	884	GLY	0	0.053	0.035	15.137	-0.056	-0.056	0.000	0.000	0.000	0.000
17	A	885	LYS	1	0.967	0.990	16.654	-0.305	-0.305	0.000	0.000	0.000	0.000
18	A	886	LYS	1	0.792	0.907	18.434	-0.322	-0.322	0.000	0.000	0.000	0.000
19	A	887	HIS	0	-0.083	-0.058	19.348	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	888	GLY	0	0.026	0.015	20.593	0.009	0.009	0.000	0.000	0.000	0.000
21	A	889	ILE	0	-0.006	0.021	15.554	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	890	THR	0	-0.053	-0.031	18.312	0.007	0.007	0.000	0.000	0.000	0.000
23	A	891	GLU	-1	-0.943	-0.974	14.937	0.217	0.217	0.000	0.000	0.000	0.000
24	A	892	LEU	0	-0.038	-0.024	8.464	0.045	0.045	0.000	0.000	0.000	0.000
25	A	893	HIS	0	0.015	0.011	10.654	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	894	PRO	0	0.069	0.017	8.122	0.125	0.125	0.000	0.000	0.000	0.000
27	A	895	ASP	-1	-0.901	-0.948	5.742	0.381	0.381	0.000	0.000	0.000	0.000
28	A	896	VAL	0	0.036	0.024	6.391	0.192	0.192	0.000	0.000	0.000	0.000
29	A	897	VAL	0	-0.012	-0.016	2.689	-0.709	-0.019	0.741	-0.260	-1.171	0.001
30	A	898	SER	0	0.007	-0.004	2.434	0.003	1.508	1.042	-0.828	-1.719	0.000
31	A	899	TYR	0	0.034	0.025	3.167	0.301	-0.189	0.054	0.706	-0.270	0.000
32	A	900	VAL	0	0.040	0.016	6.889	-0.206	-0.206	0.000	0.000	0.000	0.000
33	A	901	SER	0	0.022	-0.008	2.576	-3.563	-3.203	2.769	-0.829	-2.300	-0.007
34	A	902	HIS	0	-0.018	0.001	4.759	-1.269	-1.150	0.000	-0.029	-0.091	0.000
35	A	903	ALA	0	0.047	0.019	6.273	-0.168	-0.168	0.000	0.000	0.000	0.000
36	A	904	THR	0	-0.058	-0.041	7.250	-0.126	-0.126	0.000	0.000	0.000	0.000
37	A	905	GLN	0	-0.017	-0.004	6.700	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	906	GLN	0	0.007	0.010	8.647	0.033	0.033	0.000	0.000	0.000	0.000
39	A	907	ARG	1	0.943	0.976	11.853	-0.075	-0.075	0.000	0.000	0.000	0.000
40	A	908	LEU	0	-0.031	-0.035	10.190	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	909	GLN	0	0.016	0.026	12.218	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	910	ASN	0	0.058	0.029	14.002	0.015	0.015	0.000	0.000	0.000	0.000
43	A	911	LEU	0	-0.062	-0.027	16.225	0.008	0.008	0.000	0.000	0.000	0.000
44	A	912	VAL	0	0.026	0.016	15.126	0.002	0.002	0.000	0.000	0.000	0.000
45	A	913	GLU	-1	-0.892	-0.948	17.322	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	914	LYS	1	0.940	0.958	19.812	0.008	0.008	0.000	0.000	0.000	0.000
47	A	915	ILE	0	-0.077	-0.042	19.751	0.004	0.004	0.000	0.000	0.000	0.000
48	A	916	SER	0	-0.077	-0.046	21.107	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	917	GLU	-1	-1.003	-0.978	23.675	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	1	NME	0	-0.042	-0.007	25.939	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:869:MET )