FMO DATABASE

FMODB ID: 6N7RZ

Calculation Name: 2YH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YH9

Chain ID: A

ChEMBL ID:

UniProt ID: P0A937

Base Structure: X-ray

Registration Date: 2023-06-22

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-308969.951699
FMO2-HF: Nuclear repulsion	283293.333024
FMO2-HF: Total energy	-25676.618674
FMO2-MP2: Total energy	-25751.41385

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:5:VAL)

Summations of interaction energy for fragment #1(A:5:VAL)

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.
-18.473	-23.308	20.459	-7.406	-8.217	0.026

Interaction energy analysis for fragmet #1(A:5:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.023

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	7	LYS	1	0.952	0.963	1.963	-13.978	-20.861	19.150	-6.552	-5.715	0.034
4	A	8	ILE	0	0.035	0.026	2.756	-2.464	-1.408	0.208	-0.276	-0.987	0.000
5	A	9	ARG	1	0.863	0.894	5.182	-1.382	-1.384	-0.001	-0.007	0.011	0.000
6	A	10	VAL	0	0.066	0.021	8.268	0.025	0.025	0.000	0.000	0.000	0.000
7	A	11	GLY	0	0.009	0.008	10.847	0.108	0.108	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.055	0.023	8.224	0.025	0.025	0.000	0.000	0.000	0.000
9	A	13	THR	0	0.050	0.032	11.890	-0.090	-0.090	0.000	0.000	0.000	0.000
10	A	14	GLN	0	0.076	0.008	12.003	0.051	0.051	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.015	0.008	12.288	0.006	0.006	0.000	0.000	0.000	0.000
12	A	16	GLN	0	0.022	0.012	11.147	0.015	0.015	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.032	0.016	6.575	0.213	0.213	0.000	0.000	0.000	0.000
14	A	18	ALA	0	-0.012	-0.003	7.957	0.113	0.113	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.060	-0.017	10.109	0.050	0.050	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.032	-0.010	5.632	0.198	0.198	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.076	-0.049	2.272	-0.905	0.089	1.102	-0.571	-1.526	-0.008
18	A	22	GLY	0	0.041	0.041	5.785	-0.215	-0.215	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.011	-0.024	9.068	-0.122	-0.122	0.000	0.000	0.000	0.000
20	A	24	PRO	0	-0.026	-0.005	9.387	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	25	LEU	0	0.021	0.018	10.283	0.095	0.095	0.000	0.000	0.000	0.000
22	A	26	MET	0	-0.020	-0.025	12.201	0.070	0.070	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.035	-0.020	13.021	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.867	-0.946	15.380	-0.294	-0.294	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.038	0.031	18.452	0.014	0.014	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.002	-0.001	21.539	0.037	0.037	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.007	0.009	22.085	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.072	-0.022	20.031	0.020	0.020	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.036	-0.002	23.150	0.002	0.002	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.015	0.001	24.236	0.014	0.014	0.000	0.000	0.000	0.000
31	A	35	TRP	0	-0.036	-0.006	23.659	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	36	PHE	0	0.003	-0.009	23.992	0.015	0.015	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.004	0.011	25.102	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.015	-0.011	26.135	0.013	0.013	0.000	0.000	0.000	0.000
35	A	39	PHE	0	-0.001	0.005	28.313	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.972	0.987	22.975	0.140	0.140	0.000	0.000	0.000	0.000
37	A	41	GLN	0	-0.052	-0.041	28.748	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	42	GLN	0	0.028	0.027	30.949	0.001	0.001	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.002	-0.014	34.248	0.005	0.005	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.030	0.012	37.992	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	45	HIS	0	0.024	0.046	34.891	0.000	0.000	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.921	-0.953	38.403	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	47	GLY	0	-0.013	-0.006	39.579	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.029	-0.025	40.526	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.030	-0.032	35.236	0.004	0.004	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.080	-0.027	30.334	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	51	GLN	0	0.060	0.029	33.696	0.001	0.001	0.000	0.000	0.000	0.000
48	A	52	THR	0	-0.077	-0.038	29.797	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.010	-0.010	30.184	0.005	0.005	0.000	0.000	0.000	0.000
50	A	54	THR	0	0.013	0.006	27.898	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.031	-0.004	28.915	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.036	0.018	28.525	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.016	-0.003	27.837	0.004	0.004	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.023	0.018	29.396	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.059	0.007	28.279	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	60	SER	0	-0.064	-0.025	28.908	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.009	0.012	29.306	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.030	-0.012	30.139	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.007	-0.001	32.342	0.003	0.003	0.000	0.000	0.000	0.000
60	A	64	THR	0	-0.068	-0.045	33.077	0.007	0.007	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.041	-0.020	33.726	0.006	0.006	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.027	0.010	33.615	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.889	-0.932	32.958	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	68	ASN	0	-0.011	-0.013	33.508	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.970	0.977	32.912	0.031	0.031	0.000	0.000	0.000	0.000
66	A	70	PRO	0	0.036	0.030	35.092	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:VAL)