FMO DATABASE

FMODB ID: R9MK8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-309218.926927
FMO2-HF: Nuclear repulsion	283541.75302
FMO2-HF: Total energy	-25677.173907
FMO2-MP2: Total energy	-25751.833935

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.
-14.474	-8.572	2.102	-2.751	-5.251	0.014

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 : 0.059 / q_NPA : 0.019

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	0.960	0.992	2.936	-12.393	-8.338	0.837	-1.929	-2.962	0.016
4	A	8	ILE	0	0.046	0.030	3.142	-1.481	-0.757	0.045	-0.156	-0.613	0.000
5	A	9	ARG	1	0.858	0.893	5.721	-0.921	-0.921	0.000	0.000	0.000	0.000
6	A	10	VAL	0	0.053	0.019	8.639	0.013	0.013	0.000	0.000	0.000	0.000
7	A	11	GLY	0	0.026	0.015	10.764	0.056	0.056	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.077	0.008	8.746	0.053	0.053	0.000	0.000	0.000	0.000
9	A	13	THR	0	0.063	0.029	12.183	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	14	GLN	0	0.043	0.006	11.997	0.066	0.066	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.045	0.019	12.110	0.038	0.038	0.000	0.000	0.000	0.000
12	A	16	GLN	0	0.034	0.022	11.197	0.022	0.022	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.016	0.002	6.690	0.223	0.223	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.000	0.001	7.950	0.217	0.217	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.041	-0.014	10.591	0.041	0.041	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.037	-0.014	6.263	0.157	0.157	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.083	-0.059	2.545	0.006	1.129	1.220	-0.666	-1.676	-0.002
18	A	22	GLY	0	0.044	0.047	6.346	-0.366	-0.366	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.017	-0.019	9.518	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	24	PRO	0	-0.024	-0.007	9.143	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	25	LEU	0	0.002	-0.006	10.100	0.052	0.052	0.000	0.000	0.000	0.000
22	A	26	MET	0	-0.015	-0.011	12.117	0.034	0.034	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.029	-0.015	12.768	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.843	-0.919	15.216	-0.185	-0.185	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.035	0.028	18.311	0.014	0.014	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.006	0.007	21.392	0.027	0.027	0.000	0.000	0.000	0.000
27	A	31	GLY	0	-0.001	0.002	21.938	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.073	-0.041	20.023	0.016	0.016	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.030	0.006	23.044	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.049	-0.031	24.425	0.011	0.011	0.000	0.000	0.000	0.000
31	A	35	TRP	0	-0.030	0.004	23.770	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	36	PHE	0	0.028	-0.008	24.308	0.010	0.010	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.004	0.015	25.156	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.010	-0.010	25.631	0.009	0.009	0.000	0.000	0.000	0.000
35	A	39	PHE	0	0.025	0.019	28.033	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.961	0.995	23.338	0.082	0.082	0.000	0.000	0.000	0.000
37	A	41	GLN	0	-0.034	-0.031	28.060	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	42	GLN	0	0.032	0.024	31.503	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.004	-0.018	34.169	0.005	0.005	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.025	0.014	38.002	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.013	0.018	34.284	0.001	0.001	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.923	-0.949	38.181	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	47	GLY	0	-0.019	-0.011	39.284	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.014	-0.020	40.391	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.028	-0.020	35.178	0.002	0.002	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.056	-0.033	30.081	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	51	GLN	0	0.047	0.027	33.257	0.001	0.001	0.000	0.000	0.000	0.000
48	A	52	THR	0	-0.052	-0.035	29.348	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.016	0.000	30.212	0.003	0.003	0.000	0.000	0.000	0.000
50	A	54	THR	0	-0.021	-0.006	27.675	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.039	-0.004	28.829	0.003	0.003	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.012	0.002	28.515	0.001	0.001	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.009	-0.003	27.801	0.000	0.000	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.053	0.027	29.426	0.001	0.001	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.044	0.009	27.773	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	60	SER	0	-0.056	-0.023	28.590	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.013	0.011	28.902	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.030	-0.010	29.718	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.009	-0.002	32.206	0.003	0.003	0.000	0.000	0.000	0.000
60	A	64	THR	0	-0.065	-0.043	32.882	0.004	0.004	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.034	-0.023	33.506	0.003	0.003	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.052	0.014	33.496	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.760	-0.845	32.611	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	68	ASN	0	-0.004	-0.007	33.396	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.819	0.886	32.624	0.006	0.006	0.000	0.000	0.000	0.000
66	A	70	PRO	0	0.036	0.030	34.801	-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:5:VAL)