FMO DATABASE

FMODB ID: R5J28

Calculation Name: 5D60-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D60

Chain ID: A

ChEMBL ID:

UniProt ID: G0SB31

Base Structure: X-ray

Registration Date: 2023-06-20

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-218212.270983
FMO2-HF: Nuclear repulsion	195854.681398
FMO2-HF: Total energy	-22357.589585
FMO2-MP2: Total energy	-22420.851807

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:160:SER)

Summations of interaction energy for fragment #1(A:160:SER)

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.
-17.086	-10.427	4.908	-4.648	-6.919	0.017

Interaction energy analysis for fragmet #1(A:160:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.012

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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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	162	GLN	0	0.072	0.039	2.625	-4.993	-2.042	0.981	-1.549	-2.383	0.010
4	A	163	GLN	0	-0.008	-0.002	2.275	-10.861	-7.945	3.917	-2.859	-3.973	0.007
5	A	164	ILE	0	0.034	0.010	3.677	-0.980	-0.188	0.010	-0.240	-0.563	0.000
6	A	165	ALA	0	0.011	0.021	5.978	-0.078	-0.078	0.000	0.000	0.000	0.000
7	A	166	ALA	0	0.018	0.007	6.970	-0.223	-0.223	0.000	0.000	0.000	0.000
8	A	167	LEU	0	-0.004	-0.012	6.855	-0.101	-0.101	0.000	0.000	0.000	0.000
9	A	168	SER	0	-0.028	-0.023	9.611	0.048	0.048	0.000	0.000	0.000	0.000
10	A	169	GLU	-1	-0.881	-0.933	11.632	0.134	0.134	0.000	0.000	0.000	0.000
11	A	170	SER	0	-0.009	-0.003	12.379	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	171	LEU	0	-0.036	-0.001	12.637	0.001	0.001	0.000	0.000	0.000	0.000
13	A	172	GLN	0	-0.006	-0.007	15.667	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	173	ALA	0	0.027	0.017	17.128	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	174	THR	0	-0.013	-0.019	17.315	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	175	GLN	0	-0.018	-0.022	19.783	0.017	0.017	0.000	0.000	0.000	0.000
17	A	176	GLN	0	-0.034	-0.013	21.399	0.000	0.000	0.000	0.000	0.000	0.000
18	A	177	GLN	0	-0.008	-0.008	21.097	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	178	LEU	0	-0.001	0.004	23.100	0.000	0.000	0.000	0.000	0.000	0.000
20	A	179	GLN	0	0.028	0.020	25.847	0.002	0.002	0.000	0.000	0.000	0.000
21	A	180	ALA	0	-0.016	0.003	27.359	0.004	0.004	0.000	0.000	0.000	0.000
22	A	181	LEU	0	0.027	0.009	26.676	0.001	0.001	0.000	0.000	0.000	0.000
23	A	182	GLN	0	-0.017	-0.015	28.178	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	183	GLN	0	0.016	0.011	31.906	0.002	0.002	0.000	0.000	0.000	0.000
25	A	184	GLN	0	0.006	-0.008	31.052	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	185	CYS	0	-0.027	-0.016	33.289	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	186	TYR	0	-0.004	-0.001	34.952	0.002	0.002	0.000	0.000	0.000	0.000
28	A	187	GLU	-1	-0.858	-0.909	37.741	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	188	LEU	0	0.010	0.013	36.868	0.000	0.000	0.000	0.000	0.000	0.000
30	A	189	GLU	-1	-0.855	-0.882	40.116	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	190	LYS	1	0.911	0.933	41.110	0.011	0.011	0.000	0.000	0.000	0.000
32	A	191	THR	0	-0.026	-0.023	42.985	0.001	0.001	0.000	0.000	0.000	0.000
33	A	192	ASN	0	-0.030	-0.033	42.864	0.000	0.000	0.000	0.000	0.000	0.000
34	A	193	ARG	1	0.808	0.875	44.272	0.013	0.013	0.000	0.000	0.000	0.000
35	A	194	LEU	0	0.011	0.018	48.218	0.001	0.001	0.000	0.000	0.000	0.000
36	A	195	LEU	0	0.010	0.001	47.321	0.000	0.000	0.000	0.000	0.000	0.000
37	A	196	VAL	0	-0.010	-0.009	49.791	0.000	0.000	0.000	0.000	0.000	0.000
38	A	197	SER	0	-0.033	-0.024	52.257	0.001	0.001	0.000	0.000	0.000	0.000
39	A	198	GLU	-1	-0.845	-0.914	53.966	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	199	VAL	0	-0.004	0.006	53.888	0.000	0.000	0.000	0.000	0.000	0.000
41	A	200	MET	0	-0.020	-0.017	54.789	0.001	0.001	0.000	0.000	0.000	0.000
42	A	201	THR	0	-0.023	0.005	58.266	0.002	0.002	0.000	0.000	0.000	0.000
43	A	202	LEU	0	0.045	0.003	57.789	0.000	0.000	0.000	0.000	0.000	0.000
44	A	203	GLN	0	-0.006	-0.005	57.888	0.001	0.001	0.000	0.000	0.000	0.000
45	A	204	LYS	1	0.871	0.933	60.879	0.011	0.011	0.000	0.000	0.000	0.000
46	A	205	MET	0	0.012	0.018	63.521	0.000	0.000	0.000	0.000	0.000	0.000
47	A	206	VAL	0	0.036	0.021	63.898	0.000	0.000	0.000	0.000	0.000	0.000
48	A	207	LYS	1	0.927	0.961	65.102	0.013	0.013	0.000	0.000	0.000	0.000
49	A	208	ALA	0	0.039	0.025	68.598	0.000	0.000	0.000	0.000	0.000	0.000
50	A	209	GLN	0	0.006	0.005	68.248	0.000	0.000	0.000	0.000	0.000	0.000
51	A	210	ASN	0	-0.015	0.001	70.586	0.001	0.001	0.000	0.000	0.000	0.000
52	A	211	GLN	0	0.010	0.001	72.400	0.000	0.000	0.000	0.000	0.000	0.000
53	A	212	ALA	0	-0.015	-0.005	74.323	0.000	0.000	0.000	0.000	0.000	0.000
54	A	213	SER	0	-0.048	-0.024	74.039	0.000	0.000	0.000	0.000	0.000	0.000
55	A	214	ASN	0	-0.133	-0.061	75.770	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:160:SER)