FMO DATABASE

FMODB ID: 66Q2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-217682.196117
FMO2-HF: Nuclear repulsion	195325.161336
FMO2-HF: Total energy	-22357.034781
FMO2-MP2: Total energy	-22420.301052

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.
-18.809	-13.256	6.865	-4.823	-7.594	0.024

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 : 0.037 / q_NPA : 0.010

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	162	GLN	0	0.058	0.032	2.494	-4.350	-1.717	1.699	-1.613	-2.719	0.011
4	A	163	GLN	0	-0.021	-0.017	2.109	-12.589	-10.440	5.150	-2.960	-4.339	0.012
5	A	164	ILE	0	0.031	0.007	3.797	-1.471	-0.700	0.016	-0.250	-0.536	0.001
6	A	165	ALA	0	0.027	0.020	5.970	-0.172	-0.172	0.000	0.000	0.000	0.000
7	A	166	ALA	0	0.026	0.013	6.942	-0.254	-0.254	0.000	0.000	0.000	0.000
8	A	167	LEU	0	-0.002	-0.010	7.292	-0.131	-0.131	0.000	0.000	0.000	0.000
9	A	168	SER	0	-0.022	-0.002	9.976	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	169	GLU	-1	-0.934	-0.969	11.469	0.179	0.179	0.000	0.000	0.000	0.000
11	A	170	SER	0	-0.040	-0.024	12.643	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	171	LEU	0	0.010	-0.003	13.341	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	172	GLN	0	-0.005	0.013	15.968	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	173	ALA	0	0.041	0.025	17.496	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	174	THR	0	-0.010	0.001	17.916	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	175	GLN	0	-0.010	-0.016	19.667	0.014	0.014	0.000	0.000	0.000	0.000
17	A	176	GLN	0	-0.011	-0.002	21.958	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	177	GLN	0	0.003	-0.010	21.642	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	178	LEU	0	-0.012	-0.010	23.053	0.000	0.000	0.000	0.000	0.000	0.000
20	A	179	GLN	0	0.010	0.016	26.325	0.003	0.003	0.000	0.000	0.000	0.000
21	A	180	ALA	0	-0.006	0.003	27.787	0.003	0.003	0.000	0.000	0.000	0.000
22	A	181	LEU	0	0.015	0.003	27.376	0.000	0.000	0.000	0.000	0.000	0.000
23	A	182	GLN	0	-0.028	-0.015	29.154	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	183	GLN	0	-0.016	-0.003	32.338	0.002	0.002	0.000	0.000	0.000	0.000
25	A	184	GLN	0	0.034	0.015	32.006	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	185	CYS	0	-0.017	-0.014	33.940	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	186	TYR	0	-0.005	0.005	34.960	0.002	0.002	0.000	0.000	0.000	0.000
28	A	187	GLU	-1	-0.973	-0.989	38.292	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	188	LEU	0	-0.018	-0.013	37.699	0.000	0.000	0.000	0.000	0.000	0.000
30	A	189	GLU	-1	-0.919	-0.958	40.689	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	190	LYS	1	0.991	0.998	42.239	0.009	0.009	0.000	0.000	0.000	0.000
32	A	191	THR	0	-0.020	-0.016	43.977	0.001	0.001	0.000	0.000	0.000	0.000
33	A	192	ASN	0	0.023	0.006	43.436	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	193	ARG	1	0.880	0.945	44.849	0.011	0.011	0.000	0.000	0.000	0.000
35	A	194	LEU	0	0.001	0.010	48.680	0.001	0.001	0.000	0.000	0.000	0.000
36	A	195	LEU	0	0.039	0.016	47.882	0.000	0.000	0.000	0.000	0.000	0.000
37	A	196	VAL	0	-0.017	-0.003	50.194	0.000	0.000	0.000	0.000	0.000	0.000
38	A	197	SER	0	0.021	0.015	52.714	0.001	0.001	0.000	0.000	0.000	0.000
39	A	198	GLU	-1	-0.923	-0.965	54.207	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	199	VAL	0	-0.011	-0.006	54.377	0.000	0.000	0.000	0.000	0.000	0.000
41	A	200	MET	0	-0.054	-0.034	55.872	0.001	0.001	0.000	0.000	0.000	0.000
42	A	201	THR	0	0.022	0.017	58.847	0.001	0.001	0.000	0.000	0.000	0.000
43	A	202	LEU	0	0.017	-0.005	58.163	0.000	0.000	0.000	0.000	0.000	0.000
44	A	203	GLN	0	-0.010	0.003	58.694	0.001	0.001	0.000	0.000	0.000	0.000
45	A	204	LYS	1	0.944	0.965	62.866	0.008	0.008	0.000	0.000	0.000	0.000
46	A	205	MET	0	-0.014	0.001	64.184	0.000	0.000	0.000	0.000	0.000	0.000
47	A	206	VAL	0	0.036	0.026	64.518	0.000	0.000	0.000	0.000	0.000	0.000
48	A	207	LYS	1	0.947	0.957	66.107	0.012	0.012	0.000	0.000	0.000	0.000
49	A	208	ALA	0	0.006	0.009	68.999	0.000	0.000	0.000	0.000	0.000	0.000
50	A	209	GLN	0	0.027	0.012	67.963	0.000	0.000	0.000	0.000	0.000	0.000
51	A	210	ASN	0	-0.010	-0.004	71.193	0.000	0.000	0.000	0.000	0.000	0.000
52	A	211	GLN	0	-0.035	-0.011	72.961	0.000	0.000	0.000	0.000	0.000	0.000
53	A	212	ALA	0	-0.013	0.000	74.874	0.000	0.000	0.000	0.000	0.000	0.000
54	A	213	SER	0	-0.054	-0.018	74.795	0.000	0.000	0.000	0.000	0.000	0.000
55	A	214	ASN	0	-0.092	-0.040	76.424	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)