FMO DATABASE

FMODB ID: YZ9Y2

Calculation Name: 5COS-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5COS

Chain ID: C

ChEMBL ID:

UniProt ID: A0A084

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-317490.011082
FMO2-HF: Nuclear repulsion	293315.313415
FMO2-HF: Total energy	-24174.697667
FMO2-MP2: Total energy	-24243.246942

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(C:8:SER)

Summations of interaction energy for fragment #1(C:8: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.
1.028	2.469	-0.016	-0.589	-0.836	0.002

Interaction energy analysis for fragmet #1(C:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.022

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	C	10	PRO	0	0.027	0.013	3.876	0.506	1.811	-0.015	-0.562	-0.728	0.002
4	C	11	GLY	0	0.046	0.021	6.574	0.368	0.368	0.000	0.000	0.000	0.000
5	C	12	GLU	-1	-0.855	-0.918	8.938	-0.509	-0.509	0.000	0.000	0.000	0.000
6	C	13	VAL	0	-0.062	-0.033	8.351	0.123	0.123	0.000	0.000	0.000	0.000
7	C	14	ALA	0	-0.004	-0.005	7.223	0.161	0.161	0.000	0.000	0.000	0.000
8	C	15	GLU	-1	-0.882	-0.945	9.249	-0.035	-0.035	0.000	0.000	0.000	0.000
9	C	16	GLN	0	0.037	0.022	12.781	-0.011	-0.011	0.000	0.000	0.000	0.000
10	C	17	ALA	0	-0.004	-0.004	10.544	0.029	0.029	0.000	0.000	0.000	0.000
11	C	18	MET	0	-0.027	-0.011	12.482	0.083	0.083	0.000	0.000	0.000	0.000
12	C	19	HIS	0	-0.001	0.007	13.957	0.003	0.003	0.000	0.000	0.000	0.000
13	C	20	TRP	0	0.040	-0.012	16.012	0.027	0.027	0.000	0.000	0.000	0.000
14	C	21	HIS	0	-0.060	-0.043	14.469	0.020	0.020	0.000	0.000	0.000	0.000
15	C	22	LEU	0	-0.019	-0.014	16.639	0.005	0.005	0.000	0.000	0.000	0.000
16	C	23	GLU	-1	-0.841	-0.921	19.443	-0.005	-0.005	0.000	0.000	0.000	0.000
17	C	24	LEU	0	-0.080	-0.047	19.422	-0.013	-0.013	0.000	0.000	0.000	0.000
18	C	25	GLN	0	-0.086	-0.045	19.217	0.045	0.045	0.000	0.000	0.000	0.000
19	C	26	GLU	-1	-0.845	-0.906	22.304	0.071	0.071	0.000	0.000	0.000	0.000
20	C	27	PRO	0	-0.076	-0.039	25.620	-0.003	-0.003	0.000	0.000	0.000	0.000
21	C	28	ALA	0	-0.030	-0.012	28.623	-0.004	-0.004	0.000	0.000	0.000	0.000
22	C	29	VAL	0	0.022	0.023	24.517	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	30	SER	0	0.016	0.011	27.601	-0.007	-0.007	0.000	0.000	0.000	0.000
24	C	31	ALA	0	0.067	0.010	27.772	-0.003	-0.003	0.000	0.000	0.000	0.000
25	C	32	ALA	0	-0.001	0.003	28.178	-0.008	-0.008	0.000	0.000	0.000	0.000
26	C	33	THR	0	0.012	0.019	23.522	-0.015	-0.015	0.000	0.000	0.000	0.000
27	C	34	LEU	0	0.000	0.001	23.476	-0.010	-0.010	0.000	0.000	0.000	0.000
28	C	35	ALA	0	-0.004	-0.003	23.443	-0.012	-0.012	0.000	0.000	0.000	0.000
29	C	36	ALA	0	0.004	0.008	23.130	-0.020	-0.020	0.000	0.000	0.000	0.000
30	C	37	CYS	0	-0.002	0.020	19.053	-0.033	-0.033	0.000	0.000	0.000	0.000
31	C	38	MET	0	-0.044	-0.029	18.756	-0.027	-0.027	0.000	0.000	0.000	0.000
32	C	39	SER	0	0.004	0.014	19.454	-0.034	-0.034	0.000	0.000	0.000	0.000
33	C	40	TRP	0	0.007	-0.021	11.806	-0.039	-0.039	0.000	0.000	0.000	0.000
34	C	41	ARG	1	0.817	0.866	14.802	0.023	0.023	0.000	0.000	0.000	0.000
35	C	42	GLN	0	-0.019	-0.018	15.012	-0.059	-0.059	0.000	0.000	0.000	0.000
36	C	43	ALA	0	-0.022	0.007	17.102	-0.026	-0.026	0.000	0.000	0.000	0.000
37	C	44	HIS	0	0.027	0.006	10.479	-0.108	-0.108	0.000	0.000	0.000	0.000
38	C	45	PRO	0	0.051	0.034	11.117	-0.019	-0.019	0.000	0.000	0.000	0.000
39	C	46	LEU	0	-0.005	-0.009	5.023	-0.078	-0.078	0.000	0.000	0.000	0.000
40	C	47	HIS	1	0.875	0.951	8.473	0.528	0.528	0.000	0.000	0.000	0.000
41	C	48	GLU	-1	-0.709	-0.810	11.255	-0.026	-0.026	0.000	0.000	0.000	0.000
42	C	49	HIS	0	-0.022	-0.011	3.675	0.572	0.708	-0.001	-0.027	-0.108	0.000
43	C	50	ALA	0	0.019	0.006	7.009	0.291	0.291	0.000	0.000	0.000	0.000
44	C	51	TRP	0	0.040	0.031	8.015	0.434	0.434	0.000	0.000	0.000	0.000
45	C	52	GLN	0	-0.016	-0.022	10.536	0.213	0.213	0.000	0.000	0.000	0.000
46	C	53	ARG	1	0.872	0.931	5.222	-0.633	-0.633	0.000	0.000	0.000	0.000
47	C	54	THR	0	0.020	-0.001	8.214	0.286	0.286	0.000	0.000	0.000	0.000
48	C	55	GLN	0	0.034	0.025	10.177	0.021	0.021	0.000	0.000	0.000	0.000
49	C	56	VAL	0	0.004	0.009	10.746	0.006	0.006	0.000	0.000	0.000	0.000
50	C	57	PHE	0	-0.016	-0.027	7.412	0.014	0.014	0.000	0.000	0.000	0.000
51	C	58	ALA	0	0.044	0.033	11.785	-0.044	-0.044	0.000	0.000	0.000	0.000
52	C	59	GLN	0	-0.103	-0.041	14.587	-0.061	-0.061	0.000	0.000	0.000	0.000
53	C	60	ARG	1	0.970	0.984	11.670	-0.618	-0.618	0.000	0.000	0.000	0.000
54	C	61	LEU	0	-0.020	-0.011	14.619	-0.036	-0.036	0.000	0.000	0.000	0.000
55	C	62	ARG	1	0.821	0.885	16.751	-0.298	-0.298	0.000	0.000	0.000	0.000
56	C	63	GLU	-1	-0.854	-0.919	18.637	0.287	0.287	0.000	0.000	0.000	0.000
57	C	64	MET	0	-0.065	-0.015	17.092	0.007	0.007	0.000	0.000	0.000	0.000
58	C	65	ARG	1	0.920	0.977	19.162	-0.299	-0.299	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:8:SER)