FMO DATABASE

FMODB ID: V5VR1

Calculation Name: 5CFF-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CFF

Chain ID: E

ChEMBL ID:

UniProt ID: P25159

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-402426.30283
FMO2-HF: Nuclear repulsion	375266.745487
FMO2-HF: Total energy	-27159.557343
FMO2-MP2: Total energy	-27238.865528

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(E:949:GLY)

Summations of interaction energy for fragment #1(E:949:GLY)

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.
-1.298	0.489	0.267	-0.722	-1.332	-0.001

Interaction energy analysis for fragmet #1(E:949:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.011

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	E	951	MET	0	0.042	0.019	3.817	-1.501	-0.799	-0.007	-0.360	-0.335	0.001
4	E	952	LYS	1	0.955	0.975	6.765	-0.278	-0.278	0.000	0.000	0.000	0.000
5	E	953	GLU	-1	-0.887	-0.953	2.537	-1.786	-0.986	0.274	-0.328	-0.746	-0.002
6	E	954	GLN	0	-0.014	-0.003	3.908	0.432	0.717	0.000	-0.034	-0.251	0.000
7	E	955	LEU	0	0.008	0.007	5.979	0.314	0.314	0.000	0.000	0.000	0.000
8	E	956	LEU	0	0.016	0.013	7.611	0.137	0.137	0.000	0.000	0.000	0.000
9	E	957	TYR	0	-0.034	-0.019	6.750	0.139	0.139	0.000	0.000	0.000	0.000
10	E	958	LEU	0	0.011	-0.013	8.634	0.119	0.119	0.000	0.000	0.000	0.000
11	E	959	SER	0	-0.059	-0.014	11.424	0.083	0.083	0.000	0.000	0.000	0.000
12	E	960	LYS	1	0.892	0.946	7.636	0.441	0.441	0.000	0.000	0.000	0.000
13	E	961	LEU	0	-0.082	-0.025	12.647	0.033	0.033	0.000	0.000	0.000	0.000
14	E	962	LEU	0	-0.057	-0.052	14.458	0.029	0.029	0.000	0.000	0.000	0.000
15	E	963	ASP	-1	-0.970	-0.956	16.743	-0.103	-0.103	0.000	0.000	0.000	0.000
16	E	964	PHE	0	-0.033	-0.005	14.232	0.005	0.005	0.000	0.000	0.000	0.000
17	E	965	GLU	-1	-0.867	-0.942	16.578	-0.097	-0.097	0.000	0.000	0.000	0.000
18	E	966	VAL	0	-0.021	-0.028	12.865	-0.018	-0.018	0.000	0.000	0.000	0.000
19	E	967	ASN	0	-0.026	-0.005	15.940	0.037	0.037	0.000	0.000	0.000	0.000
20	E	968	PHE	0	0.019	-0.004	11.217	-0.004	-0.004	0.000	0.000	0.000	0.000
21	E	969	SER	0	-0.038	-0.014	16.686	0.015	0.015	0.000	0.000	0.000	0.000
22	E	970	ASP	-1	-0.790	-0.860	16.484	0.095	0.095	0.000	0.000	0.000	0.000
23	E	971	TYR	0	-0.029	-0.009	19.495	0.004	0.004	0.000	0.000	0.000	0.000
24	E	972	PRO	0	0.011	-0.013	21.865	0.003	0.003	0.000	0.000	0.000	0.000
25	E	973	LYS	1	0.961	0.996	23.038	-0.077	-0.077	0.000	0.000	0.000	0.000
26	E	974	GLY	0	0.015	0.011	24.620	-0.010	-0.010	0.000	0.000	0.000	0.000
27	E	975	ASN	0	-0.029	-0.027	27.988	0.005	0.005	0.000	0.000	0.000	0.000
28	E	976	HIS	0	0.026	0.028	26.895	-0.008	-0.008	0.000	0.000	0.000	0.000
29	E	977	ASN	0	-0.007	-0.006	26.473	0.009	0.009	0.000	0.000	0.000	0.000
30	E	978	GLU	-1	-0.978	-1.010	22.014	-0.001	-0.001	0.000	0.000	0.000	0.000
31	E	979	PHE	0	-0.017	0.007	19.433	0.007	0.007	0.000	0.000	0.000	0.000
32	E	980	LEU	0	0.051	0.026	20.530	-0.014	-0.014	0.000	0.000	0.000	0.000
33	E	981	THR	0	-0.033	-0.013	15.256	0.018	0.018	0.000	0.000	0.000	0.000
34	E	982	ILE	0	-0.007	-0.008	18.459	-0.023	-0.023	0.000	0.000	0.000	0.000
35	E	983	VAL	0	0.005	-0.004	14.247	0.014	0.014	0.000	0.000	0.000	0.000
36	E	984	THR	0	-0.052	-0.021	17.454	-0.011	-0.011	0.000	0.000	0.000	0.000
37	E	985	LEU	0	0.042	0.009	15.193	-0.007	-0.007	0.000	0.000	0.000	0.000
38	E	986	SER	0	0.001	-0.001	18.777	0.008	0.008	0.000	0.000	0.000	0.000
39	E	987	THR	0	-0.018	-0.005	18.673	-0.004	-0.004	0.000	0.000	0.000	0.000
40	E	988	HIS	0	-0.033	0.010	21.591	0.015	0.015	0.000	0.000	0.000	0.000
41	E	989	PRO	0	0.013	-0.015	24.869	-0.004	-0.004	0.000	0.000	0.000	0.000
42	E	990	PRO	0	0.050	0.025	22.967	-0.013	-0.013	0.000	0.000	0.000	0.000
43	E	991	GLN	0	0.006	0.001	19.721	0.002	0.002	0.000	0.000	0.000	0.000
44	E	992	ILE	0	-0.001	-0.003	21.224	0.006	0.006	0.000	0.000	0.000	0.000
45	E	993	CYS	0	-0.037	-0.001	17.742	-0.007	-0.007	0.000	0.000	0.000	0.000
46	E	994	HIS	0	0.026	0.006	19.229	0.011	0.011	0.000	0.000	0.000	0.000
47	E	995	GLY	0	0.016	0.009	16.815	-0.030	-0.030	0.000	0.000	0.000	0.000
48	E	996	VAL	0	-0.009	0.007	17.876	0.027	0.027	0.000	0.000	0.000	0.000
49	E	997	GLY	0	0.084	0.027	17.252	-0.012	-0.012	0.000	0.000	0.000	0.000
50	E	998	LYS	1	0.827	0.914	18.102	-0.037	-0.037	0.000	0.000	0.000	0.000
51	E	999	SER	0	0.021	-0.007	15.762	0.026	0.026	0.000	0.000	0.000	0.000
52	E	1000	SER	0	0.029	0.009	16.539	-0.023	-0.023	0.000	0.000	0.000	0.000
53	E	1001	GLU	-1	-0.905	-0.941	10.373	0.781	0.781	0.000	0.000	0.000	0.000
54	E	1002	GLU	-1	-0.929	-0.976	11.967	0.047	0.047	0.000	0.000	0.000	0.000
55	E	1003	SER	0	0.000	-0.012	13.631	-0.056	-0.056	0.000	0.000	0.000	0.000
56	E	1004	GLN	0	0.006	-0.009	11.717	0.026	0.026	0.000	0.000	0.000	0.000
57	E	1005	ASN	0	-0.023	-0.022	8.108	-0.184	-0.184	0.000	0.000	0.000	0.000
58	E	1006	ASP	-1	-0.852	-0.923	10.690	-0.279	-0.279	0.000	0.000	0.000	0.000
59	E	1007	ALA	0	0.011	0.007	13.697	-0.039	-0.039	0.000	0.000	0.000	0.000
60	E	1008	ALA	0	-0.008	-0.009	9.996	-0.024	-0.024	0.000	0.000	0.000	0.000
61	E	1009	SER	0	-0.034	-0.011	11.248	-0.084	-0.084	0.000	0.000	0.000	0.000
62	E	1010	ASN	0	-0.022	-0.025	12.205	-0.017	-0.017	0.000	0.000	0.000	0.000
63	E	1011	ALA	0	0.020	0.016	13.825	0.016	0.016	0.000	0.000	0.000	0.000
64	E	1012	LEU	0	0.005	0.001	8.824	0.017	0.017	0.000	0.000	0.000	0.000
65	E	1013	LYS	1	0.889	0.958	13.407	0.282	0.282	0.000	0.000	0.000	0.000
66	E	1014	ILE	0	0.016	0.003	16.041	0.019	0.019	0.000	0.000	0.000	0.000
67	E	1015	LEU	0	0.023	-0.001	14.698	0.014	0.014	0.000	0.000	0.000	0.000
68	E	1016	SER	0	-0.078	-0.023	15.547	0.017	0.017	0.000	0.000	0.000	0.000
69	E	1017	LYS	1	0.881	0.939	17.401	0.174	0.174	0.000	0.000	0.000	0.000
70	E	1018	LEU	0	-0.048	0.001	20.466	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:949:GLY)