FMO DATABASE

FMODB ID: 82ZVY

Calculation Name: 5CLV-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CLV

Chain ID: E

ChEMBL ID:

UniProt ID: P03052

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	OptHSide
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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356131.337774
FMO2-HF: Nuclear repulsion	331824.338138
FMO2-HF: Total energy	-24306.999636
FMO2-MP2: Total energy	-24379.884025

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:2:LYS)

Summations of interaction energy for fragment #1(E:2:LYS)

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.
-6.781	-4.999	-0.024	-0.765	-0.992	-0.001

Interaction energy analysis for fragmet #1(E:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.957

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	E	4	ARG	1	0.852	0.917	3.691	26.042	27.824	-0.024	-0.765	-0.992	-0.001
4	E	5	LEU	0	-0.010	0.018	5.986	0.069	0.069	0.000	0.000	0.000	0.000
5	E	6	THR	0	0.013	-0.019	9.790	0.698	0.698	0.000	0.000	0.000	0.000
6	E	7	GLU	-1	-0.817	-0.931	12.629	-13.459	-13.459	0.000	0.000	0.000	0.000
7	E	8	SER	0	-0.019	0.008	15.175	0.487	0.487	0.000	0.000	0.000	0.000
8	E	9	GLN	0	0.112	0.067	12.051	0.033	0.033	0.000	0.000	0.000	0.000
9	E	10	PHE	0	-0.012	-0.002	12.221	0.077	0.077	0.000	0.000	0.000	0.000
10	E	11	GLN	0	-0.047	-0.029	14.731	0.747	0.747	0.000	0.000	0.000	0.000
11	E	12	GLU	-1	-0.916	-0.951	18.102	-13.451	-13.451	0.000	0.000	0.000	0.000
12	E	13	ALA	0	-0.013	-0.001	15.594	0.381	0.381	0.000	0.000	0.000	0.000
13	E	14	ILE	0	-0.030	-0.026	16.723	0.355	0.355	0.000	0.000	0.000	0.000
14	E	15	GLN	0	-0.003	0.016	19.208	0.681	0.681	0.000	0.000	0.000	0.000
15	E	16	GLY	0	0.021	0.009	22.585	-0.139	-0.139	0.000	0.000	0.000	0.000
16	E	17	LEU	0	-0.040	-0.013	18.349	0.075	0.075	0.000	0.000	0.000	0.000
17	E	18	GLU	-1	-0.887	-0.935	22.608	-9.889	-9.889	0.000	0.000	0.000	0.000
18	E	19	VAL	0	-0.079	-0.045	19.053	-0.240	-0.240	0.000	0.000	0.000	0.000
19	E	20	GLY	0	0.041	0.018	22.265	0.243	0.243	0.000	0.000	0.000	0.000
20	E	21	GLN	0	0.023	-0.004	21.254	-0.140	-0.140	0.000	0.000	0.000	0.000
21	E	22	GLN	0	0.017	-0.005	19.478	-0.250	-0.250	0.000	0.000	0.000	0.000
22	E	23	THR	0	-0.035	-0.017	16.957	-0.381	-0.381	0.000	0.000	0.000	0.000
23	E	24	ILE	0	0.073	0.049	15.975	-0.871	-0.871	0.000	0.000	0.000	0.000
24	E	25	GLU	-1	-0.770	-0.876	15.594	-13.483	-13.483	0.000	0.000	0.000	0.000
25	E	26	ILE	0	-0.067	-0.030	13.173	-0.669	-0.669	0.000	0.000	0.000	0.000
26	E	27	ALA	0	-0.003	-0.007	11.415	-1.074	-1.074	0.000	0.000	0.000	0.000
27	E	28	ARG	1	0.869	0.930	10.888	12.259	12.259	0.000	0.000	0.000	0.000
28	E	29	GLY	0	0.014	-0.008	11.431	-0.581	-0.581	0.000	0.000	0.000	0.000
29	E	30	VAL	0	-0.052	-0.017	6.623	-1.052	-1.052	0.000	0.000	0.000	0.000
30	E	31	LEU	0	-0.029	-0.009	6.300	-2.221	-2.221	0.000	0.000	0.000	0.000
31	E	32	VAL	0	0.056	0.041	7.774	-1.108	-1.108	0.000	0.000	0.000	0.000
32	E	33	ASP	-1	-0.842	-0.896	9.908	-16.766	-16.766	0.000	0.000	0.000	0.000
33	E	34	GLY	0	-0.059	-0.018	5.931	-0.476	-0.476	0.000	0.000	0.000	0.000
34	E	35	LYS	1	0.827	0.897	6.786	15.077	15.077	0.000	0.000	0.000	0.000
35	E	36	PRO	0	0.041	0.009	7.699	-0.893	-0.893	0.000	0.000	0.000	0.000
36	E	37	GLN	0	0.100	0.042	8.255	2.265	2.265	0.000	0.000	0.000	0.000
37	E	38	ALA	0	-0.027	-0.016	10.552	1.232	1.232	0.000	0.000	0.000	0.000
38	E	39	THR	0	0.009	0.013	12.063	1.239	1.239	0.000	0.000	0.000	0.000
39	E	40	PHE	0	0.073	0.054	11.754	0.908	0.908	0.000	0.000	0.000	0.000
40	E	41	ALA	0	-0.034	-0.023	14.768	0.652	0.652	0.000	0.000	0.000	0.000
41	E	42	THR	0	-0.052	-0.037	16.659	0.643	0.643	0.000	0.000	0.000	0.000
42	E	43	SER	0	-0.050	-0.041	17.407	0.578	0.578	0.000	0.000	0.000	0.000
43	E	44	LEU	0	-0.013	-0.002	17.765	0.473	0.473	0.000	0.000	0.000	0.000
44	E	45	GLY	0	0.023	0.032	20.474	0.464	0.464	0.000	0.000	0.000	0.000
45	E	46	LEU	0	-0.040	-0.004	18.302	0.235	0.235	0.000	0.000	0.000	0.000
46	E	47	THR	0	0.057	0.009	19.205	-0.685	-0.685	0.000	0.000	0.000	0.000
47	E	48	ARG	1	1.013	0.974	13.885	17.777	17.777	0.000	0.000	0.000	0.000
48	E	49	GLY	0	0.017	0.020	14.621	-0.848	-0.848	0.000	0.000	0.000	0.000
49	E	50	ALA	0	0.036	0.022	16.239	-0.307	-0.307	0.000	0.000	0.000	0.000
50	E	51	VAL	0	0.008	0.007	12.318	-0.031	-0.031	0.000	0.000	0.000	0.000
51	E	52	SER	0	0.023	0.012	11.771	-0.902	-0.902	0.000	0.000	0.000	0.000
52	E	53	GLN	0	-0.034	-0.018	12.798	-0.079	-0.079	0.000	0.000	0.000	0.000
53	E	54	ALA	0	-0.056	-0.029	15.240	0.153	0.153	0.000	0.000	0.000	0.000
54	E	55	VAL	0	0.024	-0.001	8.647	0.064	0.064	0.000	0.000	0.000	0.000
55	E	56	HIS	0	-0.016	0.001	11.655	-1.160	-1.160	0.000	0.000	0.000	0.000
56	E	57	ARG	1	0.946	0.974	12.627	13.999	13.999	0.000	0.000	0.000	0.000
57	E	58	VAL	0	0.033	0.015	13.556	0.251	0.251	0.000	0.000	0.000	0.000
58	E	59	TRP	0	-0.064	-0.056	7.904	-1.179	-1.179	0.000	0.000	0.000	0.000
59	E	60	ALA	0	0.023	-0.007	12.267	-0.091	-0.091	0.000	0.000	0.000	0.000
60	E	61	ALA	0	0.046	0.038	14.482	0.461	0.461	0.000	0.000	0.000	0.000
61	E	62	PHE	0	0.010	-0.015	11.548	0.375	0.375	0.000	0.000	0.000	0.000
62	E	63	GLU	-1	-0.904	-0.933	10.922	-22.546	-22.546	0.000	0.000	0.000	0.000
63	E	64	ASP	-1	-0.918	-0.954	14.829	-14.121	-14.121	0.000	0.000	0.000	0.000
64	E	65	LYS	1	0.719	0.869	18.272	13.566	13.566	0.000	0.000	0.000	0.000
65	E	66	ASN	0	-0.057	-0.023	14.518	-0.248	-0.248	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:2:LYS)