FMO DATABASE

FMODB ID: 7GR5K

Calculation Name: 4ZC3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZC3

Chain ID: A

ChEMBL ID:

UniProt ID: P68928

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	57
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-299207.659282
FMO2-HF: Nuclear repulsion	277336.547251
FMO2-HF: Total energy	-21871.112031
FMO2-MP2: Total energy	-21935.648954

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:6:LEU)

Summations of interaction energy for fragment #1(A:6:LEU)

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.
-11.488	-4.987	1.519	-3.061	-4.956	-0.014

Interaction energy analysis for fragmet #1(A:6:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.019

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	8	PRO	0	0.109	0.044	3.853	-2.064	-0.593	-0.012	-0.686	-0.772	0.003
4	A	9	LYS	1	0.899	0.969	6.543	-0.177	-0.177	0.000	0.000	0.000	0.000
5	A	10	GLN	0	-0.038	-0.031	4.089	1.521	1.739	0.000	-0.020	-0.198	0.000
6	A	11	GLU	-1	-0.822	-0.902	2.978	-8.904	-5.479	0.283	-1.822	-1.886	-0.018
7	A	12	ARG	1	0.854	0.913	6.004	0.567	0.567	0.000	0.000	0.000	0.000
8	A	13	PHE	0	0.002	-0.006	8.436	0.103	0.103	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.004	0.003	5.337	0.078	0.078	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.846	-0.928	9.338	-0.565	-0.565	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.823	-0.897	11.598	-0.124	-0.124	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.034	-0.022	12.489	0.058	0.058	0.000	0.000	0.000	0.000
13	A	18	PHE	0	-0.026	-0.014	11.617	0.018	0.018	0.000	0.000	0.000	0.000
14	A	19	ILE	0	-0.001	0.016	15.243	0.016	0.016	0.000	0.000	0.000	0.000
15	A	20	ASN	0	-0.097	-0.066	17.115	0.032	0.032	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.887	-0.936	19.275	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	22	MET	0	-0.025	-0.018	15.624	0.017	0.017	0.000	0.000	0.000	0.000
18	A	23	ASN	0	0.001	0.021	18.129	0.059	0.059	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.046	-0.001	15.455	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	25	THR	0	0.041	0.018	15.952	0.038	0.038	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.928	0.958	18.098	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.049	0.049	13.794	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	28	ALA	0	-0.027	-0.017	13.532	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	29	ILE	0	-0.025	-0.023	14.597	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.011	0.001	16.088	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.012	0.000	11.101	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	32	GLY	0	0.013	0.013	12.686	0.008	0.008	0.000	0.000	0.000	0.000
28	A	33	TYR	0	-0.069	-0.037	9.015	0.022	0.022	0.000	0.000	0.000	0.000
29	A	34	SER	0	0.019	0.011	15.362	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	35	LYS	1	1.054	0.998	18.906	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	36	ASN	0	-0.005	-0.003	21.218	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	37	SER	0	0.011	0.012	18.356	0.000	0.000	0.000	0.000	0.000	0.000
33	A	38	ALA	0	-0.018	0.011	17.032	0.042	0.042	0.000	0.000	0.000	0.000
34	A	39	SER	0	-0.003	-0.003	17.180	0.018	0.018	0.000	0.000	0.000	0.000
35	A	40	ALA	0	0.039	0.018	18.433	0.011	0.011	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.035	0.014	12.625	0.033	0.033	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.009	0.005	13.395	0.079	0.079	0.000	0.000	0.000	0.000
38	A	43	ALA	0	-0.019	-0.015	14.062	0.025	0.025	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.929	-0.962	12.566	0.983	0.983	0.000	0.000	0.000	0.000
40	A	45	ASN	0	0.007	-0.022	9.216	0.409	0.409	0.000	0.000	0.000	0.000
41	A	46	LEU	0	-0.046	-0.008	10.105	0.081	0.081	0.000	0.000	0.000	0.000
42	A	47	GLN	0	-0.035	-0.020	12.238	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.944	0.992	6.522	-2.820	-2.820	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.047	0.027	8.729	0.013	0.013	0.000	0.000	0.000	0.000
45	A	50	ALA	0	-0.006	-0.014	3.372	-0.427	-0.147	0.021	-0.064	-0.236	0.000
46	A	51	ILE	0	-0.022	-0.005	4.919	-0.159	-0.159	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.941	0.961	6.720	-0.561	-0.561	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.016	0.011	6.247	-0.158	-0.158	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.860	0.918	2.388	0.326	1.433	1.227	-0.469	-1.864	0.001
50	A	55	ILE	0	0.000	0.002	6.730	-0.134	-0.134	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.820	-0.908	10.200	0.088	0.088	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.073	-0.032	8.085	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.907	0.953	9.322	0.457	0.457	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.033	-0.026	11.551	0.014	0.014	0.000	0.000	0.000	0.000
55	A	60	LYS	1	0.926	0.978	12.206	0.296	0.296	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.972	-0.996	10.778	-0.527	-0.527	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.053	-0.006	15.011	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LEU)