FMO DATABASE

FMODB ID: R99N8

Calculation Name: 3ZGX-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ZGX

Chain ID: C

ChEMBL ID:

UniProt ID: P35154

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-332291.673691
FMO2-HF: Nuclear repulsion	305219.835391
FMO2-HF: Total energy	-27071.838299
FMO2-MP2: Total energy	-27150.553851

3D Structure Molmil

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:10:THR)

Summations of interaction energy for fragment #1(C:10:THR)

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.
-3.473	1.075	-0.042	-2.527	-1.979	0.003

Interaction energy analysis for fragmet #1(C:10:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.002

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	C	12	GLU	-1	-0.818	-0.886	3.817	-3.058	1.349	-0.042	-2.503	-1.861	0.003
4	C	13	GLY	0	-0.004	0.005	6.075	-0.436	-0.436	0.000	0.000	0.000	0.000
5	C	14	PRO	0	0.001	-0.009	6.719	0.123	0.123	0.000	0.000	0.000	0.000
6	C	15	LEU	0	0.030	-0.001	8.038	0.211	0.211	0.000	0.000	0.000	0.000
7	C	16	ASP	-1	-0.721	-0.886	9.254	-0.463	-0.463	0.000	0.000	0.000	0.000
8	C	17	LEU	0	-0.019	0.011	4.144	0.245	0.386	0.000	-0.024	-0.118	0.000
9	C	18	LEU	0	0.000	-0.009	8.250	0.274	0.274	0.000	0.000	0.000	0.000
10	C	19	LEU	0	0.018	0.019	10.669	0.022	0.022	0.000	0.000	0.000	0.000
11	C	20	HIS	1	0.737	0.859	8.424	-0.104	-0.104	0.000	0.000	0.000	0.000
12	C	21	LEU	0	-0.046	-0.015	9.912	0.050	0.050	0.000	0.000	0.000	0.000
13	C	22	ILE	0	0.026	0.012	12.378	0.000	0.000	0.000	0.000	0.000	0.000
14	C	23	ASN	0	0.048	0.020	15.524	-0.012	-0.012	0.000	0.000	0.000	0.000
15	C	24	ARG	1	0.927	0.965	13.050	-0.867	-0.867	0.000	0.000	0.000	0.000
16	C	25	LEU	0	-0.047	-0.026	14.956	0.019	0.019	0.000	0.000	0.000	0.000
17	C	26	GLU	-1	-0.886	-0.935	18.202	0.154	0.154	0.000	0.000	0.000	0.000
18	C	27	ILE	0	0.018	-0.016	19.520	-0.011	-0.011	0.000	0.000	0.000	0.000
19	C	28	ASP	-1	-0.925	-0.970	19.229	0.477	0.477	0.000	0.000	0.000	0.000
20	C	29	ILE	0	-0.126	-0.043	21.239	-0.012	-0.012	0.000	0.000	0.000	0.000
21	C	30	TYR	0	-0.031	-0.032	23.525	-0.023	-0.023	0.000	0.000	0.000	0.000
22	C	31	ASP	-1	-0.912	-0.945	24.554	0.174	0.174	0.000	0.000	0.000	0.000
23	C	32	ILE	0	-0.034	0.009	24.911	0.007	0.007	0.000	0.000	0.000	0.000
24	C	33	PRO	0	-0.033	-0.038	26.873	-0.020	-0.020	0.000	0.000	0.000	0.000
25	C	34	VAL	0	-0.083	-0.042	29.948	-0.011	-0.011	0.000	0.000	0.000	0.000
26	C	35	ALA	0	0.108	0.085	29.049	0.010	0.010	0.000	0.000	0.000	0.000
27	C	36	LYS	1	0.879	0.941	30.398	-0.157	-0.157	0.000	0.000	0.000	0.000
28	C	37	ILE	0	0.037	0.020	31.204	0.004	0.004	0.000	0.000	0.000	0.000
29	C	38	THR	0	0.009	-0.006	30.844	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	39	GLU	-1	-0.884	-0.943	32.497	0.073	0.073	0.000	0.000	0.000	0.000
31	C	40	GLN	0	0.002	-0.028	29.720	-0.013	-0.013	0.000	0.000	0.000	0.000
32	C	41	TYR	0	0.030	0.031	26.118	-0.002	-0.002	0.000	0.000	0.000	0.000
33	C	42	LEU	0	-0.005	-0.008	28.497	-0.005	-0.005	0.000	0.000	0.000	0.000
34	C	43	LEU	0	-0.036	-0.001	28.328	-0.007	-0.007	0.000	0.000	0.000	0.000
35	C	44	TYR	0	-0.003	0.002	21.157	-0.009	-0.009	0.000	0.000	0.000	0.000
36	C	45	VAL	0	0.030	0.016	25.544	-0.007	-0.007	0.000	0.000	0.000	0.000
37	C	46	HIS	0	-0.013	0.007	27.034	-0.011	-0.011	0.000	0.000	0.000	0.000
38	C	47	THR	0	-0.011	-0.034	25.521	-0.007	-0.007	0.000	0.000	0.000	0.000
39	C	48	MET	0	-0.006	0.011	20.460	-0.017	-0.017	0.000	0.000	0.000	0.000
40	C	49	ARG	1	0.945	0.960	24.273	-0.031	-0.031	0.000	0.000	0.000	0.000
41	C	50	VAL	0	-0.055	-0.024	26.698	-0.011	-0.011	0.000	0.000	0.000	0.000
42	C	51	LEU	0	0.047	0.034	20.789	-0.013	-0.013	0.000	0.000	0.000	0.000
43	C	52	GLU	-1	-0.925	-0.967	22.446	-0.015	-0.015	0.000	0.000	0.000	0.000
44	C	53	LEU	0	-0.057	-0.010	24.649	-0.014	-0.014	0.000	0.000	0.000	0.000
45	C	54	ASP	-1	-0.807	-0.911	27.040	-0.052	-0.052	0.000	0.000	0.000	0.000
46	C	55	ILE	0	-0.030	-0.004	20.974	-0.015	-0.015	0.000	0.000	0.000	0.000
47	C	56	ALA	0	-0.039	-0.020	25.012	-0.016	-0.016	0.000	0.000	0.000	0.000
48	C	57	SER	0	-0.068	-0.068	26.934	-0.004	-0.004	0.000	0.000	0.000	0.000
49	C	58	GLU	-1	-0.897	-0.951	26.063	-0.114	-0.114	0.000	0.000	0.000	0.000
50	C	59	TYR	0	-0.044	-0.034	20.544	-0.020	-0.020	0.000	0.000	0.000	0.000
51	C	60	LEU	0	-0.048	-0.002	27.284	-0.002	-0.002	0.000	0.000	0.000	0.000
52	C	61	VAL	0	0.046	0.019	30.903	0.000	0.000	0.000	0.000	0.000	0.000
53	C	62	MET	0	-0.015	0.016	27.371	-0.001	-0.001	0.000	0.000	0.000	0.000
54	C	63	ALA	0	0.015	0.015	30.134	-0.005	-0.005	0.000	0.000	0.000	0.000
55	C	64	ALA	0	0.003	-0.006	31.326	0.001	0.001	0.000	0.000	0.000	0.000
56	C	65	THR	0	-0.037	-0.048	32.523	0.004	0.004	0.000	0.000	0.000	0.000
57	C	66	LEU	0	0.025	0.005	28.909	0.003	0.003	0.000	0.000	0.000	0.000
58	C	67	LEU	0	0.018	0.035	33.659	0.002	0.002	0.000	0.000	0.000	0.000
59	C	68	SER	0	0.033	0.027	36.435	0.004	0.004	0.000	0.000	0.000	0.000
60	C	69	ILE	0	0.029	0.036	33.916	0.004	0.004	0.000	0.000	0.000	0.000
61	C	70	LYS	1	0.947	0.963	35.993	0.132	0.132	0.000	0.000	0.000	0.000
62	C	71	SER	0	-0.147	-0.105	37.881	0.005	0.005	0.000	0.000	0.000	0.000
63	C	72	ARG	1	0.957	0.965	40.599	0.099	0.099	0.000	0.000	0.000	0.000
64	C	73	MET	0	-0.060	-0.019	37.779	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	74	LEU	0	-0.066	-0.013	41.285	0.001	0.001	0.000	0.000	0.000	0.000
66	C	75	LEU	0	0.017	0.005	44.176	0.004	0.004	0.000	0.000	0.000	0.000
67	C	76	PRO	0	0.007	0.014	45.899	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:10:THR)