FMO DATABASE

FMODB ID: 1JG5Z

Calculation Name: 1GMJ-D-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GMJ

Chain ID: D

ChEMBL ID:

UniProt ID: P01096

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	58
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-251416.494083
FMO2-HF: Nuclear repulsion	227857.430759
FMO2-HF: Total energy	-23559.063324
FMO2-MP2: Total energy	-23629.780489

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(D:22:ACE )

Summations of interaction energy for fragment #1(D:22:ACE )

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.
0.541	2.758	0.236	-1.253	-1.201	-0.006

Interaction energy analysis for fragmet #1(D:22:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.031

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	D	24	LYS	1	0.952	0.973	3.818	2.067	2.701	-0.005	-0.321	-0.308	0.001
4	D	25	ARG	1	0.890	0.935	6.571	0.899	0.899	0.000	0.000	0.000	0.000
5	D	26	GLU	-1	-0.868	-0.929	3.154	-3.271	-2.266	0.224	-0.638	-0.592	-0.005
6	D	27	GLN	0	0.001	-0.007	5.305	0.746	0.746	0.000	0.000	0.000	0.000
7	D	28	ALA	0	0.012	0.022	7.271	0.112	0.112	0.000	0.000	0.000	0.000
8	D	29	GLU	-1	-0.948	-0.972	5.352	1.189	1.189	0.000	0.000	0.000	0.000
9	D	30	GLU	-1	-0.893	-0.947	3.472	0.398	0.976	0.017	-0.294	-0.301	-0.002
10	D	31	GLU	-1	-0.923	-0.961	6.346	0.029	0.029	0.000	0.000	0.000	0.000
11	D	32	ARG	1	0.915	0.942	10.049	-0.213	-0.213	0.000	0.000	0.000	0.000
12	D	33	TYR	0	0.060	0.043	7.851	-0.071	-0.071	0.000	0.000	0.000	0.000
13	D	34	PHE	0	0.050	0.008	7.305	-0.070	-0.070	0.000	0.000	0.000	0.000
14	D	35	ARG	1	0.891	0.963	11.312	-0.237	-0.237	0.000	0.000	0.000	0.000
15	D	36	ALA	0	-0.033	-0.021	13.232	-0.047	-0.047	0.000	0.000	0.000	0.000
16	D	37	ARG	1	0.944	0.965	11.373	-0.544	-0.544	0.000	0.000	0.000	0.000
17	D	38	ALA	0	0.019	0.018	14.823	-0.039	-0.039	0.000	0.000	0.000	0.000
18	D	39	LYS	1	0.940	0.970	17.089	-0.186	-0.186	0.000	0.000	0.000	0.000
19	D	40	GLU	-1	-0.937	-0.971	17.912	0.211	0.211	0.000	0.000	0.000	0.000
20	D	41	GLN	0	0.091	0.036	18.258	-0.034	-0.034	0.000	0.000	0.000	0.000
21	D	42	LEU	0	-0.052	-0.016	20.408	-0.022	-0.022	0.000	0.000	0.000	0.000
22	D	43	ALA	0	-0.041	-0.029	22.591	-0.016	-0.016	0.000	0.000	0.000	0.000
23	D	44	ALA	0	0.013	0.013	23.209	-0.013	-0.013	0.000	0.000	0.000	0.000
24	D	45	LEU	0	0.047	0.019	23.729	-0.014	-0.014	0.000	0.000	0.000	0.000
25	D	46	LYS	1	0.897	0.921	26.523	-0.093	-0.093	0.000	0.000	0.000	0.000
26	D	47	LYS	1	1.004	1.005	27.520	-0.122	-0.122	0.000	0.000	0.000	0.000
27	D	48	HIS	0	0.010	-0.002	25.730	-0.011	-0.011	0.000	0.000	0.000	0.000
28	D	49	LYS	1	0.926	0.992	29.505	-0.089	-0.089	0.000	0.000	0.000	0.000
29	D	50	GLU	-1	-0.937	-0.962	32.470	0.063	0.063	0.000	0.000	0.000	0.000
30	D	51	ASN	0	-0.021	-0.015	32.114	-0.006	-0.006	0.000	0.000	0.000	0.000
31	D	52	GLU	-1	-0.907	-0.936	34.462	0.058	0.058	0.000	0.000	0.000	0.000
32	D	53	ILE	0	-0.008	-0.007	36.280	-0.005	-0.005	0.000	0.000	0.000	0.000
33	D	54	SER	0	-0.029	-0.026	38.025	-0.005	-0.005	0.000	0.000	0.000	0.000
34	D	55	HIS	0	-0.009	-0.003	38.308	-0.001	-0.001	0.000	0.000	0.000	0.000
35	D	56	HIS	0	0.052	0.011	39.760	-0.004	-0.004	0.000	0.000	0.000	0.000
36	D	57	ALA	0	-0.023	0.000	42.474	-0.003	-0.003	0.000	0.000	0.000	0.000
37	D	58	LYS	1	0.964	0.984	42.612	-0.052	-0.052	0.000	0.000	0.000	0.000
38	D	59	GLU	-1	-0.894	-0.950	44.524	0.041	0.041	0.000	0.000	0.000	0.000
39	D	60	ILE	0	-0.029	-0.017	46.405	-0.003	-0.003	0.000	0.000	0.000	0.000
40	D	61	GLU	-1	-0.946	-0.965	48.338	0.036	0.036	0.000	0.000	0.000	0.000
41	D	62	ARG	1	0.943	0.964	47.893	-0.038	-0.038	0.000	0.000	0.000	0.000
42	D	63	LEU	0	0.023	0.000	49.706	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	64	GLN	0	-0.017	-0.011	52.511	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	65	LYS	1	0.962	0.987	51.963	-0.035	-0.035	0.000	0.000	0.000	0.000
45	D	66	GLU	-1	-0.977	-0.983	54.238	0.028	0.028	0.000	0.000	0.000	0.000
46	D	67	ILE	0	-0.012	-0.006	56.170	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	68	GLU	-1	-0.922	-0.945	58.482	0.023	0.023	0.000	0.000	0.000	0.000
48	D	69	ARG	1	0.940	0.960	58.179	-0.027	-0.027	0.000	0.000	0.000	0.000
49	D	70	HIS	0	0.022	-0.004	59.334	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	71	LYS	1	0.987	0.982	62.561	-0.023	-0.023	0.000	0.000	0.000	0.000
51	D	72	GLN	0	0.022	0.007	64.310	-0.001	-0.001	0.000	0.000	0.000	0.000
52	D	73	SER	0	-0.024	-0.014	65.206	-0.001	-0.001	0.000	0.000	0.000	0.000
53	D	74	ILE	0	-0.021	0.018	67.018	-0.001	-0.001	0.000	0.000	0.000	0.000
54	D	75	LYS	1	0.953	0.958	68.839	-0.020	-0.020	0.000	0.000	0.000	0.000
55	D	76	LYS	1	0.941	0.979	70.352	-0.018	-0.018	0.000	0.000	0.000	0.000
56	D	77	LEU	0	-0.048	-0.028	70.291	-0.001	-0.001	0.000	0.000	0.000	0.000
57	D	78	LYS	1	0.907	0.973	71.891	-0.017	-0.017	0.000	0.000	0.000	0.000
58	D	79	NME	0	-0.007	0.019	75.339	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:22:ACE )