FMO DATABASE

FMODB ID: YZGM2

Calculation Name: 3A7P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A7P

Chain ID: A

ChEMBL ID:

UniProt ID: Q03818

Base Structure: X-ray

Registration Date: 2023-09-19

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-409449.173722
FMO2-HF: Nuclear repulsion	374708.694482
FMO2-HF: Total energy	-34740.479241
FMO2-MP2: Total energy	-34843.636454

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(A:55:GLY)

Summations of interaction energy for fragment #1(A:55: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.
-4.041	-1.486	2.255	-1.78	-3.03	-0.002

Interaction energy analysis for fragmet #1(A:55:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.008

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	A	57	ILE	0	0.066	0.028	3.820	-1.970	-0.638	-0.004	-0.613	-0.715	0.001
4	A	58	VAL	0	0.025	0.020	2.039	-2.608	-2.091	2.243	-0.946	-1.813	-0.002
5	A	59	SER	0	-0.005	0.017	3.588	0.244	0.852	0.017	-0.211	-0.415	-0.001
6	A	60	HIS	0	-0.004	-0.008	4.850	0.514	0.612	-0.001	-0.010	-0.087	0.000
7	A	61	ASP	-1	-0.860	-0.949	7.219	-0.112	-0.112	0.000	0.000	0.000	0.000
8	A	62	ASP	-1	-0.890	-0.940	7.142	-1.166	-1.166	0.000	0.000	0.000	0.000
9	A	63	ALA	0	-0.034	-0.011	9.175	0.173	0.173	0.000	0.000	0.000	0.000
10	A	64	LEU	0	-0.026	-0.011	11.184	0.135	0.135	0.000	0.000	0.000	0.000
11	A	65	LEU	0	0.000	-0.011	11.305	0.090	0.090	0.000	0.000	0.000	0.000
12	A	66	ASN	0	0.004	0.010	12.076	0.091	0.091	0.000	0.000	0.000	0.000
13	A	67	THR	0	-0.015	-0.002	14.968	0.066	0.066	0.000	0.000	0.000	0.000
14	A	68	LEU	0	-0.024	-0.011	16.848	0.040	0.040	0.000	0.000	0.000	0.000
15	A	69	ALA	0	0.004	0.001	17.673	0.031	0.031	0.000	0.000	0.000	0.000
16	A	70	ILE	0	-0.030	-0.015	18.400	0.027	0.027	0.000	0.000	0.000	0.000
17	A	71	LEU	0	0.045	0.013	21.014	0.025	0.025	0.000	0.000	0.000	0.000
18	A	72	GLN	0	-0.029	0.000	22.535	0.009	0.009	0.000	0.000	0.000	0.000
19	A	73	LYS	1	0.928	0.955	23.849	0.157	0.157	0.000	0.000	0.000	0.000
20	A	74	GLU	-1	-0.919	-0.966	24.717	-0.131	-0.131	0.000	0.000	0.000	0.000
21	A	75	LEU	0	0.016	0.011	26.596	0.012	0.012	0.000	0.000	0.000	0.000
22	A	76	LYS	1	0.988	0.976	28.620	0.101	0.101	0.000	0.000	0.000	0.000
23	A	77	SER	0	-0.045	-0.011	29.823	0.010	0.010	0.000	0.000	0.000	0.000
24	A	78	LYS	1	1.019	0.995	29.894	0.099	0.099	0.000	0.000	0.000	0.000
25	A	79	GLU	-1	-0.903	-0.933	32.060	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	80	GLN	0	-0.087	-0.044	33.368	0.002	0.002	0.000	0.000	0.000	0.000
27	A	81	GLU	-1	-0.940	-0.971	35.813	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	82	ILE	0	-0.006	-0.010	35.714	0.005	0.005	0.000	0.000	0.000	0.000
29	A	83	ARG	1	0.924	0.958	35.572	0.065	0.065	0.000	0.000	0.000	0.000
30	A	84	ARG	1	0.960	0.979	36.783	0.068	0.068	0.000	0.000	0.000	0.000
31	A	85	LEU	0	0.039	0.012	40.239	0.003	0.003	0.000	0.000	0.000	0.000
32	A	86	LYS	1	0.931	0.971	41.354	0.046	0.046	0.000	0.000	0.000	0.000
33	A	87	GLU	-1	-0.851	-0.918	45.002	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	88	VAL	0	-0.033	-0.014	46.112	0.002	0.002	0.000	0.000	0.000	0.000
35	A	89	ILE	0	-0.016	-0.015	46.090	0.002	0.002	0.000	0.000	0.000	0.000
36	A	90	ALA	0	0.038	0.026	49.121	0.002	0.002	0.000	0.000	0.000	0.000
37	A	91	LEU	0	-0.007	0.004	51.019	0.002	0.002	0.000	0.000	0.000	0.000
38	A	92	LYS	1	0.932	0.959	51.156	0.036	0.036	0.000	0.000	0.000	0.000
39	A	93	ASN	0	0.053	0.028	52.316	0.002	0.002	0.000	0.000	0.000	0.000
40	A	94	LYS	1	1.001	1.017	55.187	0.030	0.030	0.000	0.000	0.000	0.000
41	A	95	ASN	0	-0.115	-0.077	56.983	0.001	0.001	0.000	0.000	0.000	0.000
42	A	96	THR	0	-0.030	-0.019	57.031	0.001	0.001	0.000	0.000	0.000	0.000
43	A	97	GLU	-1	-0.883	-0.935	57.771	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	98	ARG	1	0.935	0.967	59.718	0.025	0.025	0.000	0.000	0.000	0.000
45	A	99	LEU	0	-0.010	0.007	61.233	0.001	0.001	0.000	0.000	0.000	0.000
46	A	100	ASN	0	-0.002	-0.012	61.809	0.000	0.000	0.000	0.000	0.000	0.000
47	A	101	ALA	0	-0.001	0.009	65.048	0.001	0.001	0.000	0.000	0.000	0.000
48	A	102	ALA	0	0.020	0.006	67.420	0.001	0.001	0.000	0.000	0.000	0.000
49	A	103	LEU	0	0.014	0.004	67.204	0.001	0.001	0.000	0.000	0.000	0.000
50	A	104	ILE	0	0.011	0.021	67.269	0.001	0.001	0.000	0.000	0.000	0.000
51	A	105	SER	0	-0.022	-0.015	70.876	0.001	0.001	0.000	0.000	0.000	0.000
52	A	106	GLY	0	0.057	0.021	72.790	0.001	0.001	0.000	0.000	0.000	0.000
53	A	107	THR	0	-0.028	-0.021	72.319	0.000	0.000	0.000	0.000	0.000	0.000
54	A	108	ILE	0	-0.029	-0.015	74.165	0.001	0.001	0.000	0.000	0.000	0.000
55	A	109	GLU	-1	-0.858	-0.933	77.136	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	110	ASN	0	-0.051	-0.021	77.712	0.001	0.001	0.000	0.000	0.000	0.000
57	A	111	ASN	0	0.030	0.007	79.168	0.000	0.000	0.000	0.000	0.000	0.000
58	A	112	VAL	0	-0.012	-0.001	80.981	0.001	0.001	0.000	0.000	0.000	0.000
59	A	113	LEU	0	-0.031	-0.022	81.621	0.000	0.000	0.000	0.000	0.000	0.000
60	A	114	GLN	0	-0.042	-0.014	81.852	0.000	0.000	0.000	0.000	0.000	0.000
61	A	115	GLN	0	0.007	0.012	84.923	0.000	0.000	0.000	0.000	0.000	0.000
62	A	116	LYS	1	0.965	0.994	86.661	0.011	0.011	0.000	0.000	0.000	0.000
63	A	117	LEU	0	-0.006	-0.003	87.577	0.000	0.000	0.000	0.000	0.000	0.000
64	A	118	SER	0	-0.016	-0.011	88.961	0.000	0.000	0.000	0.000	0.000	0.000
65	A	119	ASP	-1	-0.901	-0.969	90.731	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	120	LEU	0	-0.004	-0.001	92.716	0.000	0.000	0.000	0.000	0.000	0.000
67	A	121	LYS	1	0.943	0.975	89.837	0.011	0.011	0.000	0.000	0.000	0.000
68	A	122	LYS	1	0.974	0.995	95.154	0.008	0.008	0.000	0.000	0.000	0.000
69	A	123	GLU	-1	-0.946	-0.971	97.084	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	124	HIS	0	0.029	-0.007	98.167	0.000	0.000	0.000	0.000	0.000	0.000
71	A	125	SER	0	0.003	0.009	98.654	0.000	0.000	0.000	0.000	0.000	0.000
72	A	126	GLN	0	-0.051	-0.031	100.983	0.000	0.000	0.000	0.000	0.000	0.000
73	A	127	LEU	0	0.010	0.014	103.020	0.000	0.000	0.000	0.000	0.000	0.000
74	A	128	VAL	0	0.054	0.028	102.005	0.000	0.000	0.000	0.000	0.000	0.000
75	A	129	ALA	0	-0.024	-0.007	105.011	0.000	0.000	0.000	0.000	0.000	0.000
76	A	130	ARG	1	0.930	0.958	106.719	0.007	0.007	0.000	0.000	0.000	0.000
77	A	131	TRP	0	0.013	0.008	108.288	0.000	0.000	0.000	0.000	0.000	0.000
78	A	132	LEU	0	0.086	0.043	107.559	0.000	0.000	0.000	0.000	0.000	0.000
79	A	133	LYS	1	0.920	0.968	109.395	0.007	0.007	0.000	0.000	0.000	0.000
80	A	134	LYS	1	0.824	0.918	112.750	0.007	0.007	0.000	0.000	0.000	0.000
81	A	135	THR	0	0.011	-0.003	112.972	0.000	0.000	0.000	0.000	0.000	0.000
82	A	136	GLU	-1	-0.916	-0.967	114.369	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	137	LYS	1	0.936	0.959	116.536	0.006	0.006	0.000	0.000	0.000	0.000
84	A	138	GLU	-1	-0.934	-0.971	117.339	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	139	THR	0	-0.011	-0.007	118.360	0.000	0.000	0.000	0.000	0.000	0.000
86	A	140	GLU	-1	-0.992	-0.970	120.620	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	141	ALA	0	-0.079	-0.045	122.454	0.000	0.000	0.000	0.000	0.000	0.000
88	A	142	MET	0	-0.052	-0.006	122.455	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:55:GLY)