FMO DATABASE

FMODB ID: QY62Y

Calculation Name: 1GD2-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GD2

Chain ID: E

ChEMBL ID:

UniProt ID: Q01663

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-291433.168903
FMO2-HF: Nuclear repulsion	264850.428945
FMO2-HF: Total energy	-26582.739957
FMO2-MP2: Total energy	-26662.082314

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:75:ASP)

Summations of interaction energy for fragment #1(E:75:ASP)

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.
-113.981	-110.679	0.144	-1.508	-1.939	0.009

Interaction energy analysis for fragmet #1(E:75:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.880 / q_NPA : -0.944

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	77	GLU	-1	-0.853	-0.892	2.829	17.640	20.875	0.145	-1.487	-1.893	0.009
4	E	78	PRO	0	-0.012	-0.009	4.369	-3.441	-3.374	-0.001	-0.021	-0.046	0.000
5	E	79	SER	0	0.110	0.045	7.173	-0.854	-0.854	0.000	0.000	0.000	0.000
6	E	80	SER	0	0.058	0.016	8.871	-1.130	-1.130	0.000	0.000	0.000	0.000
7	E	81	LYS	1	0.997	0.985	11.200	-16.611	-16.611	0.000	0.000	0.000	0.000
8	E	82	ARG	1	0.935	0.969	11.088	-20.160	-20.160	0.000	0.000	0.000	0.000
9	E	83	LYS	1	0.807	0.888	7.662	-28.034	-28.034	0.000	0.000	0.000	0.000
10	E	84	ALA	0	-0.021	-0.018	12.698	-0.993	-0.993	0.000	0.000	0.000	0.000
11	E	85	GLN	0	0.069	0.046	15.831	-0.070	-0.070	0.000	0.000	0.000	0.000
12	E	86	ASN	0	0.046	0.021	13.347	-1.489	-1.489	0.000	0.000	0.000	0.000
13	E	87	ARG	1	0.962	0.991	14.313	-17.047	-17.047	0.000	0.000	0.000	0.000
14	E	88	ALA	0	-0.003	0.001	18.568	-0.703	-0.703	0.000	0.000	0.000	0.000
15	E	89	ALA	0	0.036	0.010	20.123	-0.632	-0.632	0.000	0.000	0.000	0.000
16	E	90	GLN	0	0.067	0.029	20.171	-0.550	-0.550	0.000	0.000	0.000	0.000
17	E	91	ARG	1	0.921	0.967	22.123	-11.232	-11.232	0.000	0.000	0.000	0.000
18	E	92	ALA	0	0.017	0.006	24.460	-0.474	-0.474	0.000	0.000	0.000	0.000
19	E	93	PHE	0	-0.015	-0.007	24.800	-0.405	-0.405	0.000	0.000	0.000	0.000
20	E	94	ARG	1	0.922	0.943	22.092	-12.607	-12.607	0.000	0.000	0.000	0.000
21	E	95	LYS	1	0.796	0.887	27.765	-9.145	-9.145	0.000	0.000	0.000	0.000
22	E	96	ARG	1	1.008	1.004	26.471	-10.936	-10.936	0.000	0.000	0.000	0.000
23	E	97	LYS	1	0.948	0.978	28.851	-10.787	-10.787	0.000	0.000	0.000	0.000
24	E	98	GLU	-1	-0.812	-0.891	31.998	8.514	8.514	0.000	0.000	0.000	0.000
25	E	99	ASP	-1	-0.819	-0.887	33.813	8.500	8.500	0.000	0.000	0.000	0.000
26	E	100	HIS	0	0.007	-0.002	35.474	-0.245	-0.245	0.000	0.000	0.000	0.000
27	E	101	LEU	0	-0.008	0.013	35.850	-0.172	-0.172	0.000	0.000	0.000	0.000
28	E	102	LYS	1	0.920	0.924	36.236	-8.475	-8.475	0.000	0.000	0.000	0.000
29	E	103	ALA	0	0.010	0.028	39.981	-0.226	-0.226	0.000	0.000	0.000	0.000
30	E	104	LEU	0	0.006	0.006	39.190	-0.197	-0.197	0.000	0.000	0.000	0.000
31	E	105	GLU	-1	-0.926	-0.964	41.177	7.218	7.218	0.000	0.000	0.000	0.000
32	E	106	THR	0	-0.027	-0.017	43.678	-0.198	-0.198	0.000	0.000	0.000	0.000
33	E	107	GLN	0	-0.009	-0.003	45.491	-0.055	-0.055	0.000	0.000	0.000	0.000
34	E	108	VAL	0	0.006	-0.014	45.416	-0.168	-0.168	0.000	0.000	0.000	0.000
35	E	109	VAL	0	-0.005	0.007	47.897	-0.122	-0.122	0.000	0.000	0.000	0.000
36	E	110	THR	0	0.009	-0.002	49.894	-0.147	-0.147	0.000	0.000	0.000	0.000
37	E	111	LEU	0	-0.023	-0.024	49.639	-0.125	-0.125	0.000	0.000	0.000	0.000
38	E	112	LYS	1	0.915	0.962	48.566	-6.576	-6.576	0.000	0.000	0.000	0.000
39	E	113	GLU	-1	-0.916	-0.957	53.635	5.735	5.735	0.000	0.000	0.000	0.000
40	E	114	LEU	0	0.009	0.018	55.615	-0.122	-0.122	0.000	0.000	0.000	0.000
41	E	115	HIS	0	-0.006	0.009	56.287	-0.092	-0.092	0.000	0.000	0.000	0.000
42	E	116	SER	0	0.010	0.005	57.920	-0.092	-0.092	0.000	0.000	0.000	0.000
43	E	117	SER	0	-0.013	0.001	59.826	-0.107	-0.107	0.000	0.000	0.000	0.000
44	E	118	THR	0	-0.016	-0.030	60.404	-0.084	-0.084	0.000	0.000	0.000	0.000
45	E	119	THR	0	-0.031	-0.022	61.158	-0.069	-0.069	0.000	0.000	0.000	0.000
46	E	120	LEU	0	-0.005	0.003	63.792	-0.082	-0.082	0.000	0.000	0.000	0.000
47	E	121	GLU	-1	-0.909	-0.949	65.849	4.758	4.758	0.000	0.000	0.000	0.000
48	E	122	ASN	0	-0.027	-0.019	66.306	-0.100	-0.100	0.000	0.000	0.000	0.000
49	E	123	ASP	-1	-0.857	-0.935	67.347	4.699	4.699	0.000	0.000	0.000	0.000
50	E	124	GLN	0	-0.056	-0.022	69.702	-0.072	-0.072	0.000	0.000	0.000	0.000
51	E	125	LEU	0	0.017	-0.004	70.261	-0.096	-0.096	0.000	0.000	0.000	0.000
52	E	126	ARG	1	0.904	0.958	67.268	-4.794	-4.794	0.000	0.000	0.000	0.000
53	E	127	GLN	0	-0.043	-0.019	73.962	-0.100	-0.100	0.000	0.000	0.000	0.000
54	E	128	LYS	1	0.929	0.949	75.863	-4.089	-4.089	0.000	0.000	0.000	0.000
55	E	129	VAL	0	0.025	0.016	76.045	-0.046	-0.046	0.000	0.000	0.000	0.000
56	E	130	ARG	1	0.928	0.964	74.330	-4.279	-4.279	0.000	0.000	0.000	0.000
57	E	131	GLN	0	-0.007	0.000	79.388	-0.065	-0.065	0.000	0.000	0.000	0.000
58	E	132	LEU	0	0.006	-0.006	80.617	-0.048	-0.048	0.000	0.000	0.000	0.000
59	E	133	GLU	-1	-0.893	-0.929	81.512	3.945	3.945	0.000	0.000	0.000	0.000
60	E	134	GLU	-1	-0.921	-0.943	84.518	3.696	3.696	0.000	0.000	0.000	0.000
61	E	135	GLU	-1	-0.934	-0.971	86.360	3.596	3.596	0.000	0.000	0.000	0.000
62	E	136	LEU	0	-0.072	-0.029	86.539	-0.043	-0.043	0.000	0.000	0.000	0.000
63	E	137	ARG	1	0.808	0.890	84.171	-3.808	-3.808	0.000	0.000	0.000	0.000
64	E	138	ILE	0	-0.023	-0.002	90.375	-0.039	-0.039	0.000	0.000	0.000	0.000
65	E	139	LEU	0	-0.033	-0.003	92.705	-0.049	-0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:75:ASP)