FMO DATABASE

FMODB ID: R9278

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	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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-291378.084714
FMO2-HF: Nuclear repulsion	264795.858449
FMO2-HF: Total energy	-26582.226265
FMO2-MP2: Total energy	-26661.609798

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.
-113.265	-110.045	0.161	-1.428	-1.952	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 : -0.878 / q_NPA : -0.942

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	-0.916	-0.945	2.822	17.518	20.663	0.162	-1.409	-1.897	0.009
4	E	78	PRO	0	-0.018	-0.013	4.362	-3.516	-3.441	-0.001	-0.019	-0.055	0.000
5	E	79	SER	0	0.111	0.046	7.167	-0.926	-0.926	0.000	0.000	0.000	0.000
6	E	80	SER	0	0.058	0.015	8.868	-1.167	-1.167	0.000	0.000	0.000	0.000
7	E	81	LYS	1	1.005	0.987	11.195	-16.682	-16.682	0.000	0.000	0.000	0.000
8	E	82	ARG	1	0.977	1.006	11.066	-20.144	-20.144	0.000	0.000	0.000	0.000
9	E	83	LYS	1	0.861	0.933	7.918	-27.376	-27.376	0.000	0.000	0.000	0.000
10	E	84	ALA	0	-0.012	-0.014	12.691	-0.965	-0.965	0.000	0.000	0.000	0.000
11	E	85	GLN	0	0.049	0.027	15.842	-0.091	-0.091	0.000	0.000	0.000	0.000
12	E	86	ASN	0	0.017	0.006	13.129	-1.465	-1.465	0.000	0.000	0.000	0.000
13	E	87	ARG	1	0.963	0.990	14.115	-17.019	-17.019	0.000	0.000	0.000	0.000
14	E	88	ALA	0	-0.008	-0.001	18.560	-0.702	-0.702	0.000	0.000	0.000	0.000
15	E	89	ALA	0	0.034	0.007	20.162	-0.628	-0.628	0.000	0.000	0.000	0.000
16	E	90	GLN	0	0.030	0.017	20.171	-0.205	-0.205	0.000	0.000	0.000	0.000
17	E	91	ARG	1	0.932	0.960	22.114	-11.300	-11.300	0.000	0.000	0.000	0.000
18	E	92	ALA	0	0.009	0.002	24.451	-0.482	-0.482	0.000	0.000	0.000	0.000
19	E	93	PHE	0	-0.017	-0.005	24.865	-0.413	-0.413	0.000	0.000	0.000	0.000
20	E	94	ARG	1	0.966	0.968	21.831	-12.636	-12.636	0.000	0.000	0.000	0.000
21	E	95	LYS	1	0.848	0.932	27.756	-9.215	-9.215	0.000	0.000	0.000	0.000
22	E	96	ARG	1	1.002	1.000	26.546	-10.951	-10.951	0.000	0.000	0.000	0.000
23	E	97	LYS	1	0.944	0.976	28.400	-10.954	-10.954	0.000	0.000	0.000	0.000
24	E	98	GLU	-1	-0.874	-0.946	31.988	8.605	8.605	0.000	0.000	0.000	0.000
25	E	99	ASP	-1	-0.857	-0.922	33.804	8.493	8.493	0.000	0.000	0.000	0.000
26	E	100	HIS	0	-0.008	-0.009	35.466	-0.249	-0.249	0.000	0.000	0.000	0.000
27	E	101	LEU	0	-0.014	0.013	35.819	-0.167	-0.167	0.000	0.000	0.000	0.000
28	E	102	LYS	1	0.991	0.981	36.749	-8.392	-8.392	0.000	0.000	0.000	0.000
29	E	103	ALA	0	0.010	0.024	39.971	-0.227	-0.227	0.000	0.000	0.000	0.000
30	E	104	LEU	0	0.015	0.007	39.360	-0.199	-0.199	0.000	0.000	0.000	0.000
31	E	105	GLU	-1	-0.930	-0.962	41.012	7.311	7.311	0.000	0.000	0.000	0.000
32	E	106	THR	0	-0.029	-0.013	43.668	-0.205	-0.205	0.000	0.000	0.000	0.000
33	E	107	GLN	0	-0.008	-0.011	45.528	-0.024	-0.024	0.000	0.000	0.000	0.000
34	E	108	VAL	0	-0.004	-0.014	45.382	-0.169	-0.169	0.000	0.000	0.000	0.000
35	E	109	VAL	0	0.002	0.010	47.918	-0.126	-0.126	0.000	0.000	0.000	0.000
36	E	110	THR	0	0.013	0.006	49.938	-0.154	-0.154	0.000	0.000	0.000	0.000
37	E	111	LEU	0	-0.020	-0.025	49.565	-0.125	-0.125	0.000	0.000	0.000	0.000
38	E	112	LYS	1	0.917	0.959	49.640	-6.481	-6.481	0.000	0.000	0.000	0.000
39	E	113	GLU	-1	-0.929	-0.962	53.625	5.721	5.721	0.000	0.000	0.000	0.000
40	E	114	LEU	0	0.007	0.017	55.606	-0.122	-0.122	0.000	0.000	0.000	0.000
41	E	115	HIS	0	-0.012	0.003	56.292	-0.109	-0.109	0.000	0.000	0.000	0.000
42	E	116	SER	0	-0.008	-0.004	57.909	-0.127	-0.127	0.000	0.000	0.000	0.000
43	E	117	SER	0	-0.013	0.005	59.815	-0.127	-0.127	0.000	0.000	0.000	0.000
44	E	118	THR	0	0.019	-0.017	60.417	-0.079	-0.079	0.000	0.000	0.000	0.000
45	E	119	THR	0	-0.041	-0.022	61.104	-0.065	-0.065	0.000	0.000	0.000	0.000
46	E	120	LEU	0	0.016	0.018	63.783	-0.082	-0.082	0.000	0.000	0.000	0.000
47	E	121	GLU	-1	-0.914	-0.955	65.842	4.732	4.732	0.000	0.000	0.000	0.000
48	E	122	ASN	0	-0.042	-0.023	66.390	-0.112	-0.112	0.000	0.000	0.000	0.000
49	E	123	ASP	-1	-0.900	-0.963	67.072	4.735	4.735	0.000	0.000	0.000	0.000
50	E	124	GLN	0	-0.064	-0.030	69.828	-0.068	-0.068	0.000	0.000	0.000	0.000
51	E	125	LEU	0	0.021	-0.003	70.119	-0.098	-0.098	0.000	0.000	0.000	0.000
52	E	126	ARG	1	0.949	0.980	67.570	-4.753	-4.753	0.000	0.000	0.000	0.000
53	E	127	GLN	0	-0.062	-0.024	73.847	-0.087	-0.087	0.000	0.000	0.000	0.000
54	E	128	LYS	1	0.974	0.977	75.856	-4.103	-4.103	0.000	0.000	0.000	0.000
55	E	129	VAL	0	0.017	0.014	75.921	-0.047	-0.047	0.000	0.000	0.000	0.000
56	E	130	ARG	1	0.970	0.989	74.444	-4.273	-4.273	0.000	0.000	0.000	0.000
57	E	131	GLN	0	-0.053	-0.036	79.657	-0.056	-0.056	0.000	0.000	0.000	0.000
58	E	132	LEU	0	0.003	-0.003	80.636	-0.050	-0.050	0.000	0.000	0.000	0.000
59	E	133	GLU	-1	-0.949	-0.964	81.324	3.980	3.980	0.000	0.000	0.000	0.000
60	E	134	GLU	-1	-0.932	-0.952	84.368	3.692	3.692	0.000	0.000	0.000	0.000
61	E	135	GLU	-1	-0.914	-0.964	86.313	3.591	3.591	0.000	0.000	0.000	0.000
62	E	136	LEU	0	-0.063	-0.022	86.413	-0.043	-0.043	0.000	0.000	0.000	0.000
63	E	137	ARG	1	0.851	0.921	84.034	-3.799	-3.799	0.000	0.000	0.000	0.000
64	E	138	ILE	0	-0.029	-0.004	90.210	-0.040	-0.040	0.000	0.000	0.000	0.000
65	E	139	LEU	0	-0.034	-0.005	92.631	-0.048	-0.048	0.000	0.000	0.000	0.000

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