FMO DATABASE

FMODB ID: K9543

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	OptAll
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	-291875.58956
FMO2-HF: Nuclear repulsion	265292.647961
FMO2-HF: Total energy	-26582.9416
FMO2-MP2: Total energy	-26662.267541

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.
-116.269	-113.006	0.174	-1.573	-1.865	0.01

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 : -0.874 / q_NPA : -0.938

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	-0.822	-0.886	2.764	17.431	20.619	0.175	-1.553	-1.810	0.010
4	E	78	PRO	0	-0.016	-0.016	4.437	-3.815	-3.740	-0.001	-0.020	-0.055	0.000
5	E	79	SER	0	0.103	0.039	7.428	-1.150	-1.150	0.000	0.000	0.000	0.000
6	E	80	SER	0	0.035	0.008	8.539	-1.497	-1.497	0.000	0.000	0.000	0.000
7	E	81	LYS	1	1.004	0.993	11.047	-16.580	-16.580	0.000	0.000	0.000	0.000
8	E	82	ARG	1	0.933	0.971	10.909	-20.137	-20.137	0.000	0.000	0.000	0.000
9	E	83	LYS	1	0.806	0.894	7.033	-28.777	-28.777	0.000	0.000	0.000	0.000
10	E	84	ALA	0	-0.029	-0.019	12.663	-1.026	-1.026	0.000	0.000	0.000	0.000
11	E	85	GLN	0	0.064	0.037	15.885	-0.015	-0.015	0.000	0.000	0.000	0.000
12	E	86	ASN	0	0.054	0.029	13.851	-1.361	-1.361	0.000	0.000	0.000	0.000
13	E	87	ARG	1	0.955	0.986	14.334	-17.021	-17.021	0.000	0.000	0.000	0.000
14	E	88	ALA	0	0.003	0.003	18.653	-0.696	-0.696	0.000	0.000	0.000	0.000
15	E	89	ALA	0	0.030	0.014	20.059	-0.613	-0.613	0.000	0.000	0.000	0.000
16	E	90	GLN	0	0.079	0.028	20.259	-1.015	-1.015	0.000	0.000	0.000	0.000
17	E	91	ARG	1	0.934	0.981	22.163	-11.189	-11.189	0.000	0.000	0.000	0.000
18	E	92	ALA	0	0.030	0.009	24.490	-0.455	-0.455	0.000	0.000	0.000	0.000
19	E	93	PHE	0	-0.044	-0.020	24.837	-0.403	-0.403	0.000	0.000	0.000	0.000
20	E	94	ARG	1	0.905	0.934	22.345	-12.569	-12.569	0.000	0.000	0.000	0.000
21	E	95	LYS	1	0.802	0.889	27.910	-9.137	-9.137	0.000	0.000	0.000	0.000
22	E	96	ARG	1	1.015	1.006	26.244	-10.902	-10.902	0.000	0.000	0.000	0.000
23	E	97	LYS	1	0.959	0.987	29.339	-10.599	-10.599	0.000	0.000	0.000	0.000
24	E	98	GLU	-1	-0.817	-0.900	32.102	8.445	8.445	0.000	0.000	0.000	0.000
25	E	99	ASP	-1	-0.819	-0.887	33.920	8.486	8.486	0.000	0.000	0.000	0.000
26	E	100	HIS	0	0.013	0.003	35.513	-0.226	-0.226	0.000	0.000	0.000	0.000
27	E	101	LEU	0	-0.013	0.008	35.912	-0.181	-0.181	0.000	0.000	0.000	0.000
28	E	102	LYS	1	0.914	0.933	36.280	-8.439	-8.439	0.000	0.000	0.000	0.000
29	E	103	ALA	0	0.001	0.020	39.921	-0.226	-0.226	0.000	0.000	0.000	0.000
30	E	104	LEU	0	0.001	0.001	38.956	-0.180	-0.180	0.000	0.000	0.000	0.000
31	E	105	GLU	-1	-0.906	-0.956	41.525	7.100	7.100	0.000	0.000	0.000	0.000
32	E	106	THR	0	-0.026	-0.019	43.856	-0.206	-0.206	0.000	0.000	0.000	0.000
33	E	107	GLN	0	-0.014	0.005	45.302	-0.063	-0.063	0.000	0.000	0.000	0.000
34	E	108	VAL	0	0.010	-0.011	45.193	-0.175	-0.175	0.000	0.000	0.000	0.000
35	E	109	VAL	0	-0.016	-0.005	47.757	-0.124	-0.124	0.000	0.000	0.000	0.000
36	E	110	THR	0	0.029	0.004	49.852	-0.156	-0.156	0.000	0.000	0.000	0.000
37	E	111	LEU	0	-0.024	-0.022	49.649	-0.129	-0.129	0.000	0.000	0.000	0.000
38	E	112	LYS	1	0.901	0.965	48.210	-6.605	-6.605	0.000	0.000	0.000	0.000
39	E	113	GLU	-1	-0.911	-0.951	53.743	5.715	5.715	0.000	0.000	0.000	0.000
40	E	114	LEU	0	0.014	0.009	55.630	-0.123	-0.123	0.000	0.000	0.000	0.000
41	E	115	HIS	0	0.022	0.027	56.337	-0.086	-0.086	0.000	0.000	0.000	0.000
42	E	116	SER	0	0.002	0.004	57.915	-0.100	-0.100	0.000	0.000	0.000	0.000
43	E	117	SER	0	-0.019	-0.007	59.860	-0.112	-0.112	0.000	0.000	0.000	0.000
44	E	118	THR	0	-0.004	-0.022	60.337	-0.082	-0.082	0.000	0.000	0.000	0.000
45	E	119	THR	0	-0.042	-0.027	61.084	-0.078	-0.078	0.000	0.000	0.000	0.000
46	E	120	LEU	0	-0.022	-0.008	63.693	-0.092	-0.092	0.000	0.000	0.000	0.000
47	E	121	GLU	-1	-0.901	-0.947	65.514	4.766	4.766	0.000	0.000	0.000	0.000
48	E	122	ASN	0	0.000	-0.003	66.324	-0.100	-0.100	0.000	0.000	0.000	0.000
49	E	123	ASP	-1	-0.821	-0.916	67.636	4.641	4.641	0.000	0.000	0.000	0.000
50	E	124	GLN	0	-0.032	-0.013	69.459	-0.097	-0.097	0.000	0.000	0.000	0.000
51	E	125	LEU	0	0.016	0.009	70.202	-0.095	-0.095	0.000	0.000	0.000	0.000
52	E	126	ARG	1	0.837	0.915	66.495	-4.815	-4.815	0.000	0.000	0.000	0.000
53	E	127	GLN	0	-0.034	-0.002	73.837	-0.107	-0.107	0.000	0.000	0.000	0.000
54	E	128	LYS	1	0.911	0.945	75.815	-4.078	-4.078	0.000	0.000	0.000	0.000
55	E	129	VAL	0	0.041	0.015	76.261	-0.061	-0.061	0.000	0.000	0.000	0.000
56	E	130	ARG	1	0.930	0.950	74.477	-4.293	-4.293	0.000	0.000	0.000	0.000
57	E	131	GLN	0	-0.013	-0.001	79.048	-0.064	-0.064	0.000	0.000	0.000	0.000
58	E	132	LEU	0	-0.003	-0.003	80.513	-0.046	-0.046	0.000	0.000	0.000	0.000
59	E	133	GLU	-1	-0.889	-0.923	81.886	3.912	3.912	0.000	0.000	0.000	0.000
60	E	134	GLU	-1	-0.867	-0.919	84.371	3.694	3.694	0.000	0.000	0.000	0.000
61	E	135	GLU	-1	-0.932	-0.973	86.383	3.593	3.593	0.000	0.000	0.000	0.000
62	E	136	LEU	0	-0.064	-0.039	86.535	-0.047	-0.047	0.000	0.000	0.000	0.000
63	E	137	ARG	1	0.754	0.861	84.552	-3.812	-3.812	0.000	0.000	0.000	0.000
64	E	138	ILE	0	-0.046	-0.010	90.157	-0.041	-0.041	0.000	0.000	0.000	0.000
65	E	139	LEU	0	-0.052	-0.014	92.365	-0.056	-0.056	0.000	0.000	0.000	0.000

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