FMO DATABASE

FMODB ID: R9JV8

Calculation Name: 3GHD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZN4

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-400617.472781
FMO2-HF: Nuclear repulsion	374001.295759
FMO2-HF: Total energy	-26616.177022
FMO2-MP2: Total energy	-26694.064194

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(A:14:LYS)

Summations of interaction energy for fragment #1(A:14:LYS)

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.
-27.174	-34.12	36.257	-15.19	-14.121	-0.128

Interaction energy analysis for fragmet #1(A:14:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.908

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

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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	16	ILE	0	-0.011	-0.010	3.487	-7.587	-4.655	-0.006	-1.351	-1.575	-0.002
4	A	17	VAL	0	0.009	0.010	5.822	2.454	2.454	0.000	0.000	0.000	0.000
5	A	18	VAL	0	-0.050	-0.018	9.425	-0.634	-0.634	0.000	0.000	0.000	0.000
6	A	19	GLN	0	0.014	0.005	12.184	1.425	1.425	0.000	0.000	0.000	0.000
7	A	20	PRO	0	-0.008	-0.004	15.985	-0.248	-0.248	0.000	0.000	0.000	0.000
8	A	21	LYS	1	0.859	0.908	18.297	13.387	13.387	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.831	-0.899	14.662	-18.841	-18.841	0.000	0.000	0.000	0.000
10	A	23	THR	0	-0.002	-0.023	17.253	-0.077	-0.077	0.000	0.000	0.000	0.000
11	A	24	VAL	0	0.040	0.018	15.642	-1.374	-1.374	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.821	-0.906	14.965	-17.721	-17.721	0.000	0.000	0.000	0.000
13	A	26	ARG	1	0.892	0.936	13.977	18.842	18.842	0.000	0.000	0.000	0.000
14	A	27	VAL	0	0.072	0.029	10.746	-1.800	-1.800	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.035	0.026	10.216	-2.923	-2.923	0.000	0.000	0.000	0.000
16	A	29	LYS	1	0.885	0.951	10.520	16.640	16.640	0.000	0.000	0.000	0.000
17	A	30	ILE	0	-0.060	-0.025	7.437	-2.320	-2.320	0.000	0.000	0.000	0.000
18	A	31	LEU	0	0.064	0.044	5.815	-5.393	-5.393	0.000	0.000	0.000	0.000
19	A	32	SER	0	0.048	0.027	5.391	-8.789	-8.789	0.000	0.000	0.000	0.000
20	A	33	ARG	1	0.927	0.970	6.361	27.505	27.505	0.000	0.000	0.000	0.000
21	A	34	ASN	0	-0.052	-0.025	3.599	-2.178	-0.203	0.006	-1.088	-0.892	-0.005
22	A	35	LYS	1	0.946	0.999	1.560	-4.201	-18.493	29.907	-10.137	-5.479	-0.085
23	A	36	ALA	0	-0.035	-0.026	2.117	-22.402	-19.887	6.125	-3.690	-4.949	-0.035
24	A	37	GLY	0	0.056	0.036	2.748	8.812	8.357	0.226	1.144	-0.915	-0.001
25	A	38	SER	0	-0.038	-0.028	3.801	7.313	7.692	-0.001	-0.068	-0.311	0.000
26	A	39	ALA	0	0.008	0.002	5.508	-4.184	-4.184	0.000	0.000	0.000	0.000
27	A	40	VAL	0	-0.007	-0.013	7.432	2.301	2.301	0.000	0.000	0.000	0.000
28	A	41	VAL	0	0.006	0.011	9.990	-0.318	-0.318	0.000	0.000	0.000	0.000
29	A	42	MET	0	0.005	-0.009	12.413	0.412	0.412	0.000	0.000	0.000	0.000
30	A	43	GLU	-1	-0.910	-0.961	15.311	-13.736	-13.736	0.000	0.000	0.000	0.000
31	A	44	GLY	0	-0.010	-0.009	19.000	0.457	0.457	0.000	0.000	0.000	0.000
32	A	45	ASP	-1	-0.852	-0.928	17.510	-14.901	-14.901	0.000	0.000	0.000	0.000
33	A	46	GLU	-1	-0.917	-0.923	17.739	-13.045	-13.045	0.000	0.000	0.000	0.000
34	A	47	ILE	0	-0.018	-0.016	11.617	-0.450	-0.450	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.005	-0.003	15.357	0.716	0.716	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.017	-0.024	14.496	0.940	0.940	0.000	0.000	0.000	0.000
37	A	50	VAL	0	-0.034	0.001	8.206	-1.170	-1.170	0.000	0.000	0.000	0.000
38	A	51	VAL	0	0.028	0.032	10.147	1.406	1.406	0.000	0.000	0.000	0.000
39	A	52	THR	0	0.000	0.007	7.653	-2.557	-2.557	0.000	0.000	0.000	0.000
40	A	53	GLU	-1	-0.875	-0.960	7.929	-30.718	-30.718	0.000	0.000	0.000	0.000
41	A	54	ARG	1	0.843	0.902	10.152	18.943	18.943	0.000	0.000	0.000	0.000
42	A	55	ASP	-1	-0.817	-0.903	11.824	-17.162	-17.162	0.000	0.000	0.000	0.000
43	A	56	ILE	0	0.002	0.000	11.705	1.232	1.232	0.000	0.000	0.000	0.000
44	A	57	LEU	0	-0.030	-0.022	13.611	1.208	1.208	0.000	0.000	0.000	0.000
45	A	58	ASP	-1	-0.777	-0.879	15.941	-14.866	-14.866	0.000	0.000	0.000	0.000
46	A	59	LYS	1	0.881	0.940	16.067	16.010	16.010	0.000	0.000	0.000	0.000
47	A	60	VAL	0	-0.050	-0.018	17.439	0.585	0.585	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.002	0.004	18.049	0.620	0.620	0.000	0.000	0.000	0.000
49	A	62	ALA	0	0.001	0.007	20.262	0.636	0.636	0.000	0.000	0.000	0.000
50	A	63	LYS	1	0.876	0.946	21.929	12.283	12.283	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.018	0.018	23.790	0.429	0.429	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.939	0.976	22.601	12.196	12.196	0.000	0.000	0.000	0.000
53	A	66	ASN	0	0.044	0.015	23.396	-0.908	-0.908	0.000	0.000	0.000	0.000
54	A	67	PRO	0	0.007	-0.009	18.615	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	68	LYS	1	0.928	0.957	20.125	13.314	13.314	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.938	-0.963	21.939	-11.146	-11.146	0.000	0.000	0.000	0.000
57	A	70	VAL	0	-0.018	0.007	19.605	0.304	0.304	0.000	0.000	0.000	0.000
58	A	71	LYS	1	0.918	0.974	19.572	11.688	11.688	0.000	0.000	0.000	0.000
59	A	72	VAL	0	0.022	0.004	13.833	0.156	0.156	0.000	0.000	0.000	0.000
60	A	73	GLU	-1	-0.810	-0.915	16.620	-13.275	-13.275	0.000	0.000	0.000	0.000
61	A	74	GLU	-1	-0.906	-0.968	18.685	-12.405	-12.405	0.000	0.000	0.000	0.000
62	A	75	ILE	0	-0.052	-0.029	15.062	0.351	0.351	0.000	0.000	0.000	0.000
63	A	76	MET	0	-0.069	-0.016	14.449	-0.604	-0.604	0.000	0.000	0.000	0.000
64	A	77	THR	0	-0.022	0.004	13.538	1.275	1.275	0.000	0.000	0.000	0.000
65	A	78	LYS	1	0.894	0.940	14.884	13.133	13.133	0.000	0.000	0.000	0.000
66	A	79	ASN	0	0.017	-0.012	14.757	-0.380	-0.380	0.000	0.000	0.000	0.000
67	A	80	PRO	0	-0.001	0.008	13.830	0.665	0.665	0.000	0.000	0.000	0.000
68	A	81	VAL	0	-0.005	0.000	13.727	0.440	0.440	0.000	0.000	0.000	0.000
69	A	82	LYS	1	0.815	0.906	16.676	12.733	12.733	0.000	0.000	0.000	0.000
70	A	83	ILE	0	0.016	0.012	18.980	0.416	0.416	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:LYS)