FMO DATABASE

FMODB ID: K3N33

Calculation Name: 3KBL-A-Xray372

Preferred Name: Female germline-specific tumor suppressor gld-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3KBL

Chain ID: A

ChEMBL ID: CHEMBL1293302

UniProt ID: Q17339

Base Structure: X-ray

Registration Date: 2023-06-20

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-271491.905501
FMO2-HF: Nuclear repulsion	249648.328711
FMO2-HF: Total energy	-21843.576789
FMO2-MP2: Total energy	-21908.330111

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:-1:SER)

Summations of interaction energy for fragment #1(A:-1:SER)

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.
-4.139	-1.767	0.745	-1.079	-2.037	-0.002

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.036

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	144	GLU	-1	-0.870	-0.928	3.813	-4.252	-3.058	-0.010	-0.543	-0.641	0.002
4	A	145	ALA	0	-0.018	0.003	5.769	0.717	0.717	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.052	0.018	7.788	0.301	0.301	0.000	0.000	0.000	0.000
6	A	147	VAL	0	0.030	-0.003	11.391	0.034	0.034	0.000	0.000	0.000	0.000
7	A	148	GLU	-1	-0.935	-0.963	14.395	-0.458	-0.458	0.000	0.000	0.000	0.000
8	A	149	TYR	0	0.008	-0.026	5.669	0.150	0.150	0.000	0.000	0.000	0.000
9	A	150	LEU	0	0.003	0.002	11.435	0.118	0.118	0.000	0.000	0.000	0.000
10	A	151	ALA	0	-0.051	-0.032	12.169	0.100	0.100	0.000	0.000	0.000	0.000
11	A	152	ASP	-1	-0.913	-0.956	12.789	-0.279	-0.279	0.000	0.000	0.000	0.000
12	A	153	LEU	0	0.047	0.023	8.398	0.105	0.105	0.000	0.000	0.000	0.000
13	A	154	VAL	0	-0.036	-0.018	12.852	0.088	0.088	0.000	0.000	0.000	0.000
14	A	155	LYS	1	0.890	0.952	15.994	0.205	0.205	0.000	0.000	0.000	0.000
15	A	156	GLU	-1	-0.906	-0.957	13.382	-0.121	-0.121	0.000	0.000	0.000	0.000
16	A	157	LYS	1	0.897	0.929	15.681	0.090	0.090	0.000	0.000	0.000	0.000
17	A	158	LYS	1	0.933	0.967	17.312	0.118	0.118	0.000	0.000	0.000	0.000
18	A	159	HIS	0	-0.069	-0.029	19.587	0.003	0.003	0.000	0.000	0.000	0.000
19	A	160	LEU	0	0.078	0.040	16.069	0.011	0.011	0.000	0.000	0.000	0.000
20	A	161	THR	0	-0.072	-0.039	20.492	0.012	0.012	0.000	0.000	0.000	0.000
21	A	162	LEU	0	-0.067	-0.035	23.405	0.004	0.004	0.000	0.000	0.000	0.000
22	A	163	PHE	0	-0.048	-0.028	22.318	0.005	0.005	0.000	0.000	0.000	0.000
23	A	164	PRO	0	0.062	0.023	23.939	0.008	0.008	0.000	0.000	0.000	0.000
24	A	165	HIS	0	-0.028	-0.022	24.516	0.007	0.007	0.000	0.000	0.000	0.000
25	A	166	MET	0	-0.054	-0.012	24.004	0.004	0.004	0.000	0.000	0.000	0.000
26	A	167	PHE	0	0.019	0.014	18.486	0.011	0.011	0.000	0.000	0.000	0.000
27	A	168	SER	0	0.032	0.013	18.523	0.005	0.005	0.000	0.000	0.000	0.000
28	A	169	ALA	0	0.002	0.000	16.149	0.003	0.003	0.000	0.000	0.000	0.000
29	A	170	VAL	0	0.038	0.008	13.887	0.023	0.023	0.000	0.000	0.000	0.000
30	A	171	GLU	-1	-0.853	-0.935	13.946	0.015	0.015	0.000	0.000	0.000	0.000
31	A	172	ARG	1	0.921	0.975	14.022	-0.204	-0.204	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.006	-0.003	10.026	0.007	0.007	0.000	0.000	0.000	0.000
33	A	174	LEU	0	-0.003	0.029	9.758	-0.039	-0.039	0.000	0.000	0.000	0.000
34	A	175	ASP	-1	-0.839	-0.928	11.041	-0.090	-0.090	0.000	0.000	0.000	0.000
35	A	176	ASP	-1	-0.935	-0.964	9.093	0.183	0.183	0.000	0.000	0.000	0.000
36	A	177	GLU	-1	-0.786	-0.852	4.505	-1.874	-1.673	-0.001	-0.031	-0.168	0.000
37	A	178	ILE	0	-0.015	-0.010	7.488	-0.159	-0.159	0.000	0.000	0.000	0.000
38	A	179	GLY	0	-0.034	-0.015	10.345	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	180	ARG	1	0.834	0.892	2.946	0.753	1.730	0.756	-0.505	-1.228	-0.004
40	A	181	VAL	0	0.011	0.007	6.311	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	182	ARG	1	0.923	0.961	8.212	0.190	0.190	0.000	0.000	0.000	0.000
42	A	183	VAL	0	0.000	0.009	10.182	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	184	ALA	0	0.010	0.005	7.676	0.013	0.013	0.000	0.000	0.000	0.000
44	A	185	LEU	0	0.005	0.002	9.825	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	186	PHE	0	0.001	0.004	12.630	0.030	0.030	0.000	0.000	0.000	0.000
46	A	187	GLN	0	0.009	-0.024	11.552	0.077	0.077	0.000	0.000	0.000	0.000
47	A	188	THR	0	-0.073	-0.033	11.282	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	189	GLU	-1	-0.919	-0.946	14.171	-0.244	-0.244	0.000	0.000	0.000	0.000
49	A	190	PHE	0	-0.104	-0.050	17.199	0.025	0.025	0.000	0.000	0.000	0.000
50	A	191	PRO	0	0.049	0.020	16.245	0.031	0.031	0.000	0.000	0.000	0.000
51	A	192	ARG	1	0.887	0.938	17.326	0.088	0.088	0.000	0.000	0.000	0.000
52	A	193	VAL	0	-0.050	-0.006	18.196	0.017	0.017	0.000	0.000	0.000	0.000
53	A	194	GLU	-1	-0.949	-0.959	14.421	0.151	0.151	0.000	0.000	0.000	0.000
54	A	195	LEU	0	-0.055	-0.020	14.311	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-1:SER)