FMO DATABASE

FMODB ID: 9GN32

Calculation Name: 3KBL-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	56
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-275077.214892
FMO2-HF: Nuclear repulsion	253062.669914
FMO2-HF: Total energy	-22014.544978
FMO2-MP2: Total energy	-22079.836568

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:-2:ACE )

Summations of interaction energy for fragment #1(A:-2:ACE )

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.
0.242	1.008	-0.006	-0.311	-0.449	0

Interaction energy analysis for fragmet #1(A:-2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.013

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].
3	A	0	HIS	0	-0.019	0.004	3.813	1.004	1.770	-0.006	-0.311	-0.449
4	A	144	GLU	-1	-0.871	-0.928	6.766	-0.330	-0.330	0.000	0.000	0.000
5	A	145	ALA	0	-0.016	0.004	9.358	-0.016	-0.016	0.000	0.000	0.000
6	A	146	THR	0	0.053	0.017	12.136	0.076	0.076	0.000	0.000	0.000
7	A	147	VAL	0	0.028	-0.004	15.496	-0.024	-0.024	0.000	0.000	0.000
8	A	148	GLU	-1	-0.935	-0.963	17.396	-0.147	-0.147	0.000	0.000	0.000
9	A	149	TYR	0	0.009	-0.026	9.752	0.041	0.041	0.000	0.000	0.000
10	A	150	LEU	0	-0.001	0.001	15.151	-0.006	-0.006	0.000	0.000	0.000
11	A	151	ALA	0	-0.047	-0.030	16.940	0.013	0.013	0.000	0.000	0.000
12	A	152	ASP	-1	-0.910	-0.955	16.121	-0.231	-0.231	0.000	0.000	0.000
13	A	153	LEU	0	0.037	0.020	12.997	0.017	0.017	0.000	0.000	0.000
14	A	154	VAL	0	-0.029	-0.016	17.042	0.024	0.024	0.000	0.000	0.000
15	A	155	LYS	1	0.890	0.952	20.591	0.149	0.149	0.000	0.000	0.000
16	A	156	GLU	-1	-0.906	-0.958	16.704	-0.256	-0.256	0.000	0.000	0.000
17	A	157	LYS	1	0.898	0.929	19.997	0.235	0.235	0.000	0.000	0.000
18	A	158	LYS	1	0.933	0.967	21.352	0.133	0.133	0.000	0.000	0.000
19	A	159	HIS	0	-0.068	-0.029	22.928	0.017	0.017	0.000	0.000	0.000
20	A	160	LEU	0	0.077	0.040	19.525	0.014	0.014	0.000	0.000	0.000
21	A	161	THR	0	-0.070	-0.038	24.075	0.012	0.012	0.000	0.000	0.000
22	A	162	LEU	0	-0.070	-0.035	27.131	0.011	0.011	0.000	0.000	0.000
23	A	163	PHE	0	-0.048	-0.028	25.541	0.011	0.011	0.000	0.000	0.000
24	A	164	PRO	0	0.063	0.023	27.125	-0.008	-0.008	0.000	0.000	0.000
25	A	165	HIS	0	-0.029	-0.022	27.451	0.002	0.002	0.000	0.000	0.000
26	A	166	MET	0	-0.054	-0.011	26.629	0.005	0.005	0.000	0.000	0.000
27	A	167	PHE	0	0.019	0.013	21.275	0.003	0.003	0.000	0.000	0.000
28	A	168	SER	0	0.032	0.013	21.343	-0.020	-0.020	0.000	0.000	0.000
29	A	169	ALA	0	0.002	0.000	17.797	-0.014	-0.014	0.000	0.000	0.000
30	A	170	VAL	0	0.038	0.008	16.543	-0.035	-0.035	0.000	0.000	0.000
31	A	171	GLU	-1	-0.849	-0.935	17.170	-0.219	-0.219	0.000	0.000	0.000
32	A	172	ARG	1	0.918	0.975	16.923	0.231	0.231	0.000	0.000	0.000
33	A	173	LEU	0	-0.006	-0.002	12.200	-0.028	-0.028	0.000	0.000	0.000
34	A	174	LEU	0	-0.003	0.029	13.611	-0.078	-0.078	0.000	0.000	0.000
35	A	175	ASP	-1	-0.840	-0.928	15.603	-0.274	-0.274	0.000	0.000	0.000
36	A	176	ASP	-1	-0.933	-0.963	13.202	-0.408	-0.408	0.000	0.000	0.000
37	A	177	GLU	-1	-0.785	-0.852	9.164	-1.381	-1.381	0.000	0.000	0.000
38	A	178	ILE	0	-0.021	-0.013	12.393	0.019	0.019	0.000	0.000	0.000
39	A	179	GLY	0	-0.029	-0.013	15.593	0.030	0.030	0.000	0.000	0.000
40	A	180	ARG	1	0.834	0.893	8.153	1.284	1.284	0.000	0.000	0.000
41	A	181	VAL	0	0.013	0.007	11.720	0.020	0.020	0.000	0.000	0.000
42	A	182	ARG	1	0.921	0.960	13.658	0.303	0.303	0.000	0.000	0.000
43	A	183	VAL	0	0.001	0.009	15.007	0.040	0.040	0.000	0.000	0.000
44	A	184	ALA	0	0.012	0.005	12.229	0.037	0.037	0.000	0.000	0.000
45	A	185	LEU	0	0.004	0.001	14.296	0.047	0.047	0.000	0.000	0.000
46	A	186	PHE	0	0.001	0.004	17.153	0.038	0.038	0.000	0.000	0.000
47	A	187	GLN	0	0.016	-0.025	15.670	0.007	0.007	0.000	0.000	0.000
48	A	188	THR	0	-0.073	-0.033	15.517	0.022	0.022	0.000	0.000	0.000
49	A	189	GLU	-1	-0.919	-0.946	18.273	-0.087	-0.087	0.000	0.000	0.000
50	A	190	PHE	0	-0.104	-0.050	21.376	0.022	0.022	0.000	0.000	0.000
51	A	191	PRO	0	0.048	0.019	19.862	-0.005	-0.005	0.000	0.000	0.000
52	A	192	ARG	1	0.887	0.938	20.775	0.061	0.061	0.000	0.000	0.000
53	A	193	VAL	0	-0.048	-0.005	22.209	0.007	0.007	0.000	0.000	0.000
54	A	194	GLU	-1	-0.955	-0.962	17.395	-0.145	-0.145	0.000	0.000	0.000
55	A	195	LEU	0	-0.078	-0.039	18.819	0.011	0.011	0.000	0.000	0.000
56	A	196	NME	0	0.014	0.017	16.159	0.008	0.008	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ACE )