FMO DATABASE

FMODB ID: 53M3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-272482.118588
FMO2-HF: Nuclear repulsion	250637.973623
FMO2-HF: Total energy	-21844.144965
FMO2-MP2: Total energy	-21908.897127

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.
-4.663	-1.997	2.276	-1.887	-3.054	-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 : -0.037 / q_NPA : -0.032

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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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	-0.819	-0.896	3.883	-4.306	-3.100	-0.007	-0.605	-0.594	0.002
4	A	145	ALA	0	-0.019	-0.005	5.989	0.514	0.514	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.044	0.018	7.817	0.346	0.346	0.000	0.000	0.000	0.000
6	A	147	VAL	0	0.036	0.001	11.274	0.019	0.019	0.000	0.000	0.000	0.000
7	A	148	GLU	-1	-0.957	-0.972	14.133	-0.431	-0.431	0.000	0.000	0.000	0.000
8	A	149	TYR	0	-0.002	-0.030	5.405	0.220	0.220	0.000	0.000	0.000	0.000
9	A	150	LEU	0	0.007	0.006	11.173	0.077	0.077	0.000	0.000	0.000	0.000
10	A	151	ALA	0	-0.030	-0.018	11.977	0.082	0.082	0.000	0.000	0.000	0.000
11	A	152	ASP	-1	-0.832	-0.902	12.943	-0.242	-0.242	0.000	0.000	0.000	0.000
12	A	153	LEU	0	0.050	0.022	7.969	0.096	0.096	0.000	0.000	0.000	0.000
13	A	154	VAL	0	-0.034	-0.023	12.602	0.075	0.075	0.000	0.000	0.000	0.000
14	A	155	LYS	1	0.745	0.856	15.732	0.251	0.251	0.000	0.000	0.000	0.000
15	A	156	GLU	-1	-0.872	-0.926	12.784	-0.114	-0.114	0.000	0.000	0.000	0.000
16	A	157	LYS	1	0.845	0.890	15.376	0.124	0.124	0.000	0.000	0.000	0.000
17	A	158	LYS	1	0.937	0.971	17.056	0.126	0.126	0.000	0.000	0.000	0.000
18	A	159	HIS	0	-0.031	-0.007	18.839	0.008	0.008	0.000	0.000	0.000	0.000
19	A	160	LEU	0	0.033	0.020	15.614	0.013	0.013	0.000	0.000	0.000	0.000
20	A	161	THR	0	-0.100	-0.058	20.067	0.013	0.013	0.000	0.000	0.000	0.000
21	A	162	LEU	0	-0.053	-0.022	23.067	0.006	0.006	0.000	0.000	0.000	0.000
22	A	163	PHE	0	-0.014	-0.012	21.969	0.007	0.007	0.000	0.000	0.000	0.000
23	A	164	PRO	0	0.029	0.006	23.729	0.005	0.005	0.000	0.000	0.000	0.000
24	A	165	HIS	0	-0.020	-0.022	23.733	0.006	0.006	0.000	0.000	0.000	0.000
25	A	166	MET	0	-0.063	-0.003	23.428	0.005	0.005	0.000	0.000	0.000	0.000
26	A	167	PHE	0	0.012	0.008	18.233	0.009	0.009	0.000	0.000	0.000	0.000
27	A	168	SER	0	0.041	0.029	17.873	0.003	0.003	0.000	0.000	0.000	0.000
28	A	169	ALA	0	-0.003	-0.004	16.021	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	170	VAL	0	0.018	0.007	13.198	0.006	0.006	0.000	0.000	0.000	0.000
30	A	171	GLU	-1	-0.823	-0.932	13.505	-0.043	-0.043	0.000	0.000	0.000	0.000
31	A	172	ARG	1	0.823	0.902	12.727	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.003	-0.007	9.560	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	174	LEU	0	-0.001	0.012	9.373	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	175	ASP	-1	-0.785	-0.876	10.709	-0.152	-0.152	0.000	0.000	0.000	0.000
35	A	176	ASP	-1	-0.853	-0.906	8.992	0.071	0.071	0.000	0.000	0.000	0.000
36	A	177	GLU	-1	-0.775	-0.830	4.134	-2.492	-2.171	0.001	-0.105	-0.216	0.000
37	A	178	ILE	0	-0.026	-0.019	7.077	-0.108	-0.108	0.000	0.000	0.000	0.000
38	A	179	GLY	0	-0.026	-0.012	9.920	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	180	ARG	1	0.794	0.859	2.604	0.939	2.078	2.282	-1.177	-2.244	-0.004
40	A	181	VAL	0	0.014	0.005	6.056	0.003	0.003	0.000	0.000	0.000	0.000
41	A	182	ARG	1	0.929	0.966	7.859	0.239	0.239	0.000	0.000	0.000	0.000
42	A	183	VAL	0	-0.004	0.003	9.975	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	184	ALA	0	0.012	0.006	7.619	0.009	0.009	0.000	0.000	0.000	0.000
44	A	185	LEU	0	0.013	0.001	9.750	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	186	PHE	0	-0.024	-0.012	12.448	0.032	0.032	0.000	0.000	0.000	0.000
46	A	187	GLN	0	-0.042	-0.050	12.102	0.061	0.061	0.000	0.000	0.000	0.000
47	A	188	THR	0	-0.033	-0.012	11.422	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	189	GLU	-1	-0.968	-0.965	14.158	-0.215	-0.215	0.000	0.000	0.000	0.000
49	A	190	PHE	0	-0.093	-0.047	17.004	0.022	0.022	0.000	0.000	0.000	0.000
50	A	191	PRO	0	0.039	0.013	16.207	0.031	0.031	0.000	0.000	0.000	0.000
51	A	192	ARG	1	0.856	0.933	17.252	0.061	0.061	0.000	0.000	0.000	0.000
52	A	193	VAL	0	-0.029	-0.011	18.278	0.009	0.009	0.000	0.000	0.000	0.000
53	A	194	GLU	-1	-0.861	-0.916	13.606	0.176	0.176	0.000	0.000	0.000	0.000
54	A	195	LEU	0	-0.037	-0.006	14.000	-0.016	-0.016	0.000	0.000	0.000	0.000

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