FMO DATABASE

FMODB ID: 4373N

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	OptHSide
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	-271576.239767
FMO2-HF: Nuclear repulsion	249732.276225
FMO2-HF: Total energy	-21843.963542
FMO2-MP2: Total energy	-21908.712831

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.
-4.398	-1.657	1.067	-1.419	-2.389	-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 : -0.043 / q_NPA : -0.034

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	-0.828	-0.904	3.813	-4.174	-2.837	-0.010	-0.639	-0.688	0.002
4	A	145	ALA	0	-0.028	0.002	5.743	0.626	0.626	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.037	0.009	7.744	0.273	0.273	0.000	0.000	0.000	0.000
6	A	147	VAL	0	0.039	0.002	11.351	0.025	0.025	0.000	0.000	0.000	0.000
7	A	148	GLU	-1	-0.932	-0.961	14.351	-0.395	-0.395	0.000	0.000	0.000	0.000
8	A	149	TYR	0	0.007	-0.026	5.654	0.177	0.177	0.000	0.000	0.000	0.000
9	A	150	LEU	0	0.003	0.003	11.394	0.095	0.095	0.000	0.000	0.000	0.000
10	A	151	ALA	0	-0.041	-0.024	12.127	0.083	0.083	0.000	0.000	0.000	0.000
11	A	152	ASP	-1	-0.855	-0.925	12.879	-0.216	-0.216	0.000	0.000	0.000	0.000
12	A	153	LEU	0	0.035	0.015	8.283	0.092	0.092	0.000	0.000	0.000	0.000
13	A	154	VAL	0	-0.028	-0.019	12.817	0.074	0.074	0.000	0.000	0.000	0.000
14	A	155	LYS	1	0.833	0.926	15.959	0.224	0.224	0.000	0.000	0.000	0.000
15	A	156	GLU	-1	-0.929	-0.972	13.032	-0.125	-0.125	0.000	0.000	0.000	0.000
16	A	157	LYS	1	0.839	0.893	15.608	0.092	0.092	0.000	0.000	0.000	0.000
17	A	158	LYS	1	0.944	0.973	17.286	0.111	0.111	0.000	0.000	0.000	0.000
18	A	159	HIS	0	-0.058	-0.024	19.295	0.005	0.005	0.000	0.000	0.000	0.000
19	A	160	LEU	0	0.055	0.032	16.169	0.011	0.011	0.000	0.000	0.000	0.000
20	A	161	THR	0	-0.085	-0.042	20.505	0.012	0.012	0.000	0.000	0.000	0.000
21	A	162	LEU	0	-0.063	-0.033	23.420	0.005	0.005	0.000	0.000	0.000	0.000
22	A	163	PHE	0	-0.040	-0.027	22.260	0.006	0.006	0.000	0.000	0.000	0.000
23	A	164	PRO	0	0.049	0.017	23.950	0.005	0.005	0.000	0.000	0.000	0.000
24	A	165	HIS	0	-0.032	-0.024	24.515	0.005	0.005	0.000	0.000	0.000	0.000
25	A	166	MET	0	-0.043	0.000	23.925	0.004	0.004	0.000	0.000	0.000	0.000
26	A	167	PHE	0	0.003	0.005	18.556	0.008	0.008	0.000	0.000	0.000	0.000
27	A	168	SER	0	0.061	0.032	18.531	0.000	0.000	0.000	0.000	0.000	0.000
28	A	169	ALA	0	-0.017	-0.012	16.248	0.001	0.001	0.000	0.000	0.000	0.000
29	A	170	VAL	0	0.045	0.005	13.743	0.009	0.009	0.000	0.000	0.000	0.000
30	A	171	GLU	-1	-0.847	-0.932	13.956	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	172	ARG	1	0.901	0.966	13.766	-0.123	-0.123	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.003	-0.002	9.704	0.004	0.004	0.000	0.000	0.000	0.000
33	A	174	LEU	0	-0.004	0.020	9.752	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	175	ASP	-1	-0.781	-0.889	11.023	-0.110	-0.110	0.000	0.000	0.000	0.000
35	A	176	ASP	-1	-0.928	-0.959	9.212	0.104	0.104	0.000	0.000	0.000	0.000
36	A	177	GLU	-1	-0.765	-0.825	4.436	-1.978	-1.766	-0.001	-0.045	-0.167	0.000
37	A	178	ILE	0	-0.013	-0.011	7.471	-0.112	-0.112	0.000	0.000	0.000	0.000
38	A	179	GLY	0	-0.032	-0.012	10.319	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	180	ARG	1	0.804	0.860	2.859	0.557	1.749	1.078	-0.735	-1.534	-0.004
40	A	181	VAL	0	0.018	0.006	6.209	0.021	0.021	0.000	0.000	0.000	0.000
41	A	182	ARG	1	0.923	0.961	8.181	0.174	0.174	0.000	0.000	0.000	0.000
42	A	183	VAL	0	-0.001	0.005	10.217	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	184	ALA	0	0.007	0.008	7.655	0.010	0.010	0.000	0.000	0.000	0.000
44	A	185	LEU	0	-0.002	0.004	9.803	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	186	PHE	0	-0.012	-0.010	12.585	0.024	0.024	0.000	0.000	0.000	0.000
46	A	187	GLN	0	-0.038	-0.041	12.046	0.057	0.057	0.000	0.000	0.000	0.000
47	A	188	THR	0	-0.024	-0.007	11.384	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	189	GLU	-1	-0.971	-0.966	14.112	-0.199	-0.199	0.000	0.000	0.000	0.000
49	A	190	PHE	0	-0.100	-0.052	17.129	0.018	0.018	0.000	0.000	0.000	0.000
50	A	191	PRO	0	0.057	0.024	16.197	0.030	0.030	0.000	0.000	0.000	0.000
51	A	192	ARG	1	0.877	0.937	17.269	0.054	0.054	0.000	0.000	0.000	0.000
52	A	193	VAL	0	-0.057	-0.018	18.505	0.012	0.012	0.000	0.000	0.000	0.000
53	A	194	GLU	-1	-0.864	-0.924	13.936	0.194	0.194	0.000	0.000	0.000	0.000
54	A	195	LEU	0	-0.053	-0.014	14.141	-0.015	-0.015	0.000	0.000	0.000	0.000

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