FMO DATABASE

FMODB ID: RY7N8

Calculation Name: 3KBL-A-Xray540

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: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-271480.194545
FMO2-HF: Nuclear repulsion	249648.328711
FMO2-HF: Total energy	-21831.865834
FMO2-MP2: Total energy	-21896.336468

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.
-0.913	0.242	0.005	-0.373	-0.788	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 : 0.085 / q_NPA : 0.018

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].
4	A	0	HIS	0	-0.114	0.080	4.293	0.365	0.612	0.000	-0.135	-0.112	0.000
5	A	144	GLU	0	0.098	-0.100	3.813	-3.206	-2.323	-0.004	-0.498	-0.381	0.002
6	A	144	GLU	-1	-0.980	-0.835	7.357	-1.878	-1.878	0.000	0.000	0.000	0.000
7	A	145	ALA	0	0.040	-0.122	6.620	0.495	0.495	0.000	0.000	0.000	0.000
8	A	145	ALA	0	-0.039	0.137	7.583	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	146	THR	0	0.015	-0.098	8.608	0.127	0.127	0.000	0.000	0.000	0.000
10	A	146	THR	0	0.014	0.073	10.688	0.058	0.058	0.000	0.000	0.000	0.000
11	A	147	VAL	0	0.116	-0.090	12.184	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	147	VAL	0	-0.050	0.119	16.212	0.006	0.006	0.000	0.000	0.000	0.000
13	A	148	GLU	0	0.073	-0.125	14.961	0.016	0.016	0.000	0.000	0.000	0.000
14	A	148	GLU	-1	-0.999	-0.831	14.569	-0.078	-0.078	0.000	0.000	0.000	0.000
15	A	149	TYR	0	0.107	-0.074	10.394	0.149	0.149	0.000	0.000	0.000	0.000
16	A	149	TYR	0	-0.099	0.060	5.669	0.167	0.167	0.000	0.000	0.000	0.000
17	A	150	LEU	0	0.147	-0.100	11.700	0.096	0.096	0.000	0.000	0.000	0.000
18	A	150	LEU	0	-0.126	0.095	12.735	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	151	ALA	0	0.032	-0.129	12.965	0.050	0.050	0.000	0.000	0.000	0.000
20	A	151	ALA	0	-0.100	0.098	16.552	0.004	0.004	0.000	0.000	0.000	0.000
21	A	152	ASP	0	0.052	-0.137	13.810	0.016	0.016	0.000	0.000	0.000	0.000
22	A	152	ASP	-1	-0.963	-0.819	12.789	0.248	0.248	0.000	0.000	0.000	0.000
23	A	153	LEU	0	0.105	-0.099	12.107	0.104	0.104	0.000	0.000	0.000	0.000
24	A	153	LEU	0	-0.086	0.102	8.979	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	154	VAL	0	0.086	-0.085	13.021	0.054	0.054	0.000	0.000	0.000	0.000
26	A	154	VAL	0	-0.119	0.078	15.532	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	155	LYS	0	0.066	-0.098	16.462	0.011	0.011	0.000	0.000	0.000	0.000
28	A	155	LYS	1	0.855	1.062	17.597	-0.078	-0.078	0.000	0.000	0.000	0.000
29	A	156	GLU	0	0.050	-0.165	15.261	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	156	GLU	-1	-0.969	-0.794	13.382	0.450	0.450	0.000	0.000	0.000	0.000
31	A	157	LYS	0	0.147	-0.105	16.199	0.041	0.041	0.000	0.000	0.000	0.000
32	A	157	LYS	1	0.771	1.018	15.993	0.129	0.129	0.000	0.000	0.000	0.000
33	A	158	LYS	0	0.118	-0.085	17.407	0.006	0.006	0.000	0.000	0.000	0.000
34	A	158	LYS	1	0.813	1.051	20.876	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	159	HIS	0	-0.007	-0.114	20.013	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	159	HIS	0	-0.058	0.094	19.587	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	160	LEU	0	0.064	-0.114	19.196	0.005	0.005	0.000	0.000	0.000	0.000
38	A	160	LEU	0	-0.031	0.150	16.069	0.005	0.005	0.000	0.000	0.000	0.000
39	A	161	THR	0	0.033	-0.064	20.492	0.009	0.009	0.000	0.000	0.000	0.000
40	A	161	THR	0	-0.094	0.014	21.944	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	162	LEU	0	0.014	-0.131	23.405	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	162	LEU	0	-0.080	0.108	24.715	0.000	0.000	0.000	0.000	0.000	0.000
43	A	163	PHE	0	-0.034	-0.114	23.972	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	163	PHE	0	-0.115	0.072	22.318	0.006	0.006	0.000	0.000	0.000	0.000
45	A	164	PRO	0	0.121	-0.084	23.939	0.008	0.008	0.000	0.000	0.000	0.000
46	A	165	HIS	0	0.036	0.009	24.516	0.007	0.007	0.000	0.000	0.000	0.000
47	A	165	HIS	0	-0.090	0.076	26.645	0.002	0.002	0.000	0.000	0.000	0.000
48	A	166	MET	0	0.089	-0.095	24.004	0.001	0.001	0.000	0.000	0.000	0.000
49	A	166	MET	0	-0.122	0.102	24.045	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	167	PHE	0	0.006	-0.120	19.563	0.021	0.021	0.000	0.000	0.000	0.000
51	A	167	PHE	0	-0.033	0.100	18.486	0.008	0.008	0.000	0.000	0.000	0.000
52	A	168	SER	0	0.177	-0.023	18.523	0.013	0.013	0.000	0.000	0.000	0.000
53	A	168	SER	0	-0.045	0.072	20.888	0.004	0.004	0.000	0.000	0.000	0.000
54	A	169	ALA	0	0.121	-0.112	16.961	-0.050	-0.050	0.000	0.000	0.000	0.000
55	A	169	ALA	0	-0.089	0.112	16.149	0.012	0.012	0.000	0.000	0.000	0.000
56	A	170	VAL	0	-0.007	-0.108	13.887	0.003	0.003	0.000	0.000	0.000	0.000
57	A	170	VAL	0	-0.039	0.103	13.962	0.010	0.010	0.000	0.000	0.000	0.000
58	A	171	GLU	0	0.155	-0.104	13.946	0.013	0.013	0.000	0.000	0.000	0.000
59	A	171	GLU	-1	-0.996	-0.844	17.870	0.135	0.135	0.000	0.000	0.000	0.000
60	A	172	ARG	0	0.174	-0.039	15.146	-0.065	-0.065	0.000	0.000	0.000	0.000
61	A	172	ARG	1	0.822	1.041	14.516	0.048	0.048	0.000	0.000	0.000	0.000
62	A	173	LEU	0	0.027	-0.116	11.085	-0.154	-0.154	0.000	0.000	0.000	0.000
63	A	173	LEU	0	-0.086	0.089	10.026	0.040	0.040	0.000	0.000	0.000	0.000
64	A	174	LEU	0	0.116	-0.070	10.126	-0.087	-0.087	0.000	0.000	0.000	0.000
65	A	174	LEU	0	-0.109	0.126	11.614	0.000	0.000	0.000	0.000	0.000	0.000
66	A	175	ASP	0	0.085	-0.149	11.703	-0.128	-0.128	0.000	0.000	0.000	0.000
67	A	175	ASP	-1	-0.941	-0.804	15.002	-0.137	-0.137	0.000	0.000	0.000	0.000
68	A	176	ASP	0	0.111	-0.102	10.739	-0.118	-0.118	0.000	0.000	0.000	0.000
69	A	176	ASP	-1	-1.030	-0.857	9.882	-0.317	-0.317	0.000	0.000	0.000	0.000
70	A	177	GLU	0	0.083	-0.111	7.644	-0.433	-0.433	0.000	0.000	0.000	0.000
71	A	177	GLU	-1	-0.847	-0.722	5.016	-1.444	-1.386	-0.001	-0.002	-0.056	0.000
72	A	178	ILE	0	0.076	-0.102	8.513	-0.375	-0.375	0.000	0.000	0.000	0.000
73	A	178	ILE	0	-0.112	0.081	12.143	0.008	0.008	0.000	0.000	0.000	0.000
74	A	179	GLY	0	-0.049	-0.113	11.432	-0.081	-0.081	0.000	0.000	0.000	0.000
75	A	180	ARG	0	0.137	-0.005	7.493	0.142	0.142	0.000	0.000	0.000	0.000
76	A	180	ARG	1	0.732	1.004	3.958	4.843	4.810	0.010	0.262	-0.239	0.000
77	A	181	VAL	0	0.038	-0.112	8.527	-0.398	-0.398	0.000	0.000	0.000	0.000
78	A	181	VAL	0	-0.052	0.119	7.377	0.015	0.015	0.000	0.000	0.000	0.000
79	A	182	ARG	0	0.111	-0.092	9.216	0.041	0.041	0.000	0.000	0.000	0.000
80	A	182	ARG	1	0.819	1.047	13.497	0.531	0.531	0.000	0.000	0.000	0.000
81	A	183	VAL	0	0.046	-0.113	11.828	0.131	0.131	0.000	0.000	0.000	0.000
82	A	183	VAL	0	-0.076	0.120	11.010	0.016	0.016	0.000	0.000	0.000	0.000
83	A	184	ALA	0	0.094	-0.079	9.143	0.213	0.213	0.000	0.000	0.000	0.000
84	A	184	ALA	0	-0.040	0.099	8.361	-0.124	-0.124	0.000	0.000	0.000	0.000
85	A	185	LEU	0	0.076	-0.102	10.511	0.032	0.032	0.000	0.000	0.000	0.000
86	A	185	LEU	0	-0.080	0.096	11.904	0.044	0.044	0.000	0.000	0.000	0.000
87	A	186	PHE	0	0.124	-0.063	13.368	0.105	0.105	0.000	0.000	0.000	0.000
88	A	186	PHE	0	-0.121	0.067	15.277	0.032	0.032	0.000	0.000	0.000	0.000
89	A	187	GLN	0	0.062	-0.137	13.929	0.140	0.140	0.000	0.000	0.000	0.000
90	A	187	GLN	0	-0.038	0.094	12.333	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	188	THR	0	-0.080	-0.066	14.216	0.059	0.059	0.000	0.000	0.000	0.000
92	A	188	THR	0	-0.045	0.041	12.497	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	189	GLU	0	0.098	-0.094	15.363	0.053	0.053	0.000	0.000	0.000	0.000
94	A	189	GLU	-1	-1.050	-0.881	18.396	-0.502	-0.502	0.000	0.000	0.000	0.000
95	A	190	PHE	0	-0.011	-0.118	18.137	0.063	0.063	0.000	0.000	0.000	0.000
96	A	190	PHE	0	-0.171	0.082	19.384	0.024	0.024	0.000	0.000	0.000	0.000
97	A	191	PRO	0	0.117	-0.076	17.391	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	192	ARG	0	0.082	0.036	18.479	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	192	ARG	1	0.824	1.019	22.418	0.410	0.410	0.000	0.000	0.000	0.000
100	A	193	VAL	0	0.021	-0.120	19.624	0.052	0.052	0.000	0.000	0.000	0.000
101	A	193	VAL	0	-0.075	0.097	18.910	0.009	0.009	0.000	0.000	0.000	0.000
102	A	194	GLU	0	0.066	-0.123	16.564	-0.082	-0.082	0.000	0.000	0.000	0.000
103	A	194	GLU	-1	-0.961	-0.810	15.267	-0.890	-0.890	0.000	0.000	0.000	0.000
104	A	195	LEU	0	-0.126	-0.141	14.777	0.104	0.104	0.000	0.000	0.000	0.000
105	A	195	LEU	0	0.020	0.015	15.472	0.006	0.006	0.000	0.000	0.000	0.000

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