FMO DATABASE

FMODB ID: ZN4RN

Calculation Name: 3KBL-A-Xray540

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

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-272471.023438
FMO2-HF: Nuclear repulsion	250637.973623
FMO2-HF: Total energy	-21833.049815
FMO2-MP2: Total energy	-21897.517341

3D Structure Molmil

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.
-0.103	0.151	0.047	0.597	-0.897	0.003

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 : 0.075 / q_NPA : 0.027

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	-0.117	0.078	4.384	0.289	0.554	0.000	-0.143	-0.122	0.000
5	A	144	GLU	0	0.117	-0.087	3.883	-3.548	-2.585	-0.002	-0.596	-0.365	0.003
6	A	144	GLU	-1	-0.942	-0.817	7.775	-1.636	-1.636	0.000	0.000	0.000	0.000
7	A	145	ALA	0	0.020	-0.118	6.773	0.470	0.470	0.000	0.000	0.000	0.000
8	A	145	ALA	0	-0.035	0.127	7.384	-0.069	-0.069	0.000	0.000	0.000	0.000
9	A	146	THR	0	0.014	-0.072	8.561	0.138	0.138	0.000	0.000	0.000	0.000
10	A	146	THR	0	-0.002	0.060	10.758	0.021	0.021	0.000	0.000	0.000	0.000
11	A	147	VAL	0	0.132	-0.083	11.982	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	147	VAL	0	-0.055	0.100	15.827	0.007	0.007	0.000	0.000	0.000	0.000
13	A	148	GLU	0	0.099	-0.116	14.949	0.008	0.008	0.000	0.000	0.000	0.000
14	A	148	GLU	-1	-1.044	-0.847	14.477	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	149	TYR	0	0.105	-0.082	10.247	0.126	0.126	0.000	0.000	0.000	0.000
16	A	149	TYR	0	-0.100	0.058	5.405	0.273	0.273	0.000	0.000	0.000	0.000
17	A	150	LEU	0	0.128	-0.092	11.555	0.073	0.073	0.000	0.000	0.000	0.000
18	A	150	LEU	0	-0.114	0.088	12.230	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	151	ALA	0	0.057	-0.122	12.764	0.035	0.035	0.000	0.000	0.000	0.000
20	A	151	ALA	0	-0.091	0.104	16.527	0.004	0.004	0.000	0.000	0.000	0.000
21	A	152	ASP	0	0.046	-0.120	14.024	0.007	0.007	0.000	0.000	0.000	0.000
22	A	152	ASP	-1	-0.902	-0.784	12.943	0.243	0.243	0.000	0.000	0.000	0.000
23	A	153	LEU	0	0.105	-0.110	11.588	0.118	0.118	0.000	0.000	0.000	0.000
24	A	153	LEU	0	-0.054	0.114	8.356	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	154	VAL	0	0.090	-0.075	12.689	0.034	0.034	0.000	0.000	0.000	0.000
26	A	154	VAL	0	-0.112	0.074	15.244	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	155	LYS	0	0.080	-0.110	16.140	0.007	0.007	0.000	0.000	0.000	0.000
28	A	155	LYS	1	0.684	0.965	16.135	-0.195	-0.195	0.000	0.000	0.000	0.000
29	A	156	GLU	0	0.024	-0.133	14.467	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	156	GLU	-1	-0.913	-0.808	12.784	0.370	0.370	0.000	0.000	0.000	0.000
31	A	157	LYS	0	0.150	-0.088	15.704	0.036	0.036	0.000	0.000	0.000	0.000
32	A	157	LYS	1	0.721	0.987	15.610	0.156	0.156	0.000	0.000	0.000	0.000
33	A	158	LYS	0	0.107	-0.083	17.071	0.001	0.001	0.000	0.000	0.000	0.000
34	A	158	LYS	1	0.843	1.058	20.464	0.002	0.002	0.000	0.000	0.000	0.000
35	A	159	HIS	0	0.017	-0.103	19.553	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	159	HIS	0	-0.096	0.092	18.839	0.003	0.003	0.000	0.000	0.000	0.000
37	A	160	LEU	0	0.108	-0.096	18.770	0.009	0.009	0.000	0.000	0.000	0.000
38	A	160	LEU	0	-0.063	0.121	15.614	0.001	0.001	0.000	0.000	0.000	0.000
39	A	161	THR	0	-0.028	-0.100	20.067	0.003	0.003	0.000	0.000	0.000	0.000
40	A	161	THR	0	-0.083	0.018	21.648	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	162	LEU	0	-0.001	-0.110	23.067	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	162	LEU	0	-0.059	0.104	24.194	0.001	0.001	0.000	0.000	0.000	0.000
43	A	163	PHE	0	-0.010	-0.100	23.548	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	163	PHE	0	-0.090	0.075	21.969	0.007	0.007	0.000	0.000	0.000	0.000
45	A	164	PRO	0	0.090	-0.105	23.729	0.005	0.005	0.000	0.000	0.000	0.000
46	A	165	HIS	0	0.031	0.019	23.733	0.006	0.006	0.000	0.000	0.000	0.000
47	A	165	HIS	0	-0.087	0.071	25.770	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	166	MET	0	0.096	-0.103	23.682	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	166	MET	0	-0.101	0.100	23.428	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	167	PHE	0	-0.015	-0.095	19.292	0.019	0.019	0.000	0.000	0.000	0.000
51	A	167	PHE	0	-0.046	0.104	18.233	0.010	0.010	0.000	0.000	0.000	0.000
52	A	168	SER	0	0.202	-0.024	17.873	0.026	0.026	0.000	0.000	0.000	0.000
53	A	168	SER	0	-0.046	0.064	20.564	0.004	0.004	0.000	0.000	0.000	0.000
54	A	169	ALA	0	0.085	-0.091	16.644	-0.058	-0.058	0.000	0.000	0.000	0.000
55	A	169	ALA	0	-0.076	0.094	16.021	0.010	0.010	0.000	0.000	0.000	0.000
56	A	170	VAL	0	0.039	-0.118	13.531	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	170	VAL	0	-0.049	0.107	13.198	0.011	0.011	0.000	0.000	0.000	0.000
58	A	171	GLU	0	0.071	-0.103	13.505	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	171	GLU	-1	-0.924	-0.840	17.555	0.115	0.115	0.000	0.000	0.000	0.000
60	A	172	ARG	0	0.134	-0.062	14.825	-0.066	-0.066	0.000	0.000	0.000	0.000
61	A	172	ARG	1	0.739	0.987	13.414	0.269	0.269	0.000	0.000	0.000	0.000
62	A	173	LEU	0	0.043	-0.108	10.927	-0.176	-0.176	0.000	0.000	0.000	0.000
63	A	173	LEU	0	-0.078	0.091	9.560	0.033	0.033	0.000	0.000	0.000	0.000
64	A	174	LEU	0	0.121	-0.075	9.663	-0.104	-0.104	0.000	0.000	0.000	0.000
65	A	174	LEU	0	-0.121	0.109	10.854	0.009	0.009	0.000	0.000	0.000	0.000
66	A	175	ASP	0	0.094	-0.108	11.343	-0.128	-0.128	0.000	0.000	0.000	0.000
67	A	175	ASP	-1	-0.919	-0.791	14.707	-0.229	-0.229	0.000	0.000	0.000	0.000
68	A	176	ASP	0	0.101	-0.073	10.581	-0.120	-0.120	0.000	0.000	0.000	0.000
69	A	176	ASP	-1	-0.941	-0.825	9.701	-0.456	-0.456	0.000	0.000	0.000	0.000
70	A	177	GLU	0	0.130	-0.082	7.178	-0.473	-0.473	0.000	0.000	0.000	0.000
71	A	177	GLU	-1	-0.869	-0.734	4.736	-2.135	-2.081	-0.001	-0.005	-0.047	0.000
72	A	178	ILE	0	0.089	-0.097	8.074	-0.410	-0.410	0.000	0.000	0.000	0.000
73	A	178	ILE	0	-0.119	0.080	11.392	0.015	0.015	0.000	0.000	0.000	0.000
74	A	179	GLY	0	-0.038	-0.125	11.000	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	180	ARG	0	0.103	0.017	6.768	0.270	0.270	0.000	0.000	0.000	0.000
76	A	180	ARG	1	0.716	0.950	3.583	6.479	5.451	0.050	1.341	-0.363	0.000
77	A	181	VAL	0	0.074	-0.097	8.178	-0.280	-0.280	0.000	0.000	0.000	0.000
78	A	181	VAL	0	-0.095	0.111	7.122	0.031	0.031	0.000	0.000	0.000	0.000
79	A	182	ARG	0	0.121	-0.078	8.859	0.085	0.085	0.000	0.000	0.000	0.000
80	A	182	ARG	1	0.820	1.036	12.975	0.577	0.577	0.000	0.000	0.000	0.000
81	A	183	VAL	0	0.070	-0.103	11.433	0.165	0.165	0.000	0.000	0.000	0.000
82	A	183	VAL	0	-0.094	0.105	10.760	0.021	0.021	0.000	0.000	0.000	0.000
83	A	184	ALA	0	0.114	-0.065	9.028	0.239	0.239	0.000	0.000	0.000	0.000
84	A	184	ALA	0	-0.073	0.086	8.267	-0.127	-0.127	0.000	0.000	0.000	0.000
85	A	185	LEU	0	0.095	-0.078	10.416	0.080	0.080	0.000	0.000	0.000	0.000
86	A	185	LEU	0	-0.095	0.070	11.766	0.054	0.054	0.000	0.000	0.000	0.000
87	A	186	PHE	0	0.107	-0.066	13.198	0.116	0.116	0.000	0.000	0.000	0.000
88	A	186	PHE	0	-0.132	0.056	15.158	0.031	0.031	0.000	0.000	0.000	0.000
89	A	187	GLN	0	0.061	-0.108	13.937	0.150	0.150	0.000	0.000	0.000	0.000
90	A	187	GLN	0	-0.137	0.052	12.930	-0.148	-0.148	0.000	0.000	0.000	0.000
91	A	188	THR	0	-0.024	-0.097	14.160	0.050	0.050	0.000	0.000	0.000	0.000
92	A	188	THR	0	-0.031	0.068	12.691	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	189	GLU	0	0.102	-0.094	15.378	0.067	0.067	0.000	0.000	0.000	0.000
94	A	189	GLU	-1	-1.049	-0.870	17.685	-0.477	-0.477	0.000	0.000	0.000	0.000
95	A	190	PHE	0	-0.055	-0.115	17.979	0.070	0.070	0.000	0.000	0.000	0.000
96	A	190	PHE	0	-0.138	0.075	19.217	0.022	0.022	0.000	0.000	0.000	0.000
97	A	191	PRO	0	0.120	-0.088	17.395	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	192	ARG	0	0.009	0.033	18.462	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	192	ARG	1	0.834	1.012	22.532	0.382	0.382	0.000	0.000	0.000	0.000
100	A	193	VAL	0	0.044	-0.107	19.270	0.057	0.057	0.000	0.000	0.000	0.000
101	A	193	VAL	0	-0.065	0.088	19.362	0.008	0.008	0.000	0.000	0.000	0.000
102	A	194	GLU	0	0.135	-0.092	16.293	-0.068	-0.068	0.000	0.000	0.000	0.000
103	A	194	GLU	-1	-0.939	-0.805	14.629	-0.977	-0.977	0.000	0.000	0.000	0.000
104	A	195	LEU	0	-0.139	-0.149	14.499	0.108	0.108	0.000	0.000	0.000	0.000
105	A	195	LEU	0	0.055	0.028	15.153	0.001	0.001	0.000	0.000	0.000	0.000

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