FMO DATABASE

FMODB ID: 6G1LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-271565.21874
FMO2-HF: Nuclear repulsion	249732.276225
FMO2-HF: Total energy	-21832.942515
FMO2-MP2: Total energy	-21897.405341

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.
-1.187	-0.095	0.027	-0.272	-0.849	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 : 0.064 / q_NPA : 0.019

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	-0.132	0.071	4.301	0.314	0.605	0.001	-0.164	-0.129	0.000
5	A	144	GLU	0	0.119	-0.094	3.813	-3.546	-2.527	-0.005	-0.609	-0.405	0.003
6	A	144	GLU	-1	-0.960	-0.822	7.446	-1.725	-1.725	0.000	0.000	0.000	0.000
7	A	145	ALA	0	0.029	-0.120	6.620	0.470	0.470	0.000	0.000	0.000	0.000
8	A	145	ALA	0	-0.034	0.131	7.500	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	146	THR	0	-0.032	-0.090	8.566	0.131	0.131	0.000	0.000	0.000	0.000
10	A	146	THR	0	0.017	0.059	10.649	0.046	0.046	0.000	0.000	0.000	0.000
11	A	147	VAL	0	0.146	-0.069	12.150	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	147	VAL	0	-0.057	0.106	16.162	0.006	0.006	0.000	0.000	0.000	0.000
13	A	148	GLU	0	0.108	-0.122	14.961	0.008	0.008	0.000	0.000	0.000	0.000
14	A	148	GLU	-1	-1.020	-0.833	14.556	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	149	TYR	0	0.101	-0.073	10.408	0.134	0.134	0.000	0.000	0.000	0.000
16	A	149	TYR	0	-0.093	0.057	5.656	0.234	0.234	0.000	0.000	0.000	0.000
17	A	150	LEU	0	0.139	-0.085	11.720	0.087	0.087	0.000	0.000	0.000	0.000
18	A	150	LEU	0	-0.118	0.088	12.478	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	151	ALA	0	0.046	-0.126	12.988	0.038	0.038	0.000	0.000	0.000	0.000
20	A	151	ALA	0	-0.097	0.100	16.616	0.004	0.004	0.000	0.000	0.000	0.000
21	A	152	ASP	0	0.064	-0.127	13.962	0.009	0.009	0.000	0.000	0.000	0.000
22	A	152	ASP	-1	-0.923	-0.796	12.879	0.237	0.237	0.000	0.000	0.000	0.000
23	A	153	LEU	0	0.076	-0.107	12.039	0.101	0.101	0.000	0.000	0.000	0.000
24	A	153	LEU	0	-0.080	0.098	8.890	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	154	VAL	0	0.098	-0.081	13.041	0.046	0.046	0.000	0.000	0.000	0.000
26	A	154	VAL	0	-0.114	0.075	15.473	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	155	LYS	0	0.107	-0.102	16.483	0.007	0.007	0.000	0.000	0.000	0.000
28	A	155	LYS	1	0.766	1.031	17.371	-0.139	-0.139	0.000	0.000	0.000	0.000
29	A	156	GLU	0	0.036	-0.163	15.268	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	156	GLU	-1	-0.966	-0.815	13.032	0.423	0.423	0.000	0.000	0.000	0.000
31	A	157	LYS	0	0.125	-0.094	16.230	0.038	0.038	0.000	0.000	0.000	0.000
32	A	157	LYS	1	0.723	0.984	15.963	0.142	0.142	0.000	0.000	0.000	0.000
33	A	158	LYS	0	0.110	-0.080	17.424	0.004	0.004	0.000	0.000	0.000	0.000
34	A	158	LYS	1	0.833	1.051	20.903	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	159	HIS	0	-0.004	-0.105	20.038	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	159	HIS	0	-0.089	0.084	19.295	0.002	0.002	0.000	0.000	0.000	0.000
37	A	160	LEU	0	0.097	-0.101	19.176	0.006	0.006	0.000	0.000	0.000	0.000
38	A	160	LEU	0	-0.040	0.139	16.169	0.004	0.004	0.000	0.000	0.000	0.000
39	A	161	THR	0	-0.011	-0.091	20.505	0.006	0.006	0.000	0.000	0.000	0.000
40	A	161	THR	0	-0.076	0.023	22.038	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	162	LEU	0	-0.001	-0.113	23.420	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	162	LEU	0	-0.070	0.100	24.697	0.001	0.001	0.000	0.000	0.000	0.000
43	A	163	PHE	0	-0.019	-0.103	23.953	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	163	PHE	0	-0.114	0.065	22.260	0.006	0.006	0.000	0.000	0.000	0.000
45	A	164	PRO	0	0.112	-0.094	23.950	0.005	0.005	0.000	0.000	0.000	0.000
46	A	165	HIS	0	0.013	0.030	24.515	0.008	0.008	0.000	0.000	0.000	0.000
47	A	165	HIS	0	-0.099	0.069	26.551	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	166	MET	0	0.111	-0.116	23.987	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	166	MET	0	-0.096	0.101	23.925	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	167	PHE	0	-0.020	-0.095	19.615	0.020	0.020	0.000	0.000	0.000	0.000
51	A	167	PHE	0	-0.055	0.100	18.556	0.010	0.010	0.000	0.000	0.000	0.000
52	A	168	SER	0	0.224	-0.032	18.531	0.008	0.008	0.000	0.000	0.000	0.000
53	A	168	SER	0	-0.038	0.068	20.803	0.005	0.005	0.000	0.000	0.000	0.000
54	A	169	ALA	0	0.073	-0.079	16.966	-0.049	-0.049	0.000	0.000	0.000	0.000
55	A	169	ALA	0	-0.079	0.089	16.248	0.011	0.011	0.000	0.000	0.000	0.000
56	A	170	VAL	0	0.048	-0.125	13.899	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	170	VAL	0	-0.033	0.115	13.743	0.009	0.009	0.000	0.000	0.000	0.000
58	A	171	GLU	0	0.093	-0.097	13.956	0.004	0.004	0.000	0.000	0.000	0.000
59	A	171	GLU	-1	-0.971	-0.847	17.904	0.100	0.100	0.000	0.000	0.000	0.000
60	A	172	ARG	0	0.153	-0.063	15.157	-0.064	-0.064	0.000	0.000	0.000	0.000
61	A	172	ARG	1	0.820	1.050	14.235	0.160	0.160	0.000	0.000	0.000	0.000
62	A	173	LEU	0	0.048	-0.093	11.103	-0.155	-0.155	0.000	0.000	0.000	0.000
63	A	173	LEU	0	-0.092	0.085	9.704	0.036	0.036	0.000	0.000	0.000	0.000
64	A	174	LEU	0	0.113	-0.079	10.140	-0.102	-0.102	0.000	0.000	0.000	0.000
65	A	174	LEU	0	-0.101	0.114	11.436	0.002	0.002	0.000	0.000	0.000	0.000
66	A	175	ASP	0	0.089	-0.112	11.721	-0.117	-0.117	0.000	0.000	0.000	0.000
67	A	175	ASP	-1	-0.915	-0.791	15.193	-0.195	-0.195	0.000	0.000	0.000	0.000
68	A	176	ASP	0	0.094	-0.096	10.844	-0.098	-0.098	0.000	0.000	0.000	0.000
69	A	176	ASP	-1	-1.014	-0.867	9.989	-0.413	-0.413	0.000	0.000	0.000	0.000
70	A	177	GLU	0	0.134	-0.096	7.632	-0.406	-0.406	0.000	0.000	0.000	0.000
71	A	177	GLU	-1	-0.854	-0.715	5.004	-2.028	-1.989	-0.001	-0.002	-0.037	0.000
72	A	178	ILE	0	0.086	-0.096	8.495	-0.348	-0.348	0.000	0.000	0.000	0.000
73	A	178	ILE	0	-0.116	0.084	11.942	0.011	0.011	0.000	0.000	0.000	0.000
74	A	179	GLY	0	-0.049	-0.123	11.405	-0.065	-0.065	0.000	0.000	0.000	0.000
75	A	180	ARG	0	0.122	0.004	7.423	0.178	0.178	0.000	0.000	0.000	0.000
76	A	180	ARG	1	0.731	0.955	3.847	5.483	5.226	0.032	0.503	-0.278	0.000
77	A	181	VAL	0	0.051	-0.095	8.498	-0.369	-0.369	0.000	0.000	0.000	0.000
78	A	181	VAL	0	-0.080	0.116	7.270	0.020	0.020	0.000	0.000	0.000	0.000
79	A	182	ARG	0	0.124	-0.082	9.178	0.055	0.055	0.000	0.000	0.000	0.000
80	A	182	ARG	1	0.821	1.039	13.449	0.533	0.533	0.000	0.000	0.000	0.000
81	A	183	VAL	0	0.054	-0.113	11.783	0.136	0.136	0.000	0.000	0.000	0.000
82	A	183	VAL	0	-0.082	0.118	11.021	0.020	0.020	0.000	0.000	0.000	0.000
83	A	184	ALA	0	0.096	-0.073	9.090	0.211	0.211	0.000	0.000	0.000	0.000
84	A	184	ALA	0	-0.058	0.092	8.330	-0.122	-0.122	0.000	0.000	0.000	0.000
85	A	185	LEU	0	0.072	-0.080	10.472	0.039	0.039	0.000	0.000	0.000	0.000
86	A	185	LEU	0	-0.093	0.072	11.778	0.047	0.047	0.000	0.000	0.000	0.000
87	A	186	PHE	0	0.120	-0.067	13.326	0.109	0.109	0.000	0.000	0.000	0.000
88	A	186	PHE	0	-0.132	0.057	15.282	0.033	0.033	0.000	0.000	0.000	0.000
89	A	187	GLN	0	0.110	-0.094	13.943	0.138	0.138	0.000	0.000	0.000	0.000
90	A	187	GLN	0	-0.140	0.066	12.937	-0.117	-0.117	0.000	0.000	0.000	0.000
91	A	188	THR	0	-0.065	-0.114	14.198	0.057	0.057	0.000	0.000	0.000	0.000
92	A	188	THR	0	-0.021	0.067	12.648	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	189	GLU	0	0.093	-0.087	15.325	0.061	0.061	0.000	0.000	0.000	0.000
94	A	189	GLU	-1	-1.055	-0.875	17.940	-0.472	-0.472	0.000	0.000	0.000	0.000
95	A	190	PHE	0	-0.029	-0.119	18.090	0.063	0.063	0.000	0.000	0.000	0.000
96	A	190	PHE	0	-0.156	0.069	19.399	0.022	0.022	0.000	0.000	0.000	0.000
97	A	191	PRO	0	0.122	-0.075	17.362	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	192	ARG	0	0.067	0.035	18.447	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	192	ARG	1	0.830	1.013	22.460	0.385	0.385	0.000	0.000	0.000	0.000
100	A	193	VAL	0	0.018	-0.114	19.618	0.047	0.047	0.000	0.000	0.000	0.000
101	A	193	VAL	0	-0.085	0.093	19.251	0.009	0.009	0.000	0.000	0.000	0.000
102	A	194	GLU	0	0.118	-0.102	16.552	-0.068	-0.068	0.000	0.000	0.000	0.000
103	A	194	GLU	-1	-0.944	-0.806	14.952	-0.953	-0.953	0.000	0.000	0.000	0.000
104	A	195	LEU	0	-0.120	-0.143	14.646	0.104	0.104	0.000	0.000	0.000	0.000
105	A	195	LEU	0	0.033	0.018	15.415	0.005	0.005	0.000	0.000	0.000	0.000

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