FMO DATABASE

FMODB ID: L6ZN9

Calculation Name: 3D0F-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphate ion | glycerol

Ligand 3-letter code: PO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D0F

Chain ID: A

ChEMBL ID:

UniProt ID: Q81ZZ3

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
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. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-666894.457988
FMO2-HF: Nuclear repulsion	627142.766712
FMO2-HF: Total energy	-39751.691276
FMO2-MP2: Total energy	-39869.830158

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:316:ASN)

Summations of interaction energy for fragment #1(A:316:ASN)

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.
44.61	46.265	-0.009	-0.738	-0.909	-0.001

Interaction energy analysis for fragmet #1(A:316:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.911

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].
3	A	318	TYR	0	0.049	0.022	3.849	-8.408	-6.987	-0.010	-0.652	-0.760	0.000
4	A	319	ARG	1	0.936	0.954	3.492	50.527	50.761	0.001	-0.086	-0.149	-0.001
5	A	320	GLY	0	0.025	0.035	8.285	2.351	2.351	0.000	0.000	0.000	0.000
6	A	321	PRO	0	-0.032	-0.023	10.904	-1.654	-1.654	0.000	0.000	0.000	0.000
7	A	322	GLU	-1	-0.944	-0.960	13.068	-20.200	-20.200	0.000	0.000	0.000	0.000
8	A	323	ALA	0	0.013	0.011	14.195	0.863	0.863	0.000	0.000	0.000	0.000
9	A	324	PHE	0	-0.029	-0.024	17.028	-0.365	-0.365	0.000	0.000	0.000	0.000
10	A	325	LEU	0	0.041	0.031	20.674	0.369	0.369	0.000	0.000	0.000	0.000
11	A	326	LYS	1	0.910	0.950	23.949	10.164	10.164	0.000	0.000	0.000	0.000
12	A	327	LEU	0	0.049	0.025	24.912	0.218	0.218	0.000	0.000	0.000	0.000
13	A	328	PRO	0	0.044	0.036	28.497	0.289	0.289	0.000	0.000	0.000	0.000
14	A	329	LYS	1	0.935	0.945	31.602	8.176	8.176	0.000	0.000	0.000	0.000
15	A	330	ASP	-1	-0.865	-0.926	34.050	-8.895	-8.895	0.000	0.000	0.000	0.000
16	A	331	LEU	0	-0.007	-0.010	28.467	-0.110	-0.110	0.000	0.000	0.000	0.000
17	A	332	LYS	1	0.895	0.941	30.743	8.990	8.990	0.000	0.000	0.000	0.000
18	A	333	ASP	-1	-0.836	-0.906	33.341	-8.833	-8.833	0.000	0.000	0.000	0.000
19	A	334	ARG	1	0.930	0.936	31.427	9.195	9.195	0.000	0.000	0.000	0.000
20	A	335	GLU	-1	-0.942	-0.941	31.806	-8.520	-8.520	0.000	0.000	0.000	0.000
21	A	336	ALA	0	0.056	0.017	32.440	-0.248	-0.248	0.000	0.000	0.000	0.000
22	A	337	LEU	0	-0.075	-0.057	27.271	-0.333	-0.333	0.000	0.000	0.000	0.000
23	A	338	GLN	0	-0.033	-0.009	27.537	-0.543	-0.543	0.000	0.000	0.000	0.000
24	A	339	ASP	-1	-0.862	-0.920	28.438	-9.647	-9.647	0.000	0.000	0.000	0.000
25	A	340	ILE	0	-0.115	-0.062	26.352	-0.215	-0.215	0.000	0.000	0.000	0.000
26	A	341	MET	0	-0.036	-0.032	21.801	-0.499	-0.499	0.000	0.000	0.000	0.000
27	A	342	GLN	0	0.011	0.032	24.709	-0.117	-0.117	0.000	0.000	0.000	0.000
28	A	343	ASP	-1	-0.905	-0.939	24.470	-11.404	-11.404	0.000	0.000	0.000	0.000
29	A	344	ILE	0	-0.080	-0.050	19.155	-0.601	-0.601	0.000	0.000	0.000	0.000
30	A	345	GLY	0	0.063	0.037	20.180	0.363	0.363	0.000	0.000	0.000	0.000
31	A	346	ASN	0	-0.029	-0.018	21.211	0.518	0.518	0.000	0.000	0.000	0.000
32	A	347	SER	0	-0.035	-0.019	20.394	0.338	0.338	0.000	0.000	0.000	0.000
33	A	348	ASP	-1	-0.879	-0.935	19.951	-15.346	-15.346	0.000	0.000	0.000	0.000
34	A	349	ASP	-1	-0.950	-1.003	22.103	-11.908	-11.908	0.000	0.000	0.000	0.000
35	A	350	ILE	0	-0.042	-0.005	23.843	0.577	0.577	0.000	0.000	0.000	0.000
36	A	351	LEU	0	-0.030	-0.014	21.529	-0.513	-0.513	0.000	0.000	0.000	0.000
37	A	352	ALA	0	-0.019	-0.018	22.839	0.459	0.459	0.000	0.000	0.000	0.000
38	A	353	ALA	0	-0.011	-0.016	24.532	-0.257	-0.257	0.000	0.000	0.000	0.000
39	A	354	VAL	0	-0.008	0.009	27.127	0.176	0.176	0.000	0.000	0.000	0.000
40	A	355	VAL	0	-0.016	-0.011	29.319	0.094	0.094	0.000	0.000	0.000	0.000
41	A	356	LEU	0	-0.008	-0.003	31.271	0.026	0.026	0.000	0.000	0.000	0.000
42	A	357	SER	0	0.000	-0.003	34.847	0.272	0.272	0.000	0.000	0.000	0.000
43	A	358	ALA	0	0.026	0.002	37.620	-0.166	-0.166	0.000	0.000	0.000	0.000
44	A	359	THR	0	-0.023	-0.010	39.904	0.228	0.228	0.000	0.000	0.000	0.000
45	A	360	PRO	0	0.036	0.001	42.470	-0.131	-0.131	0.000	0.000	0.000	0.000
46	A	361	GLY	0	0.001	0.019	44.409	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	362	ALA	0	-0.039	-0.035	40.660	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	363	VAL	0	0.009	0.020	35.208	0.065	0.065	0.000	0.000	0.000	0.000
49	A	364	GLU	-1	-0.867	-0.922	34.999	-8.371	-8.371	0.000	0.000	0.000	0.000
50	A	365	ALA	0	0.009	-0.006	30.649	0.009	0.009	0.000	0.000	0.000	0.000
51	A	366	PHE	0	0.017	0.033	24.526	-0.131	-0.131	0.000	0.000	0.000	0.000
52	A	367	ARG	1	0.906	0.938	23.727	11.894	11.894	0.000	0.000	0.000	0.000
53	A	368	LYS	1	0.959	0.960	17.901	15.815	15.815	0.000	0.000	0.000	0.000
54	A	369	ASN	0	-0.057	-0.035	20.439	-0.404	-0.404	0.000	0.000	0.000	0.000
55	A	370	GLY	0	0.020	0.021	21.466	0.003	0.003	0.000	0.000	0.000	0.000
56	A	371	GLU	-1	-0.826	-0.879	24.194	-11.025	-11.025	0.000	0.000	0.000	0.000
57	A	372	THR	0	0.004	-0.007	27.065	-0.074	-0.074	0.000	0.000	0.000	0.000
58	A	373	ILE	0	-0.031	-0.006	29.063	0.148	0.148	0.000	0.000	0.000	0.000
59	A	374	ARG	1	0.918	0.948	31.733	7.905	7.905	0.000	0.000	0.000	0.000
60	A	375	ILE	0	-0.031	-0.003	32.472	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	376	THR	0	0.025	-0.004	36.609	0.219	0.219	0.000	0.000	0.000	0.000
62	A	377	GLY	0	0.054	0.025	40.068	-0.083	-0.083	0.000	0.000	0.000	0.000
63	A	378	ASP	-1	-0.830	-0.914	40.566	-7.378	-7.378	0.000	0.000	0.000	0.000
64	A	379	GLY	0	-0.002	0.009	37.189	-0.117	-0.117	0.000	0.000	0.000	0.000
65	A	380	LEU	0	0.007	-0.003	36.921	-0.243	-0.243	0.000	0.000	0.000	0.000
66	A	381	LYS	1	0.882	0.934	39.464	7.223	7.223	0.000	0.000	0.000	0.000
67	A	382	ALA	0	0.014	0.013	36.965	0.147	0.147	0.000	0.000	0.000	0.000
68	A	383	ALA	0	0.019	0.013	37.111	0.031	0.031	0.000	0.000	0.000	0.000
69	A	384	HIS	0	-0.005	-0.008	39.040	0.220	0.220	0.000	0.000	0.000	0.000
70	A	385	ARG	1	0.900	0.942	42.463	7.173	7.173	0.000	0.000	0.000	0.000
71	A	386	PHE	0	0.005	0.012	39.306	0.135	0.135	0.000	0.000	0.000	0.000
72	A	387	LEU	0	0.015	0.010	39.319	-0.107	-0.107	0.000	0.000	0.000	0.000
73	A	388	SER	0	-0.051	-0.038	42.854	0.174	0.174	0.000	0.000	0.000	0.000
74	A	389	ASN	0	-0.020	-0.011	45.723	0.030	0.030	0.000	0.000	0.000	0.000
75	A	390	ASP	-1	-0.756	-0.865	46.424	-6.543	-6.543	0.000	0.000	0.000	0.000
76	A	391	PRO	0	0.029	0.001	47.106	-0.149	-0.149	0.000	0.000	0.000	0.000
77	A	392	LYS	1	0.928	0.972	47.493	6.241	6.241	0.000	0.000	0.000	0.000
78	A	393	ILE	0	-0.072	-0.015	41.750	-0.126	-0.126	0.000	0.000	0.000	0.000
79	A	394	GLY	0	0.046	0.024	43.516	-0.110	-0.110	0.000	0.000	0.000	0.000
80	A	395	GLU	-1	-0.808	-0.901	41.881	-7.641	-7.641	0.000	0.000	0.000	0.000
81	A	396	LYS	1	0.928	0.968	39.183	7.359	7.359	0.000	0.000	0.000	0.000
82	A	397	ARG	1	0.813	0.909	38.847	7.247	7.247	0.000	0.000	0.000	0.000
83	A	398	ILE	0	-0.005	-0.004	35.955	-0.169	-0.169	0.000	0.000	0.000	0.000
84	A	399	ARG	1	0.887	0.934	37.143	8.506	8.506	0.000	0.000	0.000	0.000
85	A	400	PRO	0	0.021	-0.006	36.037	-0.243	-0.243	0.000	0.000	0.000	0.000
86	A	401	GLY	0	0.015	0.006	32.668	0.099	0.099	0.000	0.000	0.000	0.000
87	A	402	ALA	0	-0.030	-0.001	32.245	-0.232	-0.232	0.000	0.000	0.000	0.000
88	A	403	LEU	0	-0.010	-0.003	25.696	-0.163	-0.163	0.000	0.000	0.000	0.000
89	A	404	ILE	0	0.003	0.003	29.758	0.132	0.132	0.000	0.000	0.000	0.000
90	A	405	ARG	1	0.946	0.973	22.288	12.258	12.258	0.000	0.000	0.000	0.000
91	A	406	VAL	0	-0.020	-0.011	27.383	0.470	0.470	0.000	0.000	0.000	0.000
92	A	407	LYS	1	0.941	0.987	26.580	11.002	11.002	0.000	0.000	0.000	0.000
93	A	408	LYS	1	0.910	0.966	28.340	10.678	10.678	0.000	0.000	0.000	0.000
94	A	409	THR	0	-0.002	-0.016	30.005	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	410	GLU	-1	-0.869	-0.942	32.264	-9.345	-9.345	0.000	0.000	0.000	0.000
96	A	411	LYS	1	0.926	0.964	33.593	7.821	7.821	0.000	0.000	0.000	0.000
97	A	412	GLY	0	-0.001	0.004	32.766	0.151	0.151	0.000	0.000	0.000	0.000
98	A	413	SER	0	-0.008	-0.005	33.220	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	414	TRP	0	0.029	0.009	26.028	-0.267	-0.267	0.000	0.000	0.000	0.000
100	A	415	GLN	0	-0.019	-0.012	32.375	0.205	0.205	0.000	0.000	0.000	0.000
101	A	416	ILE	0	-0.007	-0.004	32.147	-0.350	-0.350	0.000	0.000	0.000	0.000
102	A	417	VAL	0	-0.041	-0.019	29.300	0.239	0.239	0.000	0.000	0.000	0.000
103	A	418	GLN	0	-0.040	-0.024	30.107	0.045	0.045	0.000	0.000	0.000	0.000
104	A	419	LEU	0	-0.027	-0.025	23.873	-0.109	-0.109	0.000	0.000	0.000	0.000
105	A	420	PRO	-1	-0.886	-0.922	26.077	-10.756	-10.756	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:316:ASN)