FMO DATABASE

FMODB ID: Y9LK2

Calculation Name: 2DXQ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DXQ

Chain ID: A

ChEMBL ID:

UniProt ID: A9CI53

Base Structure: X-ray

Registration Date: 2025-10-04

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1238680.837068
FMO2-HF: Nuclear repulsion	1183422.757725
FMO2-HF: Total energy	-55258.079342
FMO2-MP2: Total energy	-55419.894637

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:4:ASP)

Summations of interaction energy for fragment #1(A:4:ASP)

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.
-9.052	-2.946	0.608	-3.241	-3.472	-0.004

Interaction energy analysis for fragmet #1(A:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.025

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	6	ILE	0	0.006	0.009	3.014	-8.539	-4.437	0.059	-2.079	-2.081	0.010
4	A	7	SER	0	-0.039	-0.017	2.680	-1.802	0.110	0.550	-1.152	-1.310	-0.014
5	A	8	LEU	0	0.010	0.005	4.673	0.865	0.957	-0.001	-0.010	-0.081	0.000
6	A	9	ARG	1	0.771	0.857	7.615	6.015	6.015	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.058	0.033	10.560	0.270	0.270	0.000	0.000	0.000	0.000
8	A	11	ALA	0	-0.038	-0.015	12.469	-0.709	-0.709	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.044	0.011	14.309	0.272	0.272	0.000	0.000	0.000	0.000
10	A	13	PRO	0	0.006	-0.016	15.689	-0.071	-0.071	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.003	0.006	14.583	0.169	0.169	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.749	-0.838	11.930	-4.594	-4.594	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.019	0.014	14.764	0.161	0.161	0.000	0.000	0.000	0.000
14	A	17	PRO	0	0.051	0.016	16.845	0.165	0.165	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.031	0.019	15.124	0.129	0.129	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.047	-0.033	16.204	0.202	0.202	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.003	0.019	18.184	0.191	0.191	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.838	-0.911	18.066	-1.743	-1.743	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.054	-0.036	15.184	0.183	0.183	0.000	0.000	0.000	0.000
20	A	23	TYR	0	-0.003	-0.023	19.736	0.178	0.178	0.000	0.000	0.000	0.000
21	A	24	GLN	0	0.015	0.005	23.057	0.037	0.037	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.071	-0.036	21.157	0.097	0.097	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.110	-0.046	23.323	0.104	0.104	0.000	0.000	0.000	0.000
24	A	27	ASN	0	-0.056	-0.032	24.879	0.124	0.124	0.000	0.000	0.000	0.000
25	A	28	PRO	0	-0.002	-0.001	27.667	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.034	-0.020	29.247	0.018	0.018	0.000	0.000	0.000	0.000
27	A	30	ASP	-1	-0.872	-0.915	29.232	-0.506	-0.506	0.000	0.000	0.000	0.000
28	A	31	PRO	0	-0.039	-0.019	30.605	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.888	-0.950	27.182	-0.854	-0.854	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.057	-0.015	26.761	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	34	THR	0	0.014	-0.026	25.753	-0.115	-0.115	0.000	0.000	0.000	0.000
32	A	35	THR	0	-0.007	-0.028	21.217	0.017	0.017	0.000	0.000	0.000	0.000
33	A	36	GLN	0	-0.011	-0.012	23.861	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.839	-0.884	27.050	-0.829	-0.829	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.025	0.015	24.656	0.038	0.038	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.016	0.013	24.220	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.004	-0.005	25.289	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	41	VAL	0	0.045	0.021	26.780	0.023	0.023	0.000	0.000	0.000	0.000
39	A	42	PHE	0	-0.009	-0.003	17.518	0.015	0.015	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.006	-0.003	23.192	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.002	0.000	24.678	0.026	0.026	0.000	0.000	0.000	0.000
42	A	45	MET	0	-0.035	-0.030	23.419	0.031	0.031	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.038	-0.024	18.601	0.006	0.006	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.012	0.010	22.421	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	48	GLN	0	-0.031	0.006	25.725	0.078	0.078	0.000	0.000	0.000	0.000
46	A	49	PRO	0	-0.003	-0.016	25.867	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	50	GLY	0	-0.009	-0.002	25.842	0.043	0.043	0.000	0.000	0.000	0.000
48	A	51	LEU	0	-0.023	0.013	22.110	0.065	0.065	0.000	0.000	0.000	0.000
49	A	52	THR	0	-0.042	-0.033	17.525	-0.080	-0.080	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.028	0.032	17.030	0.117	0.117	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.025	0.002	13.892	-0.228	-0.228	0.000	0.000	0.000	0.000
52	A	55	VAL	0	0.029	0.012	10.862	0.131	0.131	0.000	0.000	0.000	0.000
53	A	56	ALA	0	-0.009	0.004	9.470	-0.099	-0.099	0.000	0.000	0.000	0.000
54	A	57	THR	0	-0.015	-0.027	6.559	-0.381	-0.381	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.744	-0.822	6.785	0.523	0.523	0.000	0.000	0.000	0.000
56	A	59	ASN	0	-0.034	-0.040	5.783	-0.337	-0.337	0.000	0.000	0.000	0.000
57	A	60	GLY	0	0.005	0.017	6.035	-1.217	-1.217	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.901	0.953	6.673	3.240	3.240	0.000	0.000	0.000	0.000
59	A	62	PRO	0	0.004	-0.002	10.253	0.294	0.294	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.037	-0.013	10.596	0.355	0.355	0.000	0.000	0.000	0.000
61	A	64	ALA	0	-0.025	-0.023	13.065	0.471	0.471	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.029	-0.015	13.857	-0.329	-0.329	0.000	0.000	0.000	0.000
63	A	66	ALA	0	0.031	0.008	16.371	0.242	0.242	0.000	0.000	0.000	0.000
64	A	67	THR	0	0.007	0.019	18.447	-0.185	-0.185	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.028	-0.006	20.462	0.141	0.141	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.023	0.010	22.128	-0.092	-0.092	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.008	-0.013	23.231	0.095	0.095	0.000	0.000	0.000	0.000
68	A	71	VAL	0	0.008	0.003	26.962	-0.048	-0.048	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.013	0.010	30.784	0.048	0.048	0.000	0.000	0.000	0.000
70	A	73	ASN	0	0.007	-0.017	33.156	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	74	LEU	0	0.093	0.045	36.107	0.011	0.011	0.000	0.000	0.000	0.000
72	A	75	THR	0	-0.052	-0.044	38.085	0.029	0.029	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.907	0.940	36.688	-0.077	-0.077	0.000	0.000	0.000	0.000
74	A	77	ALA	0	0.040	0.013	37.187	0.010	0.010	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.004	0.009	37.533	0.003	0.003	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.888	0.979	30.462	-0.166	-0.166	0.000	0.000	0.000	0.000
77	A	80	PRO	0	0.051	0.034	29.416	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	81	TYR	0	-0.061	-0.034	30.191	0.055	0.055	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.052	0.022	25.633	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	83	PHE	0	-0.026	-0.011	27.423	0.061	0.061	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.022	-0.018	21.461	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.861	-0.937	23.695	-0.266	-0.266	0.000	0.000	0.000	0.000
83	A	86	ASN	0	-0.029	-0.013	22.807	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	87	VAL	0	-0.034	-0.012	19.850	-0.067	-0.067	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.015	0.019	19.087	0.065	0.065	0.000	0.000	0.000	0.000
86	A	89	THR	0	-0.028	-0.016	16.983	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	90	LEU	0	0.044	0.026	15.781	0.018	0.018	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.786	-0.878	19.011	0.228	0.228	0.000	0.000	0.000	0.000
89	A	92	ALA	0	0.005	-0.001	18.899	0.132	0.132	0.000	0.000	0.000	0.000
90	A	93	ARG	1	0.750	0.834	13.188	0.259	0.259	0.000	0.000	0.000	0.000
91	A	94	ARG	1	0.937	0.965	17.075	-0.082	-0.082	0.000	0.000	0.000	0.000
92	A	95	GLY	0	-0.027	-0.021	19.262	0.088	0.088	0.000	0.000	0.000	0.000
93	A	96	ARG	1	0.922	0.963	13.837	-1.168	-1.168	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.022	0.019	13.857	0.319	0.319	0.000	0.000	0.000	0.000
95	A	98	TYR	0	0.001	-0.027	9.186	0.134	0.134	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.079	0.026	13.231	-0.158	-0.158	0.000	0.000	0.000	0.000
97	A	100	ARG	1	0.913	0.942	16.540	-1.214	-1.214	0.000	0.000	0.000	0.000
98	A	101	THR	0	-0.023	-0.014	10.608	0.195	0.195	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.001	0.004	13.433	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	103	VAL	0	0.006	0.002	14.600	-0.093	-0.093	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.902	0.961	16.768	-1.133	-1.133	0.000	0.000	0.000	0.000
102	A	105	HIS	0	0.059	0.041	13.123	0.055	0.055	0.000	0.000	0.000	0.000
103	A	106	ALA	0	0.000	0.020	15.976	-0.096	-0.096	0.000	0.000	0.000	0.000
104	A	107	ILE	0	0.005	-0.007	18.891	-0.035	-0.035	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.916	-0.968	17.180	1.160	1.160	0.000	0.000	0.000	0.000
106	A	109	THR	0	-0.022	-0.020	17.522	-0.063	-0.063	0.000	0.000	0.000	0.000
107	A	110	ALA	0	-0.004	-0.004	19.926	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	111	PHE	0	-0.033	-0.025	23.353	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	112	GLY	0	0.022	0.023	22.156	0.010	0.010	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.036	-0.015	23.206	-0.035	-0.035	0.000	0.000	0.000	0.000
111	A	114	ASN	0	0.008	-0.002	25.269	0.001	0.001	0.000	0.000	0.000	0.000
112	A	115	CYS	0	-0.028	0.004	26.553	-0.029	-0.029	0.000	0.000	0.000	0.000
113	A	116	TYR	0	-0.067	-0.047	28.870	0.061	0.061	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.857	0.927	30.149	0.024	0.024	0.000	0.000	0.000	0.000
115	A	118	VAL	0	0.058	0.032	24.368	-0.045	-0.045	0.000	0.000	0.000	0.000
116	A	119	MET	0	-0.057	-0.013	27.765	0.046	0.046	0.000	0.000	0.000	0.000
117	A	120	LEU	0	0.039	0.019	24.656	-0.035	-0.035	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.010	0.006	28.375	0.041	0.041	0.000	0.000	0.000	0.000
119	A	122	THR	0	0.046	0.010	28.086	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	123	GLY	0	0.030	0.024	30.348	0.021	0.021	0.000	0.000	0.000	0.000
121	A	124	ARG	1	0.873	0.940	26.190	0.045	0.045	0.000	0.000	0.000	0.000
122	A	125	HIS	0	0.086	0.036	31.436	0.026	0.026	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.853	-0.921	29.181	0.177	0.177	0.000	0.000	0.000	0.000
124	A	127	PRO	0	0.072	0.023	30.383	0.014	0.014	0.000	0.000	0.000	0.000
125	A	128	ALA	0	-0.013	0.001	27.078	0.046	0.046	0.000	0.000	0.000	0.000
126	A	129	VAL	0	-0.025	-0.021	25.797	0.045	0.045	0.000	0.000	0.000	0.000
127	A	130	HIS	0	-0.032	-0.015	26.636	0.036	0.036	0.000	0.000	0.000	0.000
128	A	131	ALA	0	0.087	0.042	27.997	0.025	0.025	0.000	0.000	0.000	0.000
129	A	132	PHE	0	-0.048	-0.006	19.221	0.103	0.103	0.000	0.000	0.000	0.000
130	A	133	TYR	0	0.076	0.033	23.200	0.074	0.074	0.000	0.000	0.000	0.000
131	A	134	GLU	-1	-0.902	-0.943	25.033	0.421	0.421	0.000	0.000	0.000	0.000
132	A	135	SER	0	-0.084	-0.041	22.730	0.099	0.099	0.000	0.000	0.000	0.000
133	A	136	CYS	0	-0.094	-0.062	20.956	0.140	0.140	0.000	0.000	0.000	0.000
134	A	137	GLY	0	-0.013	0.000	22.051	0.028	0.028	0.000	0.000	0.000	0.000
135	A	138	PHE	0	-0.033	-0.011	23.723	-0.045	-0.045	0.000	0.000	0.000	0.000
136	A	139	VAL	0	0.042	0.004	27.477	0.036	0.036	0.000	0.000	0.000	0.000
137	A	140	GLN	0	0.001	0.018	31.165	-0.043	-0.043	0.000	0.000	0.000	0.000
138	A	141	ASN	0	0.017	0.010	33.641	-0.035	-0.035	0.000	0.000	0.000	0.000
139	A	142	LYS	1	0.850	0.910	35.008	-0.153	-0.153	0.000	0.000	0.000	0.000
140	A	143	THR	0	0.045	0.031	36.568	0.013	0.013	0.000	0.000	0.000	0.000
141	A	144	GLY	0	0.009	0.006	36.200	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	145	PHE	0	-0.018	-0.016	36.952	0.006	0.006	0.000	0.000	0.000	0.000
143	A	146	GLN	0	0.027	0.012	36.238	-0.038	-0.038	0.000	0.000	0.000	0.000
144	A	147	ILE	0	-0.006	0.006	39.025	0.015	0.015	0.000	0.000	0.000	0.000
145	A	148	ARG	1	0.892	0.926	34.420	0.252	0.252	0.000	0.000	0.000	0.000
146	A	149	GLN	0	-0.036	-0.010	40.399	0.034	0.034	0.000	0.000	0.000	0.000
147	A	150	ASP	-2	-1.848	-1.909	40.058	-0.590	-0.590	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASP)