FMO DATABASE

FMODB ID: Y1VK2

Calculation Name: 3LD3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3LD3

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GJ02

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1737176.743501
FMO2-HF: Nuclear repulsion	1670848.46609
FMO2-HF: Total energy	-66328.277411
FMO2-MP2: Total energy	-66520.381909

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:5:ASP)

Summations of interaction energy for fragment #1(A:5: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.
-14.213	-12.225	0.017	-0.85	-1.155	-0.002

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.087 / q_NPA : -0.055

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	7	GLY	0	0.006	0.011	3.101	2.174	3.795	0.017	-0.718	-0.920	-0.001
4	A	8	SER	0	0.112	0.051	4.322	3.102	3.253	-0.001	-0.027	-0.123	0.000
57	A	61	ASN	0	-0.053	-0.046	3.888	-7.444	-7.228	0.001	-0.105	-0.112	-0.001
5	A	9	GLY	0	0.041	0.025	7.607	1.719	1.719	0.000	0.000	0.000	0.000
6	A	10	SER	0	-0.038	-0.032	9.564	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	11	ASN	0	-0.049	-0.015	11.055	0.207	0.207	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.028	0.050	11.636	0.286	0.286	0.000	0.000	0.000	0.000
9	A	13	PRO	0	-0.028	-0.024	13.545	0.025	0.025	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.812	-0.904	15.882	-1.236	-1.236	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.876	-0.952	15.565	-0.644	-0.644	0.000	0.000	0.000	0.000
12	A	16	VAL	0	-0.025	-0.011	12.285	-0.314	-0.314	0.000	0.000	0.000	0.000
13	A	17	ASN	0	-0.083	-0.047	7.380	1.942	1.942	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.017	0.001	10.466	-0.749	-0.749	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.007	0.003	7.736	0.619	0.619	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.023	-0.010	10.875	-0.064	-0.064	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.844	-0.934	13.955	-2.054	-2.054	0.000	0.000	0.000	0.000
18	A	22	VAL	0	-0.007	-0.014	16.084	0.250	0.250	0.000	0.000	0.000	0.000
19	A	23	SER	0	-0.025	-0.023	19.745	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.004	0.002	21.385	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.894	-0.960	24.184	-0.308	-0.308	0.000	0.000	0.000	0.000
22	A	26	SER	0	-0.064	-0.035	24.217	0.065	0.065	0.000	0.000	0.000	0.000
23	A	27	HIS	0	0.018	-0.008	26.724	-0.050	-0.050	0.000	0.000	0.000	0.000
24	A	28	PRO	0	0.022	0.031	26.373	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	29	VAL	0	-0.040	-0.032	23.212	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	30	LYS	1	0.802	0.893	18.558	1.480	1.480	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.001	-0.020	17.906	0.104	0.104	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.796	-0.880	16.214	-1.688	-1.688	0.000	0.000	0.000	0.000
29	A	33	PHE	0	-0.043	-0.023	10.894	0.349	0.349	0.000	0.000	0.000	0.000
30	A	34	ASP	-1	-0.816	-0.890	13.039	-1.942	-1.942	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.930	-0.972	8.181	-6.503	-6.503	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.898	0.959	9.728	0.892	0.892	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.090	-0.067	11.835	0.509	0.509	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.027	0.026	9.385	0.638	0.638	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.049	-0.018	10.051	0.389	0.389	0.000	0.000	0.000	0.000
36	A	40	LEU	0	-0.031	-0.008	13.150	-0.407	-0.407	0.000	0.000	0.000	0.000
37	A	41	TRP	0	-0.037	-0.027	14.892	0.334	0.334	0.000	0.000	0.000	0.000
38	A	42	VAL	0	-0.030	-0.025	18.176	-0.055	-0.055	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.840	-0.891	20.682	-0.995	-0.995	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.766	0.859	22.321	0.991	0.991	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.002	0.000	25.388	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.019	-0.004	25.988	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.009	0.000	29.360	0.051	0.051	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.047	-0.035	31.646	0.041	0.041	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.012	-0.003	32.599	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	50	MET	0	-0.057	-0.020	31.142	0.006	0.006	0.000	0.000	0.000	0.000
47	A	51	TYR	0	0.000	0.009	28.230	0.003	0.003	0.000	0.000	0.000	0.000
48	A	52	TYR	0	0.085	0.035	22.707	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	53	PRO	0	0.000	0.005	25.992	0.045	0.045	0.000	0.000	0.000	0.000
50	A	54	CYS	0	-0.066	-0.041	22.503	0.006	0.006	0.000	0.000	0.000	0.000
51	A	55	ASN	0	0.025	0.016	19.058	0.109	0.109	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.017	0.004	18.093	0.008	0.008	0.000	0.000	0.000	0.000
53	A	57	GLY	0	0.052	0.017	14.794	0.162	0.162	0.000	0.000	0.000	0.000
54	A	58	PHE	0	0.061	0.053	8.089	-0.086	-0.086	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.009	0.007	9.752	-0.315	-0.315	0.000	0.000	0.000	0.000
56	A	60	PRO	0	-0.009	0.002	5.211	-0.628	-0.628	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.028	-0.029	6.962	1.601	1.601	0.000	0.000	0.000	0.000
59	A	63	ILE	0	0.008	0.016	10.803	-0.213	-0.213	0.000	0.000	0.000	0.000
60	A	64	ALA	0	0.019	0.002	13.766	0.264	0.264	0.000	0.000	0.000	0.000
61	A	65	GLY	0	-0.036	-0.027	17.023	0.031	0.031	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.850	-0.919	18.864	-2.171	-2.171	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.040	-0.018	17.130	0.097	0.097	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.822	-0.895	14.975	-2.878	-2.878	0.000	0.000	0.000	0.000
65	A	69	PRO	0	-0.045	-0.033	10.666	-0.184	-0.184	0.000	0.000	0.000	0.000
66	A	70	VAL	0	-0.009	-0.013	12.657	0.599	0.599	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.732	-0.841	13.990	-2.587	-2.587	0.000	0.000	0.000	0.000
68	A	72	VAL	0	-0.086	-0.063	14.932	0.144	0.144	0.000	0.000	0.000	0.000
69	A	73	LEU	0	0.001	0.007	17.552	0.110	0.110	0.000	0.000	0.000	0.000
70	A	74	VAL	0	0.017	-0.008	16.847	0.027	0.027	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.017	0.018	20.201	0.122	0.122	0.000	0.000	0.000	0.000
72	A	76	ALA	0	-0.034	-0.028	21.799	0.008	0.008	0.000	0.000	0.000	0.000
73	A	77	ARG	1	0.824	0.895	23.954	0.105	0.105	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.034	-0.015	24.453	0.058	0.058	0.000	0.000	0.000	0.000
75	A	79	PRO	0	0.013	0.011	23.103	-0.046	-0.046	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.015	0.002	16.616	0.122	0.122	0.000	0.000	0.000	0.000
77	A	81	MET	0	-0.011	0.015	16.283	-0.049	-0.049	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.035	0.007	15.933	-0.064	-0.064	0.000	0.000	0.000	0.000
79	A	83	GLY	0	-0.002	-0.006	11.758	0.280	0.280	0.000	0.000	0.000	0.000
80	A	84	ALA	0	-0.068	-0.011	11.033	0.349	0.349	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.009	-0.002	7.613	-0.503	-0.503	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.031	-0.012	10.979	0.562	0.562	0.000	0.000	0.000	0.000
83	A	87	CYS	0	0.001	0.021	13.156	-0.377	-0.377	0.000	0.000	0.000	0.000
84	A	88	VAL	0	0.011	-0.006	14.549	0.352	0.352	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.913	0.951	16.609	0.592	0.592	0.000	0.000	0.000	0.000
86	A	90	PRO	0	-0.005	0.001	17.306	0.110	0.110	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.044	-0.018	20.021	0.096	0.096	0.000	0.000	0.000	0.000
88	A	92	GLY	0	0.015	-0.001	23.082	0.122	0.122	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.030	-0.008	22.186	-0.133	-0.133	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.002	0.016	24.059	0.112	0.112	0.000	0.000	0.000	0.000
91	A	95	MET	0	0.022	0.012	24.167	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	96	MET	0	-0.035	-0.009	25.116	0.132	0.132	0.000	0.000	0.000	0.000
93	A	97	ASN	0	0.001	0.018	25.999	-0.136	-0.136	0.000	0.000	0.000	0.000
94	A	98	ASP	-1	-0.789	-0.919	24.688	-1.251	-1.251	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.839	-0.921	26.272	-1.064	-1.064	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.772	0.889	19.411	1.954	1.954	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.008	0.002	24.098	-0.061	-0.061	0.000	0.000	0.000	0.000
98	A	102	GLU	-1	-0.907	-0.961	23.055	-1.365	-1.365	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.766	-0.876	20.836	-1.911	-1.911	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.059	-0.032	21.873	0.036	0.036	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.740	0.866	19.864	1.617	1.617	0.000	0.000	0.000	0.000
102	A	106	VAL	0	-0.008	-0.006	17.939	0.161	0.161	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.015	0.001	20.515	0.048	0.048	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.005	-0.008	18.946	-0.040	-0.040	0.000	0.000	0.000	0.000
105	A	109	VAL	0	0.004	0.010	20.849	0.133	0.133	0.000	0.000	0.000	0.000
106	A	110	PRO	0	0.017	0.002	19.443	-0.114	-0.114	0.000	0.000	0.000	0.000
107	A	111	ALA	0	0.033	0.030	18.000	0.018	0.018	0.000	0.000	0.000	0.000
108	A	112	THR	0	0.012	-0.007	20.005	0.127	0.127	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.770	0.866	15.163	0.656	0.656	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.044	-0.013	17.255	0.147	0.147	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.774	-0.886	20.536	-0.080	-0.080	0.000	0.000	0.000	0.000
112	A	116	GLN	0	0.008	0.006	23.901	-0.083	-0.083	0.000	0.000	0.000	0.000
113	A	117	TYR	0	-0.049	-0.010	27.012	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	118	TYR	0	0.067	0.015	25.007	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	119	GLY	0	-0.013	-0.008	26.891	-0.067	-0.067	0.000	0.000	0.000	0.000
116	A	120	ASN	0	-0.041	-0.027	27.897	-0.037	-0.037	0.000	0.000	0.000	0.000
117	A	121	ILE	0	-0.008	0.020	26.937	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.003	0.000	26.430	-0.069	-0.069	0.000	0.000	0.000	0.000
119	A	123	ASN	0	0.012	-0.018	26.179	-0.167	-0.167	0.000	0.000	0.000	0.000
120	A	124	TYR	0	0.048	0.016	26.990	0.054	0.054	0.000	0.000	0.000	0.000
121	A	125	SER	0	-0.013	-0.007	28.379	0.030	0.030	0.000	0.000	0.000	0.000
122	A	126	ASP	-1	-0.861	-0.911	30.533	-0.574	-0.574	0.000	0.000	0.000	0.000
123	A	127	LEU	0	-0.034	-0.015	27.195	0.046	0.046	0.000	0.000	0.000	0.000
124	A	128	PRO	0	0.000	-0.006	31.859	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	129	SER	0	0.056	0.029	33.671	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	130	SER	0	0.040	0.018	34.756	-0.033	-0.033	0.000	0.000	0.000	0.000
127	A	131	PHE	0	0.007	0.011	27.050	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	132	LEU	0	0.048	0.037	29.243	-0.040	-0.040	0.000	0.000	0.000	0.000
129	A	133	ASP	-1	-0.881	-0.930	31.230	-0.589	-0.589	0.000	0.000	0.000	0.000
130	A	134	SER	0	-0.088	-0.060	31.476	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	135	ILE	0	0.032	0.017	26.341	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	136	SER	0	0.001	-0.021	29.090	-0.056	-0.056	0.000	0.000	0.000	0.000
133	A	137	HIS	0	-0.031	-0.001	31.002	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	138	PHE	0	0.019	-0.001	25.489	0.014	0.014	0.000	0.000	0.000	0.000
135	A	139	PHE	0	0.023	-0.001	23.219	0.000	0.000	0.000	0.000	0.000	0.000
136	A	140	SER	0	-0.009	-0.007	28.668	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	141	PHE	0	-0.081	-0.063	32.160	0.033	0.033	0.000	0.000	0.000	0.000
138	A	142	TYR	0	0.035	0.016	24.652	0.021	0.021	0.000	0.000	0.000	0.000
139	A	143	LYS	1	0.865	0.939	24.934	1.166	1.166	0.000	0.000	0.000	0.000
140	A	144	LYS	1	0.893	0.959	30.703	0.621	0.621	0.000	0.000	0.000	0.000
141	A	145	LEU	0	-0.025	-0.007	33.946	0.032	0.032	0.000	0.000	0.000	0.000
142	A	146	GLU	-1	-0.822	-0.898	28.660	-0.749	-0.749	0.000	0.000	0.000	0.000
143	A	147	LYS	1	0.837	0.888	32.775	0.513	0.513	0.000	0.000	0.000	0.000
144	A	148	ASP	-1	-0.857	-0.898	32.075	-0.598	-0.598	0.000	0.000	0.000	0.000
145	A	149	LYS	1	0.854	0.933	25.913	0.857	0.857	0.000	0.000	0.000	0.000
146	A	150	PHE	0	-0.060	-0.026	29.831	0.077	0.077	0.000	0.000	0.000	0.000
147	A	151	VAL	0	0.031	0.005	28.098	-0.065	-0.065	0.000	0.000	0.000	0.000
148	A	152	SER	0	-0.093	-0.029	30.482	0.085	0.085	0.000	0.000	0.000	0.000
149	A	153	VAL	0	0.023	0.006	29.344	-0.067	-0.067	0.000	0.000	0.000	0.000
150	A	154	GLY	0	-0.003	0.007	29.945	0.057	0.057	0.000	0.000	0.000	0.000
151	A	155	CYS	0	-0.062	-0.041	31.529	0.050	0.050	0.000	0.000	0.000	0.000
152	A	156	TRP	0	0.029	0.006	25.533	-0.083	-0.083	0.000	0.000	0.000	0.000
153	A	157	GLN	0	-0.030	-0.016	26.718	-0.018	-0.018	0.000	0.000	0.000	0.000
154	A	158	ASP	-1	-0.801	-0.888	27.097	-1.069	-1.069	0.000	0.000	0.000	0.000
155	A	159	ALA	0	0.053	0.021	23.914	-0.109	-0.109	0.000	0.000	0.000	0.000
156	A	160	ALA	0	-0.053	-0.022	22.985	-0.132	-0.132	0.000	0.000	0.000	0.000
157	A	161	SER	0	0.002	-0.025	23.393	-0.114	-0.114	0.000	0.000	0.000	0.000
158	A	162	ALA	0	-0.005	0.003	21.191	-0.131	-0.131	0.000	0.000	0.000	0.000
159	A	163	LYS	1	0.800	0.891	18.889	1.133	1.133	0.000	0.000	0.000	0.000
160	A	164	GLU	-1	-0.819	-0.903	18.676	-2.015	-2.015	0.000	0.000	0.000	0.000
161	A	165	LEU	0	0.011	0.021	18.224	-0.168	-0.168	0.000	0.000	0.000	0.000
162	A	166	ILE	0	0.024	0.006	13.963	-0.264	-0.264	0.000	0.000	0.000	0.000
163	A	167	ARG	1	0.860	0.921	14.766	1.523	1.523	0.000	0.000	0.000	0.000
164	A	168	SER	0	-0.060	-0.044	15.670	-0.213	-0.213	0.000	0.000	0.000	0.000
165	A	169	ALA	0	0.061	0.039	14.496	-0.099	-0.099	0.000	0.000	0.000	0.000
166	A	170	ILE	0	-0.026	-0.013	10.301	-0.629	-0.629	0.000	0.000	0.000	0.000
167	A	171	ILE	0	-0.106	-0.055	11.966	-0.310	-0.310	0.000	0.000	0.000	0.000
168	A	172	ALA	0	-0.021	-0.010	14.627	-0.001	-0.001	0.000	0.000	0.000	0.000
169	A	173	ALA	0	0.019	0.027	9.493	0.039	0.039	0.000	0.000	0.000	0.000
170	A	174	LYS	1	0.848	0.930	10.291	2.669	2.669	0.000	0.000	0.000	0.000
171	A	175	LYS	0	0.023	0.028	11.991	-0.891	-0.891	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)