FMO DATABASE

FMODB ID: 5G9ZZ

Calculation Name: 2LDR-A-Other547

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine | zinc ion

Ligand 3-letter code: PTR | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2LDR

Chain ID: A

ChEMBL ID:

UniProt ID: Q13191

Base Structure: SolutionNMR

Registration Date: 2025-10-06

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-516865.126975
FMO2-HF: Nuclear repulsion	481822.461266
FMO2-HF: Total energy	-35042.665708
FMO2-MP2: Total energy	-35134.747024

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:345:GLY)

Summations of interaction energy for fragment #1(A:345:GLY)

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.
-123.383	-120.568	0.491	-1.925	-1.381	-0.019

Interaction energy analysis for fragmet #1(A:345:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.919

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	347	HIS	1	0.908	0.942	2.608	24.334	27.117	0.492	-1.920	-1.355	-0.019
74	A	419	GLU	-1	-0.819	-0.917	4.796	-49.171	-49.139	-0.001	-0.005	-0.026	0.000
4	A	348	MET	0	0.005	0.015	5.091	-2.694	-2.694	0.000	0.000	0.000	0.000
5	A	349	GLY	0	-0.011	-0.003	6.456	2.618	2.618	0.000	0.000	0.000	0.000
6	A	350	SER	0	-0.035	-0.039	8.798	-2.135	-2.135	0.000	0.000	0.000	0.000
7	A	351	ASP	-1	-0.880	-0.939	10.249	-27.552	-27.552	0.000	0.000	0.000	0.000
8	A	352	HIS	0	-0.003	-0.003	11.986	0.421	0.421	0.000	0.000	0.000	0.000
9	A	353	ILE	0	-0.056	-0.029	14.019	0.080	0.080	0.000	0.000	0.000	0.000
10	A	354	LYS	1	0.817	0.905	17.395	13.010	13.010	0.000	0.000	0.000	0.000
11	A	355	VAL	0	-0.028	-0.005	21.175	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	356	THR	0	-0.020	-0.060	23.425	0.262	0.262	0.000	0.000	0.000	0.000
13	A	357	GLN	0	-0.003	-0.015	26.338	0.023	0.023	0.000	0.000	0.000	0.000
14	A	358	GLU	-1	-0.859	-0.875	26.650	-11.640	-11.640	0.000	0.000	0.000	0.000
15	A	359	GLN	0	0.019	0.003	22.294	-0.063	-0.063	0.000	0.000	0.000	0.000
16	A	360	TYR	0	0.028	0.001	26.992	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	361	GLU	-1	-0.874	-0.941	29.036	-9.102	-9.102	0.000	0.000	0.000	0.000
18	A	362	LEU	0	-0.008	-0.005	28.309	0.151	0.151	0.000	0.000	0.000	0.000
19	A	363	TYR	0	-0.041	-0.031	24.505	-0.154	-0.154	0.000	0.000	0.000	0.000
20	A	364	CYS	0	-0.049	-0.022	30.028	0.193	0.193	0.000	0.000	0.000	0.000
21	A	365	GLU	-1	-0.979	-0.980	33.353	-8.719	-8.719	0.000	0.000	0.000	0.000
22	A	366	MET	0	-0.074	-0.030	30.744	0.205	0.205	0.000	0.000	0.000	0.000
23	A	367	GLY	0	-0.026	0.006	33.526	0.048	0.048	0.000	0.000	0.000	0.000
24	A	368	SER	0	-0.042	-0.028	28.846	-0.270	-0.270	0.000	0.000	0.000	0.000
25	A	369	THR	0	0.073	0.035	26.929	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	370	PHE	0	0.050	0.021	19.495	-0.325	-0.325	0.000	0.000	0.000	0.000
27	A	371	GLN	0	0.032	0.006	21.020	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	372	LEU	0	0.095	0.063	21.184	-0.682	-0.682	0.000	0.000	0.000	0.000
29	A	373	CYS	0	-0.113	-0.039	20.901	-0.124	-0.124	0.000	0.000	0.000	0.000
30	A	374	LYS	1	0.815	0.876	22.202	13.514	13.514	0.000	0.000	0.000	0.000
31	A	375	ILE	0	-0.018	-0.012	19.644	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	376	CYS	0	-0.016	-0.014	22.873	0.348	0.348	0.000	0.000	0.000	0.000
33	A	377	ALA	0	-0.020	-0.008	25.320	0.416	0.416	0.000	0.000	0.000	0.000
34	A	378	GLU	-1	-0.916	-0.947	25.620	-10.767	-10.767	0.000	0.000	0.000	0.000
35	A	379	ASN	0	0.009	-0.009	20.709	0.465	0.465	0.000	0.000	0.000	0.000
36	A	380	ASP	-1	-0.800	-0.905	20.253	-13.989	-13.989	0.000	0.000	0.000	0.000
37	A	381	LYS	1	0.705	0.865	16.841	15.126	15.126	0.000	0.000	0.000	0.000
38	A	382	ASP	-1	-0.858	-0.930	14.833	-18.902	-18.902	0.000	0.000	0.000	0.000
39	A	383	VAL	0	-0.031	-0.014	10.657	-2.104	-2.104	0.000	0.000	0.000	0.000
40	A	384	LYS	1	0.901	0.964	10.896	23.973	23.973	0.000	0.000	0.000	0.000
41	A	385	ILE	0	0.006	0.001	10.144	-3.015	-3.015	0.000	0.000	0.000	0.000
42	A	386	GLU	-1	-0.896	-0.936	9.720	-24.464	-24.464	0.000	0.000	0.000	0.000
43	A	387	PRO	0	-0.001	-0.030	10.947	-1.492	-1.492	0.000	0.000	0.000	0.000
44	A	388	CYS	0	-0.043	-0.018	13.146	1.276	1.276	0.000	0.000	0.000	0.000
45	A	389	GLY	0	0.031	0.012	14.404	1.023	1.023	0.000	0.000	0.000	0.000
46	A	390	HIS	0	0.016	0.003	15.785	1.259	1.259	0.000	0.000	0.000	0.000
47	A	391	LEU	0	-0.011	-0.012	14.921	-1.365	-1.365	0.000	0.000	0.000	0.000
48	A	392	MET	0	-0.024	-0.015	15.481	1.116	1.116	0.000	0.000	0.000	0.000
49	A	393	CYS	0	0.076	0.051	16.205	0.046	0.046	0.000	0.000	0.000	0.000
50	A	394	THR	0	0.039	0.025	12.078	-0.158	-0.158	0.000	0.000	0.000	0.000
51	A	395	SER	0	0.008	0.000	14.774	-0.116	-0.116	0.000	0.000	0.000	0.000
52	A	397	LEU	0	-0.006	0.007	12.336	0.500	0.500	0.000	0.000	0.000	0.000
53	A	398	THR	0	-0.013	-0.017	15.366	-0.343	-0.343	0.000	0.000	0.000	0.000
54	A	399	ALA	0	0.034	0.011	16.497	0.371	0.371	0.000	0.000	0.000	0.000
55	A	400	TRP	0	-0.042	-0.018	16.369	1.343	1.343	0.000	0.000	0.000	0.000
56	A	401	GLN	0	-0.020	-0.040	13.594	0.366	0.366	0.000	0.000	0.000	0.000
57	A	402	GLU	-1	-0.957	-0.963	17.036	-15.588	-15.588	0.000	0.000	0.000	0.000
58	A	403	SER	0	-0.107	-0.046	19.985	0.988	0.988	0.000	0.000	0.000	0.000
59	A	404	ASP	-1	-0.909	-0.961	20.401	-14.332	-14.332	0.000	0.000	0.000	0.000
60	A	405	GLY	0	0.024	0.021	16.519	-0.293	-0.293	0.000	0.000	0.000	0.000
61	A	406	GLN	0	-0.018	0.006	15.721	-0.633	-0.633	0.000	0.000	0.000	0.000
62	A	407	GLY	0	0.015	0.011	13.749	0.388	0.388	0.000	0.000	0.000	0.000
63	A	408	CYS	0	-0.062	-0.013	14.798	0.501	0.501	0.000	0.000	0.000	0.000
64	A	409	PRO	0	0.052	0.018	15.976	0.956	0.956	0.000	0.000	0.000	0.000
65	A	410	PHE	0	-0.009	-0.023	18.949	0.660	0.660	0.000	0.000	0.000	0.000
66	A	411	CYS	0	-0.071	-0.034	18.272	0.259	0.259	0.000	0.000	0.000	0.000
67	A	412	ARG	1	0.878	0.955	19.697	14.058	14.058	0.000	0.000	0.000	0.000
68	A	413	CYS	0	-0.012	0.002	16.050	0.415	0.415	0.000	0.000	0.000	0.000
69	A	414	GLU	-1	-0.853	-0.926	12.448	-23.192	-23.192	0.000	0.000	0.000	0.000
70	A	415	ILE	0	-0.053	-0.021	9.551	0.294	0.294	0.000	0.000	0.000	0.000
71	A	416	LYS	1	0.909	0.945	8.617	21.470	21.470	0.000	0.000	0.000	0.000
72	A	417	GLY	0	-0.019	-0.005	6.225	-5.450	-5.450	0.000	0.000	0.000	0.000
73	A	418	THR	0	-0.011	-0.019	5.404	3.531	3.531	0.000	0.000	0.000	0.000
75	A	420	PRO	0	0.019	0.016	6.897	3.889	3.889	0.000	0.000	0.000	0.000
76	A	421	ILE	0	-0.030	0.032	10.052	0.493	0.493	0.000	0.000	0.000	0.000
77	A	422	ILE	0	0.047	0.018	12.158	1.121	1.121	0.000	0.000	0.000	0.000
78	A	423	VAL	0	-0.064	-0.041	15.924	0.041	0.041	0.000	0.000	0.000	0.000
79	A	424	ASP	-1	-0.841	-0.919	18.637	-14.599	-14.599	0.000	0.000	0.000	0.000
80	A	425	PRO	0	-0.038	-0.032	21.748	0.001	0.001	0.000	0.000	0.000	0.000
81	A	426	PHE	-1	-0.858	-0.904	25.067	-11.330	-11.330	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:345:GLY)