FMO DATABASE

FMODB ID: YVGN2

Calculation Name: 2CI9-A-Xray372

Preferred Name: Nck adaptor protein 1

Target Type: SINGLE PROTEIN

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 2CI9

Chain ID: A

ChEMBL ID: CHEMBL4846

UniProt ID: P16333

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-797869.517626
FMO2-HF: Nuclear repulsion	756837.99203
FMO2-HF: Total energy	-41031.525596
FMO2-MP2: Total energy	-41151.664341

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:276:GLY)

Summations of interaction energy for fragment #1(A:276: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.
-3.101	0.736	4.879	-3.471	-5.246	-0.005

Interaction energy analysis for fragmet #1(A:276:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.013

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	278	LEU	0	0.053	0.013	3.780	-0.521	1.218	-0.021	-0.933	-0.786	0.005
4	A	279	GLY	0	-0.014	-0.004	6.561	0.191	0.191	0.000	0.000	0.000	0.000
5	A	280	SER	0	0.000	-0.010	6.842	0.088	0.088	0.000	0.000	0.000	0.000
6	A	281	PRO	0	0.027	0.021	8.232	-0.181	-0.181	0.000	0.000	0.000	0.000
7	A	282	TRP	0	-0.003	-0.001	5.073	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	283	TYR	0	-0.077	-0.063	2.289	-2.109	-1.957	4.657	-1.683	-3.126	-0.007
9	A	284	TYR	0	-0.031	-0.003	6.664	0.085	0.085	0.000	0.000	0.000	0.000
10	A	285	GLY	0	0.046	0.000	5.145	-0.046	-0.046	0.000	0.000	0.000	0.000
11	A	286	LYS	1	0.953	0.993	4.620	-3.524	-3.433	-0.001	-0.009	-0.081	0.000
12	A	287	VAL	0	-0.015	0.000	6.028	0.064	0.064	0.000	0.000	0.000	0.000
13	A	288	THR	0	0.038	0.006	9.464	0.011	0.011	0.000	0.000	0.000	0.000
14	A	289	ARG	1	0.935	0.952	11.879	-0.243	-0.243	0.000	0.000	0.000	0.000
15	A	290	HIS	0	0.023	0.006	14.168	-0.048	-0.048	0.000	0.000	0.000	0.000
16	A	291	GLN	0	0.047	0.025	12.536	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	292	ALA	0	-0.004	-0.003	12.187	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	293	GLU	-1	-0.834	-0.916	13.968	0.012	0.012	0.000	0.000	0.000	0.000
19	A	294	MET	0	-0.011	0.009	17.619	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	295	ALA	0	0.001	0.004	15.154	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	296	LEU	0	-0.012	-0.013	15.515	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	297	ASN	0	-0.028	-0.018	18.364	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	298	GLU	-1	-0.945	-0.946	20.407	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	299	ARG	1	0.871	0.928	15.313	0.150	0.150	0.000	0.000	0.000	0.000
25	A	300	GLY	0	-0.031	-0.003	20.229	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	301	HIS	0	-0.030	-0.018	20.905	0.023	0.023	0.000	0.000	0.000	0.000
27	A	302	GLU	-1	-0.861	-0.945	22.198	-0.070	-0.070	0.000	0.000	0.000	0.000
28	A	303	GLY	0	0.018	0.005	21.791	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	304	ASP	-1	-0.804	-0.890	18.364	-0.189	-0.189	0.000	0.000	0.000	0.000
30	A	305	PHE	0	-0.035	-0.032	13.371	0.027	0.027	0.000	0.000	0.000	0.000
31	A	306	LEU	0	-0.010	-0.004	10.122	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	307	ILE	0	-0.005	-0.002	7.577	0.103	0.103	0.000	0.000	0.000	0.000
33	A	308	ARG	1	0.882	0.951	6.108	-0.444	-0.444	0.000	0.000	0.000	0.000
34	A	309	ASP	-1	-0.756	-0.869	3.224	2.965	4.412	0.214	-0.735	-0.926	-0.004
35	A	310	SER	0	-0.104	-0.043	5.819	-0.225	-0.225	0.000	0.000	0.000	0.000
36	A	311	GLU	-1	-0.839	-0.937	9.388	0.633	0.633	0.000	0.000	0.000	0.000
37	A	312	SER	0	-0.039	-0.028	11.458	0.033	0.033	0.000	0.000	0.000	0.000
38	A	313	SER	0	-0.078	-0.056	12.158	-0.044	-0.044	0.000	0.000	0.000	0.000
39	A	314	PRO	0	0.024	-0.005	8.860	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	315	ASN	0	0.013	0.032	6.999	0.664	0.664	0.000	0.000	0.000	0.000
41	A	316	ASP	-1	-0.828	-0.884	7.536	0.044	0.044	0.000	0.000	0.000	0.000
42	A	317	PHE	0	0.047	0.010	3.133	-0.022	0.386	0.030	-0.111	-0.327	0.001
43	A	318	SER	0	-0.097	-0.064	8.256	0.066	0.066	0.000	0.000	0.000	0.000
44	A	319	VAL	0	0.011	0.023	10.205	-0.081	-0.081	0.000	0.000	0.000	0.000
45	A	320	SER	0	-0.016	-0.027	12.788	0.067	0.067	0.000	0.000	0.000	0.000
46	A	321	LEU	0	0.009	0.002	14.551	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	322	LYS	1	0.906	0.957	17.812	0.072	0.072	0.000	0.000	0.000	0.000
48	A	323	ALA	0	0.010	-0.002	20.454	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	324	GLN	0	0.030	0.017	23.710	0.009	0.009	0.000	0.000	0.000	0.000
50	A	325	GLY	0	-0.020	0.002	27.140	0.003	0.003	0.000	0.000	0.000	0.000
51	A	326	LYS	1	0.905	0.943	23.188	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	327	ASN	0	0.027	0.020	19.346	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	328	LYS	1	0.903	0.965	19.840	0.027	0.027	0.000	0.000	0.000	0.000
54	A	329	HIS	0	-0.028	-0.022	15.430	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	330	PHE	0	-0.007	0.003	15.405	0.022	0.022	0.000	0.000	0.000	0.000
56	A	331	LYS	1	0.932	0.970	13.294	-0.255	-0.255	0.000	0.000	0.000	0.000
57	A	332	VAL	0	0.020	0.004	10.778	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	333	GLN	0	-0.046	-0.023	10.799	0.055	0.055	0.000	0.000	0.000	0.000
59	A	334	LEU	0	0.017	0.024	7.500	-0.088	-0.088	0.000	0.000	0.000	0.000
60	A	335	LYS	1	0.928	0.960	10.872	0.046	0.046	0.000	0.000	0.000	0.000
61	A	336	GLU	-1	-0.902	-0.952	13.890	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	337	THR	0	-0.037	-0.026	12.281	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	338	VAL	0	0.003	0.014	13.294	-0.056	-0.056	0.000	0.000	0.000	0.000
64	A	339	TYR	0	0.036	0.016	7.575	0.071	0.071	0.000	0.000	0.000	0.000
65	A	340	CYS	0	-0.072	-0.036	13.282	0.018	0.018	0.000	0.000	0.000	0.000
66	A	341	ILE	0	0.062	0.028	15.010	0.019	0.019	0.000	0.000	0.000	0.000
67	A	342	GLY	0	0.014	0.016	17.092	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	343	GLN	0	-0.010	-0.019	20.517	0.005	0.005	0.000	0.000	0.000	0.000
69	A	344	ARG	1	0.912	0.974	20.289	0.108	0.108	0.000	0.000	0.000	0.000
70	A	345	LYS	1	0.950	0.964	17.918	0.058	0.058	0.000	0.000	0.000	0.000
71	A	346	PHE	0	0.019	0.015	15.622	0.010	0.010	0.000	0.000	0.000	0.000
72	A	347	SER	0	0.041	0.018	15.499	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	348	THR	0	0.079	0.047	12.705	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	349	MET	0	0.007	0.005	8.368	0.133	0.133	0.000	0.000	0.000	0.000
75	A	350	GLU	-1	-0.866	-0.956	11.768	-0.710	-0.710	0.000	0.000	0.000	0.000
76	A	351	GLU	-1	-0.898	-0.948	14.307	-0.222	-0.222	0.000	0.000	0.000	0.000
77	A	352	LEU	0	-0.079	-0.023	13.198	0.048	0.048	0.000	0.000	0.000	0.000
78	A	353	VAL	0	-0.021	-0.037	13.548	0.040	0.040	0.000	0.000	0.000	0.000
79	A	354	GLU	-1	-0.819	-0.906	16.414	-0.251	-0.251	0.000	0.000	0.000	0.000
80	A	355	HIS	0	-0.038	-0.011	19.417	0.041	0.041	0.000	0.000	0.000	0.000
81	A	356	TYR	0	-0.052	-0.040	17.942	0.030	0.030	0.000	0.000	0.000	0.000
82	A	357	LYS	1	0.890	0.974	18.572	0.297	0.297	0.000	0.000	0.000	0.000
83	A	358	LYS	1	0.893	0.946	22.219	0.128	0.128	0.000	0.000	0.000	0.000
84	A	359	ALA	0	-0.016	0.001	24.178	0.015	0.015	0.000	0.000	0.000	0.000
85	A	360	PRO	0	-0.005	-0.011	23.780	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	361	ILE	0	-0.012	-0.003	17.499	0.000	0.000	0.000	0.000	0.000	0.000
87	A	362	PHE	0	-0.029	-0.030	22.115	0.016	0.016	0.000	0.000	0.000	0.000
88	A	363	THR	0	0.011	-0.003	24.484	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	364	SER	0	-0.018	0.010	28.299	0.005	0.005	0.000	0.000	0.000	0.000
90	A	365	GLU	-1	-0.917	-0.972	30.550	0.000	0.000	0.000	0.000	0.000	0.000
91	A	366	GLN	0	-0.068	-0.032	33.209	0.000	0.000	0.000	0.000	0.000	0.000
92	A	367	GLY	0	0.015	0.017	33.593	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	368	GLU	-1	-0.883	-0.941	30.397	-0.031	-0.031	0.000	0.000	0.000	0.000
94	A	369	LYS	1	0.874	0.938	28.233	0.057	0.057	0.000	0.000	0.000	0.000
95	A	370	LEU	0	-0.002	0.009	23.742	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	371	TYR	0	0.004	-0.008	22.979	0.003	0.003	0.000	0.000	0.000	0.000
97	A	372	LEU	0	-0.035	-0.009	16.358	0.004	0.004	0.000	0.000	0.000	0.000
98	A	373	VAL	0	0.029	0.013	20.156	0.000	0.000	0.000	0.000	0.000	0.000
99	A	374	LYS	1	0.865	0.919	18.464	0.174	0.174	0.000	0.000	0.000	0.000
100	A	375	HIS	0	0.047	0.033	11.870	0.054	0.054	0.000	0.000	0.000	0.000
101	A	376	LEU	0	-0.044	-0.011	14.315	0.019	0.019	0.000	0.000	0.000	0.000
102	A	377	SER	0	0.054	0.025	13.857	-0.022	-0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:276:GLY)