FMO DATABASE

FMODB ID: 1NL6Z

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	OptAll
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	-800520.422654
FMO2-HF: Nuclear repulsion	759488.300965
FMO2-HF: Total energy	-41032.121689
FMO2-MP2: Total energy	-41152.335071

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.
-5.489	-1.29	4.488	-3.931	-4.757	-0.022

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 : -0.001 / q_NPA : -0.007

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	0.064	0.014	3.879	0.191	1.121	-0.007	-0.375	-0.549	0.001
4	A	279	GLY	0	-0.009	-0.005	6.426	0.235	0.235	0.000	0.000	0.000	0.000
5	A	280	SER	0	0.003	0.012	6.681	0.297	0.297	0.000	0.000	0.000	0.000
6	A	281	PRO	0	0.006	-0.007	7.837	-0.184	-0.184	0.000	0.000	0.000	0.000
7	A	282	TRP	0	0.002	0.010	5.947	-0.056	-0.056	0.000	0.000	0.000	0.000
8	A	283	TYR	0	-0.047	-0.055	2.634	-0.966	-0.206	4.160	-2.377	-2.542	-0.011
9	A	284	TYR	0	-0.020	-0.008	6.816	0.084	0.084	0.000	0.000	0.000	0.000
10	A	285	GLY	0	0.055	0.012	4.740	0.048	0.068	-0.001	-0.004	-0.015	0.000
11	A	286	LYS	1	0.832	0.914	3.739	-1.079	-0.899	0.000	-0.040	-0.140	0.000
12	A	287	VAL	0	-0.014	0.001	5.915	0.135	0.135	0.000	0.000	0.000	0.000
13	A	288	THR	0	0.028	-0.001	9.645	-0.042	-0.042	0.000	0.000	0.000	0.000
14	A	289	ARG	1	0.953	0.961	12.081	0.013	0.013	0.000	0.000	0.000	0.000
15	A	290	HIS	0	0.022	0.010	14.629	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	291	GLN	0	0.052	0.029	12.514	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	292	ALA	0	0.011	0.013	12.748	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	293	GLU	-1	-0.752	-0.859	14.423	-0.085	-0.085	0.000	0.000	0.000	0.000
19	A	294	MET	0	-0.005	0.012	17.992	0.003	0.003	0.000	0.000	0.000	0.000
20	A	295	ALA	0	-0.015	-0.008	15.237	0.000	0.000	0.000	0.000	0.000	0.000
21	A	296	LEU	0	-0.015	-0.019	15.913	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	297	ASN	0	-0.036	-0.023	18.700	0.003	0.003	0.000	0.000	0.000	0.000
23	A	298	GLU	-1	-0.917	-0.943	20.250	-0.082	-0.082	0.000	0.000	0.000	0.000
24	A	299	ARG	1	0.860	0.923	15.264	0.202	0.202	0.000	0.000	0.000	0.000
25	A	300	GLY	0	-0.025	0.003	20.351	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	301	HIS	0	-0.021	-0.017	20.974	0.020	0.020	0.000	0.000	0.000	0.000
27	A	302	GLU	-1	-0.823	-0.914	22.595	-0.109	-0.109	0.000	0.000	0.000	0.000
28	A	303	GLY	0	0.023	0.011	22.314	0.001	0.001	0.000	0.000	0.000	0.000
29	A	304	ASP	-1	-0.800	-0.877	18.738	-0.203	-0.203	0.000	0.000	0.000	0.000
30	A	305	PHE	0	-0.017	-0.017	13.901	0.015	0.015	0.000	0.000	0.000	0.000
31	A	306	LEU	0	-0.006	0.007	10.620	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	307	ILE	0	-0.008	-0.007	8.064	0.066	0.066	0.000	0.000	0.000	0.000
33	A	308	ARG	1	0.805	0.910	6.480	0.054	0.054	0.000	0.000	0.000	0.000
34	A	309	ASP	-1	-0.661	-0.810	2.730	-4.626	-2.702	0.319	-1.023	-1.220	-0.012
35	A	310	SER	0	-0.059	-0.026	5.797	0.156	0.156	0.000	0.000	0.000	0.000
36	A	311	GLU	-1	-0.769	-0.873	9.159	0.054	0.054	0.000	0.000	0.000	0.000
37	A	312	SER	0	-0.029	-0.013	10.906	0.047	0.047	0.000	0.000	0.000	0.000
38	A	313	SER	0	-0.058	-0.048	11.327	0.023	0.023	0.000	0.000	0.000	0.000
39	A	314	PRO	0	0.028	0.001	7.985	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	315	ASN	0	0.016	0.023	6.273	0.413	0.413	0.000	0.000	0.000	0.000
41	A	316	ASP	-1	-0.796	-0.853	7.236	0.038	0.038	0.000	0.000	0.000	0.000
42	A	317	PHE	0	0.022	-0.010	3.269	-0.414	-0.029	0.017	-0.112	-0.291	0.000
43	A	318	SER	0	-0.042	-0.037	8.017	0.182	0.182	0.000	0.000	0.000	0.000
44	A	319	VAL	0	0.014	0.027	10.440	-0.087	-0.087	0.000	0.000	0.000	0.000
45	A	320	SER	0	-0.022	-0.028	12.909	0.049	0.049	0.000	0.000	0.000	0.000
46	A	321	LEU	0	-0.002	-0.003	15.056	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	322	LYS	1	0.901	0.962	18.200	0.127	0.127	0.000	0.000	0.000	0.000
48	A	323	ALA	0	-0.024	-0.018	20.895	0.000	0.000	0.000	0.000	0.000	0.000
49	A	324	GLN	0	0.023	0.001	24.264	0.009	0.009	0.000	0.000	0.000	0.000
50	A	325	GLY	0	-0.020	0.006	27.755	0.002	0.002	0.000	0.000	0.000	0.000
51	A	326	LYS	1	0.792	0.866	21.348	0.067	0.067	0.000	0.000	0.000	0.000
52	A	327	ASN	0	-0.009	-0.012	19.982	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	328	LYS	1	0.867	0.955	20.269	0.091	0.091	0.000	0.000	0.000	0.000
54	A	329	HIS	0	-0.019	-0.028	15.715	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	330	PHE	0	0.008	0.005	15.404	0.027	0.027	0.000	0.000	0.000	0.000
56	A	331	LYS	1	0.821	0.908	12.094	-0.049	-0.049	0.000	0.000	0.000	0.000
57	A	332	VAL	0	-0.004	-0.002	10.745	0.014	0.014	0.000	0.000	0.000	0.000
58	A	333	GLN	0	-0.008	-0.008	10.636	0.011	0.011	0.000	0.000	0.000	0.000
59	A	334	LEU	0	0.011	0.014	7.294	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	335	LYS	1	0.900	0.953	11.019	0.024	0.024	0.000	0.000	0.000	0.000
61	A	336	GLU	-1	-0.885	-0.940	14.009	0.075	0.075	0.000	0.000	0.000	0.000
62	A	337	THR	0	-0.055	-0.030	12.202	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	338	VAL	0	0.014	0.014	13.038	-0.060	-0.060	0.000	0.000	0.000	0.000
64	A	339	TYR	0	0.054	0.034	8.114	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	340	CYS	0	-0.062	-0.041	13.249	0.010	0.010	0.000	0.000	0.000	0.000
66	A	341	ILE	0	0.046	0.017	14.998	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	342	GLY	0	0.006	0.006	17.141	0.004	0.004	0.000	0.000	0.000	0.000
68	A	343	GLN	0	0.032	0.005	20.485	0.009	0.009	0.000	0.000	0.000	0.000
69	A	344	ARG	1	0.843	0.941	20.368	0.102	0.102	0.000	0.000	0.000	0.000
70	A	345	LYS	1	0.916	0.942	17.860	0.033	0.033	0.000	0.000	0.000	0.000
71	A	346	PHE	0	0.015	0.015	15.682	0.003	0.003	0.000	0.000	0.000	0.000
72	A	347	SER	0	0.056	0.029	15.599	0.001	0.001	0.000	0.000	0.000	0.000
73	A	348	THR	0	-0.011	-0.036	12.674	0.016	0.016	0.000	0.000	0.000	0.000
74	A	349	MET	0	0.022	0.020	8.444	0.087	0.087	0.000	0.000	0.000	0.000
75	A	350	GLU	-1	-0.806	-0.896	12.060	-0.514	-0.514	0.000	0.000	0.000	0.000
76	A	351	GLU	-1	-0.894	-0.943	14.714	-0.157	-0.157	0.000	0.000	0.000	0.000
77	A	352	LEU	0	-0.077	-0.025	13.428	0.030	0.030	0.000	0.000	0.000	0.000
78	A	353	VAL	0	-0.004	-0.023	13.845	0.022	0.022	0.000	0.000	0.000	0.000
79	A	354	GLU	-1	-0.792	-0.885	16.678	-0.229	-0.229	0.000	0.000	0.000	0.000
80	A	355	HIS	0	0.024	0.033	19.747	0.040	0.040	0.000	0.000	0.000	0.000
81	A	356	TYR	0	-0.029	-0.023	18.260	0.021	0.021	0.000	0.000	0.000	0.000
82	A	357	LYS	1	0.855	0.932	18.957	0.250	0.250	0.000	0.000	0.000	0.000
83	A	358	LYS	1	0.861	0.926	22.532	0.123	0.123	0.000	0.000	0.000	0.000
84	A	359	ALA	0	-0.012	0.002	24.295	0.013	0.013	0.000	0.000	0.000	0.000
85	A	360	PRO	0	0.002	-0.008	23.864	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	361	ILE	0	-0.017	-0.008	17.355	0.001	0.001	0.000	0.000	0.000	0.000
87	A	362	PHE	0	0.001	-0.017	22.027	0.006	0.006	0.000	0.000	0.000	0.000
88	A	363	THR	0	-0.010	-0.015	24.439	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	364	SER	0	-0.081	-0.057	28.267	0.002	0.002	0.000	0.000	0.000	0.000
90	A	365	GLU	-1	-0.928	-0.968	30.915	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	366	GLN	0	-0.006	0.002	34.052	0.002	0.002	0.000	0.000	0.000	0.000
92	A	367	GLY	0	0.010	0.013	33.939	0.000	0.000	0.000	0.000	0.000	0.000
93	A	368	GLU	-1	-0.862	-0.898	30.923	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	369	LYS	1	0.906	0.942	28.476	0.063	0.063	0.000	0.000	0.000	0.000
95	A	370	LEU	0	-0.008	0.005	24.120	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	371	TYR	0	0.000	-0.006	23.064	0.005	0.005	0.000	0.000	0.000	0.000
97	A	372	LEU	0	-0.030	0.000	16.724	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	373	VAL	0	0.022	0.013	20.270	0.009	0.009	0.000	0.000	0.000	0.000
99	A	374	LYS	1	0.841	0.889	18.526	0.185	0.185	0.000	0.000	0.000	0.000
100	A	375	HIS	0	0.029	0.019	11.559	0.055	0.055	0.000	0.000	0.000	0.000
101	A	376	LEU	0	-0.047	-0.011	14.369	0.023	0.023	0.000	0.000	0.000	0.000
102	A	377	SER	0	0.045	0.022	13.642	-0.019	-0.019	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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