FMO DATABASE

FMODB ID: VQGK1

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	OptHSide
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	-799286.007479
FMO2-HF: Nuclear repulsion	758254.036437
FMO2-HF: Total energy	-41031.971041
FMO2-MP2: Total energy	-41152.167916

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.
-5.892	-1.545	3.048	-2.877	-4.515	-0.013

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 : -0.016

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	0.047	0.015	3.780	-0.742	0.579	-0.018	-0.676	-0.627	0.003
4	A	279	GLY	0	-0.003	0.000	6.561	0.384	0.384	0.000	0.000	0.000	0.000
5	A	280	SER	0	0.002	-0.009	6.848	0.317	0.317	0.000	0.000	0.000	0.000
6	A	281	PRO	0	0.024	0.015	7.943	-0.119	-0.119	0.000	0.000	0.000	0.000
7	A	282	TRP	0	-0.006	-0.003	5.911	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	283	TYR	0	-0.065	-0.065	2.498	-2.137	-1.051	2.923	-1.330	-2.678	-0.010
9	A	284	TYR	0	-0.013	0.002	6.445	-0.144	-0.144	0.000	0.000	0.000	0.000
10	A	285	GLY	0	0.045	0.003	5.254	-0.143	-0.143	0.000	0.000	0.000	0.000
11	A	286	LYS	1	0.847	0.923	4.110	0.707	0.829	-0.001	-0.011	-0.109	0.000
12	A	287	VAL	0	-0.016	0.004	6.298	0.173	0.173	0.000	0.000	0.000	0.000
13	A	288	THR	0	0.023	-0.010	9.689	0.056	0.056	0.000	0.000	0.000	0.000
14	A	289	ARG	1	0.952	0.965	11.983	-0.096	-0.096	0.000	0.000	0.000	0.000
15	A	290	HIS	0	0.006	-0.003	14.358	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	291	GLN	0	0.043	0.028	12.665	-0.030	-0.030	0.000	0.000	0.000	0.000
17	A	292	ALA	0	0.001	0.002	12.277	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	293	GLU	-1	-0.790	-0.895	14.107	0.008	0.008	0.000	0.000	0.000	0.000
19	A	294	MET	0	-0.007	0.012	17.767	0.007	0.007	0.000	0.000	0.000	0.000
20	A	295	ALA	0	-0.004	0.002	15.222	0.000	0.000	0.000	0.000	0.000	0.000
21	A	296	LEU	0	-0.006	-0.011	15.496	0.003	0.003	0.000	0.000	0.000	0.000
22	A	297	ASN	0	-0.023	-0.012	18.417	0.014	0.014	0.000	0.000	0.000	0.000
23	A	298	GLU	-1	-0.941	-0.948	20.467	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	299	ARG	1	0.880	0.929	15.502	0.207	0.207	0.000	0.000	0.000	0.000
25	A	300	GLY	0	-0.034	-0.002	20.229	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	301	HIS	0	-0.034	-0.017	20.900	0.015	0.015	0.000	0.000	0.000	0.000
27	A	302	GLU	-1	-0.826	-0.917	22.141	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	303	GLY	0	0.015	0.005	21.688	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	304	ASP	-1	-0.781	-0.862	18.315	-0.080	-0.080	0.000	0.000	0.000	0.000
30	A	305	PHE	0	-0.027	-0.030	13.272	0.017	0.017	0.000	0.000	0.000	0.000
31	A	306	LEU	0	-0.014	-0.004	10.197	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	307	ILE	0	-0.005	0.001	7.508	0.072	0.072	0.000	0.000	0.000	0.000
33	A	308	ARG	1	0.823	0.917	6.148	-0.219	-0.219	0.000	0.000	0.000	0.000
34	A	309	ASP	-1	-0.675	-0.811	2.962	-3.503	-2.148	0.127	-0.668	-0.813	-0.007
35	A	310	SER	0	-0.105	-0.044	5.922	-0.249	-0.249	0.000	0.000	0.000	0.000
36	A	311	GLU	-1	-0.743	-0.874	8.917	0.066	0.066	0.000	0.000	0.000	0.000
37	A	312	SER	0	-0.039	-0.023	11.056	0.017	0.017	0.000	0.000	0.000	0.000
38	A	313	SER	0	-0.045	-0.040	11.802	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	314	PRO	0	0.028	-0.003	8.254	0.126	0.126	0.000	0.000	0.000	0.000
40	A	315	ASN	0	0.012	0.028	6.688	0.286	0.286	0.000	0.000	0.000	0.000
41	A	316	ASP	-1	-0.806	-0.859	8.200	0.938	0.938	0.000	0.000	0.000	0.000
42	A	317	PHE	0	0.041	0.001	3.320	-0.711	-0.248	0.017	-0.192	-0.288	0.001
43	A	318	SER	0	-0.050	-0.041	8.458	-0.154	-0.154	0.000	0.000	0.000	0.000
44	A	319	VAL	0	-0.001	0.016	10.171	-0.048	-0.048	0.000	0.000	0.000	0.000
45	A	320	SER	0	-0.012	-0.021	12.716	0.002	0.002	0.000	0.000	0.000	0.000
46	A	321	LEU	0	0.004	0.001	14.548	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	322	LYS	1	0.912	0.963	17.775	0.046	0.046	0.000	0.000	0.000	0.000
48	A	323	ALA	0	-0.005	-0.012	20.442	0.005	0.005	0.000	0.000	0.000	0.000
49	A	324	GLN	0	0.014	0.003	23.696	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	325	GLY	0	-0.015	0.005	27.155	0.006	0.006	0.000	0.000	0.000	0.000
51	A	326	LYS	1	0.858	0.920	21.349	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	327	ASN	0	-0.029	-0.016	19.423	0.004	0.004	0.000	0.000	0.000	0.000
53	A	328	LYS	1	0.885	0.962	19.818	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	329	HIS	0	-0.020	-0.028	15.504	0.005	0.005	0.000	0.000	0.000	0.000
55	A	330	PHE	0	-0.002	0.004	15.359	0.004	0.004	0.000	0.000	0.000	0.000
56	A	331	LYS	1	0.833	0.912	12.592	-0.470	-0.470	0.000	0.000	0.000	0.000
57	A	332	VAL	0	0.018	0.006	11.100	-0.048	-0.048	0.000	0.000	0.000	0.000
58	A	333	GLN	0	-0.022	-0.015	11.375	0.114	0.114	0.000	0.000	0.000	0.000
59	A	334	LEU	0	0.029	0.032	8.367	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	335	LYS	1	0.896	0.941	11.838	-0.366	-0.366	0.000	0.000	0.000	0.000
61	A	336	GLU	-1	-0.893	-0.945	14.821	0.288	0.288	0.000	0.000	0.000	0.000
62	A	337	THR	0	-0.044	-0.032	13.261	-0.082	-0.082	0.000	0.000	0.000	0.000
63	A	338	VAL	0	0.008	0.016	14.289	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	339	TYR	0	0.032	0.018	8.902	0.165	0.165	0.000	0.000	0.000	0.000
65	A	340	CYS	0	-0.060	-0.031	14.107	-0.112	-0.112	0.000	0.000	0.000	0.000
66	A	341	ILE	0	0.073	0.029	15.634	0.040	0.040	0.000	0.000	0.000	0.000
67	A	342	GLY	0	0.006	0.013	17.555	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	343	GLN	0	-0.004	-0.017	21.059	0.022	0.022	0.000	0.000	0.000	0.000
69	A	344	ARG	1	0.840	0.936	20.802	-0.136	-0.136	0.000	0.000	0.000	0.000
70	A	345	LYS	1	0.947	0.962	18.677	-0.196	-0.196	0.000	0.000	0.000	0.000
71	A	346	PHE	0	0.023	0.017	16.200	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	347	SER	0	0.058	0.028	16.327	0.054	0.054	0.000	0.000	0.000	0.000
73	A	348	THR	0	0.015	-0.020	13.417	0.042	0.042	0.000	0.000	0.000	0.000
74	A	349	MET	0	0.010	0.013	8.349	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	350	GLU	-1	-0.821	-0.912	12.092	0.055	0.055	0.000	0.000	0.000	0.000
76	A	351	GLU	-1	-0.891	-0.940	14.390	0.071	0.071	0.000	0.000	0.000	0.000
77	A	352	LEU	0	-0.088	-0.029	13.486	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	353	VAL	0	-0.011	-0.028	13.333	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	354	GLU	-1	-0.797	-0.876	16.285	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	355	HIS	0	0.011	0.018	19.482	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	356	TYR	0	-0.041	-0.035	18.165	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	357	LYS	1	0.880	0.949	18.503	0.003	0.003	0.000	0.000	0.000	0.000
83	A	358	LYS	1	0.885	0.941	21.988	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	359	ALA	0	-0.024	-0.003	24.072	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	360	PRO	0	-0.004	-0.010	23.633	0.003	0.003	0.000	0.000	0.000	0.000
86	A	361	ILE	0	-0.018	-0.006	17.350	0.011	0.011	0.000	0.000	0.000	0.000
87	A	362	PHE	0	-0.008	-0.020	21.965	0.010	0.010	0.000	0.000	0.000	0.000
88	A	363	THR	0	-0.003	-0.012	24.378	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	364	SER	0	-0.068	-0.038	28.194	0.006	0.006	0.000	0.000	0.000	0.000
90	A	365	GLU	-1	-0.912	-0.962	30.483	0.053	0.053	0.000	0.000	0.000	0.000
91	A	366	GLN	0	-0.042	-0.021	33.509	0.002	0.002	0.000	0.000	0.000	0.000
92	A	367	GLY	0	0.004	0.010	33.481	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	368	GLU	-1	-0.841	-0.896	30.420	0.026	0.026	0.000	0.000	0.000	0.000
94	A	369	LYS	1	0.895	0.944	28.119	-0.030	-0.030	0.000	0.000	0.000	0.000
95	A	370	LEU	0	-0.001	0.005	23.639	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	371	TYR	0	-0.006	-0.013	22.811	0.011	0.011	0.000	0.000	0.000	0.000
97	A	372	LEU	0	-0.032	-0.005	16.179	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	373	VAL	0	0.019	0.004	19.987	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	374	LYS	1	0.835	0.890	18.290	0.092	0.092	0.000	0.000	0.000	0.000
100	A	375	HIS	0	0.039	0.026	11.210	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	376	LEU	0	-0.055	-0.016	14.275	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	377	SER	0	0.059	0.028	13.777	-0.021	-0.021	0.000	0.000	0.000	0.000

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