FMO DATABASE

FMODB ID: MVYMZ

Calculation Name: 4HRN-C-Xray372

Preferred Name: Receptor protein-tyrosine kinase erbB-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4HRN

Chain ID: C

ChEMBL ID: CHEMBL1824

UniProt ID: P04626

Base Structure: X-ray

Registration Date: 2023-09-19

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-406783.861542
FMO2-HF: Nuclear repulsion	376351.474797
FMO2-HF: Total energy	-30432.386745
FMO2-MP2: Total energy	-30511.856508

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(C:9:CYS)

Summations of interaction energy for fragment #1(C:9:CYS)

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.
-30.875	-19.062	15.815	-11.062	-16.568	0.058

Interaction energy analysis for fragmet #1(C:9:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : 0.012

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

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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	C	11	GLN	0	-0.037	-0.027	2.640	-7.299	-4.410	6.197	-3.890	-5.196	0.025
4	C	12	PHE	0	0.006	0.001	4.037	-2.664	-2.713	0.195	0.637	-0.783	-0.002
5	C	13	LEU	0	0.032	0.020	2.587	-3.085	2.456	3.334	-3.177	-5.699	-0.006
6	C	14	ARG	1	0.824	0.897	1.923	-16.980	-17.903	6.051	-2.849	-2.279	0.037
7	C	15	GLY	0	0.017	0.018	3.471	-3.750	-3.344	0.087	-0.073	-0.420	0.001
8	C	16	GLN	0	-0.035	-0.029	3.822	1.468	2.735	-0.016	-0.496	-0.755	-0.003
11	C	20	GLU	-1	-0.868	-0.950	3.786	0.517	3.199	-0.033	-1.214	-1.436	0.006
12	C	21	GLU	-1	-0.917	-0.966	6.942	1.666	1.666	0.000	0.000	0.000	0.000
13	C	22	CYS	0	-0.116	-0.052	6.372	-0.815	-0.815	0.000	0.000	0.000	0.000
14	C	23	ARG	1	0.918	0.945	9.328	-1.284	-1.284	0.000	0.000	0.000	0.000
15	C	24	VAL	0	-0.005	-0.004	12.181	-0.151	-0.151	0.000	0.000	0.000	0.000
16	C	25	LEU	0	0.029	0.003	14.980	-0.134	-0.134	0.000	0.000	0.000	0.000
17	C	26	GLN	0	-0.016	0.010	13.918	-0.128	-0.128	0.000	0.000	0.000	0.000
18	C	27	GLY	0	0.008	0.004	14.195	0.133	0.133	0.000	0.000	0.000	0.000
19	C	28	LEU	0	-0.035	0.000	14.614	0.062	0.062	0.000	0.000	0.000	0.000
20	C	29	PRO	0	0.017	-0.008	12.691	-0.122	-0.122	0.000	0.000	0.000	0.000
21	C	30	ARG	1	0.897	0.926	13.229	-0.407	-0.407	0.000	0.000	0.000	0.000
22	C	31	GLU	-1	-0.744	-0.831	9.329	2.656	2.656	0.000	0.000	0.000	0.000
23	C	32	TYR	0	0.036	0.015	13.198	-0.078	-0.078	0.000	0.000	0.000	0.000
24	C	33	VAL	0	0.001	-0.016	10.143	0.280	0.280	0.000	0.000	0.000	0.000
25	C	34	ASN	0	-0.008	-0.013	11.444	-0.395	-0.395	0.000	0.000	0.000	0.000
26	C	35	ALA	0	0.065	0.043	10.688	0.333	0.333	0.000	0.000	0.000	0.000
27	C	36	ARG	1	0.844	0.920	6.224	-3.311	-3.311	0.000	0.000	0.000	0.000
28	C	37	HIS	0	-0.001	0.001	6.557	1.685	1.685	0.000	0.000	0.000	0.000
29	C	39	LEU	0	0.000	-0.003	7.964	0.062	0.062	0.000	0.000	0.000	0.000
30	C	40	PRO	0	0.000	0.006	10.734	-0.115	-0.115	0.000	0.000	0.000	0.000
31	C	41	CYS	0	-0.054	-0.026	13.207	-0.083	-0.083	0.000	0.000	0.000	0.000
32	C	42	HIS	0	0.095	0.048	16.767	-0.054	-0.054	0.000	0.000	0.000	0.000
33	C	43	PRO	0	-0.019	-0.031	19.061	-0.003	-0.003	0.000	0.000	0.000	0.000
34	C	44	GLU	-1	-0.801	-0.891	20.705	0.170	0.170	0.000	0.000	0.000	0.000
35	C	45	CYS	0	-0.119	-0.029	20.805	0.056	0.056	0.000	0.000	0.000	0.000
36	C	46	GLN	0	0.025	0.002	22.371	-0.009	-0.009	0.000	0.000	0.000	0.000
37	C	47	PRO	0	-0.033	-0.018	20.083	0.050	0.050	0.000	0.000	0.000	0.000
38	C	48	GLN	0	-0.071	-0.027	21.353	-0.068	-0.068	0.000	0.000	0.000	0.000
39	C	49	ASP	-1	-0.859	-0.930	21.694	0.371	0.371	0.000	0.000	0.000	0.000
40	C	50	GLY	0	-0.050	-0.017	23.279	0.024	0.024	0.000	0.000	0.000	0.000
41	C	51	SER	0	-0.046	-0.044	23.009	-0.018	-0.018	0.000	0.000	0.000	0.000
42	C	52	VAL	0	0.054	0.037	18.311	0.018	0.018	0.000	0.000	0.000	0.000
43	C	53	THR	0	0.025	0.014	18.409	-0.094	-0.094	0.000	0.000	0.000	0.000
44	C	55	PHE	0	-0.028	-0.014	19.173	0.064	0.064	0.000	0.000	0.000	0.000
45	C	56	GLY	0	-0.004	-0.003	17.647	0.038	0.038	0.000	0.000	0.000	0.000
46	C	57	PRO	0	-0.031	-0.015	16.158	0.007	0.007	0.000	0.000	0.000	0.000
47	C	58	GLU	-1	-0.895	-0.939	17.934	0.392	0.392	0.000	0.000	0.000	0.000
48	C	59	ALA	0	-0.007	-0.012	21.688	0.018	0.018	0.000	0.000	0.000	0.000
49	C	60	ASP	-1	-0.909	-0.955	24.393	0.364	0.364	0.000	0.000	0.000	0.000
50	C	61	GLN	0	-0.005	-0.002	21.053	0.051	0.051	0.000	0.000	0.000	0.000
51	C	63	VAL	0	-0.006	0.009	23.023	-0.023	-0.023	0.000	0.000	0.000	0.000
52	C	64	ALA	0	0.002	-0.016	25.175	-0.040	-0.040	0.000	0.000	0.000	0.000
53	C	65	CYS	0	-0.098	-0.015	25.613	0.005	0.005	0.000	0.000	0.000	0.000
54	C	66	ALA	0	0.006	0.006	24.984	-0.011	-0.011	0.000	0.000	0.000	0.000
55	C	67	HIS	0	-0.105	-0.073	26.434	-0.038	-0.038	0.000	0.000	0.000	0.000
56	C	68	TYR	0	-0.024	-0.001	30.352	-0.010	-0.010	0.000	0.000	0.000	0.000
57	C	69	LYS	1	0.923	0.960	29.920	-0.268	-0.268	0.000	0.000	0.000	0.000
58	C	70	ASP	-1	-0.923	-0.965	32.229	0.138	0.138	0.000	0.000	0.000	0.000
59	C	71	PRO	0	-0.082	-0.004	33.065	0.013	0.013	0.000	0.000	0.000	0.000
60	C	72	PRO	0	0.008	-0.009	30.430	-0.014	-0.014	0.000	0.000	0.000	0.000
61	C	73	PHE	0	0.061	0.002	27.489	0.024	0.024	0.000	0.000	0.000	0.000
62	C	75	VAL	0	0.025	0.002	27.559	0.005	0.005	0.000	0.000	0.000	0.000
63	C	76	ALA	0	0.086	0.046	28.354	-0.008	-0.008	0.000	0.000	0.000	0.000
64	C	77	ARG	1	0.879	0.925	29.877	-0.081	-0.081	0.000	0.000	0.000	0.000
65	C	78	CYS	0	0.035	0.030	33.586	0.010	0.010	0.000	0.000	0.000	0.000
66	C	79	PRO	0	-0.004	0.008	35.902	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:9:CYS)