FMO DATABASE

FMODB ID: 949Y2

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-406918.01812
FMO2-HF: Nuclear repulsion	376485.91939
FMO2-HF: Total energy	-30432.09873
FMO2-MP2: Total energy	-30511.598225

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.
-29.294	-21.133	18.926	-10.68	-16.407	0.059

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 : -0.048 / q_NPA : -0.018

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	-0.039	-0.027	2.535	-5.887	-6.596	10.438	-4.062	-5.667	0.023
4	C	12	PHE	0	-0.010	-0.005	3.979	-2.415	-2.683	0.198	0.902	-0.833	-0.002
5	C	13	LEU	0	0.027	0.018	2.694	-2.963	2.671	2.205	-2.876	-4.962	-0.003
6	C	14	ARG	1	0.860	0.930	1.924	-16.354	-17.220	6.044	-2.868	-2.310	0.037
7	C	15	GLY	0	0.008	0.015	3.471	-3.823	-3.413	0.087	-0.075	-0.422	0.001
8	C	16	GLN	0	-0.033	-0.030	3.822	0.959	2.207	-0.016	-0.487	-0.744	-0.003
11	C	20	GLU	-1	-0.863	-0.948	3.786	0.645	3.357	-0.030	-1.214	-1.469	0.006
12	C	21	GLU	-1	-0.952	-0.983	6.801	1.930	1.930	0.000	0.000	0.000	0.000
13	C	22	CYS	0	-0.107	-0.041	6.241	-0.752	-0.752	0.000	0.000	0.000	0.000
14	C	23	ARG	1	0.920	0.957	9.328	-0.918	-0.918	0.000	0.000	0.000	0.000
15	C	24	VAL	0	0.022	0.014	12.181	-0.165	-0.165	0.000	0.000	0.000	0.000
16	C	25	LEU	0	0.033	-0.001	14.980	-0.132	-0.132	0.000	0.000	0.000	0.000
17	C	26	GLN	0	0.018	0.026	13.541	-0.132	-0.132	0.000	0.000	0.000	0.000
18	C	27	GLY	0	0.003	0.003	14.195	0.127	0.127	0.000	0.000	0.000	0.000
19	C	28	LEU	0	-0.038	-0.002	14.630	0.072	0.072	0.000	0.000	0.000	0.000
20	C	29	PRO	0	0.025	-0.008	12.944	-0.123	-0.123	0.000	0.000	0.000	0.000
21	C	30	ARG	1	0.890	0.921	13.229	-0.397	-0.397	0.000	0.000	0.000	0.000
22	C	31	GLU	-1	-0.787	-0.891	9.109	2.665	2.665	0.000	0.000	0.000	0.000
23	C	32	TYR	0	0.023	0.012	13.198	-0.066	-0.066	0.000	0.000	0.000	0.000
24	C	33	VAL	0	0.002	-0.009	10.208	0.260	0.260	0.000	0.000	0.000	0.000
25	C	34	ASN	0	0.000	-0.011	11.442	-0.367	-0.367	0.000	0.000	0.000	0.000
26	C	35	ALA	0	0.051	0.036	10.575	0.298	0.298	0.000	0.000	0.000	0.000
27	C	36	ARG	1	0.859	0.925	6.020	-3.995	-3.995	0.000	0.000	0.000	0.000
28	C	37	HIS	0	0.008	0.008	6.613	1.477	1.477	0.000	0.000	0.000	0.000
29	C	39	LEU	0	-0.003	-0.007	7.964	-0.018	-0.018	0.000	0.000	0.000	0.000
30	C	40	PRO	0	0.004	0.011	10.734	-0.085	-0.085	0.000	0.000	0.000	0.000
31	C	41	CYS	0	-0.035	-0.016	13.207	-0.082	-0.082	0.000	0.000	0.000	0.000
32	C	42	HIS	0	0.094	0.058	16.767	-0.060	-0.060	0.000	0.000	0.000	0.000
33	C	43	PRO	0	-0.022	-0.034	19.212	0.004	0.004	0.000	0.000	0.000	0.000
34	C	44	GLU	-1	-0.819	-0.912	20.705	0.111	0.111	0.000	0.000	0.000	0.000
35	C	45	CYS	0	-0.111	-0.026	20.814	0.067	0.067	0.000	0.000	0.000	0.000
36	C	46	GLN	0	0.056	0.009	22.371	-0.013	-0.013	0.000	0.000	0.000	0.000
37	C	47	PRO	0	-0.053	-0.013	20.183	0.053	0.053	0.000	0.000	0.000	0.000
38	C	48	GLN	0	-0.077	-0.044	21.365	-0.062	-0.062	0.000	0.000	0.000	0.000
39	C	49	ASP	-1	-0.857	-0.921	21.694	0.344	0.344	0.000	0.000	0.000	0.000
40	C	50	GLY	0	-0.059	-0.025	23.279	0.029	0.029	0.000	0.000	0.000	0.000
41	C	51	SER	0	-0.062	-0.068	23.015	-0.011	-0.011	0.000	0.000	0.000	0.000
42	C	52	VAL	0	0.057	0.044	18.762	0.013	0.013	0.000	0.000	0.000	0.000
43	C	53	THR	0	0.045	0.034	18.445	-0.099	-0.099	0.000	0.000	0.000	0.000
44	C	55	PHE	0	-0.041	-0.021	19.173	0.078	0.078	0.000	0.000	0.000	0.000
45	C	56	GLY	0	-0.016	-0.010	17.652	0.044	0.044	0.000	0.000	0.000	0.000
46	C	57	PRO	0	-0.033	-0.013	16.238	0.007	0.007	0.000	0.000	0.000	0.000
47	C	58	GLU	-1	-0.893	-0.935	17.934	0.300	0.300	0.000	0.000	0.000	0.000
48	C	59	ALA	0	-0.006	-0.016	21.688	0.023	0.023	0.000	0.000	0.000	0.000
49	C	60	ASP	-1	-0.908	-0.950	24.393	0.331	0.331	0.000	0.000	0.000	0.000
50	C	61	GLN	0	0.004	0.001	21.286	0.028	0.028	0.000	0.000	0.000	0.000
51	C	63	VAL	0	-0.010	0.008	22.916	-0.017	-0.017	0.000	0.000	0.000	0.000
52	C	64	ALA	0	0.005	-0.020	25.175	-0.037	-0.037	0.000	0.000	0.000	0.000
53	C	65	CYS	0	-0.088	-0.008	25.613	0.006	0.006	0.000	0.000	0.000	0.000
54	C	66	ALA	0	0.003	0.011	25.010	-0.008	-0.008	0.000	0.000	0.000	0.000
55	C	67	HIS	0	-0.104	-0.062	26.807	-0.036	-0.036	0.000	0.000	0.000	0.000
56	C	68	TYR	0	-0.033	-0.007	30.352	-0.006	-0.006	0.000	0.000	0.000	0.000
57	C	69	LYS	1	0.940	0.966	30.447	-0.231	-0.231	0.000	0.000	0.000	0.000
58	C	70	ASP	-1	-0.945	-0.970	32.229	0.111	0.111	0.000	0.000	0.000	0.000
59	C	71	PRO	0	-0.091	-0.012	33.094	0.012	0.012	0.000	0.000	0.000	0.000
60	C	72	PRO	0	0.006	-0.008	30.407	-0.014	-0.014	0.000	0.000	0.000	0.000
61	C	73	PHE	0	0.070	0.009	27.303	0.024	0.024	0.000	0.000	0.000	0.000
62	C	75	VAL	0	0.024	0.002	27.559	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	76	ALA	0	0.087	0.040	28.404	-0.006	-0.006	0.000	0.000	0.000	0.000
64	C	77	ARG	1	0.891	0.928	29.877	-0.033	-0.033	0.000	0.000	0.000	0.000
65	C	78	CYS	0	0.016	0.020	33.586	0.011	0.011	0.000	0.000	0.000	0.000
66	C	79	PRO	0	0.018	0.018	36.056	-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)