FMO DATABASE

FMODB ID: 727JK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-407143.788013
FMO2-HF: Nuclear repulsion	376711.220962
FMO2-HF: Total energy	-30432.567051
FMO2-MP2: Total energy	-30512.053475

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.
-29.477	-19.277	19.747	-10.942	-19.006	0.042

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 : 0.015

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	-0.042	-0.021	2.597	-5.967	-4.547	6.609	-3.333	-4.696	0.017
4	C	12	PHE	0	0.008	-0.001	3.830	-3.297	-3.584	0.442	0.808	-0.964	-0.003
5	C	13	LEU	0	0.018	0.007	2.378	-3.498	2.610	6.425	-4.651	-7.882	-0.012
6	C	14	ARG	1	0.804	0.886	1.936	-18.281	-18.926	6.088	-2.834	-2.608	0.037
7	C	15	GLY	0	0.024	0.011	3.257	-3.158	-3.338	0.211	0.758	-0.789	0.000
8	C	16	GLN	0	-0.049	-0.035	3.850	1.962	3.057	-0.009	-0.367	-0.719	-0.002
11	C	20	GLU	-1	-0.854	-0.944	3.857	1.017	3.706	-0.019	-1.323	-1.348	0.005
12	C	21	GLU	-1	-0.917	-0.957	7.190	1.685	1.685	0.000	0.000	0.000	0.000
13	C	22	CYS	0	-0.079	-0.031	6.130	0.034	0.034	0.000	0.000	0.000	0.000
14	C	23	ARG	1	0.916	0.956	9.237	-1.679	-1.679	0.000	0.000	0.000	0.000
15	C	24	VAL	0	-0.013	-0.014	12.033	-0.249	-0.249	0.000	0.000	0.000	0.000
16	C	25	LEU	0	0.017	0.001	14.666	-0.165	-0.165	0.000	0.000	0.000	0.000
17	C	26	GLN	0	-0.002	0.004	13.657	-0.184	-0.184	0.000	0.000	0.000	0.000
18	C	27	GLY	0	0.014	0.006	14.281	0.155	0.155	0.000	0.000	0.000	0.000
19	C	28	LEU	0	-0.007	0.002	14.560	0.012	0.012	0.000	0.000	0.000	0.000
20	C	29	PRO	0	0.008	-0.008	12.382	-0.069	-0.069	0.000	0.000	0.000	0.000
21	C	30	ARG	1	0.835	0.897	13.158	-0.528	-0.528	0.000	0.000	0.000	0.000
22	C	31	GLU	-1	-0.747	-0.826	8.980	3.213	3.213	0.000	0.000	0.000	0.000
23	C	32	TYR	0	0.036	0.009	12.824	-0.101	-0.101	0.000	0.000	0.000	0.000
24	C	33	VAL	0	0.005	-0.013	10.048	0.380	0.380	0.000	0.000	0.000	0.000
25	C	34	ASN	0	0.009	0.001	11.347	-0.436	-0.436	0.000	0.000	0.000	0.000
26	C	35	ALA	0	0.039	0.026	10.003	0.316	0.316	0.000	0.000	0.000	0.000
27	C	36	ARG	1	0.850	0.928	6.030	-3.087	-3.087	0.000	0.000	0.000	0.000
28	C	37	HIS	0	0.005	0.004	6.717	1.488	1.488	0.000	0.000	0.000	0.000
29	C	39	LEU	0	-0.006	-0.007	7.785	-0.054	-0.054	0.000	0.000	0.000	0.000
30	C	40	PRO	0	-0.005	0.003	10.594	-0.076	-0.076	0.000	0.000	0.000	0.000
31	C	41	CYS	0	-0.055	-0.035	13.024	-0.112	-0.112	0.000	0.000	0.000	0.000
32	C	42	HIS	0	0.099	0.047	16.610	-0.054	-0.054	0.000	0.000	0.000	0.000
33	C	43	PRO	0	-0.028	-0.029	19.048	0.003	0.003	0.000	0.000	0.000	0.000
34	C	44	GLU	-1	-0.789	-0.888	20.840	0.193	0.193	0.000	0.000	0.000	0.000
35	C	45	CYS	0	-0.091	-0.019	20.338	0.067	0.067	0.000	0.000	0.000	0.000
36	C	46	GLN	0	-0.022	-0.007	21.711	0.014	0.014	0.000	0.000	0.000	0.000
37	C	47	PRO	0	-0.009	-0.010	20.175	0.048	0.048	0.000	0.000	0.000	0.000
38	C	48	GLN	0	-0.036	-0.011	20.795	-0.072	-0.072	0.000	0.000	0.000	0.000
39	C	49	ASP	-1	-0.862	-0.921	20.829	0.535	0.535	0.000	0.000	0.000	0.000
40	C	50	GLY	0	-0.031	-0.008	22.778	0.011	0.011	0.000	0.000	0.000	0.000
41	C	51	SER	0	-0.063	-0.046	22.465	-0.028	-0.028	0.000	0.000	0.000	0.000
42	C	52	VAL	0	0.056	0.032	17.748	0.039	0.039	0.000	0.000	0.000	0.000
43	C	53	THR	0	0.034	0.020	18.077	-0.105	-0.105	0.000	0.000	0.000	0.000
44	C	55	PHE	0	-0.032	-0.018	18.859	0.087	0.087	0.000	0.000	0.000	0.000
45	C	56	GLY	0	0.013	0.013	17.571	0.017	0.017	0.000	0.000	0.000	0.000
46	C	57	PRO	0	-0.022	-0.011	16.283	0.022	0.022	0.000	0.000	0.000	0.000
47	C	58	GLU	-1	-0.901	-0.946	17.921	0.340	0.340	0.000	0.000	0.000	0.000
48	C	59	ALA	0	0.018	0.006	21.697	0.025	0.025	0.000	0.000	0.000	0.000
49	C	60	ASP	-1	-0.891	-0.944	24.539	0.360	0.360	0.000	0.000	0.000	0.000
50	C	61	GLN	0	-0.041	-0.024	21.187	0.064	0.064	0.000	0.000	0.000	0.000
51	C	63	VAL	0	-0.027	-0.007	22.606	-0.038	-0.038	0.000	0.000	0.000	0.000
52	C	64	ALA	0	-0.009	-0.010	24.807	-0.045	-0.045	0.000	0.000	0.000	0.000
53	C	65	CYS	0	-0.066	-0.022	25.209	0.011	0.011	0.000	0.000	0.000	0.000
54	C	66	ALA	0	-0.012	0.000	24.632	-0.011	-0.011	0.000	0.000	0.000	0.000
55	C	67	HIS	0	-0.097	-0.055	26.352	-0.031	-0.031	0.000	0.000	0.000	0.000
56	C	68	TYR	0	-0.020	-0.008	30.134	-0.014	-0.014	0.000	0.000	0.000	0.000
57	C	69	LYS	1	0.922	0.954	29.027	-0.285	-0.285	0.000	0.000	0.000	0.000
58	C	70	ASP	-1	-0.911	-0.954	32.160	0.133	0.133	0.000	0.000	0.000	0.000
59	C	71	PRO	0	-0.060	-0.013	32.943	0.011	0.011	0.000	0.000	0.000	0.000
60	C	72	PRO	0	0.021	0.005	29.911	-0.013	-0.013	0.000	0.000	0.000	0.000
61	C	73	PHE	0	0.030	-0.005	27.444	0.023	0.023	0.000	0.000	0.000	0.000
62	C	75	VAL	0	0.000	-0.013	27.609	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	76	ALA	0	0.078	0.040	28.292	-0.006	-0.006	0.000	0.000	0.000	0.000
64	C	77	ARG	1	0.891	0.927	29.851	-0.089	-0.089	0.000	0.000	0.000	0.000
65	C	78	CYS	0	0.021	0.029	33.502	0.007	0.007	0.000	0.000	0.000	0.000
66	C	79	PRO	0	-0.021	0.005	35.478	-0.016	-0.016	0.000	0.000	0.000	0.000

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