FMO DATABASE

FMODB ID: YR672

Calculation Name: 1HDP-A-Other547

Preferred Name: POU domain, class 2, transcription factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HDP

Chain ID: A

ChEMBL ID: CHEMBL3509582

UniProt ID: P09086

Base Structure: SolutionNMR

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-380241.496103
FMO2-HF: Nuclear repulsion	353378.444837
FMO2-HF: Total energy	-26863.051266
FMO2-MP2: Total energy	-26941.004406

3D Structure Molmil

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:1:ARG)

Summations of interaction energy for fragment #1(A:1:ARG)

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.
17.436	13.496	29.456	-11.019	-14.497	-0.08

Interaction energy analysis for fragmet #1(A:1:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.895 / q_NPA : 0.946

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	A	3	LYS	0	0.023	0.041	1.708	2.773	3.430	14.841	-6.483	-9.015	-0.043
4	A	4	LYS	0	0.111	0.062	1.895	-0.955	-5.552	14.615	-4.536	-5.482	-0.037
5	A	5	ARG	1	0.911	0.933	5.761	36.486	36.486	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.070	-0.010	7.574	0.180	0.180	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.027	-0.006	9.516	-1.265	-1.265	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.050	0.043	10.387	-0.602	-0.602	0.000	0.000	0.000	0.000
9	A	9	GLU	0	-0.012	0.024	12.978	1.017	1.017	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.059	0.008	14.975	0.752	0.752	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.038	0.028	18.363	-0.270	-0.270	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.112	0.068	18.413	0.323	0.323	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.955	0.969	16.891	16.079	16.079	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.041	-0.013	19.829	0.343	0.343	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.041	0.025	22.851	0.510	0.510	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.005	-0.004	20.269	0.420	0.420	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.924	-0.945	22.102	-12.818	-12.818	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.977	0.981	23.516	10.444	10.444	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.006	-0.012	26.157	0.411	0.411	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.007	-0.018	22.886	0.092	0.092	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.010	-0.001	25.407	0.142	0.142	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.033	-0.001	27.561	0.323	0.323	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.006	-0.019	29.244	0.309	0.309	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.010	0.011	25.080	-0.427	-0.427	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.893	0.948	26.520	9.563	9.563	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.042	0.038	25.181	0.370	0.370	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.053	0.019	27.400	-0.232	-0.232	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.019	-0.032	28.506	-0.370	-0.370	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.899	-0.952	29.275	-9.241	-9.241	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.917	-0.955	29.396	-10.099	-10.099	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.038	-0.016	24.376	-0.332	-0.332	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.025	-0.012	26.712	-0.340	-0.340	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.053	0.042	28.418	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.025	-0.030	25.509	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.076	-0.045	25.002	-0.308	-0.308	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.939	-0.967	25.976	-9.795	-9.795	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.097	-0.033	28.042	0.303	0.303	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.045	-0.043	24.921	0.193	0.193	0.000	0.000	0.000	0.000
39	A	39	HIS	-1	-0.895	-0.917	21.043	-13.296	-13.296	0.000	0.000	0.000	0.000
40	A	40	MET	0	-0.090	-0.060	20.915	-0.930	-0.930	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.881	-0.932	19.726	-14.733	-14.733	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.955	0.957	20.556	12.098	12.098	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.883	-0.928	14.595	-20.460	-20.460	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.024	0.011	15.365	-0.222	-0.222	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.002	-0.008	16.899	-0.225	-0.225	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.887	0.933	19.242	15.683	15.683	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.001	-0.003	13.433	-0.134	-0.134	0.000	0.000	0.000	0.000
48	A	48	TRP	0	-0.039	-0.006	15.218	-0.653	-0.653	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.010	-0.012	16.981	0.112	0.112	0.000	0.000	0.000	0.000
50	A	50	CYS	-1	-0.791	-0.871	17.126	-15.565	-15.565	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.009	-0.011	11.127	0.670	0.670	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.792	0.901	15.531	13.990	13.990	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.925	0.943	17.667	13.197	13.197	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.036	-0.009	13.344	0.732	0.732	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.907	0.951	13.920	17.485	17.485	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.856	-0.933	17.541	-11.989	-11.989	0.000	0.000	0.000	0.000
57	A	57	LYS	0	-0.128	-0.021	20.227	0.636	0.636	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.847	0.840	16.929	13.757	13.757	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.051	0.024	20.955	0.264	0.264	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.115	-0.068	19.717	0.549	0.549	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.032	-0.007	21.199	-0.262	-0.262	0.000	0.000	0.000	0.000
62	A	62	CYS	-1	-0.835	-0.818	19.845	-12.193	-12.193	0.000	0.000	0.000	0.000
63	A	63	SER	-1	-0.893	-0.980	18.601	-15.015	-15.015	0.000	0.000	0.000	0.000

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