FMO DATABASE

FMODB ID: 19NKZ

Calculation Name: 1YMH-E-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YMH

Chain ID: E

ChEMBL ID:

UniProt ID: Q51918

Base Structure: X-ray

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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-367390.810166
FMO2-HF: Nuclear repulsion	342013.216771
FMO2-HF: Total energy	-25377.593395
FMO2-MP2: Total energy	-25452.511215

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:818:LYS)

Summations of interaction energy for fragment #1(A:818:LYS)

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.
-135.27	-132.652	-0.005	-0.981	-1.632	-0.006

Interaction energy analysis for fragmet #1(A:818:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.649 / q_NPA : 1.784

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	820	GLU	-1	-0.968	-0.967	3.771	-48.292	-46.163	-0.018	-0.893	-1.218	-0.006
23	A	840	LYS	1	0.966	0.986	3.235	91.856	92.345	0.013	-0.088	-0.414	0.000
4	A	821	VAL	0	0.055	0.034	7.077	7.252	7.252	0.000	0.000	0.000	0.000
5	A	822	THR	0	-0.037	-0.020	5.562	-7.600	-7.600	0.000	0.000	0.000	0.000
6	A	823	ILE	0	-0.018	0.011	7.945	4.753	4.753	0.000	0.000	0.000	0.000
7	A	824	LYS	1	0.920	0.968	10.755	41.822	41.822	0.000	0.000	0.000	0.000
8	A	825	VAL	0	0.042	0.011	12.587	2.410	2.410	0.000	0.000	0.000	0.000
9	A	826	ASN	0	-0.008	-0.006	15.170	-2.122	-2.122	0.000	0.000	0.000	0.000
10	A	827	LEU	0	-0.006	-0.005	16.025	0.958	0.958	0.000	0.000	0.000	0.000
11	A	828	ILE	0	0.012	-0.005	19.781	0.496	0.496	0.000	0.000	0.000	0.000
12	A	829	PHE	0	0.001	-0.005	20.691	0.335	0.335	0.000	0.000	0.000	0.000
13	A	830	ALA	0	0.055	0.029	25.753	0.521	0.521	0.000	0.000	0.000	0.000
14	A	831	ASP	-1	-0.896	-0.945	28.329	-21.243	-21.243	0.000	0.000	0.000	0.000
15	A	832	GLY	0	-0.001	0.001	28.296	0.228	0.228	0.000	0.000	0.000	0.000
16	A	833	LYS	1	0.822	0.910	24.657	21.568	21.568	0.000	0.000	0.000	0.000
17	A	834	ILE	0	0.019	0.011	20.170	-0.192	-0.192	0.000	0.000	0.000	0.000
18	A	835	GLN	0	-0.054	-0.016	17.621	-1.296	-1.296	0.000	0.000	0.000	0.000
19	A	836	THR	0	-0.002	0.000	14.534	1.130	1.130	0.000	0.000	0.000	0.000
20	A	837	ALA	0	-0.035	-0.009	12.107	-1.404	-1.404	0.000	0.000	0.000	0.000
21	A	838	GLU	-1	-0.908	-0.962	7.919	-55.779	-55.779	0.000	0.000	0.000	0.000
22	A	839	PHE	0	-0.042	-0.020	7.782	-3.785	-3.785	0.000	0.000	0.000	0.000
24	A	841	GLY	0	0.000	0.005	5.431	2.538	2.538	0.000	0.000	0.000	0.000
25	A	842	THR	0	0.050	0.009	6.396	0.970	0.970	0.000	0.000	0.000	0.000
26	A	843	PHE	0	0.051	0.038	9.959	-0.292	-0.292	0.000	0.000	0.000	0.000
27	A	844	GLU	-1	-0.862	-0.930	12.492	-37.928	-37.928	0.000	0.000	0.000	0.000
28	A	845	GLU	-1	-0.834	-0.901	10.368	-40.834	-40.834	0.000	0.000	0.000	0.000
29	A	846	ALA	0	0.005	0.013	8.758	0.456	0.456	0.000	0.000	0.000	0.000
30	A	847	THR	0	0.001	-0.025	10.209	2.072	2.072	0.000	0.000	0.000	0.000
31	A	848	ALA	0	-0.023	-0.011	13.937	2.031	2.031	0.000	0.000	0.000	0.000
32	A	849	GLU	-1	-0.981	-1.005	8.552	-58.453	-58.453	0.000	0.000	0.000	0.000
33	A	850	ALA	0	0.009	0.011	12.605	1.338	1.338	0.000	0.000	0.000	0.000
34	A	851	TYR	0	0.014	-0.003	13.917	1.423	1.423	0.000	0.000	0.000	0.000
35	A	852	ARG	1	0.853	0.912	12.735	40.826	40.826	0.000	0.000	0.000	0.000
36	A	853	TYR	0	-0.053	-0.022	13.981	0.724	0.724	0.000	0.000	0.000	0.000
37	A	854	ALA	0	0.030	0.017	16.120	1.291	1.291	0.000	0.000	0.000	0.000
38	A	855	ASP	-1	-0.796	-0.883	19.078	-26.145	-26.145	0.000	0.000	0.000	0.000
39	A	856	LEU	0	-0.117	-0.060	17.063	1.338	1.338	0.000	0.000	0.000	0.000
40	A	857	LEU	0	-0.022	-0.009	18.209	1.100	1.100	0.000	0.000	0.000	0.000
41	A	858	ALA	0	0.055	0.033	21.496	1.169	1.169	0.000	0.000	0.000	0.000
42	A	859	LYS	1	0.864	0.942	22.942	26.936	26.936	0.000	0.000	0.000	0.000
43	A	860	VAL	0	-0.051	-0.017	25.267	0.825	0.825	0.000	0.000	0.000	0.000
44	A	861	ASN	0	-0.074	-0.054	23.678	1.107	1.107	0.000	0.000	0.000	0.000
45	A	862	GLY	0	0.098	0.067	26.707	0.288	0.288	0.000	0.000	0.000	0.000
46	A	863	GLU	-1	-0.927	-0.977	26.562	-22.526	-22.526	0.000	0.000	0.000	0.000
47	A	864	TYR	0	-0.066	-0.063	21.693	-0.144	-0.144	0.000	0.000	0.000	0.000
48	A	865	THR	0	-0.045	-0.013	26.115	0.382	0.382	0.000	0.000	0.000	0.000
49	A	866	TRP	0	0.022	-0.005	21.891	-0.939	-0.939	0.000	0.000	0.000	0.000
50	A	867	ASP	-1	-0.933	-0.948	22.984	-23.619	-23.619	0.000	0.000	0.000	0.000
51	A	868	LEU	0	0.005	-0.002	19.282	-1.263	-1.263	0.000	0.000	0.000	0.000
52	A	869	GLU	-1	-0.925	-0.970	19.892	-24.624	-24.624	0.000	0.000	0.000	0.000
53	A	870	ASP	-1	-0.930	-0.973	16.769	-33.940	-33.940	0.000	0.000	0.000	0.000
54	A	871	GLY	0	0.001	-0.001	17.878	-1.420	-1.420	0.000	0.000	0.000	0.000
55	A	872	GLY	0	-0.019	-0.002	18.248	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	873	ASN	0	-0.038	-0.033	11.942	-0.205	-0.205	0.000	0.000	0.000	0.000
57	A	874	HIS	0	-0.036	-0.009	13.782	-4.145	-4.145	0.000	0.000	0.000	0.000
58	A	875	MET	0	0.025	0.024	16.290	1.627	1.627	0.000	0.000	0.000	0.000
59	A	876	ASN	0	-0.035	-0.013	18.000	-1.497	-1.497	0.000	0.000	0.000	0.000
60	A	877	ILE	0	0.017	0.001	17.807	0.614	0.614	0.000	0.000	0.000	0.000
61	A	878	LYS	1	0.906	0.956	21.598	21.912	21.912	0.000	0.000	0.000	0.000
62	A	879	PHE	0	-0.012	-0.007	20.674	0.373	0.373	0.000	0.000	0.000	0.000
63	A	880	ALA	0	-0.033	-0.017	26.269	0.468	0.468	0.000	0.000	0.000	0.000
64	A	881	GLY	0	-0.057	-0.029	29.029	0.592	0.592	0.000	0.000	0.000	0.000
65	A	882	LYS	0	0.025	0.020	30.361	-1.281	-1.281	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:818:LYS)