FMO DATABASE

FMODB ID: N6M1Q

Calculation Name: 1YDL-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YDL

Chain ID: A

ChEMBL ID:

UniProt ID: Q6ZYL4

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-391693.068894
FMO2-HF: Nuclear repulsion	362934.900749
FMO2-HF: Total energy	-28758.168144
FMO2-MP2: Total energy	-28840.149816

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:SER)

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

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.
-30.93	-29.047	0.452	-0.76	-1.572	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.910

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	3	GLY	0	0.050	0.045	3.805	7.555	8.740	-0.020	-0.452	-0.712	-0.003
4	A	4	THR	0	-0.057	-0.039	2.702	-5.999	-5.296	0.473	-0.307	-0.868	-0.003
5	A	5	ARG	1	0.975	0.991	5.270	23.386	23.381	-0.001	-0.001	0.008	0.000
6	A	6	LYS	1	0.962	0.984	8.888	26.522	26.522	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.044	0.012	11.470	0.500	0.500	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.014	0.002	14.486	-0.244	-0.244	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.029	-0.008	15.051	-0.235	-0.235	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.019	-0.011	16.887	0.525	0.525	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.872	-0.928	20.377	-13.232	-13.232	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.117	-0.048	22.496	0.396	0.396	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.780	-0.889	26.011	-10.061	-10.061	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.076	0.027	27.882	-0.097	-0.097	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.070	-0.019	28.929	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	MET	0	0.028	0.000	27.410	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.827	0.901	22.499	12.803	12.803	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.007	-0.011	26.136	-0.509	-0.509	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.039	-0.019	28.567	0.147	0.147	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.007	-0.005	24.032	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.016	0.011	22.940	-0.161	-0.161	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.023	0.022	26.145	0.089	0.089	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.002	0.004	28.233	0.181	0.181	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.778	-0.881	23.211	-12.801	-12.801	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.947	-0.971	26.268	-10.796	-10.796	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.068	-0.068	27.917	0.137	0.137	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.035	-0.025	27.659	-0.120	-0.120	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.022	0.028	29.606	0.211	0.211	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.020	-0.018	26.847	0.261	0.261	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.042	0.027	29.444	-0.113	-0.113	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.840	0.911	25.236	10.885	10.885	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.837	0.936	22.358	11.740	11.740	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.027	-0.025	21.358	-0.220	-0.220	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.021	0.019	19.049	-0.662	-0.662	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.130	-0.055	13.078	-0.391	-0.391	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.047	-0.038	12.153	-1.689	-1.689	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.787	-0.877	16.014	-13.686	-13.686	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.114	-0.057	14.418	-1.147	-1.147	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.844	-0.915	17.809	-13.815	-13.815	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.926	-0.975	21.116	-11.217	-11.217	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.024	0.005	22.958	0.380	0.380	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.043	-0.016	18.691	-0.153	-0.153	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.034	0.017	18.659	-0.168	-0.168	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.022	-0.008	11.543	-0.479	-0.479	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.035	0.016	16.365	0.237	0.237	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.029	-0.019	16.719	-1.030	-1.030	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.003	0.003	16.857	0.390	0.390	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.878	-0.950	18.734	-14.869	-14.869	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.024	0.013	21.639	0.602	0.602	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.011	-0.002	23.507	0.501	0.501	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.012	0.006	25.514	0.582	0.582	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.017	0.011	24.369	0.350	0.350	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.003	0.004	27.275	0.352	0.352	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.034	-0.019	29.528	0.312	0.312	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.956	-0.979	29.514	-10.101	-10.101	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.855	0.924	31.392	9.219	9.219	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.010	-0.021	33.158	0.283	0.283	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.006	0.006	35.222	0.273	0.273	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.912	-0.952	34.644	-8.695	-8.695	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.089	-0.036	36.537	0.174	0.174	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.043	-0.003	39.829	0.169	0.169	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.906	-0.950	42.361	-6.561	-6.561	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.009	0.021	44.011	-0.046	-0.046	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.021	-0.024	45.611	0.183	0.183	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.003	-0.006	48.645	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.004	0.004	46.922	0.021	0.021	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.005	-0.018	44.487	-0.132	-0.132	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.051	0.014	43.670	-0.121	-0.121	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.039	-0.018	44.881	-0.075	-0.075	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.095	-0.044	41.628	0.138	0.138	0.000	0.000	0.000	0.000
71	A	71	LYS	0	-0.012	0.023	39.296	-0.688	-0.688	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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