FMO DATABASE

FMODB ID: QL55Y

Calculation Name: 2YPB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YPB

Chain ID: A

ChEMBL ID:

UniProt ID: P17542

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-346104.557378
FMO2-HF: Nuclear repulsion	318837.769463
FMO2-HF: Total energy	-27266.787916
FMO2-MP2: Total energy	-27347.918773

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:181:GLY)

Summations of interaction energy for fragment #1(A:181:GLY)

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.
175.263	177.385	0.008	-0.918	-1.211	-0.004

Interaction energy analysis for fragmet #1(A:181:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.924 / q_NPA : 0.952

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	183	HIS	0	0.055	0.026	3.317	6.225	7.800	0.006	-0.714	-0.867	-0.003
4	A	184	THR	0	0.041	0.022	3.181	9.284	9.831	0.002	-0.204	-0.344	-0.001
5	A	185	LYS	1	0.957	0.980	5.489	33.662	33.662	0.000	0.000	0.000	0.000
6	A	186	VAL	0	0.011	0.001	7.677	4.224	4.224	0.000	0.000	0.000	0.000
7	A	187	VAL	0	0.075	0.042	8.149	3.477	3.477	0.000	0.000	0.000	0.000
8	A	188	ARG	1	0.988	0.995	10.095	30.545	30.545	0.000	0.000	0.000	0.000
9	A	189	ARG	1	0.985	1.018	12.127	23.622	23.622	0.000	0.000	0.000	0.000
10	A	190	ILE	0	0.041	0.025	12.126	1.741	1.741	0.000	0.000	0.000	0.000
11	A	191	PHE	0	0.026	0.028	14.308	1.569	1.569	0.000	0.000	0.000	0.000
12	A	192	THR	0	-0.036	-0.043	15.971	1.562	1.562	0.000	0.000	0.000	0.000
13	A	193	ASN	0	0.032	0.008	17.923	1.116	1.116	0.000	0.000	0.000	0.000
14	A	194	SER	0	-0.042	-0.040	18.352	1.171	1.171	0.000	0.000	0.000	0.000
15	A	195	ARG	1	0.972	0.994	19.283	16.411	16.411	0.000	0.000	0.000	0.000
16	A	196	GLU	-1	-0.774	-0.848	21.916	-11.461	-11.461	0.000	0.000	0.000	0.000
17	A	197	ARG	1	0.926	0.966	20.582	15.073	15.073	0.000	0.000	0.000	0.000
18	A	198	TRP	0	0.031	0.019	24.621	0.413	0.413	0.000	0.000	0.000	0.000
19	A	199	ARG	1	0.865	0.900	26.132	11.816	11.816	0.000	0.000	0.000	0.000
20	A	200	GLN	0	-0.029	-0.024	27.878	0.847	0.847	0.000	0.000	0.000	0.000
21	A	201	GLN	0	-0.021	-0.021	27.748	0.141	0.141	0.000	0.000	0.000	0.000
22	A	202	ASN	0	0.024	0.018	29.864	0.544	0.544	0.000	0.000	0.000	0.000
23	A	203	VAL	0	-0.007	0.012	32.412	0.353	0.353	0.000	0.000	0.000	0.000
24	A	204	ASN	0	-0.006	-0.020	32.573	0.546	0.546	0.000	0.000	0.000	0.000
25	A	205	GLY	0	0.030	0.023	34.926	0.255	0.255	0.000	0.000	0.000	0.000
26	A	206	ALA	0	0.068	0.032	36.667	0.259	0.259	0.000	0.000	0.000	0.000
27	A	207	PHE	0	-0.025	-0.028	37.719	0.229	0.229	0.000	0.000	0.000	0.000
28	A	208	ALA	0	-0.011	-0.004	39.492	0.243	0.243	0.000	0.000	0.000	0.000
29	A	209	GLU	-1	-0.962	-0.982	40.444	-7.807	-7.807	0.000	0.000	0.000	0.000
30	A	210	LEU	0	0.018	0.006	42.698	0.206	0.206	0.000	0.000	0.000	0.000
31	A	211	ARG	1	0.812	0.887	44.140	6.877	6.877	0.000	0.000	0.000	0.000
32	A	212	LYS	1	0.914	0.961	42.350	7.712	7.712	0.000	0.000	0.000	0.000
33	A	213	LEU	0	0.006	0.015	47.415	0.136	0.136	0.000	0.000	0.000	0.000
34	A	214	ILE	0	-0.037	-0.001	47.989	0.129	0.129	0.000	0.000	0.000	0.000
35	A	215	PRO	0	0.013	0.013	51.401	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	216	THR	0	-0.071	-0.056	51.403	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	217	HIS	0	0.045	0.046	54.653	0.043	0.043	0.000	0.000	0.000	0.000
38	A	218	PRO	0	0.026	0.000	53.667	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	219	PRO	0	0.071	0.034	53.768	-0.105	-0.105	0.000	0.000	0.000	0.000
40	A	220	ASP	-1	-0.878	-0.937	50.054	-6.384	-6.384	0.000	0.000	0.000	0.000
41	A	221	LYS	1	0.880	0.960	48.965	5.926	5.926	0.000	0.000	0.000	0.000
42	A	222	LYS	1	0.974	0.977	43.054	7.293	7.293	0.000	0.000	0.000	0.000
43	A	223	LEU	0	0.027	0.023	45.676	0.102	0.102	0.000	0.000	0.000	0.000
44	A	224	SER	0	0.010	0.003	43.569	-0.259	-0.259	0.000	0.000	0.000	0.000
45	A	225	LYS	1	0.903	0.939	35.882	8.960	8.960	0.000	0.000	0.000	0.000
46	A	226	ASN	0	0.029	0.012	42.107	0.159	0.159	0.000	0.000	0.000	0.000
47	A	227	GLU	-1	-0.832	-0.918	44.788	-6.725	-6.725	0.000	0.000	0.000	0.000
48	A	228	ILE	0	0.010	0.015	42.915	0.115	0.115	0.000	0.000	0.000	0.000
49	A	229	LEU	0	0.032	0.016	41.968	0.081	0.081	0.000	0.000	0.000	0.000
50	A	230	ARG	1	0.908	0.949	46.288	6.879	6.879	0.000	0.000	0.000	0.000
51	A	231	LEU	0	0.019	0.004	49.717	0.144	0.144	0.000	0.000	0.000	0.000
52	A	232	ALA	0	0.043	0.035	48.088	0.116	0.116	0.000	0.000	0.000	0.000
53	A	233	MET	0	-0.003	0.000	48.907	0.109	0.109	0.000	0.000	0.000	0.000
54	A	234	LYS	1	0.913	0.959	51.678	6.050	6.050	0.000	0.000	0.000	0.000
55	A	235	TYR	0	0.049	0.025	52.810	0.152	0.152	0.000	0.000	0.000	0.000
56	A	236	ILE	0	0.035	0.011	49.833	0.081	0.081	0.000	0.000	0.000	0.000
57	A	237	ASN	0	-0.037	-0.037	54.406	0.131	0.131	0.000	0.000	0.000	0.000
58	A	238	PHE	0	-0.039	-0.004	57.173	0.103	0.103	0.000	0.000	0.000	0.000
59	A	239	LEU	0	0.006	-0.007	55.212	0.083	0.083	0.000	0.000	0.000	0.000
60	A	240	ALA	0	0.036	0.016	57.707	0.068	0.068	0.000	0.000	0.000	0.000
61	A	241	LYS	1	0.908	0.947	59.632	5.133	5.133	0.000	0.000	0.000	0.000
62	A	242	LEU	0	-0.003	0.004	61.859	0.074	0.074	0.000	0.000	0.000	0.000
63	A	243	LEU	0	0.008	0.011	59.686	0.046	0.046	0.000	0.000	0.000	0.000
64	A	244	ASN	0	-0.054	-0.043	62.064	0.062	0.062	0.000	0.000	0.000	0.000
65	A	245	ASP	-1	-0.985	-0.980	65.779	-4.640	-4.640	0.000	0.000	0.000	0.000
66	A	246	GLN	0	-0.105	-0.054	65.728	0.019	0.019	0.000	0.000	0.000	0.000
67	A	247	GLU	-2	-1.934	-1.936	65.803	-9.590	-9.590	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:181:GLY)