FMO DATABASE

FMODB ID: KQ633

Calculation Name: 1YAB-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YAB

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F6

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-478752.846892
FMO2-HF: Nuclear repulsion	445737.762027
FMO2-HF: Total energy	-33015.084865
FMO2-MP2: Total energy	-33112.194516

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:68:SER)

Summations of interaction energy for fragment #1(A:68: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.
-36.802	-30.76	3.082	-3.677	-5.446	0.013

Interaction energy analysis for fragmet #1(A:68:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.919

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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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	70	LYS	1	0.917	0.951	2.706	43.285	46.652	0.311	-1.642	-2.036	0.010
4	A	71	LEU	0	-0.008	0.001	2.148	-2.254	-0.296	2.770	-1.861	-2.866	0.003
5	A	72	GLU	-1	-0.905	-0.953	3.954	-49.765	-49.182	0.002	-0.165	-0.421	0.000
6	A	73	LEU	0	0.014	-0.006	5.364	5.228	5.362	-0.001	-0.009	-0.123	0.000
7	A	74	LEU	0	-0.021	0.008	7.412	3.356	3.356	0.000	0.000	0.000	0.000
8	A	75	LEU	0	-0.094	-0.049	5.846	2.570	2.570	0.000	0.000	0.000	0.000
9	A	76	ASP	-1	-0.889	-0.944	9.337	-26.716	-26.716	0.000	0.000	0.000	0.000
10	A	77	ILE	0	-0.048	-0.001	11.300	2.063	2.063	0.000	0.000	0.000	0.000
11	A	78	PRO	0	-0.014	-0.023	14.168	0.476	0.476	0.000	0.000	0.000	0.000
12	A	79	LEU	0	0.022	0.024	15.641	0.676	0.676	0.000	0.000	0.000	0.000
13	A	80	LYS	1	0.936	0.970	18.498	12.530	12.530	0.000	0.000	0.000	0.000
14	A	81	VAL	0	0.017	0.003	21.931	0.235	0.235	0.000	0.000	0.000	0.000
15	A	82	THR	0	-0.086	-0.048	23.955	0.387	0.387	0.000	0.000	0.000	0.000
16	A	83	VAL	0	0.056	0.032	27.614	-0.153	-0.153	0.000	0.000	0.000	0.000
17	A	84	GLU	-1	-0.807	-0.870	30.558	-9.409	-9.409	0.000	0.000	0.000	0.000
18	A	85	LEU	0	0.036	0.008	33.735	0.015	0.015	0.000	0.000	0.000	0.000
19	A	86	GLY	0	0.047	0.019	37.312	0.097	0.097	0.000	0.000	0.000	0.000
20	A	87	ARG	1	0.725	0.846	31.392	9.322	9.322	0.000	0.000	0.000	0.000
21	A	88	THR	0	0.126	0.056	38.746	0.220	0.220	0.000	0.000	0.000	0.000
22	A	89	ARG	1	0.873	0.936	38.984	7.611	7.611	0.000	0.000	0.000	0.000
23	A	90	MET	0	0.001	-0.001	42.999	0.154	0.154	0.000	0.000	0.000	0.000
24	A	91	THR	0	0.002	0.005	44.600	-0.090	-0.090	0.000	0.000	0.000	0.000
25	A	92	LEU	0	0.081	0.025	44.343	0.031	0.031	0.000	0.000	0.000	0.000
26	A	93	LYS	1	0.877	0.935	46.557	5.788	5.788	0.000	0.000	0.000	0.000
27	A	94	ARG	1	0.982	0.985	48.516	6.480	6.480	0.000	0.000	0.000	0.000
28	A	95	VAL	0	-0.030	-0.013	43.592	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	96	LEU	0	-0.011	-0.014	46.530	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	97	GLU	-1	-0.863	-0.924	48.949	-5.834	-5.834	0.000	0.000	0.000	0.000
31	A	98	MET	0	-0.066	-0.006	44.497	0.068	0.068	0.000	0.000	0.000	0.000
32	A	99	ILE	0	0.038	0.031	50.148	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	100	HIS	0	0.029	0.010	48.662	-0.133	-0.133	0.000	0.000	0.000	0.000
34	A	101	GLY	0	0.022	0.009	50.430	0.125	0.125	0.000	0.000	0.000	0.000
35	A	102	SER	0	-0.062	-0.043	49.460	0.109	0.109	0.000	0.000	0.000	0.000
36	A	103	ILE	0	-0.002	0.004	49.223	-0.131	-0.131	0.000	0.000	0.000	0.000
37	A	104	ILE	0	-0.047	-0.034	44.549	0.073	0.073	0.000	0.000	0.000	0.000
38	A	105	GLU	-1	-0.934	-0.954	46.387	-6.527	-6.527	0.000	0.000	0.000	0.000
39	A	106	LEU	0	-0.075	-0.043	40.115	-0.084	-0.084	0.000	0.000	0.000	0.000
40	A	107	ASP	-1	-0.856	-0.948	40.285	-7.776	-7.776	0.000	0.000	0.000	0.000
41	A	108	LYS	1	0.751	0.904	35.701	8.756	8.756	0.000	0.000	0.000	0.000
42	A	109	LEU	0	-0.001	-0.002	41.556	0.191	0.191	0.000	0.000	0.000	0.000
43	A	110	THR	0	-0.029	-0.040	42.639	-0.141	-0.141	0.000	0.000	0.000	0.000
44	A	111	GLY	0	-0.004	0.006	43.554	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	112	GLU	-1	-0.894	-0.938	38.878	-8.118	-8.118	0.000	0.000	0.000	0.000
46	A	113	PRO	0	0.038	0.031	34.944	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	114	VAL	0	0.019	0.007	33.437	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	115	ASP	-1	-0.814	-0.891	31.336	-9.594	-9.594	0.000	0.000	0.000	0.000
49	A	116	ILE	0	-0.014	-0.010	26.087	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	117	LEU	0	-0.016	-0.024	25.633	-0.265	-0.265	0.000	0.000	0.000	0.000
51	A	118	VAL	0	0.022	0.021	20.182	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	119	ASN	0	0.010	-0.004	18.590	0.392	0.392	0.000	0.000	0.000	0.000
53	A	120	GLY	0	-0.035	-0.014	22.683	0.150	0.150	0.000	0.000	0.000	0.000
54	A	121	LYS	1	0.907	0.975	21.866	13.527	13.527	0.000	0.000	0.000	0.000
55	A	122	LEU	0	-0.016	-0.007	24.511	-0.360	-0.360	0.000	0.000	0.000	0.000
56	A	123	ILE	0	0.021	0.008	21.398	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	124	ALA	0	-0.017	-0.016	24.915	-0.140	-0.140	0.000	0.000	0.000	0.000
58	A	125	ARG	1	0.893	0.959	27.530	9.534	9.534	0.000	0.000	0.000	0.000
59	A	126	GLY	0	0.051	0.020	31.035	-0.230	-0.230	0.000	0.000	0.000	0.000
60	A	127	GLU	-1	-0.869	-0.923	32.644	-8.264	-8.264	0.000	0.000	0.000	0.000
61	A	128	VAL	0	-0.016	-0.020	34.520	-0.289	-0.289	0.000	0.000	0.000	0.000
62	A	129	VAL	0	-0.068	-0.036	33.367	0.183	0.183	0.000	0.000	0.000	0.000
63	A	130	VAL	0	0.015	0.000	35.916	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	131	ILE	0	-0.062	-0.018	31.513	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	132	ASP	-1	-0.877	-0.950	34.809	-9.227	-9.227	0.000	0.000	0.000	0.000
66	A	133	GLU	-1	-0.922	-0.961	36.217	-7.842	-7.842	0.000	0.000	0.000	0.000
67	A	134	ASN	0	-0.082	-0.029	33.113	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	135	PHE	0	-0.017	-0.009	34.734	0.078	0.078	0.000	0.000	0.000	0.000
69	A	136	GLY	0	0.017	0.005	31.425	-0.347	-0.347	0.000	0.000	0.000	0.000
70	A	137	VAL	0	-0.038	-0.020	29.316	0.263	0.263	0.000	0.000	0.000	0.000
71	A	138	ARG	1	0.940	0.983	30.056	8.717	8.717	0.000	0.000	0.000	0.000
72	A	139	ILE	0	-0.017	-0.019	26.437	0.228	0.228	0.000	0.000	0.000	0.000
73	A	140	THR	0	-0.062	-0.041	29.943	0.118	0.118	0.000	0.000	0.000	0.000
74	A	141	GLU	-1	-0.864	-0.930	30.610	-9.363	-9.363	0.000	0.000	0.000	0.000
75	A	142	ILE	0	-0.060	-0.038	23.067	-0.262	-0.262	0.000	0.000	0.000	0.000
76	A	143	VAL	0	0.021	0.034	22.757	0.120	0.120	0.000	0.000	0.000	0.000
77	A	144	SER	0	-0.024	-0.040	22.497	-0.636	-0.636	0.000	0.000	0.000	0.000
78	A	145	PRO	0	-0.040	-0.049	17.423	-0.158	-0.158	0.000	0.000	0.000	0.000
79	A	146	LYS	1	0.917	0.974	17.168	15.269	15.269	0.000	0.000	0.000	0.000
80	A	147	GLU	-1	-0.631	-0.805	18.449	-14.009	-14.009	0.000	0.000	0.000	0.000
81	A	148	ARG	1	0.830	0.903	18.407	14.849	14.849	0.000	0.000	0.000	0.000
82	A	149	LEU	0	-0.013	-0.004	13.023	-0.409	-0.409	0.000	0.000	0.000	0.000
83	A	150	GLU	-1	-0.940	-0.967	16.434	-14.668	-14.668	0.000	0.000	0.000	0.000
84	A	151	LEU	0	-0.110	-0.056	19.082	0.825	0.825	0.000	0.000	0.000	0.000
85	A	152	LEU	-1	-0.977	-0.975	14.911	-17.272	-17.272	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:68:SER)