FMO DATABASE

FMODB ID: VYZZ1

Calculation Name: 2YU6-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YU6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H6S0

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1343853.748246
FMO2-HF: Nuclear repulsion	1288019.410084
FMO2-HF: Total energy	-55834.338162
FMO2-MP2: Total energy	-55999.976698

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
32.027	32.909	-0.013	-0.351	-0.518	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.922

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	SER	0	0.026	0.007	3.845	2.839	3.721	-0.013	-0.351	-0.518	-0.001
4	A	4	GLY	0	0.041	0.030	6.967	0.908	0.908	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.035	-0.006	10.724	1.868	1.868	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.010	0.003	12.571	1.653	1.653	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.023	-0.002	15.111	-1.011	-1.011	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.051	-0.008	17.249	0.634	0.634	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.917	0.961	20.115	14.460	14.460	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.073	0.036	20.929	0.603	0.603	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.014	0.001	25.739	0.041	0.041	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.006	0.014	29.251	0.152	0.152	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.012	-0.008	32.404	0.095	0.095	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.889	0.940	35.491	8.200	8.200	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.001	-0.001	38.869	0.075	0.075	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.030	0.008	42.102	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.003	-0.010	45.673	0.152	0.152	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.063	0.031	44.235	-0.140	-0.140	0.000	0.000	0.000	0.000
19	A	19	ARG	1	1.007	1.005	45.444	6.134	6.134	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.014	-0.011	45.051	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.055	0.034	38.872	-0.087	-0.087	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.868	-0.931	42.449	-7.279	-7.279	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.046	-0.017	44.086	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.013	-0.019	39.103	-0.120	-0.120	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.067	-0.033	40.385	-0.134	-0.134	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.038	-0.007	41.712	0.017	0.017	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.862	0.929	43.883	6.720	6.720	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.045	0.046	39.481	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.028	-0.016	38.307	-0.247	-0.247	0.000	0.000	0.000	0.000
30	A	30	TRP	0	-0.003	0.006	36.727	0.142	0.142	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.051	0.018	39.082	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.038	-0.004	35.974	0.112	0.112	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.068	0.032	38.723	0.143	0.143	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.061	0.013	38.478	-0.257	-0.257	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.022	-0.008	37.957	-0.128	-0.128	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.035	-0.017	34.633	-0.335	-0.335	0.000	0.000	0.000	0.000
37	A	37	GLU	0	-0.041	-0.028	33.837	-0.250	-0.250	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.994	1.004	29.573	10.285	10.285	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.833	0.916	28.743	10.240	10.240	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.044	0.030	28.290	-0.406	-0.406	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.006	-0.008	29.072	-0.256	-0.256	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.894	0.947	26.022	11.799	11.799	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.009	0.005	24.473	-0.474	-0.474	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.007	-0.016	24.313	-0.526	-0.526	0.000	0.000	0.000	0.000
45	A	45	TRP	0	-0.033	-0.014	25.882	0.109	0.109	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.854	-0.920	21.515	-14.212	-14.212	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.066	-0.042	20.204	-1.229	-1.229	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.028	0.003	19.332	0.831	0.831	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.013	0.004	21.325	0.656	0.656	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.024	0.007	23.355	-0.365	-0.365	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.025	0.011	23.250	0.671	0.671	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.031	-0.015	27.310	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.042	0.019	29.401	0.173	0.173	0.000	0.000	0.000	0.000
54	A	54	PHE	0	0.022	0.008	32.119	0.191	0.191	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.005	-0.002	35.933	0.083	0.083	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.001	0.004	38.374	0.036	0.036	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.065	-0.031	42.034	-0.178	-0.178	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.029	0.020	43.695	0.025	0.025	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.002	-0.004	43.135	0.097	0.097	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.022	0.022	42.191	-0.156	-0.156	0.000	0.000	0.000	0.000
61	A	61	HIS	0	-0.043	-0.032	39.219	0.048	0.048	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.036	-0.022	33.395	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.022	-0.028	36.970	0.107	0.107	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.073	0.038	35.185	0.114	0.114	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.032	-0.020	28.434	-0.135	-0.135	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.046	0.016	32.159	0.061	0.061	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.918	0.967	26.611	11.002	11.002	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.053	-0.009	29.116	0.324	0.324	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.033	-0.016	29.471	-0.345	-0.345	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.016	-0.005	31.846	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.875	-0.939	32.331	-9.766	-9.766	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.081	-0.034	33.553	0.307	0.307	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.001	0.000	36.282	-0.040	-0.040	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.964	0.983	38.027	8.321	8.321	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.827	-0.893	38.309	-7.951	-7.951	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.940	0.952	40.946	7.346	7.346	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.014	0.009	44.280	0.020	0.020	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.004	0.011	46.393	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.880	-0.945	48.781	-6.377	-6.377	0.000	0.000	0.000	0.000
80	A	80	TRP	0	0.034	0.003	42.010	-0.206	-0.206	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.012	-0.005	48.069	0.136	0.136	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.029	-0.025	47.273	0.059	0.059	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.061	0.029	48.219	-0.109	-0.109	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.009	0.017	48.095	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.034	-0.018	42.911	-0.185	-0.185	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.034	0.015	42.927	0.131	0.131	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.035	-0.006	40.266	-0.129	-0.129	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.023	0.000	40.086	-0.055	-0.055	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.036	0.007	33.546	-0.077	-0.077	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.912	0.939	35.615	8.406	8.406	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.055	-0.032	33.539	-0.337	-0.337	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.856	-0.931	31.668	-9.418	-9.418	0.000	0.000	0.000	0.000
93	A	93	TRP	0	-0.042	-0.027	32.811	-0.208	-0.208	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.006	0.021	29.197	0.091	0.091	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.920	0.958	31.727	9.487	9.487	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.943	0.964	34.662	7.961	7.961	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.853	-0.903	37.123	-7.633	-7.633	0.000	0.000	0.000	0.000
98	A	98	SER	0	0.006	0.006	37.731	-0.231	-0.231	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.040	0.034	32.770	0.093	0.093	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.033	0.018	37.119	0.033	0.033	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.050	0.000	36.252	-0.228	-0.228	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.017	-0.009	35.906	-0.102	-0.102	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.026	0.015	33.252	-0.133	-0.133	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.033	0.001	31.467	-0.323	-0.323	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.046	-0.012	32.171	-0.327	-0.327	0.000	0.000	0.000	0.000
106	A	106	HIS	1	0.920	0.953	27.544	10.517	10.517	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.016	0.021	26.450	-0.295	-0.295	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.003	-0.010	27.715	0.427	0.427	0.000	0.000	0.000	0.000
109	A	109	ASN	0	0.051	0.013	26.142	-0.912	-0.912	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.024	-0.015	23.173	0.466	0.466	0.000	0.000	0.000	0.000
111	A	111	TRP	0	-0.045	-0.026	20.753	0.151	0.151	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.004	0.001	26.750	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.894	-0.942	30.581	-9.110	-9.110	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.023	-0.014	26.709	0.296	0.296	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.954	0.993	29.955	8.876	8.876	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.937	0.980	31.052	8.424	8.424	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.055	0.031	28.538	0.203	0.203	0.000	0.000	0.000	0.000
118	A	118	GLN	0	0.004	-0.002	31.256	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.105	-0.035	34.435	0.269	0.269	0.000	0.000	0.000	0.000
120	A	120	SER	0	0.000	-0.008	32.230	-0.262	-0.262	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.939	0.965	34.502	8.267	8.267	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.856	-0.945	35.260	-8.441	-8.441	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.023	0.008	33.498	-0.022	-0.022	0.000	0.000	0.000	0.000
124	A	124	GLN	0	-0.040	-0.006	31.509	-0.392	-0.392	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.893	-0.956	24.763	-12.521	-12.521	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.027	-0.001	25.851	0.147	0.147	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.771	-0.877	20.684	-14.825	-14.825	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.006	-0.019	18.418	0.281	0.281	0.000	0.000	0.000	0.000
129	A	129	GLN	0	-0.010	0.000	18.280	-0.170	-0.170	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.002	-0.018	19.736	0.326	0.326	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.028	-0.021	23.364	0.551	0.551	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.928	-0.971	18.248	-16.117	-16.117	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.039	-0.027	21.817	0.794	0.794	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.007	-0.003	24.356	0.524	0.524	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.037	-0.019	25.426	0.427	0.427	0.000	0.000	0.000	0.000
136	A	136	GLN	0	0.091	0.056	23.032	0.675	0.675	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.064	-0.027	27.255	0.293	0.293	0.000	0.000	0.000	0.000
138	A	138	TRP	0	-0.049	-0.043	30.514	0.178	0.178	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.955	-0.972	26.829	-11.351	-11.351	0.000	0.000	0.000	0.000
140	A	140	ARG	1	0.812	0.901	26.649	10.927	10.927	0.000	0.000	0.000	0.000
141	A	141	LEU	-1	-0.935	-0.943	32.859	-8.399	-8.399	0.000	0.000	0.000	0.000

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