FMO DATABASE

FMODB ID: 9RQQ2

Calculation Name: 2YRP-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YRP

Chain ID: A

ChEMBL ID:

UniProt ID: Q14934

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-856764.366686
FMO2-HF: Nuclear repulsion	812638.215924
FMO2-HF: Total energy	-44126.150762
FMO2-MP2: Total energy	-44255.763207

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.
23.966	24.828	-0.013	-0.326	-0.523	-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 : 0.863 / 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	0.022	0.011	3.832	1.546	2.408	-0.013	-0.326	-0.523	-0.001
4	A	4	GLY	0	0.026	0.028	6.525	3.845	3.845	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.063	0.022	8.102	3.838	3.838	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.003	0.000	8.787	-1.786	-1.786	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.017	0.022	11.154	1.193	1.193	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.026	-0.026	12.464	0.991	0.991	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.016	0.020	15.924	-0.326	-0.326	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.019	-0.009	17.587	-0.136	-0.136	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.023	-0.021	19.973	0.159	0.159	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.936	-0.969	20.786	-14.360	-14.360	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.005	-0.010	23.930	0.392	0.392	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.052	-0.039	27.680	-0.257	-0.257	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.035	0.008	30.503	0.165	0.165	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.112	0.051	33.851	-0.130	-0.130	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.007	-0.011	35.148	-0.073	-0.073	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.072	-0.038	36.193	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.002	0.019	39.150	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.075	0.029	41.203	0.149	0.149	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.054	-0.041	43.411	-0.124	-0.124	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.925	0.951	45.131	6.340	6.340	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.041	0.032	41.598	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.002	-0.003	41.616	0.117	0.117	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.875	-0.928	40.167	-7.486	-7.486	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.880	-0.933	35.208	-8.966	-8.966	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.027	-0.010	32.475	0.014	0.014	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.003	-0.002	29.499	-0.235	-0.235	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.029	-0.017	27.042	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.040	0.015	24.535	-0.218	-0.218	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.020	-0.008	22.042	0.048	0.048	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.008	0.020	17.071	-0.658	-0.658	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.047	-0.024	13.575	-1.220	-1.220	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.012	0.009	16.829	0.097	0.097	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.005	-0.005	17.250	-0.550	-0.550	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.041	0.019	21.061	0.486	0.486	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.942	-0.980	23.444	-11.429	-11.429	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.045	-0.025	22.385	0.026	0.026	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.867	0.932	24.575	10.083	10.083	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.001	-0.004	27.453	-0.328	-0.328	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.026	0.025	29.634	0.309	0.309	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.041	0.002	32.029	-0.195	-0.195	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.031	-0.009	32.874	0.081	0.081	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.886	-0.952	36.322	-7.225	-7.225	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.872	0.918	37.547	7.875	7.875	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.061	0.041	40.886	0.141	0.141	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.016	-0.027	44.219	-0.090	-0.090	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.873	-0.931	45.107	-6.731	-6.731	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.025	-0.003	43.000	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.825	0.915	40.007	6.925	6.925	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.017	-0.021	34.778	0.139	0.139	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.004	-0.001	38.549	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.015	-0.008	38.285	0.122	0.122	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.945	-0.973	36.515	-8.542	-8.542	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.889	-0.940	37.020	-7.390	-7.390	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.881	-0.928	33.377	-9.691	-9.691	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.018	0.011	33.754	0.216	0.216	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.008	-0.009	33.791	-0.277	-0.277	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.035	0.021	28.652	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.013	-0.020	32.112	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.899	0.933	28.070	10.308	10.308	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.021	0.003	29.187	-0.269	-0.269	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.049	-0.019	30.773	0.099	0.099	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.045	-0.016	26.574	-0.211	-0.211	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.007	-0.017	23.644	-0.483	-0.483	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.913	-0.956	16.607	-17.636	-17.636	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.011	-0.016	19.070	-0.681	-0.681	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.054	-0.021	21.528	0.533	0.533	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.004	0.005	24.110	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.048	0.028	27.099	0.021	0.021	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.043	-0.027	30.506	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.000	0.009	33.298	0.189	0.189	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.048	-0.019	36.664	-0.088	-0.088	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.028	0.024	36.574	0.201	0.201	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.919	-0.970	39.588	-7.186	-7.186	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.016	-0.006	42.155	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.010	0.017	43.591	0.242	0.242	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.019	-0.019	45.485	0.225	0.225	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.979	0.982	46.635	6.721	6.721	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.934	0.981	49.374	5.702	5.702	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.021	-0.005	48.450	0.107	0.107	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.051	0.012	51.941	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.925	0.957	49.962	6.274	6.274	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.006	0.015	45.058	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.001	-0.002	42.564	0.053	0.053	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.022	0.011	37.137	-0.291	-0.291	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.002	0.004	37.432	0.057	0.057	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.022	0.007	32.120	-0.156	-0.156	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.027	0.026	29.476	0.175	0.175	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.034	-0.016	26.593	-0.329	-0.329	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.053	0.031	23.826	0.219	0.219	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.030	-0.017	24.395	-0.387	-0.387	0.000	0.000	0.000	0.000
93	A	93	ASN	0	0.066	0.031	19.179	0.637	0.637	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.033	0.017	20.237	-0.717	-0.717	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.969	0.970	19.236	15.014	15.014	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.911	0.949	13.409	19.787	19.787	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.824	0.929	13.060	20.634	20.634	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.976	0.986	19.367	12.296	12.296	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.043	0.039	21.163	-0.474	-0.474	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.010	0.007	22.014	0.339	0.339	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.000	0.008	24.916	0.078	0.078	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.003	-0.003	26.351	-0.024	-0.024	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.042	-0.025	30.371	0.313	0.313	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.046	0.025	33.887	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.918	0.949	36.336	7.669	7.669	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.068	0.050	39.071	0.013	0.013	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.027	-0.033	42.616	0.143	0.143	0.000	0.000	0.000	0.000
108	A	108	PRO	0	-0.023	-0.008	45.724	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.084	0.019	48.333	0.008	0.008	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.038	-0.011	50.914	0.081	0.081	0.000	0.000	0.000	0.000
111	A	111	CYS	0	-0.042	-0.018	54.001	0.137	0.137	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.900	0.955	47.307	6.633	6.633	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.945	-0.979	51.114	-6.114	-6.114	0.000	0.000	0.000	0.000
114	A	114	GLU	-2	-1.912	-1.932	49.431	-12.284	-12.284	0.000	0.000	0.000	0.000

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