FMO DATABASE

FMODB ID: 2R12R

Calculation Name: 7K5Y-U-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7K5Y

Chain ID: U

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-395388.474186
FMO2-HF: Nuclear repulsion	369330.305187
FMO2-HF: Total energy	-26058.168999
FMO2-MP2: Total energy	-26136.233404

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:35:SER)

Summations of interaction energy for fragment #1(A:35: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.
130.49	132.047	0	-0.675	-0.881	-0.001

Interaction energy analysis for fragmet #1(A:35:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.921

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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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].	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	37	PRO	0	0.042	0.027	3.621	-3.284	-1.727	-0.675	-0.881	-0.001
4	A	38	PRO	0	0.049	0.019	6.420	-1.830	-1.830	0.000	0.000	0.000
5	A	39	VAL	0	0.040	0.000	7.959	2.123	2.123	0.000	0.000	0.000
6	A	40	SER	0	-0.005	-0.002	10.363	1.369	1.369	0.000	0.000	0.000
7	A	41	GLU	-1	-0.856	-0.900	10.632	-20.680	-20.680	0.000	0.000	0.000
8	A	42	LEU	0	0.034	0.018	8.184	1.658	1.658	0.000	0.000	0.000
9	A	43	ILE	0	-0.025	-0.016	12.572	1.799	1.799	0.000	0.000	0.000
10	A	44	THR	0	-0.033	-0.038	15.554	1.297	1.297	0.000	0.000	0.000
11	A	45	LYS	1	0.924	0.964	15.025	21.323	21.323	0.000	0.000	0.000
12	A	46	ALA	0	0.014	0.005	16.572	0.973	0.973	0.000	0.000	0.000
13	A	47	VAL	0	-0.071	-0.037	18.179	0.975	0.975	0.000	0.000	0.000
14	A	48	ALA	0	-0.024	-0.024	20.282	0.837	0.837	0.000	0.000	0.000
15	A	49	ALA	0	-0.019	-0.002	19.779	0.540	0.540	0.000	0.000	0.000
16	A	50	SER	0	-0.011	-0.003	21.815	0.451	0.451	0.000	0.000	0.000
17	A	51	LYS	1	0.878	0.950	25.084	12.602	12.602	0.000	0.000	0.000
18	A	52	GLU	-1	-0.814	-0.888	26.998	-9.787	-9.787	0.000	0.000	0.000
19	A	53	ARG	1	0.941	0.968	29.707	8.696	8.696	0.000	0.000	0.000
20	A	54	SER	0	-0.059	-0.031	31.403	0.227	0.227	0.000	0.000	0.000
21	A	55	GLY	0	0.026	0.011	27.399	-0.210	-0.210	0.000	0.000	0.000
22	A	56	VAL	0	0.040	0.042	21.673	0.233	0.233	0.000	0.000	0.000
23	A	57	SER	0	0.077	0.027	24.578	-0.242	-0.242	0.000	0.000	0.000
24	A	58	LEU	0	0.018	0.007	20.300	-0.627	-0.627	0.000	0.000	0.000
25	A	59	ALA	0	0.014	-0.007	21.207	-0.703	-0.703	0.000	0.000	0.000
26	A	60	ALA	0	-0.017	-0.004	21.959	-0.366	-0.366	0.000	0.000	0.000
27	A	61	LEU	0	0.033	0.017	17.757	-0.558	-0.558	0.000	0.000	0.000
28	A	62	LYS	1	0.948	0.973	17.007	14.433	14.433	0.000	0.000	0.000
29	A	63	LYS	1	0.964	0.995	16.789	12.326	12.326	0.000	0.000	0.000
30	A	64	ALA	0	0.015	0.017	17.703	-0.430	-0.430	0.000	0.000	0.000
31	A	65	LEU	0	-0.035	-0.028	12.581	-0.914	-0.914	0.000	0.000	0.000
32	A	66	ALA	0	-0.004	-0.002	12.761	-1.586	-1.586	0.000	0.000	0.000
33	A	67	ALA	0	-0.007	-0.007	13.809	-0.809	-0.809	0.000	0.000	0.000
34	A	68	ALA	0	-0.029	-0.009	12.968	0.053	0.053	0.000	0.000	0.000
35	A	69	GLY	0	0.018	0.032	10.305	-1.428	-1.428	0.000	0.000	0.000
36	A	70	TYR	0	-0.041	-0.038	6.879	-2.543	-2.543	0.000	0.000	0.000
37	A	71	ASP	-1	-0.782	-0.873	8.807	-23.403	-23.403	0.000	0.000	0.000
38	A	72	VAL	0	0.029	-0.004	10.613	-0.715	-0.715	0.000	0.000	0.000
39	A	73	GLU	-1	-0.887	-0.933	13.640	-16.713	-16.713	0.000	0.000	0.000
40	A	74	LYS	1	0.881	0.926	8.623	30.948	30.948	0.000	0.000	0.000
41	A	75	ASN	0	-0.067	-0.044	8.861	-0.281	-0.281	0.000	0.000	0.000
42	A	76	ASN	0	0.022	0.005	12.621	0.730	0.730	0.000	0.000	0.000
43	A	77	SER	0	-0.024	-0.012	15.797	0.828	0.828	0.000	0.000	0.000
44	A	78	ARG	1	0.999	0.990	10.617	24.536	24.536	0.000	0.000	0.000
45	A	79	ILE	0	0.047	0.029	13.239	0.291	0.291	0.000	0.000	0.000
46	A	80	LYS	1	0.945	0.977	15.144	15.039	15.039	0.000	0.000	0.000
47	A	81	LEU	0	-0.006	0.003	14.343	0.648	0.648	0.000	0.000	0.000
48	A	82	GLY	0	0.030	0.021	15.238	0.288	0.288	0.000	0.000	0.000
49	A	83	LEU	0	-0.008	-0.009	16.054	0.545	0.545	0.000	0.000	0.000
50	A	84	LYS	1	0.971	0.984	19.258	13.067	13.067	0.000	0.000	0.000
51	A	85	SER	0	0.000	0.015	17.472	0.769	0.769	0.000	0.000	0.000
52	A	86	LEU	0	0.023	-0.001	16.210	0.407	0.407	0.000	0.000	0.000
53	A	87	VAL	0	-0.009	0.005	20.153	0.538	0.538	0.000	0.000	0.000
54	A	88	SER	0	-0.073	-0.037	21.994	0.469	0.469	0.000	0.000	0.000
55	A	89	LYS	1	0.965	0.981	17.601	16.620	16.620	0.000	0.000	0.000
56	A	90	GLY	0	0.017	0.018	23.433	0.168	0.168	0.000	0.000	0.000
57	A	91	THR	0	-0.058	-0.028	20.014	-0.050	-0.050	0.000	0.000	0.000
58	A	92	LEU	0	-0.017	-0.018	20.373	-0.210	-0.210	0.000	0.000	0.000
59	A	93	VAL	0	-0.013	-0.008	23.875	0.346	0.346	0.000	0.000	0.000
60	A	94	GLN	0	-0.032	-0.028	26.488	-0.053	-0.053	0.000	0.000	0.000
61	A	95	THR	0	-0.042	-0.031	27.970	0.331	0.331	0.000	0.000	0.000
62	A	96	LYS	1	0.964	0.973	30.507	9.320	9.320	0.000	0.000	0.000
63	A	97	GLY	0	0.036	0.036	29.844	0.203	0.203	0.000	0.000	0.000
64	A	98	THR	0	0.048	0.012	29.330	0.171	0.171	0.000	0.000	0.000
65	A	99	GLY	0	0.009	0.012	25.942	-0.110	-0.110	0.000	0.000	0.000
66	A	100	ALA	0	0.009	-0.002	22.237	-0.277	-0.277	0.000	0.000	0.000
67	A	101	SER	0	0.021	0.014	23.800	-0.387	-0.387	0.000	0.000	0.000
68	A	102	GLY	0	0.012	0.011	26.866	0.166	0.166	0.000	0.000	0.000
69	A	103	SER	0	-0.008	-0.019	26.474	-0.350	-0.350	0.000	0.000	0.000
70	A	104	PHE	0	-0.029	-0.010	23.238	0.276	0.276	0.000	0.000	0.000
71	A	105	LYS	1	0.971	0.984	25.012	10.469	10.469	0.000	0.000	0.000
72	A	106	LEU	0	0.045	0.025	22.648	-0.204	-0.204	0.000	0.000	0.000
73	A	107	ASN	0	0.012	0.008	25.204	0.911	0.911	0.000	0.000	0.000
74	A	108	LYS	1	0.881	0.921	27.156	10.512	10.512	0.000	0.000	0.000
75	A	109	LYS	0	0.114	0.082	26.678	-1.271	-1.271	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:35:SER)