FMO DATABASE

FMODB ID: 7NJ3K

Calculation Name: 2PMR-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PMR

Chain ID: A

ChEMBL ID:

UniProt ID: O27725

Base Structure: X-ray

Registration Date: 2025-10-04

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-509723.9743
FMO2-HF: Nuclear repulsion	477455.401277
FMO2-HF: Total energy	-32268.573022
FMO2-MP2: Total energy	-32359.959418

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:3:CYS)

Summations of interaction energy for fragment #1(A:3:CYS)

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.
-121.873	-115.855	8.008	-5.305	-8.724	-0.044

Interaction energy analysis for fragmet #1(A:3:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.904

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	5	GLU	-1	-0.855	-0.918	3.575	-45.133	-42.726	-0.005	-0.964	-1.438	-0.004
4	A	6	ARG	1	0.905	0.955	2.946	51.284	52.543	0.136	-0.400	-0.996	0.000
5	A	7	ILE	0	0.063	0.034	1.985	2.945	3.208	2.498	-1.096	-1.665	-0.018
51	A	53	HIS	0	0.018	-0.035	2.120	-8.071	-7.716	5.189	-2.213	-3.331	-0.016
52	A	54	ILE	0	-0.012	0.004	3.277	-4.440	-3.433	0.134	-0.468	-0.674	-0.004
55	A	57	PHE	0	-0.017	-0.001	3.023	0.684	1.397	0.057	-0.162	-0.608	-0.002
56	A	58	GLY	0	0.024	0.029	5.099	2.736	2.750	-0.001	-0.002	-0.012	0.000
6	A	8	GLU	-1	-0.815	-0.910	5.560	-33.290	-33.290	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.861	0.921	8.166	33.560	33.560	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.875	-0.933	8.001	-28.198	-28.198	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.006	-0.009	9.117	2.711	2.711	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.888	-0.933	11.488	-22.288	-22.288	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.034	-0.015	13.264	1.792	1.792	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.012	0.009	13.691	1.372	1.372	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.840	-0.910	15.497	-14.479	-14.479	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.916	0.963	17.599	16.706	16.706	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.023	-0.001	17.390	1.136	1.136	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.013	0.010	18.226	0.811	0.811	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.062	-0.035	21.345	0.952	0.952	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.899	-0.930	23.031	-12.852	-12.852	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.023	0.016	22.246	0.616	0.616	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.935	0.969	24.506	12.550	12.550	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.058	-0.021	28.211	0.254	0.254	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.032	-0.014	27.985	0.431	0.431	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.897	0.950	30.959	8.843	8.843	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.004	0.002	26.942	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.017	-0.027	31.334	0.262	0.262	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.835	-0.927	30.525	-9.093	-9.093	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.919	-0.957	29.406	-9.622	-9.622	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.813	-0.881	26.862	-10.410	-10.410	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.931	-0.967	25.725	-10.382	-10.382	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.030	0.021	25.445	-0.459	-0.459	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.056	-0.025	21.879	-0.556	-0.556	0.000	0.000	0.000	0.000
32	A	34	VAL	0	0.008	-0.004	21.242	-0.779	-0.779	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.941	-0.968	20.859	-12.118	-12.118	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.886	0.942	19.130	12.921	12.921	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.006	-0.009	16.970	-0.809	-0.809	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.012	-0.009	16.140	-1.121	-1.121	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.028	0.015	16.864	-0.820	-0.820	0.000	0.000	0.000	0.000
38	A	40	TYR	0	-0.006	-0.014	13.558	-0.312	-0.312	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.789	0.877	12.449	15.673	15.673	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.831	-0.907	12.509	-18.008	-18.008	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.900	-0.952	13.021	-18.277	-18.277	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.095	-0.056	7.667	-1.918	-1.918	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.039	0.035	8.713	-3.324	-3.324	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.067	0.040	10.863	-0.905	-0.905	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.019	-0.029	8.520	0.079	0.079	0.000	0.000	0.000	0.000
46	A	48	LEU	0	-0.034	-0.011	5.336	-2.806	-2.806	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.999	-1.009	7.618	-24.628	-24.628	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.856	0.937	10.725	20.593	20.593	0.000	0.000	0.000	0.000
49	A	51	GLY	0	-0.021	0.004	6.964	0.748	0.748	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.838	-0.888	6.538	-30.480	-30.480	0.000	0.000	0.000	0.000
53	A	55	THR	0	-0.011	-0.032	5.658	1.015	1.015	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.022	-0.014	4.921	-0.267	-0.267	0.000	0.000	0.000	0.000
57	A	59	CYS	0	-0.066	-0.026	8.536	2.330	2.330	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.046	0.019	7.113	1.493	1.493	0.000	0.000	0.000	0.000
59	A	61	THR	0	-0.022	-0.031	7.987	2.189	2.189	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.026	0.009	10.521	2.070	2.070	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.013	0.007	12.868	1.230	1.230	0.000	0.000	0.000	0.000
62	A	64	HIS	0	-0.002	-0.017	11.391	2.016	2.016	0.000	0.000	0.000	0.000
63	A	65	GLY	0	-0.010	0.008	14.654	0.977	0.977	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.072	-0.037	16.663	1.026	1.026	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.019	0.006	17.942	0.774	0.774	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.812	-0.915	17.352	-15.608	-15.608	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.031	0.001	20.123	0.783	0.783	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.012	0.006	22.653	0.562	0.562	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.822	0.875	19.675	15.006	15.006	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.008	0.010	23.210	0.249	0.249	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.048	-0.016	25.746	0.548	0.548	0.000	0.000	0.000	0.000
72	A	74	HIS	1	0.749	0.849	27.712	10.606	10.606	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.895	0.952	28.760	9.385	9.385	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.020	-0.002	25.450	0.233	0.233	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.070	-0.036	21.365	-0.296	-0.296	0.000	0.000	0.000	0.000
76	A	78	GLU	-2	-1.888	-1.937	25.043	-22.231	-22.231	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:CYS)