FMO DATABASE

FMODB ID: VZ8V1

Calculation Name: 1R4P-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 3-pyridinium-1-ylpropane-1-sulfonate | 1,2-ethanediol | formic acid

Ligand 3-letter code: 1PS | EDO | FMT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1R4P

Chain ID: B

ChEMBL ID:

UniProt ID: P09385

Base Structure: X-ray

Registration Date: 2025-10-06

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	69
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-425277.544219
FMO2-HF: Nuclear repulsion	397375.860887
FMO2-HF: Total energy	-27901.683332
FMO2-MP2: Total energy	-27981.734148

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(B:1:ALA)

Summations of interaction energy for fragment #1(B:1:ALA)

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.
-69.907	-67.478	10.293	-6.581	-6.14	-0.074

Interaction energy analysis for fragmet #1(B:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.797 / q_NPA : 0.887

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	B	3	CYS	0	-0.040	-0.007	3.240	-0.916	0.815	0.564	-0.755	-1.540	-0.003
52	B	52	LYS	1	0.855	0.916	3.411	43.689	44.032	0.003	-0.116	-0.229	0.000
53	B	53	SER	0	0.041	-0.004	2.664	10.611	11.642	0.052	-0.471	-0.612	-0.002
54	B	54	SER	0	-0.013	-0.006	1.795	-45.185	-46.211	9.676	-5.193	-3.456	-0.069
55	B	55	THR	0	-0.008	-0.006	4.173	0.322	0.570	-0.001	-0.028	-0.220	0.000
63	B	64	GLU	-1	-0.931	-0.952	4.433	-54.236	-54.134	-0.001	-0.018	-0.083	0.000
4	B	4	ALA	0	0.059	0.030	5.652	5.845	5.845	0.000	0.000	0.000	0.000
5	B	5	LYS	1	0.956	0.986	9.083	23.057	23.057	0.000	0.000	0.000	0.000
6	B	6	GLY	0	0.031	0.021	11.096	1.413	1.413	0.000	0.000	0.000	0.000
7	B	7	LYS	1	0.868	0.930	14.832	16.087	16.087	0.000	0.000	0.000	0.000
8	B	8	ILE	0	-0.019	-0.009	16.041	-0.584	-0.584	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.817	-0.891	17.476	-16.281	-16.281	0.000	0.000	0.000	0.000
10	B	10	PHE	0	-0.041	-0.028	19.466	0.925	0.925	0.000	0.000	0.000	0.000
11	B	11	SER	0	-0.020	-0.024	19.028	-0.978	-0.978	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.887	0.935	20.078	15.520	15.520	0.000	0.000	0.000	0.000
13	B	13	TYR	0	-0.061	-0.049	20.708	-0.912	-0.912	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.043	-0.024	19.027	0.870	0.870	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.910	-0.967	23.113	-10.981	-10.981	0.000	0.000	0.000	0.000
16	B	16	ASP	-1	-0.851	-0.895	20.723	-14.912	-14.912	0.000	0.000	0.000	0.000
17	B	17	ASP	-1	-0.865	-0.899	22.449	-12.795	-12.795	0.000	0.000	0.000	0.000
18	B	18	THR	0	-0.099	-0.063	17.547	-0.956	-0.956	0.000	0.000	0.000	0.000
19	B	19	PHE	0	-0.016	-0.024	17.230	0.726	0.726	0.000	0.000	0.000	0.000
20	B	20	THR	0	0.010	0.010	16.237	-1.213	-1.213	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.025	-0.019	13.594	0.959	0.959	0.000	0.000	0.000	0.000
22	B	22	LYS	1	0.854	0.943	15.023	15.324	15.324	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.001	-0.013	12.581	0.525	0.525	0.000	0.000	0.000	0.000
24	B	24	ASP	-1	-0.855	-0.914	11.755	-24.795	-24.795	0.000	0.000	0.000	0.000
25	B	25	GLY	0	-0.001	-0.010	13.866	-0.400	-0.400	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.751	0.868	9.159	28.820	28.820	0.000	0.000	0.000	0.000
27	B	27	GLU	-1	-0.894	-0.962	13.668	-16.816	-16.816	0.000	0.000	0.000	0.000
28	B	28	TYR	0	-0.027	-0.022	8.282	-1.782	-1.782	0.000	0.000	0.000	0.000
29	B	29	TRP	0	-0.019	-0.001	12.514	1.483	1.483	0.000	0.000	0.000	0.000
30	B	30	THR	0	-0.013	-0.024	12.417	-1.320	-1.320	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.074	0.026	14.101	0.946	0.946	0.000	0.000	0.000	0.000
32	B	32	ARG	1	0.907	0.958	12.600	23.754	23.754	0.000	0.000	0.000	0.000
33	B	33	TRP	0	0.081	0.036	16.692	-0.171	-0.171	0.000	0.000	0.000	0.000
34	B	34	ASN	0	0.038	0.007	18.890	0.574	0.574	0.000	0.000	0.000	0.000
35	B	35	LEU	0	-0.032	-0.021	12.478	0.045	0.045	0.000	0.000	0.000	0.000
36	B	36	GLN	0	0.019	0.030	16.847	0.281	0.281	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.010	0.009	19.829	0.120	0.120	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.027	-0.008	16.515	0.180	0.180	0.000	0.000	0.000	0.000
39	B	39	LEU	0	0.023	0.006	13.640	-0.220	-0.220	0.000	0.000	0.000	0.000
40	B	40	GLN	0	0.028	0.019	17.776	0.435	0.435	0.000	0.000	0.000	0.000
41	B	41	SER	0	-0.007	0.000	21.138	0.567	0.567	0.000	0.000	0.000	0.000
42	B	42	ALA	0	0.040	0.020	17.439	0.306	0.306	0.000	0.000	0.000	0.000
43	B	43	GLN	0	0.000	0.017	19.491	-0.011	-0.011	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.053	-0.026	21.050	0.460	0.460	0.000	0.000	0.000	0.000
45	B	45	THR	0	-0.056	-0.051	22.234	0.324	0.324	0.000	0.000	0.000	0.000
46	B	46	GLY	0	0.008	0.024	22.002	0.196	0.196	0.000	0.000	0.000	0.000
47	B	47	MET	0	-0.002	0.016	17.451	-0.547	-0.547	0.000	0.000	0.000	0.000
48	B	48	THR	0	-0.129	-0.077	13.847	-0.024	-0.024	0.000	0.000	0.000	0.000
49	B	49	VAL	0	0.024	0.008	12.492	-0.424	-0.424	0.000	0.000	0.000	0.000
50	B	50	THR	0	-0.036	-0.029	7.093	0.248	0.248	0.000	0.000	0.000	0.000
51	B	51	ILE	0	0.008	0.014	7.356	-1.672	-1.672	0.000	0.000	0.000	0.000
56	B	57	GLU	-1	-0.833	-0.884	5.724	-21.221	-21.221	0.000	0.000	0.000	0.000
57	B	58	SER	0	0.019	0.002	9.443	-1.063	-1.063	0.000	0.000	0.000	0.000
58	B	59	GLY	0	0.004	-0.004	12.223	1.362	1.362	0.000	0.000	0.000	0.000
59	B	60	SER	0	-0.075	-0.034	8.014	1.795	1.795	0.000	0.000	0.000	0.000
60	B	61	GLY	0	0.048	0.032	10.654	0.901	0.901	0.000	0.000	0.000	0.000
61	B	62	PHE	0	-0.043	-0.026	7.684	-4.591	-4.591	0.000	0.000	0.000	0.000
62	B	63	ALA	0	-0.023	-0.019	8.071	3.972	3.972	0.000	0.000	0.000	0.000
64	B	65	VAL	0	0.009	-0.009	7.578	-2.389	-2.389	0.000	0.000	0.000	0.000
65	B	66	GLN	0	-0.067	-0.017	8.960	-0.580	-0.580	0.000	0.000	0.000	0.000
66	B	67	PHE	0	0.004	-0.015	10.442	-0.029	-0.029	0.000	0.000	0.000	0.000
67	B	68	ASN	0	-0.025	-0.015	13.994	-1.103	-1.103	0.000	0.000	0.000	0.000
68	B	69	ASN	0	0.027	0.012	16.200	-0.192	-0.192	0.000	0.000	0.000	0.000
69	B	70	ASP	-2	-1.759	-1.844	16.984	-33.250	-33.250	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ALA)