FMO DATABASE

FMODB ID: KVML3

Calculation Name: 3MSH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | tetraethylene glycol | glycerol | isopropyl alcohol

Ligand 3-letter code: PO4 | PG4 | GOL | IPA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MSH

Chain ID: A

ChEMBL ID:

UniProt ID: O43504

Base Structure: X-ray

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-549876.617608
FMO2-HF: Nuclear repulsion	514983.287154
FMO2-HF: Total energy	-34893.330455
FMO2-MP2: Total energy	-34989.96601

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:MET)

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

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.
-81.077	-78.842	0.977	-1.097	-2.115	-0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.903

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].	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	ALA	0	-0.005	0.001	2.437	0.987	3.052	0.978	-1.070	-1.973	-0.005
4	A	4	THR	0	-0.007	-0.013	4.354	3.044	3.110	0.000	-0.021	-0.045	0.000
8	A	8	HIS	0	0.028	0.011	4.255	-0.598	-0.494	-0.001	-0.006	-0.097	0.000
5	A	5	LEU	0	0.067	0.021	7.751	0.131	0.131	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.792	-0.883	10.066	-17.000	-17.000	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.025	0.021	6.750	-1.191	-1.191	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.017	0.025	9.348	1.440	1.440	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.826	-0.904	12.299	-15.420	-15.420	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.921	-0.965	8.184	-23.165	-23.165	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.050	-0.038	11.578	0.943	0.943	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.011	-0.002	13.796	0.952	0.952	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.831	0.921	11.498	20.136	20.136	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.022	-0.004	16.473	0.941	0.941	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.027	0.008	17.961	0.225	0.225	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.041	-0.020	21.232	0.548	0.548	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.079	-0.032	17.038	0.243	0.243	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.006	0.006	21.057	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.032	0.023	21.177	0.131	0.131	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.035	-0.012	15.541	-0.082	-0.082	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.006	0.010	18.594	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.018	0.018	15.039	-0.267	-0.267	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.009	-0.011	17.436	0.365	0.365	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.755	-0.870	18.430	-13.730	-13.730	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.036	-0.019	20.002	0.294	0.294	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.079	-0.061	23.000	0.880	0.880	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.001	0.003	23.689	0.452	0.452	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.035	0.003	20.692	0.228	0.228	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.008	-0.045	20.009	-1.007	-1.007	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.055	-0.025	15.352	-0.176	-0.176	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.038	0.019	15.896	-1.000	-1.000	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.078	-0.019	16.951	0.325	0.325	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.771	0.835	15.800	16.160	16.160	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.028	0.022	19.861	0.129	0.129	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.037	-0.071	22.815	0.055	0.055	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.066	-0.011	21.453	0.303	0.303	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.027	-0.015	22.956	-0.479	-0.479	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.842	-0.931	24.162	-11.868	-11.868	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.971	-0.963	25.834	-9.531	-9.531	0.000	0.000	0.000	0.000
41	A	41	HIS	0	0.040	0.023	25.530	-0.066	-0.066	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.011	0.023	23.473	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.043	0.010	24.694	-0.120	-0.120	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.001	-0.004	27.414	0.082	0.082	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.041	0.014	21.922	0.103	0.103	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.003	0.013	23.922	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.007	-0.013	24.827	0.113	0.113	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.018	-0.007	26.839	0.211	0.211	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.044	0.026	23.263	0.128	0.128	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.007	-0.008	24.353	-0.428	-0.428	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.009	-0.004	27.195	0.206	0.206	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.030	0.021	27.076	0.229	0.229	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.009	-0.001	25.828	0.133	0.133	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.823	0.912	27.782	9.303	9.303	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.064	-0.027	31.000	0.329	0.329	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.028	-0.014	27.925	0.188	0.188	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.036	-0.016	30.592	0.096	0.096	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.888	-0.919	25.489	-11.530	-11.530	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.044	-0.056	26.338	0.351	0.351	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.021	-0.025	21.325	-0.304	-0.304	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.911	-0.928	23.098	-10.843	-10.843	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.016	-0.008	19.971	0.316	0.316	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.028	-0.011	23.636	-0.217	-0.217	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.012	0.000	21.702	-0.232	-0.232	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.023	-0.013	24.155	0.488	0.488	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.033	-0.013	25.111	-0.380	-0.380	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.020	-0.004	27.410	0.316	0.316	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.914	-0.966	28.908	-9.221	-9.221	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.072	-0.032	31.378	0.248	0.248	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.865	-0.936	33.173	-7.702	-7.702	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.065	-0.026	30.628	0.094	0.094	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.073	0.048	29.157	-0.341	-0.341	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.034	-0.022	25.402	-0.190	-0.190	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.007	-0.005	23.891	-0.363	-0.363	0.000	0.000	0.000	0.000
75	A	75	MET	0	-0.020	-0.005	21.359	0.196	0.196	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.006	-0.011	21.357	-0.450	-0.450	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.013	0.012	18.262	0.537	0.537	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.886	0.941	17.892	12.952	12.952	0.000	0.000	0.000	0.000
79	A	79	HIS	0	-0.020	-0.013	10.049	1.460	1.460	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.876	-0.939	9.546	-23.881	-23.881	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.037	-0.013	12.801	-0.477	-0.477	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.050	-0.013	12.451	1.001	1.001	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.028	-0.022	16.028	0.248	0.248	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.004	-0.005	14.214	-0.348	-0.348	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.022	0.012	17.511	0.560	0.560	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.003	-0.014	17.198	-0.469	-0.469	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.025	0.014	20.190	0.168	0.168	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.955	0.967	19.988	11.946	11.946	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.026	-0.007	24.424	0.220	0.220	0.000	0.000	0.000	0.000
90	A	90	ALA	-1	-0.897	-0.941	27.627	-8.906	-8.906	0.000	0.000	0.000	0.000

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