FMO DATABASE

FMODB ID: 3Z2ZL

Calculation Name: 1CDT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CDT

Chain ID: A

ChEMBL ID:

UniProt ID: P01452

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	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-326751.588206
FMO2-HF: Nuclear repulsion	300861.737918
FMO2-HF: Total energy	-25889.850288
FMO2-MP2: Total energy	-25956.281603

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:LEU)

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

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.
65.493	75.373	17.319	-7.669	-19.527	-0.068

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.936

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	CYS	0	0.020	0.022	2.635	1.745	2.104	5.996	-0.564	-5.791	-0.002
4	A	4	ASN	0	0.009	-0.008	4.481	1.143	1.228	-0.001	-0.021	-0.063	0.000
13	A	13	THR	0	0.045	0.017	4.196	-3.207	-3.030	-0.001	-0.055	-0.121	0.000
14	A	14	CYS	0	-0.044	0.007	2.701	7.326	9.252	1.896	-1.093	-2.728	0.000
15	A	15	PRO	0	0.053	0.033	4.148	-5.629	-5.433	-0.001	-0.066	-0.129	0.000
19	A	19	ASN	0	0.067	0.017	3.047	-13.618	-12.910	0.056	-0.155	-0.609	-0.001
20	A	20	LEU	0	-0.016	0.007	2.243	-3.523	-3.262	3.795	-1.789	-2.266	-0.012
21	A	22	TYR	0	-0.012	-0.011	4.057	2.858	3.010	0.004	-0.018	-0.139	0.000
37	A	39	ILE	0	-0.066	-0.044	5.224	3.457	3.509	-0.001	-0.002	-0.048	0.000
51	A	54	CYS	0	0.013	0.045	4.745	3.797	4.027	0.000	-0.022	-0.207	0.000
52	A	55	SER	0	0.067	0.019	2.256	-2.563	-1.844	1.096	-0.709	-1.105	-0.002
53	A	56	THR	0	0.036	0.018	3.024	-3.823	-2.646	0.400	-0.065	-1.513	-0.007
54	A	57	ASP	-1	-0.781	-0.918	2.425	-80.905	-76.931	4.052	-3.450	-4.576	-0.044
55	A	58	ARG	1	0.804	0.888	3.350	32.665	32.529	0.028	0.340	-0.232	0.000
5	A	5	LYS	1	0.893	0.929	8.167	24.197	24.197	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.007	-0.002	11.254	0.062	0.062	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.082	0.039	14.168	0.363	0.363	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.001	-0.020	11.710	-0.544	-0.544	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.041	0.035	12.136	-1.276	-1.276	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.020	0.028	12.735	-0.351	-0.351	0.000	0.000	0.000	0.000
11	A	11	TYR	0	0.052	0.016	7.181	-1.646	-1.646	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.867	0.954	7.124	31.883	31.883	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.833	-0.922	6.182	-34.804	-34.804	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.014	0.012	7.755	2.975	2.975	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.832	0.913	6.042	27.921	27.921	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.925	0.950	7.837	18.442	18.442	0.000	0.000	0.000	0.000
23	A	24	MET	0	0.003	0.014	11.197	0.279	0.279	0.000	0.000	0.000	0.000
24	A	25	MET	0	-0.016	-0.012	14.277	0.099	0.099	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.027	0.022	17.643	0.233	0.233	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.027	-0.011	21.306	0.028	0.028	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.011	0.004	23.173	0.260	0.260	0.000	0.000	0.000	0.000
28	A	29	LYS	1	1.002	0.994	26.183	10.417	10.417	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.927	0.953	24.226	10.314	10.314	0.000	0.000	0.000	0.000
30	A	31	MET	0	0.018	0.036	18.676	-0.193	-0.193	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.028	0.021	20.370	-0.284	-0.284	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.037	-0.028	15.304	-0.177	-0.177	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.029	0.017	16.651	0.375	0.375	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.938	0.963	13.062	16.623	16.623	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.821	0.912	9.951	20.331	20.331	0.000	0.000	0.000	0.000
36	A	37	GLY	0	-0.043	-0.037	7.601	0.594	0.594	0.000	0.000	0.000	0.000
38	A	40	ASN	0	0.009	0.014	6.199	-3.229	-3.229	0.000	0.000	0.000	0.000
39	A	41	VAL	0	0.095	0.047	8.403	-0.601	-0.601	0.000	0.000	0.000	0.000
40	A	42	CYS	0	-0.037	-0.039	7.079	-0.609	-0.609	0.000	0.000	0.000	0.000
41	A	43	PRO	0	-0.010	-0.004	10.687	1.064	1.064	0.000	0.000	0.000	0.000
42	A	44	LYS	1	1.000	1.008	14.082	12.499	12.499	0.000	0.000	0.000	0.000
43	A	45	ASN	0	0.022	0.009	16.993	-0.119	-0.119	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.031	0.026	18.938	0.620	0.620	0.000	0.000	0.000	0.000
45	A	47	ALA	0	0.058	0.035	22.172	-0.132	-0.132	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.074	0.018	24.437	-0.136	-0.136	0.000	0.000	0.000	0.000
47	A	49	VAL	0	-0.017	0.000	18.336	-0.163	-0.163	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.850	0.923	17.827	12.102	12.102	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.019	-0.009	12.655	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	52	VAL	0	0.028	0.017	10.941	0.570	0.570	0.000	0.000	0.000	0.000
56	A	60	ASN	-1	-0.770	-0.841	6.450	-21.878	-21.878	0.000	0.000	0.000	0.000

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