FMO DATABASE

FMODB ID: NZ5NQ

Calculation Name: 2C7A-B-Xray547

Preferred Name: Progesterone receptor

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C7A

Chain ID: B

ChEMBL ID: CHEMBL208

UniProt ID: P06401

Base Structure: X-ray

Registration Date: 2025-10-03

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	-460873.057726
FMO2-HF: Nuclear repulsion	428527.422728
FMO2-HF: Total energy	-32345.634998
FMO2-MP2: Total energy	-32429.069584

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:563:PRO)

Summations of interaction energy for fragment #1(A:563:PRO)

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.
118.511	120.156	-0.013	-0.732	-0.9	-0.001

Interaction energy analysis for fragmet #1(A:563:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.897 / q_NPA : 0.918

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	565	LYS	1	0.964	1.000	3.769	37.094	38.739	-0.013	-0.732	-0.900	-0.001
4	A	566	ILE	0	0.071	0.041	6.012	2.756	2.756	0.000	0.000	0.000	0.000
5	A	567	CYS	0	-0.122	-0.026	8.350	2.028	2.028	0.000	0.000	0.000	0.000
6	A	568	LEU	0	0.090	0.042	11.691	0.757	0.757	0.000	0.000	0.000	0.000
7	A	569	ILE	0	0.029	0.006	13.704	0.980	0.980	0.000	0.000	0.000	0.000
8	A	570	CYS	0	-0.084	-0.046	15.063	0.714	0.714	0.000	0.000	0.000	0.000
9	A	571	GLY	0	0.057	0.022	11.593	0.521	0.521	0.000	0.000	0.000	0.000
10	A	572	ASP	-1	-0.786	-0.876	11.309	-21.749	-21.749	0.000	0.000	0.000	0.000
11	A	573	GLU	-1	-0.844	-0.905	7.720	-36.704	-36.704	0.000	0.000	0.000	0.000
12	A	574	ALA	0	-0.081	-0.059	9.627	3.019	3.019	0.000	0.000	0.000	0.000
13	A	575	SER	0	0.009	-0.004	9.851	-1.940	-1.940	0.000	0.000	0.000	0.000
14	A	576	GLY	0	0.012	-0.003	12.306	-0.188	-0.188	0.000	0.000	0.000	0.000
15	A	577	CYS	0	-0.035	-0.004	13.202	-0.122	-0.122	0.000	0.000	0.000	0.000
16	A	578	HIS	0	-0.015	-0.013	14.959	2.013	2.013	0.000	0.000	0.000	0.000
17	A	579	TYR	0	-0.019	-0.025	18.219	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	580	GLY	0	0.083	0.055	19.037	0.506	0.506	0.000	0.000	0.000	0.000
19	A	581	VAL	0	0.041	0.030	15.751	-0.618	-0.618	0.000	0.000	0.000	0.000
20	A	582	LEU	0	0.019	0.015	8.347	-0.277	-0.277	0.000	0.000	0.000	0.000
21	A	583	THR	0	0.023	-0.021	13.001	0.201	0.201	0.000	0.000	0.000	0.000
22	A	584	CYS	0	0.028	0.040	13.942	-0.306	-0.306	0.000	0.000	0.000	0.000
23	A	585	GLY	0	0.073	0.029	14.980	1.141	1.141	0.000	0.000	0.000	0.000
24	A	586	SER	0	0.032	-0.004	17.824	0.909	0.909	0.000	0.000	0.000	0.000
25	A	587	CYS	0	-0.003	0.020	17.861	0.914	0.914	0.000	0.000	0.000	0.000
26	A	588	LYS	1	0.990	1.030	19.222	14.963	14.963	0.000	0.000	0.000	0.000
27	A	589	VAL	0	0.006	-0.013	20.918	0.625	0.625	0.000	0.000	0.000	0.000
28	A	590	PHE	0	-0.040	-0.011	22.938	0.502	0.502	0.000	0.000	0.000	0.000
29	A	591	PHE	0	0.080	0.019	23.060	0.408	0.408	0.000	0.000	0.000	0.000
30	A	592	LYS	1	0.845	0.921	24.907	11.192	11.192	0.000	0.000	0.000	0.000
31	A	593	ARG	1	0.966	0.965	26.902	11.734	11.734	0.000	0.000	0.000	0.000
32	A	594	ALA	0	-0.050	-0.017	27.624	0.417	0.417	0.000	0.000	0.000	0.000
33	A	595	MET	0	-0.002	0.010	27.836	0.243	0.243	0.000	0.000	0.000	0.000
34	A	596	GLU	-1	-0.814	-0.891	30.578	-9.838	-9.838	0.000	0.000	0.000	0.000
35	A	597	GLY	0	-0.024	0.002	32.820	0.330	0.330	0.000	0.000	0.000	0.000
36	A	598	GLN	0	0.011	-0.002	34.006	-0.243	-0.243	0.000	0.000	0.000	0.000
37	A	599	HIS	0	-0.019	-0.028	32.414	0.338	0.338	0.000	0.000	0.000	0.000
38	A	600	ASN	0	-0.002	0.013	35.675	0.036	0.036	0.000	0.000	0.000	0.000
39	A	601	TYR	0	-0.009	-0.012	30.434	0.019	0.019	0.000	0.000	0.000	0.000
40	A	602	LEU	0	0.043	0.027	33.227	-0.152	-0.152	0.000	0.000	0.000	0.000
41	A	603	CYS	0	-0.166	-0.068	30.257	-0.247	-0.247	0.000	0.000	0.000	0.000
42	A	604	ALA	0	0.065	0.037	32.925	0.203	0.203	0.000	0.000	0.000	0.000
43	A	605	GLY	0	0.025	0.006	31.953	0.102	0.102	0.000	0.000	0.000	0.000
44	A	606	ARG	1	0.995	0.975	31.972	8.867	8.867	0.000	0.000	0.000	0.000
45	A	607	ASN	0	-0.041	-0.061	29.689	-0.105	-0.105	0.000	0.000	0.000	0.000
46	A	608	ASP	-1	-0.820	-0.900	27.494	-10.436	-10.436	0.000	0.000	0.000	0.000
47	A	609	CYS	0	-0.093	-0.048	25.856	-0.230	-0.230	0.000	0.000	0.000	0.000
48	A	610	ILE	0	0.050	0.015	20.069	-0.372	-0.372	0.000	0.000	0.000	0.000
49	A	611	VAL	0	-0.038	-0.005	19.668	0.015	0.015	0.000	0.000	0.000	0.000
50	A	612	ASP	-1	-0.756	-0.869	17.339	-15.661	-15.661	0.000	0.000	0.000	0.000
51	A	613	LYS	1	0.898	0.929	14.517	20.927	20.927	0.000	0.000	0.000	0.000
52	A	614	ILE	0	0.017	0.008	17.331	0.291	0.291	0.000	0.000	0.000	0.000
53	A	615	ARG	1	0.920	0.938	20.830	13.781	13.781	0.000	0.000	0.000	0.000
54	A	616	ARG	1	0.807	0.890	16.803	17.353	17.353	0.000	0.000	0.000	0.000
55	A	617	LYS	1	0.944	0.961	22.163	11.404	11.404	0.000	0.000	0.000	0.000
56	A	618	ASN	0	0.001	0.007	25.455	0.394	0.394	0.000	0.000	0.000	0.000
57	A	619	CYS	0	0.047	0.058	26.514	0.478	0.478	0.000	0.000	0.000	0.000
58	A	620	PRO	0	0.038	0.022	26.758	-0.400	-0.400	0.000	0.000	0.000	0.000
59	A	621	ALA	0	0.078	0.034	27.525	-0.203	-0.203	0.000	0.000	0.000	0.000
60	A	622	CYS	0	-0.004	0.002	25.539	0.023	0.023	0.000	0.000	0.000	0.000
61	A	623	ARG	1	0.841	0.903	20.251	13.593	13.593	0.000	0.000	0.000	0.000
62	A	624	LEU	0	0.042	0.021	23.215	-0.549	-0.549	0.000	0.000	0.000	0.000
63	A	625	ARG	1	0.997	1.013	25.448	10.018	10.018	0.000	0.000	0.000	0.000
64	A	626	LYS	1	0.922	0.962	16.967	16.135	16.135	0.000	0.000	0.000	0.000
65	A	627	CYS	0	-0.094	-0.061	21.042	-0.685	-0.685	0.000	0.000	0.000	0.000
66	A	628	CYS	0	-0.011	-0.007	22.100	-0.158	-0.158	0.000	0.000	0.000	0.000
67	A	629	GLN	0	-0.009	-0.010	22.945	-0.284	-0.284	0.000	0.000	0.000	0.000
68	A	630	ALA	0	-0.044	-0.016	18.041	-0.238	-0.238	0.000	0.000	0.000	0.000
69	A	631	GLY	0	0.040	0.029	19.188	-0.563	-0.563	0.000	0.000	0.000	0.000
70	A	632	MET	0	-0.141	-0.058	19.709	-0.171	-0.171	0.000	0.000	0.000	0.000
71	A	633	VAL	0	0.037	0.018	22.133	0.616	0.616	0.000	0.000	0.000	0.000
72	A	634	LEU	0	-0.050	-0.025	24.620	-0.434	-0.434	0.000	0.000	0.000	0.000
73	A	635	GLY	0	0.056	0.017	26.581	0.303	0.303	0.000	0.000	0.000	0.000
74	A	636	GLY	0	-0.040	-0.021	26.591	-0.396	-0.396	0.000	0.000	0.000	0.000
75	A	637	ARG	1	0.819	0.903	22.665	13.208	13.208	0.000	0.000	0.000	0.000
76	A	638	LYS	0	0.185	0.115	24.757	-0.197	-0.197	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:563:PRO)