FMO DATABASE

FMODB ID: 9R8M2

Calculation Name: 1X3H-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X3H

Chain ID: A

ChEMBL ID:

UniProt ID: O60711

Base Structure: SolutionNMR

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-427593.381925
FMO2-HF: Nuclear repulsion	395339.782712
FMO2-HF: Total energy	-32253.599212
FMO2-MP2: Total energy	-32341.527445

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:GLY)

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

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.
-8.929	-8.027	-0.016	-0.378	-0.508	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.915

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	SER	0	0.028	0.018	3.824	-0.089	0.813	-0.016	-0.378	-0.508	-0.001
4	A	4	GLY	0	0.037	0.019	6.619	1.463	1.463	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.000	0.002	10.424	0.206	0.206	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.029	-0.028	13.747	0.594	0.594	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.028	0.035	17.299	0.038	0.038	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.909	0.939	19.175	14.551	14.551	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.890	-0.926	22.843	-11.872	-11.872	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.012	0.004	23.737	-0.085	-0.085	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.009	-0.007	28.460	0.178	0.178	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.009	0.008	31.463	0.154	0.154	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.037	-0.030	33.272	0.299	0.299	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.046	0.014	36.992	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.024	0.004	39.328	0.084	0.084	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.041	0.033	41.598	-0.150	-0.150	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.875	0.918	37.607	8.277	8.277	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.028	0.027	43.706	0.112	0.112	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.060	0.019	44.821	-0.165	-0.165	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.035	-0.021	46.230	0.063	0.063	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.014	-0.010	43.589	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.017	-0.005	39.506	-0.153	-0.153	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.984	0.995	40.116	7.347	7.347	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.016	-0.006	40.144	0.104	0.104	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.000	0.002	42.815	0.049	0.049	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.029	-0.016	44.174	-0.070	-0.070	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.938	-0.976	48.301	-6.158	-6.158	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.008	-0.004	51.285	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.004	0.005	50.672	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.015	0.019	52.491	0.112	0.112	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.010	-0.027	52.139	-0.186	-0.186	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.003	0.003	52.712	0.146	0.146	0.000	0.000	0.000	0.000
33	A	33	MET	0	-0.021	-0.001	51.647	-0.170	-0.170	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.924	-0.948	50.397	-6.466	-6.466	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.011	0.007	46.472	-0.191	-0.191	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.000	0.000	46.831	0.152	0.152	0.000	0.000	0.000	0.000
37	A	37	TRP	0	-0.028	-0.029	48.422	-0.158	-0.158	0.000	0.000	0.000	0.000
38	A	38	HIS	0	0.079	0.009	46.522	-0.094	-0.094	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.009	-0.002	50.958	0.030	0.030	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.946	-0.969	49.357	-6.289	-6.289	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.059	-0.032	49.406	-0.049	-0.049	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.027	-0.006	51.847	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.002	0.001	53.959	0.128	0.128	0.000	0.000	0.000	0.000
44	A	44	CYS	-1	-0.844	-0.757	55.557	-5.459	-5.459	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.042	0.019	54.486	-0.065	-0.065	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.846	-0.929	55.246	-5.516	-5.516	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.117	-0.129	58.011	0.048	0.048	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.015	0.013	52.432	0.029	0.029	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.006	0.005	57.425	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.043	0.017	58.675	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.011	-0.007	56.587	0.109	0.109	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.010	0.002	61.038	0.020	0.020	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.024	-0.020	62.901	0.038	0.038	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.028	0.009	64.969	0.100	0.100	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.046	-0.012	63.048	-0.085	-0.085	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.007	0.001	56.811	0.016	0.016	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.005	0.000	60.499	0.067	0.067	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.902	-0.956	55.661	-5.883	-5.883	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.037	-0.037	57.070	0.104	0.104	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.894	-0.945	53.529	-6.104	-6.104	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.065	0.048	51.687	-0.120	-0.120	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.845	0.907	48.206	6.304	6.304	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.017	0.028	52.803	0.109	0.109	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.007	-0.024	55.762	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.081	-0.099	59.138	0.073	0.073	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.865	-0.943	62.425	-4.674	-4.674	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.002	-0.001	65.559	0.018	0.018	0.000	0.000	0.000	0.000
68	A	68	HIS	1	0.893	0.908	61.447	5.220	5.220	0.000	0.000	0.000	0.000
69	A	69	TYR	0	0.003	0.008	61.258	0.024	0.024	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.004	-0.013	63.233	0.016	0.016	0.000	0.000	0.000	0.000
71	A	71	HIS	0	-0.017	0.000	64.956	0.049	0.049	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.917	0.950	56.640	5.566	5.566	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.936	0.988	63.259	4.949	4.949	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.005	0.016	64.932	0.037	0.037	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.037	-0.014	67.228	0.013	0.013	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.008	-0.018	63.365	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.046	-0.007	59.011	0.033	0.033	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.033	0.000	60.062	-0.078	-0.078	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.088	-0.052	58.087	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	80	GLY	-1	-0.923	-0.939	59.291	-5.376	-5.376	0.000	0.000	0.000	0.000

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