FMO DATABASE

FMODB ID: RLZJ8

Calculation Name: 5GT0-D-Xray547

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion

Ligand 3-letter code: MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5GT0

Chain ID: D

ChEMBL ID:

UniProt ID: Q96QV6

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-611713.878603
FMO2-HF: Nuclear repulsion	573461.561784
FMO2-HF: Total energy	-38252.316819
FMO2-MP2: Total energy	-38364.897164

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:28:LYS)

Summations of interaction energy for fragment #1(A:28:LYS)

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.
265.377	266.517	-0.002	-0.458	-0.679	-0.001

Interaction energy analysis for fragmet #1(A:28:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.896 / q_NPA : 1.934

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	30	LYS	1	1.059	1.039	3.875	68.621	69.761	-0.002	-0.458	-0.679	-0.001
4	A	31	ARG	1	0.966	0.976	5.668	69.798	69.798	0.000	0.000	0.000	0.000
5	A	32	SER	0	-0.015	-0.004	9.022	1.913	1.913	0.000	0.000	0.000	0.000
6	A	33	ARG	1	1.014	1.012	11.978	33.793	33.793	0.000	0.000	0.000	0.000
7	A	34	LYS	1	0.919	0.956	14.679	35.417	35.417	0.000	0.000	0.000	0.000
8	A	35	GLU	-1	-0.896	-0.941	17.931	-27.586	-27.586	0.000	0.000	0.000	0.000
9	A	36	SER	0	0.001	-0.010	20.884	0.459	0.459	0.000	0.000	0.000	0.000
10	A	37	TYR	0	0.091	0.039	23.983	-0.109	-0.109	0.000	0.000	0.000	0.000
11	A	38	SER	0	0.005	-0.023	25.119	0.809	0.809	0.000	0.000	0.000	0.000
12	A	39	VAL	0	-0.008	-0.003	23.970	0.580	0.580	0.000	0.000	0.000	0.000
13	A	40	TYR	0	-0.014	-0.004	25.794	0.368	0.368	0.000	0.000	0.000	0.000
14	A	41	VAL	0	0.040	0.014	30.115	0.601	0.601	0.000	0.000	0.000	0.000
15	A	42	TYR	0	0.025	0.007	29.695	0.602	0.602	0.000	0.000	0.000	0.000
16	A	43	LYS	1	0.946	0.974	28.779	20.580	20.580	0.000	0.000	0.000	0.000
17	A	44	VAL	0	0.053	0.028	33.038	0.415	0.415	0.000	0.000	0.000	0.000
18	A	45	LEU	0	-0.018	-0.011	33.938	0.405	0.405	0.000	0.000	0.000	0.000
19	A	46	LYS	1	0.783	0.874	33.898	17.494	17.494	0.000	0.000	0.000	0.000
20	A	47	GLN	0	-0.023	-0.010	36.716	0.187	0.187	0.000	0.000	0.000	0.000
21	A	48	VAL	0	-0.040	-0.011	39.235	0.359	0.359	0.000	0.000	0.000	0.000
22	A	49	HIS	0	0.010	0.005	39.859	0.353	0.353	0.000	0.000	0.000	0.000
23	A	50	PRO	0	0.033	0.026	38.758	-0.429	-0.429	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.861	-0.924	37.918	-15.348	-15.348	0.000	0.000	0.000	0.000
25	A	52	THR	0	-0.022	0.007	37.872	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	53	GLY	0	-0.009	0.003	34.461	-0.451	-0.451	0.000	0.000	0.000	0.000
27	A	54	ILE	0	-0.003	-0.014	31.109	0.316	0.316	0.000	0.000	0.000	0.000
28	A	55	SER	0	0.049	0.031	30.886	-0.608	-0.608	0.000	0.000	0.000	0.000
29	A	56	SER	0	0.061	0.021	26.169	0.329	0.329	0.000	0.000	0.000	0.000
30	A	57	LYS	1	0.972	0.974	28.063	18.557	18.557	0.000	0.000	0.000	0.000
31	A	58	ALA	0	0.022	0.026	30.233	0.408	0.408	0.000	0.000	0.000	0.000
32	A	59	MET	0	0.039	0.035	27.610	0.265	0.265	0.000	0.000	0.000	0.000
33	A	60	GLY	0	0.022	0.016	28.124	-0.209	-0.209	0.000	0.000	0.000	0.000
34	A	61	ILE	0	-0.010	0.007	28.945	0.013	0.013	0.000	0.000	0.000	0.000
35	A	62	MET	0	0.041	0.020	31.623	0.249	0.249	0.000	0.000	0.000	0.000
36	A	63	ASN	0	-0.034	-0.031	26.796	-0.432	-0.432	0.000	0.000	0.000	0.000
37	A	64	SER	0	0.001	0.002	29.642	-0.224	-0.224	0.000	0.000	0.000	0.000
38	A	65	PHE	0	0.017	0.009	31.428	0.170	0.170	0.000	0.000	0.000	0.000
39	A	66	VAL	0	-0.002	0.000	31.418	0.258	0.258	0.000	0.000	0.000	0.000
40	A	67	ASN	0	-0.029	-0.033	27.593	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	68	ASP	-1	-0.812	-0.855	31.695	-16.126	-16.126	0.000	0.000	0.000	0.000
42	A	69	ILE	0	-0.011	-0.009	35.012	0.355	0.355	0.000	0.000	0.000	0.000
43	A	70	PHE	0	-0.017	-0.005	31.024	0.264	0.264	0.000	0.000	0.000	0.000
44	A	71	GLU	-1	-0.934	-0.970	33.039	-16.933	-16.933	0.000	0.000	0.000	0.000
45	A	72	ARG	1	0.847	0.897	34.896	15.788	15.788	0.000	0.000	0.000	0.000
46	A	73	ILE	0	0.003	-0.005	38.108	0.397	0.397	0.000	0.000	0.000	0.000
47	A	74	ALA	0	0.004	0.007	35.123	0.299	0.299	0.000	0.000	0.000	0.000
48	A	75	GLY	0	0.067	0.023	37.039	0.195	0.195	0.000	0.000	0.000	0.000
49	A	76	GLU	-1	-0.913	-0.948	38.448	-13.429	-13.429	0.000	0.000	0.000	0.000
50	A	77	ALA	0	0.002	-0.006	39.725	0.308	0.308	0.000	0.000	0.000	0.000
51	A	78	SER	0	-0.016	-0.006	38.032	0.319	0.319	0.000	0.000	0.000	0.000
52	A	79	ARG	1	0.892	0.943	40.265	14.669	14.669	0.000	0.000	0.000	0.000
53	A	80	LEU	0	-0.014	0.000	43.389	0.334	0.334	0.000	0.000	0.000	0.000
54	A	81	ALA	0	0.008	0.007	42.187	0.334	0.334	0.000	0.000	0.000	0.000
55	A	82	HIS	0	0.030	0.022	42.836	0.153	0.153	0.000	0.000	0.000	0.000
56	A	83	TYR	0	-0.008	-0.017	44.713	0.205	0.205	0.000	0.000	0.000	0.000
57	A	84	ASN	0	-0.106	-0.068	47.751	0.516	0.516	0.000	0.000	0.000	0.000
58	A	85	LYS	1	0.919	0.965	46.938	12.239	12.239	0.000	0.000	0.000	0.000
59	A	86	ARG	1	0.944	0.993	44.897	12.647	12.647	0.000	0.000	0.000	0.000
60	A	87	SER	0	0.012	0.011	41.207	-0.130	-0.130	0.000	0.000	0.000	0.000
61	A	88	THR	0	-0.032	-0.037	39.675	-0.344	-0.344	0.000	0.000	0.000	0.000
62	A	89	ILE	0	0.001	0.024	37.348	0.350	0.350	0.000	0.000	0.000	0.000
63	A	90	THR	0	-0.009	-0.029	39.789	-0.171	-0.171	0.000	0.000	0.000	0.000
64	A	91	SER	0	0.060	0.008	42.095	-0.088	-0.088	0.000	0.000	0.000	0.000
65	A	92	ARG	1	0.949	0.985	42.895	12.300	12.300	0.000	0.000	0.000	0.000
66	A	93	GLU	-1	-0.777	-0.865	42.946	-13.386	-13.386	0.000	0.000	0.000	0.000
67	A	94	ILE	0	0.032	0.018	38.406	0.019	0.019	0.000	0.000	0.000	0.000
68	A	95	GLN	0	0.003	0.006	42.326	0.292	0.292	0.000	0.000	0.000	0.000
69	A	96	THR	0	-0.049	-0.036	45.524	0.306	0.306	0.000	0.000	0.000	0.000
70	A	97	ALA	0	0.046	0.020	42.564	0.147	0.147	0.000	0.000	0.000	0.000
71	A	98	VAL	0	-0.029	-0.021	42.545	0.040	0.040	0.000	0.000	0.000	0.000
72	A	99	ARG	1	0.883	0.921	44.818	12.300	12.300	0.000	0.000	0.000	0.000
73	A	100	LEU	0	-0.022	0.007	46.679	0.225	0.225	0.000	0.000	0.000	0.000
74	A	101	LEU	0	-0.020	0.003	41.668	0.015	0.015	0.000	0.000	0.000	0.000
75	A	102	LEU	0	-0.039	-0.006	42.573	-0.177	-0.177	0.000	0.000	0.000	0.000
76	A	103	PRO	0	0.052	0.019	46.572	0.279	0.279	0.000	0.000	0.000	0.000
77	A	104	GLY	0	0.056	0.026	49.620	-0.085	-0.085	0.000	0.000	0.000	0.000
78	A	105	GLU	-1	-0.779	-0.877	51.732	-11.406	-11.406	0.000	0.000	0.000	0.000
79	A	106	LEU	0	0.008	0.009	44.416	-0.098	-0.098	0.000	0.000	0.000	0.000
80	A	107	ALA	0	0.007	0.005	46.969	-0.237	-0.237	0.000	0.000	0.000	0.000
81	A	108	LYS	1	0.829	0.901	48.157	11.125	11.125	0.000	0.000	0.000	0.000
82	A	109	HIS	0	-0.001	-0.001	47.273	0.016	0.016	0.000	0.000	0.000	0.000
83	A	110	ALA	0	0.041	0.033	43.650	-0.155	-0.155	0.000	0.000	0.000	0.000
84	A	111	VAL	0	-0.016	-0.013	44.553	-0.205	-0.205	0.000	0.000	0.000	0.000
85	A	112	SER	0	-0.068	-0.022	46.984	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	113	GLU	-1	-0.802	-0.903	42.920	-13.971	-13.971	0.000	0.000	0.000	0.000
87	A	114	GLY	0	0.013	0.007	42.196	-0.234	-0.234	0.000	0.000	0.000	0.000
88	A	115	THR	0	-0.035	-0.043	43.227	-0.094	-0.094	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.884	0.953	44.372	13.715	13.715	0.000	0.000	0.000	0.000
90	A	117	ALA	0	-0.026	-0.005	40.142	-0.083	-0.083	0.000	0.000	0.000	0.000
91	A	118	VAL	0	0.005	0.000	41.317	-0.163	-0.163	0.000	0.000	0.000	0.000
92	A	119	THR	0	-0.019	-0.019	42.886	0.009	0.009	0.000	0.000	0.000	0.000
93	A	120	LYS	1	0.972	0.989	41.371	14.384	14.384	0.000	0.000	0.000	0.000
94	A	121	TYR	0	-0.047	-0.009	36.081	-0.227	-0.227	0.000	0.000	0.000	0.000
95	A	122	THR	0	-0.013	-0.029	41.188	-0.105	-0.105	0.000	0.000	0.000	0.000
96	A	123	SER	0	-0.090	-0.044	43.828	0.216	0.216	0.000	0.000	0.000	0.000
97	A	124	SER	0	-0.085	-0.050	41.437	0.208	0.208	0.000	0.000	0.000	0.000
98	A	125	LYS	0	0.079	0.060	37.820	0.424	0.424	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:LYS)