FMO DATABASE

FMODB ID: 743GK

Calculation Name: 6NQB-H-Other547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6NQB

Chain ID: H

ChEMBL ID:

UniProt ID: P0A7R5

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1027910.262244
FMO2-HF: Nuclear repulsion	978401.24058
FMO2-HF: Total energy	-49509.021665
FMO2-MP2: Total energy	-49651.222329

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:SER)

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

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.
10.811	12.321	32.778	-17.866	-16.423	-0.129

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.773 / q_NPA : 0.857

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	3	GLN	0	0.042	0.014	2.893	3.410	6.472	0.363	-1.607	-1.819	0.000
4	A	4	ASP	-1	-0.723	-0.866	2.158	-34.065	-32.312	1.739	-1.532	-1.960	0.010
5	A	5	PRO	0	-0.029	0.020	1.654	-27.250	-34.463	20.736	-8.472	-5.051	-0.055
6	A	6	ILE	0	0.005	0.005	3.278	-0.242	-0.744	0.006	0.815	-0.320	-0.001
7	A	7	ALA	0	0.045	0.015	4.560	1.539	1.596	-0.001	-0.003	-0.052	0.000
8	A	8	ASP	-1	-0.828	-0.917	1.968	-110.920	-106.760	9.938	-7.026	-7.072	-0.083
9	A	9	MET	0	-0.012	-0.007	4.136	0.782	0.892	-0.001	-0.033	-0.076	0.000
12	A	12	ARG	1	0.856	0.913	4.673	46.845	46.885	-0.001	-0.005	-0.034	0.000
27	A	27	PRO	0	0.073	0.070	4.677	1.914	1.957	-0.001	-0.003	-0.039	0.000
10	A	10	LEU	0	0.034	0.010	6.072	3.677	3.677	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.010	0.008	7.278	3.993	3.993	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.031	0.014	8.808	2.395	2.395	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.905	0.947	11.866	22.504	22.504	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.012	-0.014	11.134	2.603	2.603	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.004	0.002	13.895	1.151	1.151	0.000	0.000	0.000	0.000
17	A	17	GLN	0	-0.010	-0.020	15.730	1.456	1.456	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.009	0.017	17.288	0.784	0.784	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.037	-0.021	18.174	0.607	0.607	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.005	0.010	19.951	-0.050	-0.050	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.948	0.980	15.747	18.239	18.239	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.061	0.031	19.340	-0.151	-0.151	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.034	0.016	17.368	0.080	0.080	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.067	-0.027	11.108	-0.734	-0.734	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.070	0.046	10.805	0.809	0.809	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.065	-0.025	6.460	-3.193	-3.193	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.055	-0.062	6.765	-4.140	-4.140	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.011	-0.006	8.397	3.831	3.831	0.000	0.000	0.000	0.000
30	A	30	LYS	1	1.004	0.986	10.152	20.858	20.858	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.027	0.018	9.572	0.692	0.692	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.848	0.920	4.880	47.184	47.184	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.034	0.025	11.054	0.517	0.517	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.001	0.002	14.702	0.995	0.995	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.018	-0.001	9.806	0.075	0.075	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.026	0.006	13.875	0.979	0.979	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.010	-0.020	15.344	0.966	0.966	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.010	0.007	17.409	0.796	0.796	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.026	-0.025	14.605	0.410	0.410	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.893	0.952	18.418	14.065	14.065	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.931	-0.956	20.881	-12.843	-12.843	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.956	-0.985	22.041	-11.760	-11.760	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.003	0.020	23.442	0.245	0.245	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.001	-0.003	19.703	0.102	0.102	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.057	-0.041	16.433	-0.470	-0.470	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.823	-0.895	20.571	-12.055	-12.055	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.861	-0.944	21.445	-13.641	-13.641	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.057	-0.017	16.763	-1.184	-1.184	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.996	1.023	17.923	15.715	15.715	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.047	-0.028	14.748	-1.281	-1.281	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.918	-0.960	15.696	-14.878	-14.878	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.045	0.027	15.214	-1.527	-1.527	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.869	-0.930	16.335	-16.933	-16.933	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.018	-0.025	15.580	-1.191	-1.191	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.858	0.913	10.829	21.935	21.935	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.018	0.030	11.206	0.585	0.585	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.890	-0.970	9.580	-36.046	-36.046	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.040	-0.025	11.359	1.940	1.940	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.880	-0.939	13.058	-18.157	-18.157	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.019	-0.021	12.991	0.749	0.749	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.010	-0.019	15.996	0.065	0.065	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.046	-0.032	15.503	-0.444	-0.444	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.839	0.918	19.410	13.241	13.241	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.042	-0.026	21.788	-0.156	-0.156	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.005	0.014	24.471	0.297	0.297	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.026	-0.013	27.861	0.371	0.371	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.022	0.011	27.535	-0.319	-0.319	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.791	0.885	26.064	11.268	11.268	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.034	0.001	21.329	0.082	0.082	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.017	0.004	22.527	0.341	0.341	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.045	-0.014	16.839	-0.024	-0.024	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.805	-0.867	19.340	-12.943	-12.943	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.057	-0.051	18.932	-0.073	-0.073	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.001	0.022	13.936	-0.144	-0.144	0.000	0.000	0.000	0.000
75	A	75	GLN	0	0.018	0.000	13.985	-1.170	-1.170	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.824	0.912	7.311	28.257	28.257	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.023	-0.007	12.029	0.603	0.603	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.019	-0.035	12.910	0.467	0.467	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.978	0.995	9.154	17.711	17.711	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.001	-0.004	6.660	1.856	1.856	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.004	-0.006	9.902	0.005	0.005	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.055	-0.022	12.831	1.080	1.080	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.901	0.933	10.623	20.670	20.670	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.006	0.004	15.449	0.936	0.936	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.008	-0.015	15.609	-0.128	-0.128	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.865	0.933	19.906	12.754	12.754	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.997	1.007	22.511	9.808	9.808	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.856	0.903	26.067	9.931	9.931	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.899	-0.957	27.087	-9.654	-9.654	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.841	-0.909	25.589	-10.966	-10.966	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.048	-0.008	23.427	-0.176	-0.176	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.033	-0.010	20.962	0.387	0.387	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.955	0.973	23.310	10.131	10.131	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.012	0.008	20.528	0.106	0.106	0.000	0.000	0.000	0.000
95	A	95	MET	0	0.031	0.020	23.695	0.366	0.366	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.006	-0.007	25.912	0.266	0.266	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.045	-0.026	27.163	0.334	0.334	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.013	0.009	27.854	0.126	0.126	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.016	0.028	23.504	-0.135	-0.135	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.002	-0.003	19.934	0.274	0.274	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.028	-0.026	19.977	-0.629	-0.629	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.030	0.029	15.732	0.088	0.088	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.011	-0.020	16.636	-0.676	-0.676	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.004	-0.003	15.223	-0.235	-0.235	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.048	-0.030	17.303	0.710	0.710	0.000	0.000	0.000	0.000
106	A	106	SER	0	0.011	-0.002	20.526	-0.166	-0.166	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.944	0.956	22.753	10.833	10.833	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.040	0.042	19.967	0.109	0.109	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.013	0.006	15.492	0.126	0.126	0.000	0.000	0.000	0.000
110	A	110	MET	0	0.039	0.035	18.640	-0.337	-0.337	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.054	-0.037	19.785	0.484	0.484	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.726	-0.839	21.874	-11.444	-11.444	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.904	0.936	24.757	10.633	10.633	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.025	0.008	24.513	0.403	0.403	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.010	-0.014	26.508	0.249	0.249	0.000	0.000	0.000	0.000
116	A	116	ARG	1	0.896	0.951	28.716	9.285	9.285	0.000	0.000	0.000	0.000
117	A	117	GLN	0	0.037	0.014	30.074	0.245	0.245	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.021	0.025	27.097	0.093	0.093	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.019	0.011	29.026	0.131	0.131	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.046	-0.024	24.479	0.119	0.119	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.029	0.013	23.806	-0.223	-0.223	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.033	0.010	20.307	0.056	0.056	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.821	-0.849	13.063	-19.630	-19.630	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.003	0.011	15.538	-0.167	-0.167	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.046	-0.027	11.356	-1.177	-1.177	0.000	0.000	0.000	0.000
126	A	126	CYS	0	-0.054	-0.046	12.097	-1.970	-1.970	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.007	0.012	14.298	1.046	1.046	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.003	-0.013	16.326	-1.207	-1.207	0.000	0.000	0.000	0.000
129	A	129	ALA	-1	-0.762	-0.868	18.589	-14.055	-14.055	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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