FMO DATABASE

FMODB ID: 2GL8R

Calculation Name: 3J7R-A-Other547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3J7R

Chain ID: A

ChEMBL ID:

UniProt ID: P63246

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1196056.161916
FMO2-HF: Nuclear repulsion	1140829.161749
FMO2-HF: Total energy	-55227.000166
FMO2-MP2: Total energy	-55392.420099

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:6:PRO)

Summations of interaction energy for fragment #1(A:6: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.
197.537	199.689	0.532	-1.091	-1.592	0

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.890

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	8	LYS	1	0.899	0.945	3.872	37.249	38.133	-0.008	-0.463	-0.412	-0.001
49	A	54	LYS	1	0.884	0.954	2.237	61.773	62.537	0.536	-0.391	-0.909	0.002
53	A	58	GLU	-1	-0.831	-0.901	3.895	-64.538	-64.034	0.004	-0.237	-0.271	-0.001
4	A	9	PHE	0	0.056	0.034	6.728	3.541	3.541	0.000	0.000	0.000	0.000
5	A	10	GLN	0	0.000	0.013	9.617	0.309	0.309	0.000	0.000	0.000	0.000
6	A	11	HIS	0	-0.031	-0.007	8.071	3.729	3.729	0.000	0.000	0.000	0.000
7	A	12	ILE	0	0.038	0.024	13.022	1.175	1.175	0.000	0.000	0.000	0.000
8	A	13	LEU	0	0.034	0.028	13.823	-0.128	-0.128	0.000	0.000	0.000	0.000
9	A	14	ARG	1	0.923	0.962	17.834	13.062	13.062	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.055	0.022	19.252	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	16	LEU	0	0.032	0.018	22.369	0.329	0.329	0.000	0.000	0.000	0.000
12	A	17	ASN	0	-0.008	-0.016	26.029	0.001	0.001	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.034	-0.010	24.392	0.403	0.403	0.000	0.000	0.000	0.000
14	A	19	ASN	0	0.008	-0.002	21.454	-0.120	-0.120	0.000	0.000	0.000	0.000
15	A	20	ILE	0	-0.008	0.001	16.325	0.221	0.221	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.847	-0.924	15.405	-17.893	-17.893	0.000	0.000	0.000	0.000
17	A	22	GLY	0	0.014	-0.012	11.922	-0.391	-0.391	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.915	0.941	10.485	21.940	21.940	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.944	0.981	11.712	15.893	15.893	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.967	0.994	11.047	22.445	22.445	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.134	0.061	10.334	2.257	2.257	0.000	0.000	0.000	0.000
22	A	27	ALA	0	-0.008	-0.008	13.830	1.273	1.273	0.000	0.000	0.000	0.000
23	A	28	PHE	0	-0.077	-0.046	15.770	1.237	1.237	0.000	0.000	0.000	0.000
24	A	29	ALA	0	0.005	0.010	14.788	0.881	0.881	0.000	0.000	0.000	0.000
25	A	30	ILE	0	0.076	0.036	16.956	0.855	0.855	0.000	0.000	0.000	0.000
26	A	31	THR	0	-0.110	-0.064	19.354	0.779	0.779	0.000	0.000	0.000	0.000
27	A	32	ALA	0	-0.007	0.013	20.949	0.582	0.582	0.000	0.000	0.000	0.000
28	A	33	ILE	0	-0.008	-0.001	21.439	0.636	0.636	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.950	0.975	24.437	11.426	11.426	0.000	0.000	0.000	0.000
30	A	35	GLY	0	0.056	0.006	27.804	0.069	0.069	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.004	0.015	22.913	0.156	0.156	0.000	0.000	0.000	0.000
32	A	37	GLY	0	0.043	0.028	24.539	-0.258	-0.258	0.000	0.000	0.000	0.000
33	A	38	ARG	1	1.020	0.985	20.818	13.625	13.625	0.000	0.000	0.000	0.000
34	A	39	ARG	1	0.916	0.971	21.910	11.424	11.424	0.000	0.000	0.000	0.000
35	A	40	TYR	0	-0.001	-0.006	24.169	-0.099	-0.099	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.044	0.022	19.505	-0.182	-0.182	0.000	0.000	0.000	0.000
37	A	42	HIS	0	-0.039	-0.024	19.012	-0.828	-0.828	0.000	0.000	0.000	0.000
38	A	43	VAL	0	-0.034	-0.012	19.920	-0.294	-0.294	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.021	0.013	19.727	0.003	0.003	0.000	0.000	0.000	0.000
40	A	45	LEU	0	0.029	0.011	14.760	-0.114	-0.114	0.000	0.000	0.000	0.000
41	A	46	ARG	1	0.943	0.972	17.297	14.169	14.169	0.000	0.000	0.000	0.000
42	A	47	LYS	1	0.822	0.929	19.735	12.232	12.232	0.000	0.000	0.000	0.000
43	A	48	ALA	0	-0.022	-0.026	17.379	0.316	0.316	0.000	0.000	0.000	0.000
44	A	49	ASP	-1	-0.955	-0.954	17.250	-16.711	-16.711	0.000	0.000	0.000	0.000
45	A	50	ILE	0	0.002	0.014	11.833	-0.939	-0.939	0.000	0.000	0.000	0.000
46	A	51	ASP	-1	-0.787	-0.863	9.242	-27.965	-27.965	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.031	-0.021	10.664	-1.268	-1.268	0.000	0.000	0.000	0.000
48	A	53	THR	0	-0.134	-0.116	8.829	-0.136	-0.136	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.853	0.910	6.792	36.460	36.460	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.020	-0.005	8.711	-0.645	-0.645	0.000	0.000	0.000	0.000
52	A	57	GLY	0	-0.011	0.010	9.406	1.950	1.950	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.007	-0.006	6.942	3.491	3.491	0.000	0.000	0.000	0.000
55	A	60	THR	0	0.015	-0.008	8.982	0.116	0.116	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.890	-0.956	11.809	-16.320	-16.320	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.825	-0.900	15.341	-15.891	-15.891	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.879	-0.930	11.939	-21.722	-21.722	0.000	0.000	0.000	0.000
59	A	64	VAL	0	-0.040	-0.024	13.790	0.781	0.781	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.872	-0.934	16.318	-13.028	-13.028	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.918	0.997	17.545	15.626	15.626	0.000	0.000	0.000	0.000
62	A	67	VAL	0	-0.006	-0.024	16.422	0.684	0.684	0.000	0.000	0.000	0.000
63	A	68	ILE	0	-0.008	-0.007	19.323	0.839	0.839	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.007	-0.032	22.201	0.675	0.675	0.000	0.000	0.000	0.000
65	A	70	ILE	0	-0.019	-0.003	20.806	0.656	0.656	0.000	0.000	0.000	0.000
66	A	71	MET	0	-0.056	-0.032	22.839	0.339	0.339	0.000	0.000	0.000	0.000
67	A	72	GLN	0	0.002	0.010	24.712	0.309	0.309	0.000	0.000	0.000	0.000
68	A	73	ASN	0	-0.033	-0.009	27.193	0.653	0.653	0.000	0.000	0.000	0.000
69	A	74	PRO	0	0.027	0.015	27.029	0.023	0.023	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.885	0.937	28.052	8.828	8.828	0.000	0.000	0.000	0.000
71	A	76	GLN	0	0.017	0.014	29.724	0.175	0.175	0.000	0.000	0.000	0.000
72	A	77	TYR	0	0.026	0.018	25.180	-0.063	-0.063	0.000	0.000	0.000	0.000
73	A	78	LYS	1	0.978	0.977	26.318	10.957	10.957	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.045	-0.013	24.741	-0.169	-0.169	0.000	0.000	0.000	0.000
75	A	80	PRO	0	0.022	0.015	28.971	0.240	0.240	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.834	-0.955	32.060	-8.968	-8.968	0.000	0.000	0.000	0.000
77	A	82	TRP	0	0.016	0.017	31.780	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	83	PHE	0	-0.050	-0.032	28.192	-0.209	-0.209	0.000	0.000	0.000	0.000
79	A	84	LEU	0	-0.008	-0.008	29.894	-0.248	-0.248	0.000	0.000	0.000	0.000
80	A	85	ASN	0	0.033	0.013	31.534	0.293	0.293	0.000	0.000	0.000	0.000
81	A	86	ARG	1	0.865	0.963	33.312	8.413	8.413	0.000	0.000	0.000	0.000
82	A	87	GLN	0	0.008	-0.016	35.287	0.299	0.299	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.943	0.956	38.282	7.510	7.510	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.780	-0.891	40.439	-7.683	-7.683	0.000	0.000	0.000	0.000
85	A	90	VAL	0	0.003	0.017	42.031	0.117	0.117	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.808	0.906	44.071	6.865	6.865	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.737	-0.853	43.825	-7.052	-7.052	0.000	0.000	0.000	0.000
88	A	93	GLY	0	-0.031	-0.015	43.587	-0.150	-0.150	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.934	0.956	37.389	8.159	8.159	0.000	0.000	0.000	0.000
90	A	95	TYR	0	0.011	0.028	36.946	0.058	0.058	0.000	0.000	0.000	0.000
91	A	96	SER	0	-0.060	-0.044	33.992	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	97	GLN	0	0.039	0.028	28.367	0.230	0.230	0.000	0.000	0.000	0.000
93	A	98	VAL	0	-0.017	0.007	31.046	-0.075	-0.075	0.000	0.000	0.000	0.000
94	A	99	LEU	0	0.013	-0.001	25.965	-0.087	-0.087	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.014	0.006	27.838	0.321	0.321	0.000	0.000	0.000	0.000
96	A	101	ASN	0	0.045	0.011	29.395	0.027	0.027	0.000	0.000	0.000	0.000
97	A	102	GLY	0	0.048	0.035	32.259	0.351	0.351	0.000	0.000	0.000	0.000
98	A	103	LEU	0	-0.045	-0.018	30.794	0.297	0.297	0.000	0.000	0.000	0.000
99	A	104	ASP	-1	-0.916	-0.951	34.313	-8.573	-8.573	0.000	0.000	0.000	0.000
100	A	105	ASN	0	0.040	0.028	36.096	0.427	0.427	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.884	0.933	37.209	8.112	8.112	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.022	-0.001	36.972	0.226	0.226	0.000	0.000	0.000	0.000
103	A	108	ARG	1	0.931	0.954	39.492	7.875	7.875	0.000	0.000	0.000	0.000
104	A	109	GLU	-1	-0.881	-0.946	41.942	-7.413	-7.413	0.000	0.000	0.000	0.000
105	A	110	ASP	-1	-0.829	-0.915	41.987	-7.261	-7.261	0.000	0.000	0.000	0.000
106	A	111	LEU	0	-0.063	-0.039	42.282	0.203	0.203	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.843	-0.914	45.537	-6.654	-6.654	0.000	0.000	0.000	0.000
108	A	113	ARG	1	0.840	0.925	45.354	7.108	7.108	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.062	-0.040	46.705	0.161	0.161	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.882	0.932	48.742	6.717	6.717	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.981	1.002	51.619	6.188	6.188	0.000	0.000	0.000	0.000
112	A	117	ILE	0	-0.082	-0.045	51.922	0.138	0.138	0.000	0.000	0.000	0.000
113	A	118	ARG	1	0.968	0.988	54.827	5.679	5.679	0.000	0.000	0.000	0.000
114	A	119	ALA	0	0.029	0.027	52.225	0.066	0.066	0.000	0.000	0.000	0.000
115	A	120	HIS	0	0.069	0.024	53.440	-0.174	-0.174	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.966	0.965	47.187	6.649	6.649	0.000	0.000	0.000	0.000
117	A	122	GLY	0	0.048	0.025	49.273	-0.128	-0.128	0.000	0.000	0.000	0.000
118	A	123	LEU	0	0.002	0.015	50.517	-0.047	-0.047	0.000	0.000	0.000	0.000
119	A	124	ARG	1	0.904	0.951	49.874	6.151	6.151	0.000	0.000	0.000	0.000
120	A	125	HIS	0	0.030	-0.007	42.877	0.016	0.016	0.000	0.000	0.000	0.000
121	A	126	PHE	0	-0.034	-0.002	47.671	-0.105	-0.105	0.000	0.000	0.000	0.000
122	A	127	TRP	0	-0.001	-0.005	50.023	0.023	0.023	0.000	0.000	0.000	0.000
123	A	128	GLY	0	0.038	0.043	47.073	0.004	0.004	0.000	0.000	0.000	0.000
124	A	129	LEU	0	-0.036	-0.012	47.788	-0.033	-0.033	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.907	0.954	44.225	6.987	6.987	0.000	0.000	0.000	0.000
126	A	131	VAL	0	0.030	0.008	45.669	0.154	0.154	0.000	0.000	0.000	0.000
127	A	132	ARG	1	0.916	0.958	40.908	7.691	7.691	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.034	0.015	47.550	0.024	0.024	0.000	0.000	0.000	0.000
129	A	134	GLN	0	0.020	0.006	44.340	-0.057	-0.057	0.000	0.000	0.000	0.000
130	A	135	HIS	0	0.066	0.024	49.696	-0.041	-0.041	0.000	0.000	0.000	0.000
131	A	136	THR	0	-0.016	-0.012	48.959	-0.095	-0.095	0.000	0.000	0.000	0.000
132	A	137	LYS	1	1.011	1.026	51.170	5.585	5.585	0.000	0.000	0.000	0.000
133	A	138	THR	0	0.003	0.007	50.532	0.030	0.030	0.000	0.000	0.000	0.000
134	A	139	THR	0	0.021	0.008	46.059	-0.103	-0.103	0.000	0.000	0.000	0.000
135	A	140	GLY	0	-0.042	-0.034	46.365	0.095	0.095	0.000	0.000	0.000	0.000
136	A	141	ARG	1	0.923	0.956	46.986	6.347	6.347	0.000	0.000	0.000	0.000
137	A	142	ARG	0	0.069	0.053	42.601	0.069	0.069	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)