FMO DATABASE

FMODB ID: 2GNVR

Calculation Name: 3J7Q-Y-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: 3J7Q

Chain ID: Y

ChEMBL ID:

UniProt ID: Q29195

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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1189402.410721
FMO2-HF: Nuclear repulsion	1134707.634895
FMO2-HF: Total energy	-54694.775825
FMO2-MP2: Total energy	-54856.723984

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:MET)

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

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.
294.901	299.372	1.47	-2.495	-3.444	-0.025

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

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 : 0.942

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	PHE	0	0.086	0.032	2.519	-12.019	-7.744	1.472	-2.490	-3.256	-0.025
4	A	4	ASN	0	0.030	0.004	5.096	3.335	3.449	-0.001	-0.003	-0.109	0.000
9	A	9	SER	0	0.000	0.004	4.826	-3.173	-3.091	-0.001	-0.002	-0.079	0.000
5	A	5	PRO	0	0.073	0.043	8.012	-1.159	-1.159	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.094	0.049	9.576	0.958	0.958	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.052	-0.017	8.410	0.660	0.660	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.057	-0.030	8.890	-0.123	-0.123	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.715	-0.840	6.802	-19.975	-19.975	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.985	0.995	9.514	19.498	19.498	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.009	-0.006	11.745	1.104	1.104	0.000	0.000	0.000	0.000
13	A	13	LYS	1	1.038	1.006	12.703	18.483	18.483	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.022	-0.024	10.332	0.309	0.309	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.941	0.983	14.046	14.932	14.932	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.953	0.984	16.517	13.600	13.600	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.898	0.915	13.268	18.977	18.977	0.000	0.000	0.000	0.000
18	A	18	HIS	0	0.026	0.026	17.219	0.732	0.732	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.023	-0.011	19.653	0.372	0.372	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.044	0.022	22.175	0.857	0.857	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.013	0.021	21.384	0.155	0.155	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.105	0.055	23.223	0.410	0.410	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.035	0.002	25.878	-0.483	-0.483	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.101	0.041	24.756	-0.650	-0.650	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.016	0.000	20.685	-0.230	-0.230	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.865	0.932	22.749	11.536	11.536	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.973	0.985	24.001	11.798	11.798	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.843	0.932	20.449	13.576	13.576	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.017	0.021	18.854	-0.370	-0.370	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.041	0.006	20.531	-0.093	-0.093	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.047	-0.032	20.464	0.411	0.411	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.008	0.019	22.050	-0.174	-0.174	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.015	-0.022	21.324	-0.188	-0.188	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.011	0.015	22.794	0.462	0.462	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.003	-0.015	25.312	-0.291	-0.291	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.955	0.953	23.989	12.171	12.171	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.817	-0.888	28.009	-9.298	-9.298	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.006	-0.006	28.903	-0.060	-0.060	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.879	0.934	20.605	13.528	13.528	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.006	0.005	26.034	-0.553	-0.553	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.964	0.998	28.239	9.232	9.232	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.020	-0.007	27.936	0.229	0.229	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.075	0.046	23.500	-0.752	-0.752	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.011	-0.003	23.123	-0.742	-0.742	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.940	0.968	16.300	17.499	17.499	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.037	0.002	19.213	0.105	0.105	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.004	0.016	21.995	-0.260	-0.260	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.050	-0.029	23.372	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.030	0.039	25.338	0.294	0.294	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.787	0.882	28.215	8.986	8.986	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.950	0.961	31.690	7.986	7.986	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.790	-0.908	34.984	-8.501	-8.501	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.734	-0.827	30.518	-10.043	-10.043	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.825	-0.880	33.887	-8.188	-8.188	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.005	-0.010	29.838	-0.380	-0.380	0.000	0.000	0.000	0.000
56	A	56	GLN	0	0.040	0.029	30.801	0.367	0.367	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.031	0.015	29.654	-0.494	-0.494	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.030	0.022	25.361	0.065	0.065	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.830	0.892	23.380	12.024	12.024	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.047	0.019	27.320	0.259	0.259	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.071	0.041	29.705	-0.177	-0.177	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.046	0.026	33.269	0.027	0.027	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.882	0.942	28.978	10.324	10.324	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.035	0.020	32.691	0.269	0.269	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.061	0.021	33.252	-0.551	-0.551	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.035	0.023	35.604	-0.143	-0.143	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.013	0.007	35.041	-0.193	-0.193	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.017	0.021	35.495	0.311	0.311	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.920	0.960	35.328	7.558	7.558	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.076	-0.042	31.955	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.048	0.032	35.247	0.222	0.222	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.031	-0.033	35.273	-0.094	-0.094	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.035	0.015	29.636	-0.240	-0.240	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.104	0.055	31.634	0.044	0.044	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.922	0.954	28.176	10.248	10.248	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.957	0.989	28.380	9.070	9.070	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.989	0.988	29.152	8.738	8.738	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.057	-0.028	20.555	-0.323	-0.323	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.019	0.024	26.272	-0.383	-0.383	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.037	-0.034	28.506	0.201	0.201	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.027	0.019	30.823	-0.138	-0.138	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.029	-0.001	31.168	0.033	0.033	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.830	-0.909	35.728	-7.602	-7.602	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.938	0.956	39.114	7.794	7.794	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.052	-0.014	33.976	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.010	-0.014	37.310	0.048	0.048	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.902	0.962	38.756	7.792	7.792	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.833	-0.909	41.466	-6.546	-6.546	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.848	0.928	44.023	6.821	6.821	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.068	0.020	46.030	0.088	0.088	0.000	0.000	0.000	0.000
91	A	91	ASN	0	0.047	0.027	49.105	0.011	0.011	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.095	0.059	49.982	0.078	0.078	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.071	-0.046	46.842	-0.064	-0.064	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.051	0.037	44.529	-0.119	-0.119	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.061	-0.035	39.972	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	HIS	0	0.037	0.009	37.736	-0.120	-0.120	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.030	-0.015	33.914	-0.068	-0.068	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.016	-0.010	32.034	-0.105	-0.105	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.023	0.008	28.119	-0.216	-0.216	0.000	0.000	0.000	0.000
100	A	100	HIS	0	0.039	0.000	22.918	0.104	0.104	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.002	0.012	23.862	0.065	0.065	0.000	0.000	0.000	0.000
102	A	102	SER	0	0.027	-0.001	20.031	0.092	0.092	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.874	0.936	19.764	14.214	14.214	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.029	0.029	24.597	0.452	0.452	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.020	-0.011	25.086	-0.619	-0.619	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.009	0.008	26.741	0.381	0.381	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.014	0.001	29.172	-0.225	-0.225	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.934	0.935	32.279	8.240	8.240	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.065	-0.016	28.263	-0.130	-0.130	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.939	0.980	32.366	8.507	8.507	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.033	-0.026	33.306	-0.305	-0.305	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.769	-0.870	35.221	-8.431	-8.431	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.982	0.981	35.579	8.130	8.130	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.818	-0.911	33.389	-9.090	-9.090	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.683	0.790	28.858	9.857	9.857	0.000	0.000	0.000	0.000
116	A	116	LYS	1	1.008	1.011	30.481	8.303	8.303	0.000	0.000	0.000	0.000
117	A	117	LYS	1	1.095	1.053	30.570	9.747	9.747	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.081	-0.043	25.600	-0.503	-0.503	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.015	-0.012	26.281	-0.591	-0.591	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.855	-0.917	26.917	-10.127	-10.127	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.908	0.953	23.466	12.342	12.342	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.832	0.906	20.979	13.584	13.584	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.037	0.025	22.644	-0.614	-0.614	0.000	0.000	0.000	0.000
124	A	124	LYS	1	1.012	1.003	24.622	11.131	11.131	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.019	-0.006	19.752	-0.290	-0.290	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.881	0.943	17.662	15.131	15.131	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.050	-0.025	20.882	-0.577	-0.577	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.090	0.044	21.888	-0.041	-0.041	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.012	-0.006	18.617	-0.212	-0.212	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.888	0.941	18.735	12.786	12.786	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.835	-0.910	20.643	-11.965	-11.965	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.937	0.978	16.098	18.040	18.040	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.108	-0.068	18.755	-0.554	-0.554	0.000	0.000	0.000	0.000
134	A	134	LYS	0	-0.004	0.019	19.390	-1.099	-1.099	0.000	0.000	0.000	0.000

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