FMO DATABASE

FMODB ID: G7Y21

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1226892.914509
FMO2-HF: Nuclear repulsion	1172621.219184
FMO2-HF: Total energy	-54271.695325
FMO2-MP2: Total energy	-54431.822944

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:4:VAL)

Summations of interaction energy for fragment #1(A:4:VAL)

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.
67.659	68.323	23.805	-12.614	-11.857	-0.102

Interaction energy analysis for fragmet #1(A:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.881

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	6	VAL	0	-0.009	-0.046	3.842	0.332	1.917	-0.014	-0.744	-0.828	0.003
5	A	8	ASP	-1	-0.788	-0.864	1.882	-106.478	-109.546	20.226	-10.512	-6.647	-0.097
6	A	9	VAL	0	-0.049	-0.004	3.033	1.736	2.542	0.055	-0.160	-0.702	-0.001
7	A	10	ASN	0	0.072	0.044	4.952	1.702	1.747	-0.001	-0.005	-0.039	0.000
130	A	133	ARG	1	0.907	0.964	5.188	22.063	22.056	-0.001	-0.002	0.010	0.000
132	A	135	ALA	0	0.017	0.032	4.004	1.109	1.301	0.000	-0.042	-0.149	0.000
133	A	136	GLY	0	0.021	0.006	2.420	-5.987	-4.973	1.483	-1.163	-1.335	-0.002
134	A	137	GLN	0	-0.019	-0.022	3.275	2.811	2.343	0.021	0.731	-0.283	0.000
136	A	139	ALA	0	-0.015	-0.014	2.366	1.000	1.376	2.037	-0.691	-1.722	-0.005
137	A	140	ALA	0	-0.028	-0.007	4.391	2.319	2.508	-0.001	-0.026	-0.162	0.000
4	A	7	LYS	1	0.849	0.931	5.813	35.886	35.886	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.034	0.020	8.604	2.893	2.893	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.059	-0.033	10.083	1.952	1.952	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.828	-0.935	7.944	-27.710	-27.710	0.000	0.000	0.000	0.000
11	A	14	PHE	0	0.013	0.021	6.887	1.468	1.468	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.008	-0.021	9.742	1.135	1.135	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.943	0.983	13.137	17.750	17.750	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.068	0.047	10.468	1.210	1.210	0.000	0.000	0.000	0.000
15	A	18	LEU	0	0.022	0.015	12.144	0.988	0.988	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.003	-0.007	13.708	1.169	1.169	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.006	0.004	15.316	0.935	0.935	0.000	0.000	0.000	0.000
18	A	21	PHE	0	0.013	0.007	12.703	1.015	1.015	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.018	-0.020	15.906	1.069	1.069	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.859	0.939	18.744	13.351	13.351	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.937	0.967	18.516	14.047	14.047	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.010	-0.001	18.873	0.512	0.512	0.000	0.000	0.000	0.000
23	A	26	GLY	0	0.027	0.025	20.721	0.398	0.398	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.914	0.969	20.714	14.230	14.230	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.031	-0.011	21.085	-0.582	-0.582	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.921	0.976	24.057	10.149	10.149	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.050	0.028	26.575	-0.141	-0.141	0.000	0.000	0.000	0.000
28	A	31	PRO	0	-0.054	-0.046	28.855	0.243	0.243	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.862	-0.930	32.376	-8.188	-8.188	0.000	0.000	0.000	0.000
30	A	33	TRP	0	0.009	0.002	31.892	0.008	0.008	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.053	-0.030	29.612	-0.048	-0.048	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.791	-0.896	32.132	-9.297	-9.297	0.000	0.000	0.000	0.000
33	A	36	THR	0	-0.002	0.003	34.304	0.209	0.209	0.000	0.000	0.000	0.000
34	A	37	VAL	0	-0.124	-0.043	30.213	0.024	0.024	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.945	0.977	32.910	8.570	8.570	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.024	0.015	26.492	-0.210	-0.210	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.080	-0.077	30.781	-0.186	-0.186	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.960	0.988	32.811	8.587	8.587	0.000	0.000	0.000	0.000
39	A	42	HIS	0	-0.017	0.015	30.660	0.306	0.306	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.851	0.940	28.180	10.639	10.639	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.767	-0.882	33.133	-8.200	-8.200	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.016	0.002	33.916	0.223	0.223	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.002	-0.001	32.449	-0.272	-0.272	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.076	-0.040	27.512	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.102	0.040	28.787	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.866	-0.916	22.829	-12.754	-12.754	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.880	-0.948	26.505	-9.951	-9.951	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.052	-0.028	23.840	-0.146	-0.146	0.000	0.000	0.000	0.000
49	A	52	TRP	0	0.040	0.008	23.097	-0.994	-0.994	0.000	0.000	0.000	0.000
50	A	53	PHE	0	-0.048	-0.018	22.732	-0.555	-0.555	0.000	0.000	0.000	0.000
51	A	54	TYR	0	0.055	0.012	20.164	-0.518	-0.518	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.061	0.034	17.805	-1.175	-1.175	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.863	0.931	17.983	11.875	11.875	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.003	0.013	19.917	-0.183	-0.183	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.060	0.031	14.528	-0.553	-0.553	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.014	-0.009	15.208	-1.231	-1.231	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.042	-0.042	16.631	-0.151	-0.151	0.000	0.000	0.000	0.000
58	A	61	ALA	0	0.042	0.019	15.869	-0.062	-0.062	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.924	0.957	11.762	21.416	21.416	0.000	0.000	0.000	0.000
60	A	63	HIS	0	-0.056	-0.048	13.771	-1.285	-1.285	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.046	-0.030	16.271	0.261	0.261	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.035	0.039	8.430	-0.338	-0.338	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.076	-0.042	10.757	-0.701	-0.701	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.891	0.955	13.932	18.133	18.133	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.059	0.051	17.260	-0.431	-0.431	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.086	0.057	19.226	0.845	0.845	0.000	0.000	0.000	0.000
67	A	70	ALA	0	-0.042	-0.038	21.267	0.081	0.081	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.082	0.049	23.225	0.252	0.252	0.000	0.000	0.000	0.000
69	A	72	VAL	0	0.008	-0.005	26.212	-0.191	-0.191	0.000	0.000	0.000	0.000
70	A	73	GLY	0	0.031	0.028	28.169	0.004	0.004	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.007	-0.002	24.201	0.140	0.140	0.000	0.000	0.000	0.000
72	A	75	MET	0	0.019	0.008	20.454	-0.189	-0.189	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.080	-0.060	24.697	0.100	0.100	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.954	0.990	26.559	11.958	11.958	0.000	0.000	0.000	0.000
75	A	78	ILE	0	0.022	0.013	20.603	0.106	0.106	0.000	0.000	0.000	0.000
76	A	79	TYR	0	-0.049	-0.038	20.625	-0.264	-0.264	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.049	0.034	25.324	0.476	0.476	0.000	0.000	0.000	0.000
78	A	81	GLY	0	-0.010	-0.019	28.069	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	82	ARG	1	0.979	0.973	29.305	9.720	9.720	0.000	0.000	0.000	0.000
80	A	83	GLN	0	-0.008	-0.001	32.968	-0.141	-0.141	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.909	0.950	35.271	8.631	8.631	0.000	0.000	0.000	0.000
82	A	85	ASN	0	-0.011	-0.004	39.145	-0.189	-0.189	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.024	0.019	42.087	0.174	0.174	0.000	0.000	0.000	0.000
84	A	87	VAL	0	0.073	0.029	43.441	-0.131	-0.131	0.000	0.000	0.000	0.000
85	A	88	MET	0	-0.006	0.007	43.615	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	89	PRO	0	0.064	0.032	41.073	-0.170	-0.170	0.000	0.000	0.000	0.000
87	A	90	SER	0	-0.062	-0.022	36.392	-0.077	-0.077	0.000	0.000	0.000	0.000
88	A	91	HIS	0	0.052	0.029	36.549	-0.139	-0.139	0.000	0.000	0.000	0.000
89	A	92	PHE	0	0.009	-0.003	28.439	-0.239	-0.239	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.013	-0.022	32.681	0.395	0.395	0.000	0.000	0.000	0.000
91	A	94	ARG	1	0.903	0.961	30.225	9.908	9.908	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.075	0.043	29.386	0.274	0.274	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.028	-0.020	30.426	0.258	0.258	0.000	0.000	0.000	0.000
94	A	97	LYS	1	1.002	0.977	30.030	9.100	9.100	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.015	0.001	30.579	-0.326	-0.326	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.089	0.039	28.087	-0.198	-0.198	0.000	0.000	0.000	0.000
97	A	100	ALA	0	0.022	0.028	25.943	-0.429	-0.429	0.000	0.000	0.000	0.000
98	A	101	ARG	1	0.938	0.960	26.129	9.177	9.177	0.000	0.000	0.000	0.000
99	A	102	ARG	1	0.916	0.954	28.002	9.507	9.507	0.000	0.000	0.000	0.000
100	A	103	VAL	0	0.043	0.042	22.207	-0.116	-0.116	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.008	-0.018	22.349	-0.261	-0.261	0.000	0.000	0.000	0.000
102	A	105	GLN	0	0.018	0.011	24.491	0.051	0.051	0.000	0.000	0.000	0.000
103	A	106	ALA	0	0.025	0.025	24.744	0.087	0.087	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.017	-0.015	18.595	-0.223	-0.223	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.897	-0.942	21.584	-12.413	-12.413	0.000	0.000	0.000	0.000
106	A	109	GLY	0	-0.025	-0.005	24.208	0.080	0.080	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.076	-0.053	19.756	0.113	0.113	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.958	0.993	20.626	11.622	11.622	0.000	0.000	0.000	0.000
109	A	112	MET	0	-0.012	0.002	16.078	-1.098	-1.098	0.000	0.000	0.000	0.000
110	A	113	VAL	0	-0.077	-0.052	17.790	-0.883	-0.883	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.787	-0.876	20.360	-14.000	-14.000	0.000	0.000	0.000	0.000
112	A	115	LYS	1	0.886	0.922	23.333	10.204	10.204	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.803	-0.888	22.770	-14.098	-14.098	0.000	0.000	0.000	0.000
114	A	117	GLN	0	-0.006	0.010	25.410	0.671	0.671	0.000	0.000	0.000	0.000
115	A	118	ASP	-1	-0.879	-0.950	26.845	-11.665	-11.665	0.000	0.000	0.000	0.000
116	A	119	GLY	0	-0.026	-0.001	28.510	0.235	0.235	0.000	0.000	0.000	0.000
117	A	120	GLY	0	-0.077	-0.045	26.081	-0.387	-0.387	0.000	0.000	0.000	0.000
118	A	121	ARG	1	0.874	0.937	22.871	12.286	12.286	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.964	0.978	19.481	13.936	13.936	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.032	-0.020	13.219	0.299	0.299	0.000	0.000	0.000	0.000
121	A	124	THR	0	0.029	0.012	17.892	-0.085	-0.085	0.000	0.000	0.000	0.000
122	A	125	PRO	0	0.007	-0.019	15.303	-1.157	-1.157	0.000	0.000	0.000	0.000
123	A	126	GLN	0	0.012	0.019	14.532	-0.801	-0.801	0.000	0.000	0.000	0.000
124	A	127	GLY	0	0.074	0.028	14.714	-0.686	-0.686	0.000	0.000	0.000	0.000
125	A	128	GLN	0	-0.037	-0.028	11.319	-2.956	-2.956	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.883	0.941	10.307	17.187	17.187	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.852	-0.930	9.982	-20.909	-20.909	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.057	-0.031	10.468	-0.254	-0.254	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.741	-0.871	5.970	-51.229	-51.229	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.001	-0.014	6.405	-0.781	-0.781	0.000	0.000	0.000	0.000
135	A	138	VAL	0	-0.015	-0.001	6.033	2.772	2.772	0.000	0.000	0.000	0.000
138	A	141	ALA	0	-0.024	0.011	6.070	3.030	3.030	0.000	0.000	0.000	0.000
139	A	142	ASN	0	-0.015	-0.042	9.092	2.774	2.774	0.000	0.000	0.000	0.000
140	A	143	LYS	1	0.893	0.964	7.843	22.535	22.535	0.000	0.000	0.000	0.000
141	A	144	LYS	0	0.076	0.055	9.467	0.028	0.028	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:4:VAL)