FMO DATABASE

FMODB ID: Z9V3N

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1000722.55492
FMO2-HF: Nuclear repulsion	951382.682376
FMO2-HF: Total energy	-49339.872543
FMO2-MP2: Total energy	-49479.500259

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:9:GLY)

Summations of interaction energy for fragment #1(A:9:GLY)

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.
-18.829	-17.286	0.095	-0.636	-1.001	-0.005

Interaction energy analysis for fragmet #1(A:9:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.913

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	11	VAL	0	0.004	-0.008	2.957	-0.762	0.693	0.096	-0.631	-0.920	-0.005
4	A	12	MET	0	-0.029	0.006	5.258	5.109	5.197	-0.001	-0.005	-0.081	0.000
5	A	13	ASP	-1	-0.821	-0.896	6.515	-35.890	-35.890	0.000	0.000	0.000	0.000
6	A	14	VAL	0	0.034	-0.002	9.180	1.614	1.614	0.000	0.000	0.000	0.000
7	A	15	ASN	0	-0.059	-0.032	13.010	-0.774	-0.774	0.000	0.000	0.000	0.000
8	A	16	THR	0	0.023	0.000	8.504	0.308	0.308	0.000	0.000	0.000	0.000
9	A	17	ALA	0	-0.006	0.004	11.519	-0.768	-0.768	0.000	0.000	0.000	0.000
10	A	18	LEU	0	0.061	0.008	12.370	0.254	0.254	0.000	0.000	0.000	0.000
11	A	19	GLN	0	-0.011	0.015	12.607	-0.568	-0.568	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.805	-0.883	9.392	-31.930	-31.930	0.000	0.000	0.000	0.000
13	A	21	VAL	0	-0.005	0.017	12.053	0.755	0.755	0.000	0.000	0.000	0.000
14	A	22	LEU	0	-0.022	0.002	15.348	1.182	1.182	0.000	0.000	0.000	0.000
15	A	23	LYS	1	0.877	0.942	12.625	20.412	20.412	0.000	0.000	0.000	0.000
16	A	24	THR	0	-0.017	-0.029	12.869	0.622	0.622	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.038	0.010	15.660	0.749	0.749	0.000	0.000	0.000	0.000
18	A	26	LEU	0	-0.112	-0.024	17.319	0.945	0.945	0.000	0.000	0.000	0.000
19	A	27	ILE	0	-0.028	-0.019	15.939	0.621	0.621	0.000	0.000	0.000	0.000
20	A	28	HIS	1	0.841	0.947	19.209	15.056	15.056	0.000	0.000	0.000	0.000
21	A	29	ASP	-1	-0.898	-0.933	20.926	-12.731	-12.731	0.000	0.000	0.000	0.000
22	A	30	GLY	0	-0.010	0.004	23.773	-0.040	-0.040	0.000	0.000	0.000	0.000
23	A	31	LEU	0	-0.006	-0.026	21.389	-0.151	-0.151	0.000	0.000	0.000	0.000
24	A	32	ALA	0	-0.002	0.005	25.353	0.430	0.430	0.000	0.000	0.000	0.000
25	A	33	ARG	1	0.888	0.944	23.873	12.398	12.398	0.000	0.000	0.000	0.000
26	A	34	GLY	0	0.072	0.028	27.767	0.073	0.073	0.000	0.000	0.000	0.000
27	A	35	ILE	0	0.003	0.007	30.526	0.132	0.132	0.000	0.000	0.000	0.000
28	A	36	ARG	1	0.964	0.987	33.790	8.490	8.490	0.000	0.000	0.000	0.000
29	A	37	GLU	-1	-0.889	-0.965	31.036	-10.219	-10.219	0.000	0.000	0.000	0.000
30	A	38	ALA	0	-0.006	0.003	30.477	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	39	ALA	0	0.072	0.033	31.695	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	40	LYS	1	0.790	0.891	35.209	8.444	8.444	0.000	0.000	0.000	0.000
33	A	41	ALA	0	-0.026	-0.025	30.704	0.087	0.087	0.000	0.000	0.000	0.000
34	A	42	LEU	0	0.035	0.007	30.360	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	43	ASP	-1	-0.824	-0.881	33.554	-8.196	-8.196	0.000	0.000	0.000	0.000
36	A	44	LYS	1	0.844	0.921	34.773	9.164	9.164	0.000	0.000	0.000	0.000
37	A	45	ARG	1	0.955	0.967	31.923	9.027	9.027	0.000	0.000	0.000	0.000
38	A	46	GLN	0	0.008	0.014	30.033	-0.220	-0.220	0.000	0.000	0.000	0.000
39	A	47	ALA	0	0.024	0.013	28.487	-0.390	-0.390	0.000	0.000	0.000	0.000
40	A	48	HIS	0	0.001	0.001	23.970	-0.237	-0.237	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.064	0.062	20.058	0.118	0.118	0.000	0.000	0.000	0.000
42	A	50	CYS	0	-0.074	-0.028	23.743	0.323	0.323	0.000	0.000	0.000	0.000
43	A	51	VAL	0	0.002	-0.004	21.131	-0.555	-0.555	0.000	0.000	0.000	0.000
44	A	52	GLN	0	-0.018	-0.029	23.773	0.339	0.339	0.000	0.000	0.000	0.000
45	A	53	ALA	0	0.010	0.002	25.360	-0.460	-0.460	0.000	0.000	0.000	0.000
46	A	54	SER	0	-0.079	-0.084	27.167	0.374	0.374	0.000	0.000	0.000	0.000
47	A	55	ASN	0	-0.004	0.009	29.095	0.571	0.571	0.000	0.000	0.000	0.000
48	A	56	CYS	0	-0.028	-0.040	31.136	-0.278	-0.278	0.000	0.000	0.000	0.000
49	A	57	ASP	-1	-0.884	-0.916	33.933	-8.419	-8.419	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.914	-0.954	37.381	-7.732	-7.732	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.035	0.021	36.776	-0.060	-0.060	0.000	0.000	0.000	0.000
52	A	60	MET	0	-0.031	-0.033	37.925	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	61	TYR	0	0.019	-0.010	31.092	-0.156	-0.156	0.000	0.000	0.000	0.000
54	A	62	VAL	0	0.056	0.015	31.666	-0.097	-0.097	0.000	0.000	0.000	0.000
55	A	63	LYS	1	0.998	1.010	34.082	7.663	7.663	0.000	0.000	0.000	0.000
56	A	64	LEU	0	-0.017	-0.013	36.884	0.028	0.028	0.000	0.000	0.000	0.000
57	A	65	VAL	0	-0.032	-0.017	30.378	-0.094	-0.094	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.853	-0.931	31.922	-9.711	-9.711	0.000	0.000	0.000	0.000
59	A	67	ALA	0	-0.018	-0.005	33.470	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	68	LEU	0	0.003	-0.001	34.745	0.003	0.003	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.098	-0.054	28.627	-0.164	-0.164	0.000	0.000	0.000	0.000
62	A	70	ALA	0	0.024	0.003	31.590	-0.250	-0.250	0.000	0.000	0.000	0.000
63	A	71	GLU	-1	-0.929	-0.943	33.808	-8.178	-8.178	0.000	0.000	0.000	0.000
64	A	72	HIS	0	-0.007	-0.017	34.018	-0.305	-0.305	0.000	0.000	0.000	0.000
65	A	73	GLN	0	-0.089	-0.051	29.304	-0.252	-0.252	0.000	0.000	0.000	0.000
66	A	74	ILE	0	0.003	0.029	29.120	-0.169	-0.169	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.036	-0.048	25.909	-0.392	-0.392	0.000	0.000	0.000	0.000
68	A	76	LEU	0	0.024	-0.003	25.959	0.390	0.390	0.000	0.000	0.000	0.000
69	A	77	ILE	0	-0.006	0.004	20.722	-0.580	-0.580	0.000	0.000	0.000	0.000
70	A	78	LYS	1	0.853	0.939	23.565	11.171	11.171	0.000	0.000	0.000	0.000
71	A	79	VAL	0	0.043	0.017	20.530	0.042	0.042	0.000	0.000	0.000	0.000
72	A	80	ASP	-1	-0.835	-0.889	23.207	-10.954	-10.954	0.000	0.000	0.000	0.000
73	A	81	ASP	-1	-0.786	-0.892	23.798	-12.285	-12.285	0.000	0.000	0.000	0.000
74	A	82	ASN	0	-0.023	-0.016	25.294	-0.082	-0.082	0.000	0.000	0.000	0.000
75	A	83	LYS	1	0.842	0.918	26.318	10.346	10.346	0.000	0.000	0.000	0.000
76	A	84	LYS	1	0.901	0.938	20.745	12.976	12.976	0.000	0.000	0.000	0.000
77	A	85	LEU	0	0.002	0.002	21.131	-0.561	-0.561	0.000	0.000	0.000	0.000
78	A	86	GLY	0	0.032	0.005	21.638	-0.251	-0.251	0.000	0.000	0.000	0.000
79	A	87	GLU	-1	-0.947	-0.985	18.277	-16.022	-16.022	0.000	0.000	0.000	0.000
80	A	88	TRP	0	0.023	0.008	15.988	-0.917	-0.917	0.000	0.000	0.000	0.000
81	A	89	VAL	0	0.054	0.034	16.682	-0.578	-0.578	0.000	0.000	0.000	0.000
82	A	90	GLY	0	0.030	-0.004	19.030	-0.384	-0.384	0.000	0.000	0.000	0.000
83	A	91	LEU	0	-0.078	-0.031	20.772	0.973	0.973	0.000	0.000	0.000	0.000
84	A	92	CYS	0	-0.023	-0.011	19.405	0.126	0.126	0.000	0.000	0.000	0.000
85	A	93	LYS	1	1.003	0.983	22.017	11.167	11.167	0.000	0.000	0.000	0.000
86	A	94	ILE	0	0.038	0.034	18.809	0.346	0.346	0.000	0.000	0.000	0.000
87	A	95	ASP	-1	-0.901	-0.954	21.772	-11.660	-11.660	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.906	0.951	24.262	11.679	11.679	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.875	-0.955	20.519	-13.935	-13.935	0.000	0.000	0.000	0.000
90	A	98	GLY	0	0.021	0.019	19.811	-0.577	-0.577	0.000	0.000	0.000	0.000
91	A	99	ASN	0	-0.009	0.004	17.341	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	100	PRO	0	0.027	0.027	20.696	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	101	ARG	1	0.875	0.930	21.738	12.593	12.593	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.895	0.947	23.886	11.609	11.609	0.000	0.000	0.000	0.000
95	A	103	VAL	0	0.036	0.026	24.624	0.419	0.419	0.000	0.000	0.000	0.000
96	A	104	VAL	0	0.030	0.019	26.901	0.429	0.429	0.000	0.000	0.000	0.000
97	A	105	GLY	0	-0.007	0.002	27.859	-0.307	-0.307	0.000	0.000	0.000	0.000
98	A	106	CYS	0	-0.084	-0.009	25.367	-0.123	-0.123	0.000	0.000	0.000	0.000
99	A	107	SER	0	0.032	0.001	27.146	0.267	0.267	0.000	0.000	0.000	0.000
100	A	108	CYS	0	0.025	0.021	26.629	-0.448	-0.448	0.000	0.000	0.000	0.000
101	A	109	VAL	0	-0.011	0.021	22.789	0.316	0.316	0.000	0.000	0.000	0.000
102	A	110	VAL	0	0.015	0.007	26.023	-0.082	-0.082	0.000	0.000	0.000	0.000
103	A	111	VAL	0	-0.021	-0.012	20.143	0.085	0.085	0.000	0.000	0.000	0.000
104	A	112	LYS	1	0.894	0.946	23.491	11.343	11.343	0.000	0.000	0.000	0.000
105	A	113	ASP	-1	-0.852	-0.938	23.152	-13.993	-13.993	0.000	0.000	0.000	0.000
106	A	114	TYR	0	0.061	0.035	18.557	-0.762	-0.762	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.000	-0.023	17.138	-1.041	-1.041	0.000	0.000	0.000	0.000
108	A	116	LYS	1	0.912	0.935	14.165	20.714	20.714	0.000	0.000	0.000	0.000
109	A	117	GLU	-1	-0.840	-0.912	15.953	-15.970	-15.970	0.000	0.000	0.000	0.000
110	A	118	SER	0	-0.032	-0.008	12.244	-2.342	-2.342	0.000	0.000	0.000	0.000
111	A	119	GLN	0	-0.077	-0.062	7.226	0.162	0.162	0.000	0.000	0.000	0.000
112	A	120	ALA	0	0.076	0.025	10.150	-1.096	-1.096	0.000	0.000	0.000	0.000
113	A	121	LYS	1	0.756	0.893	11.948	24.264	24.264	0.000	0.000	0.000	0.000
114	A	122	ASP	-1	-0.827	-0.918	13.910	-19.283	-19.283	0.000	0.000	0.000	0.000
115	A	123	VAL	0	-0.050	-0.017	10.785	0.422	0.422	0.000	0.000	0.000	0.000
116	A	124	ILE	0	-0.027	-0.036	14.265	0.953	0.953	0.000	0.000	0.000	0.000
117	A	125	GLU	-1	-0.914	-0.955	16.851	-13.109	-13.109	0.000	0.000	0.000	0.000
118	A	126	GLU	-1	-0.943	-0.959	17.937	-15.508	-15.508	0.000	0.000	0.000	0.000
119	A	127	TYR	0	0.031	0.020	16.246	0.771	0.771	0.000	0.000	0.000	0.000
120	A	128	PHE	0	-0.025	-0.022	19.568	0.879	0.879	0.000	0.000	0.000	0.000
121	A	129	LYS	1	0.961	0.989	22.015	13.256	13.256	0.000	0.000	0.000	0.000
122	A	130	CYS	0	-0.056	-0.023	22.785	1.008	1.008	0.000	0.000	0.000	0.000
123	A	131	LYS	1	0.825	0.919	22.497	12.334	12.334	0.000	0.000	0.000	0.000
124	A	132	LYS	0	0.014	0.023	22.340	-1.916	-1.916	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLY)