FMO DATABASE

FMODB ID: G7YN1

Calculation Name: 3J7R-P-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: P

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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1483903.813819
FMO2-HF: Nuclear repulsion	1420837.842815
FMO2-HF: Total energy	-63065.971004
FMO2-MP2: Total energy	-63246.41551

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:2:VAL)

Summations of interaction energy for fragment #1(A:2: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.
168.899	173.643	0.968	-2.017	-3.694	-0.015

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.917

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	4	TYR	0	0.008	-0.014	2.803	-12.570	-9.175	0.519	-1.653	-2.261	-0.012
4	A	5	SER	0	-0.017	-0.011	5.137	1.790	1.847	-0.001	-0.004	-0.052	0.000
17	A	18	ARG	1	0.912	0.947	2.833	45.099	46.391	0.450	-0.360	-1.381	-0.003
5	A	6	LEU	0	-0.013	-0.010	8.775	-1.357	-1.357	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.867	-0.941	8.340	-38.603	-38.603	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.049	-0.020	10.537	1.318	1.318	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.884	-0.941	13.467	-15.417	-15.417	0.000	0.000	0.000	0.000
9	A	10	ASN	0	0.017	0.006	16.471	1.199	1.199	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.005	0.010	11.836	-0.625	-0.625	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.030	0.015	13.274	-1.028	-1.028	0.000	0.000	0.000	0.000
12	A	13	LYS	1	1.031	1.022	15.840	14.202	14.202	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.033	0.010	13.118	0.497	0.497	0.000	0.000	0.000	0.000
14	A	15	CYS	0	-0.051	0.000	12.060	-1.492	-1.492	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.891	0.955	6.305	39.634	39.634	0.000	0.000	0.000	0.000
16	A	17	SER	0	0.011	0.004	8.477	0.114	0.114	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.040	0.025	7.456	0.971	0.971	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.054	-0.054	5.606	-2.904	-2.904	0.000	0.000	0.000	0.000
20	A	21	ASN	0	0.042	0.011	7.980	0.982	0.982	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.043	0.048	10.971	1.348	1.348	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.970	0.974	13.379	14.808	14.808	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.012	-0.016	15.389	0.990	0.990	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.019	0.019	18.099	-0.345	-0.345	0.000	0.000	0.000	0.000
25	A	26	PHE	0	0.036	0.008	15.387	0.537	0.537	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.925	0.966	17.654	11.581	11.581	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.023	-0.004	20.883	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.032	0.004	16.283	-0.096	-0.096	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.869	0.934	17.197	13.643	13.643	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.768	-0.886	18.136	-12.327	-12.327	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.008	-0.005	19.637	0.260	0.260	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.026	0.006	15.640	0.045	0.045	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.013	0.022	17.408	-0.611	-0.611	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.021	-0.011	19.743	0.240	0.240	0.000	0.000	0.000	0.000
35	A	36	ILE	0	0.003	0.005	18.014	0.360	0.360	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.955	0.976	16.994	15.794	15.794	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.041	0.032	19.471	0.653	0.653	0.000	0.000	0.000	0.000
38	A	39	MET	0	-0.105	-0.028	21.428	0.815	0.815	0.000	0.000	0.000	0.000
39	A	40	HIS	0	0.168	0.085	21.332	-0.962	-0.962	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.082	0.045	18.828	0.265	0.265	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.819	0.921	21.868	12.798	12.798	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.897	0.950	25.163	11.709	11.709	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.023	0.000	21.127	0.272	0.272	0.000	0.000	0.000	0.000
44	A	45	THR	0	0.000	-0.035	21.707	0.291	0.291	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.942	0.987	23.693	10.464	10.464	0.000	0.000	0.000	0.000
46	A	47	TYR	0	0.012	0.018	23.706	0.024	0.024	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.001	-0.001	19.891	0.248	0.248	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.975	0.990	24.418	12.076	12.076	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.789	-0.886	27.296	-9.576	-9.576	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.043	-0.012	25.486	0.319	0.319	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.060	-0.040	25.693	0.240	0.240	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.008	-0.015	28.299	0.227	0.227	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.056	-0.035	31.139	0.391	0.391	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.916	0.968	32.451	8.785	8.785	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.007	-0.005	30.021	0.026	0.026	0.000	0.000	0.000	0.000
56	A	57	CYS	0	-0.042	-0.005	29.918	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.010	0.019	23.984	-0.200	-0.200	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.005	0.007	26.134	0.289	0.289	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.040	-0.041	25.062	-0.508	-0.508	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.873	0.937	25.565	10.985	10.985	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.988	0.998	21.193	12.925	12.925	0.000	0.000	0.000	0.000
62	A	63	TYR	0	-0.095	-0.055	19.540	0.274	0.274	0.000	0.000	0.000	0.000
63	A	64	ASN	0	0.019	-0.010	25.826	-0.213	-0.213	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.035	0.028	29.387	0.318	0.318	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.045	0.022	31.060	-0.132	-0.132	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.152	-0.052	29.314	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.062	0.043	32.567	0.213	0.213	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.970	0.964	34.473	7.391	7.391	0.000	0.000	0.000	0.000
69	A	70	CYS	0	-0.035	0.028	33.166	0.129	0.129	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.032	0.017	36.410	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	72	GLN	0	0.046	-0.021	33.908	-0.140	-0.140	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.027	-0.015	32.495	-0.163	-0.163	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.970	0.990	33.347	7.460	7.460	0.000	0.000	0.000	0.000
74	A	75	GLN	0	0.006	0.011	32.961	-0.137	-0.137	0.000	0.000	0.000	0.000
75	A	76	TRP	0	-0.004	0.007	27.482	-0.216	-0.216	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.065	0.053	31.163	-0.203	-0.203	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.058	-0.063	29.504	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	79	THR	0	0.057	0.031	33.799	0.115	0.115	0.000	0.000	0.000	0.000
79	A	80	GLN	0	0.023	0.023	31.868	-0.057	-0.057	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.057	0.005	29.814	-0.272	-0.272	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.862	0.940	28.082	9.996	9.996	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.101	0.046	28.523	-0.219	-0.219	0.000	0.000	0.000	0.000
83	A	84	PRO	0	-0.049	-0.017	23.639	0.028	0.028	0.000	0.000	0.000	0.000
84	A	85	LYS	1	1.021	1.007	24.058	9.891	9.891	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.963	0.972	20.644	13.052	13.052	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.044	-0.027	19.380	-0.474	-0.474	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.008	0.020	19.450	-0.644	-0.644	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.845	-0.942	20.421	-13.173	-13.173	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.043	-0.035	15.917	-0.410	-0.410	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.021	-0.011	15.176	-1.010	-1.010	0.000	0.000	0.000	0.000
91	A	92	LEU	0	0.015	0.027	16.383	-0.243	-0.243	0.000	0.000	0.000	0.000
92	A	93	HIS	0	0.023	0.006	16.429	-0.422	-0.422	0.000	0.000	0.000	0.000
93	A	94	MET	0	-0.067	-0.011	10.960	-1.105	-1.105	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.029	0.017	13.571	-1.163	-1.163	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.992	1.001	16.203	14.327	14.327	0.000	0.000	0.000	0.000
96	A	97	ASN	0	0.013	0.003	11.848	0.403	0.403	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.012	0.003	12.996	-0.516	-0.516	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.856	-0.925	14.095	-14.221	-14.221	0.000	0.000	0.000	0.000
99	A	100	SER	0	-0.031	-0.021	15.403	0.178	0.178	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.026	-0.037	10.370	0.569	0.569	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.038	-0.023	13.939	-0.583	-0.583	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.851	-0.920	16.338	-13.896	-13.896	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.063	-0.030	13.562	0.069	0.069	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.745	0.869	12.022	22.854	22.854	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.017	0.025	15.990	0.245	0.245	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.114	-0.058	15.926	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.848	-0.920	19.998	-12.123	-12.123	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.033	-0.031	19.985	-0.342	-0.342	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.877	-0.945	21.837	-12.344	-12.344	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.088	0.047	23.324	0.210	0.210	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.055	-0.014	17.557	-0.601	-0.601	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.014	-0.005	20.125	0.395	0.395	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.105	-0.049	14.977	-1.121	-1.121	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.854	-0.912	15.672	-15.781	-15.781	0.000	0.000	0.000	0.000
115	A	116	HIS	0	-0.016	-0.017	9.025	2.241	2.241	0.000	0.000	0.000	0.000
116	A	117	ILE	0	-0.011	-0.020	11.955	-0.550	-0.550	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.041	0.013	8.857	1.649	1.649	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.020	-0.026	11.167	-0.417	-0.417	0.000	0.000	0.000	0.000
119	A	120	ASN	0	0.007	0.005	9.893	0.108	0.108	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.905	0.947	12.024	15.435	15.435	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.006	0.014	11.286	-1.269	-1.269	0.000	0.000	0.000	0.000
122	A	123	PRO	0	0.035	0.009	11.568	1.406	1.406	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.922	0.968	14.571	13.591	13.591	0.000	0.000	0.000	0.000
124	A	125	MET	0	0.045	0.033	17.823	0.080	0.080	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.951	0.932	19.947	11.819	11.819	0.000	0.000	0.000	0.000
126	A	127	ARG	1	0.988	1.005	23.697	11.271	11.271	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.980	0.996	27.117	8.881	8.881	0.000	0.000	0.000	0.000
128	A	129	THR	0	-0.032	-0.005	30.649	0.126	0.126	0.000	0.000	0.000	0.000
129	A	130	TYR	0	0.059	0.023	33.180	-0.044	-0.044	0.000	0.000	0.000	0.000
130	A	131	ARG	1	0.940	0.965	34.722	8.325	8.325	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.068	0.036	38.926	0.054	0.054	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.057	0.012	41.778	-0.242	-0.242	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.061	0.049	41.629	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.907	0.970	37.739	7.272	7.272	0.000	0.000	0.000	0.000
135	A	136	ILE	0	0.026	0.005	33.230	-0.082	-0.082	0.000	0.000	0.000	0.000
136	A	137	ASN	0	-0.002	0.005	32.067	0.013	0.013	0.000	0.000	0.000	0.000
137	A	138	PRO	0	0.011	0.001	26.860	-0.100	-0.100	0.000	0.000	0.000	0.000
138	A	139	TYR	0	0.013	-0.010	27.927	-0.114	-0.114	0.000	0.000	0.000	0.000
139	A	140	MET	0	-0.020	0.005	22.545	-0.331	-0.331	0.000	0.000	0.000	0.000
140	A	141	SER	0	-0.009	0.010	19.693	0.114	0.114	0.000	0.000	0.000	0.000
141	A	142	SER	0	-0.052	-0.053	18.599	-0.102	-0.102	0.000	0.000	0.000	0.000
142	A	143	PRO	0	0.035	0.039	14.414	0.371	0.371	0.000	0.000	0.000	0.000
143	A	144	CYS	0	-0.034	-0.013	12.889	0.409	0.409	0.000	0.000	0.000	0.000
144	A	145	HIS	0	0.049	0.035	7.203	-1.565	-1.565	0.000	0.000	0.000	0.000
145	A	146	ILE	0	-0.018	-0.003	9.175	1.318	1.318	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.817	-0.924	5.903	-35.435	-35.435	0.000	0.000	0.000	0.000
147	A	148	MET	0	0.042	0.018	8.033	2.932	2.932	0.000	0.000	0.000	0.000
148	A	149	ILE	0	-0.015	-0.015	9.175	-3.077	-3.077	0.000	0.000	0.000	0.000
149	A	150	LEU	0	-0.005	0.006	11.769	1.492	1.492	0.000	0.000	0.000	0.000
150	A	151	THR	0	-0.014	-0.012	15.007	-1.345	-1.345	0.000	0.000	0.000	0.000
151	A	152	GLU	-1	-0.792	-0.889	17.428	-14.121	-14.121	0.000	0.000	0.000	0.000
152	A	153	LYS	1	0.779	0.872	19.881	14.680	14.680	0.000	0.000	0.000	0.000
153	A	154	GLU	-2	-1.850	-1.900	23.371	-22.483	-22.483	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)