FMO DATABASE

FMODB ID: 86NNY

Calculation Name: 4PJ2-C-Xray549

Preferred Name:

Target Type:

Ligand Name: glycerol | magnesium ion

Ligand 3-letter code: GOL | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PJ2

Chain ID: C

ChEMBL ID:

UniProt ID: P86383

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1027449.501356
FMO2-HF: Nuclear repulsion	976475.365966
FMO2-HF: Total energy	-50974.135391
FMO2-MP2: Total energy	-51108.409837

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(C:1:PHE)

Summations of interaction energy for fragment #1(C:1:PHE)

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.
111.491	124.138	25.621	-12.094	-26.174	-0.099

Interaction energy analysis for fragmet #1(C:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.769 / q_NPA : 0.875

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	C	3	GLY	0	0.033	0.022	3.684	-4.077	-2.748	0.005	-0.625	-0.709	-0.001
8	C	8	GLN	0	0.075	0.015	1.796	-37.791	-38.987	11.365	-5.002	-5.168	-0.064
9	C	9	ARG	1	0.972	0.998	2.967	21.899	23.504	0.285	-0.733	-1.156	-0.008
11	C	11	LEU	0	0.022	0.006	2.266	-1.416	-0.084	3.376	-0.967	-3.741	0.001
12	C	12	SER	0	-0.012	-0.009	2.333	1.216	3.474	2.661	-1.434	-3.484	-0.001
13	C	13	CYS	0	-0.092	-0.048	3.006	2.024	0.624	0.233	1.695	-0.528	0.000
15	C	15	CYS	0	-0.131	-0.044	2.994	-4.392	-3.028	2.415	-0.934	-2.845	-0.005
16	C	16	LYS	1	0.906	0.945	5.106	30.804	30.913	-0.001	-0.003	-0.105	0.000
35	C	37	TYR	0	-0.015	-0.007	4.484	-0.413	-0.264	-0.001	-0.010	-0.138	0.000
36	C	38	PHE	0	-0.017	-0.013	2.782	-3.345	-1.693	1.321	-0.587	-2.386	0.005
56	C	58	CYS	0	-0.023	0.016	4.205	-2.454	-2.349	-0.002	-0.007	-0.095	0.000
60	C	62	SER	0	0.032	0.012	2.689	-2.457	-1.849	0.186	-0.232	-0.563	0.000
61	C	63	TYR	0	0.049	0.023	2.829	-11.804	-9.107	0.322	-1.263	-1.757	-0.014
63	C	66	SER	0	-0.015	-0.017	2.209	-8.744	-6.943	3.458	-1.935	-3.324	-0.012
64	C	67	LEU	0	0.029	0.001	4.140	0.816	0.971	-0.001	-0.052	-0.103	0.000
66	C	70	GLN	0	-0.033	-0.018	4.588	7.834	7.913	-0.001	-0.005	-0.072	0.000
4	C	4	GLY	0	0.004	-0.013	6.370	2.234	2.234	0.000	0.000	0.000	0.000
5	C	5	ILE	0	0.003	0.007	8.740	0.139	0.139	0.000	0.000	0.000	0.000
6	C	6	VAL	0	-0.028	0.001	6.454	1.403	1.403	0.000	0.000	0.000	0.000
7	C	7	SER	0	0.012	-0.027	6.077	-5.673	-5.673	0.000	0.000	0.000	0.000
10	C	10	CYS	0	-0.019	-0.005	5.479	1.685	1.685	0.000	0.000	0.000	0.000
14	C	14	ILE	0	0.061	0.024	6.817	1.797	1.797	0.000	0.000	0.000	0.000
17	C	17	MET	0	-0.036	0.000	6.915	2.006	2.006	0.000	0.000	0.000	0.000
18	C	18	GLU	-1	-0.845	-0.897	8.548	-18.484	-18.484	0.000	0.000	0.000	0.000
19	C	19	SER	0	-0.010	-0.010	7.099	0.932	0.932	0.000	0.000	0.000	0.000
20	C	20	GLY	0	0.019	0.015	8.970	1.121	1.121	0.000	0.000	0.000	0.000
21	C	22	ARG	1	0.935	0.953	5.729	18.464	18.464	0.000	0.000	0.000	0.000
22	C	23	ASN	0	0.046	0.016	8.160	0.245	0.245	0.000	0.000	0.000	0.000
23	C	24	VAL	0	-0.038	-0.011	9.768	1.335	1.335	0.000	0.000	0.000	0.000
24	C	25	GLY	0	0.042	0.030	12.495	1.178	1.178	0.000	0.000	0.000	0.000
25	C	26	CYS	0	-0.086	-0.055	13.463	-0.270	-0.270	0.000	0.000	0.000	0.000
26	C	27	LYS	1	0.933	0.979	14.723	15.840	15.840	0.000	0.000	0.000	0.000
27	C	28	MET	0	0.027	-0.014	17.902	-0.137	-0.137	0.000	0.000	0.000	0.000
28	C	29	ASP	-1	-0.836	-0.909	19.571	-12.844	-12.844	0.000	0.000	0.000	0.000
29	C	30	MET	0	-0.038	-0.015	17.419	0.259	0.259	0.000	0.000	0.000	0.000
30	C	31	GLY	0	0.002	0.008	20.789	-0.119	-0.119	0.000	0.000	0.000	0.000
31	C	32	SER	0	-0.030	-0.023	21.328	0.040	0.040	0.000	0.000	0.000	0.000
32	C	33	LEU	0	-0.003	0.004	18.554	-0.521	-0.521	0.000	0.000	0.000	0.000
33	C	34	SER	0	0.002	0.007	14.496	-0.542	-0.542	0.000	0.000	0.000	0.000
34	C	36	GLY	0	0.047	0.026	9.956	-1.081	-1.081	0.000	0.000	0.000	0.000
37	C	39	GLN	0	-0.011	0.001	7.608	1.989	1.989	0.000	0.000	0.000	0.000
38	C	40	ILE	0	0.023	0.032	8.394	0.604	0.604	0.000	0.000	0.000	0.000
39	C	41	LYS	1	1.009	1.005	12.472	15.055	15.055	0.000	0.000	0.000	0.000
40	C	42	GLU	-1	-0.894	-0.947	15.951	-13.757	-13.757	0.000	0.000	0.000	0.000
41	C	43	ALA	0	0.052	0.016	17.901	-0.336	-0.336	0.000	0.000	0.000	0.000
42	C	44	TYR	0	-0.030	-0.026	10.917	-0.352	-0.352	0.000	0.000	0.000	0.000
43	C	45	TRP	0	0.010	-0.029	12.645	-0.008	-0.008	0.000	0.000	0.000	0.000
44	C	46	ILE	0	-0.008	-0.014	14.801	-0.288	-0.288	0.000	0.000	0.000	0.000
45	C	47	ASP	-1	-0.792	-0.874	17.107	-14.553	-14.553	0.000	0.000	0.000	0.000
46	C	48	CYS	0	-0.158	-0.029	6.373	3.776	3.776	0.000	0.000	0.000	0.000
47	C	49	GLY	0	0.015	0.002	13.368	-1.230	-1.230	0.000	0.000	0.000	0.000
48	C	50	ARG	1	0.935	0.984	15.873	14.415	14.415	0.000	0.000	0.000	0.000
49	C	51	PRO	0	0.034	0.028	11.309	0.183	0.183	0.000	0.000	0.000	0.000
50	C	52	GLY	0	0.057	0.007	13.205	-0.522	-0.522	0.000	0.000	0.000	0.000
51	C	53	SER	0	0.034	0.021	13.973	0.590	0.590	0.000	0.000	0.000	0.000
52	C	54	SER	0	0.046	0.016	15.560	0.759	0.759	0.000	0.000	0.000	0.000
53	C	55	TRP	0	0.042	-0.001	14.024	-0.758	-0.758	0.000	0.000	0.000	0.000
54	C	56	LYS	1	0.957	0.973	13.378	12.796	12.796	0.000	0.000	0.000	0.000
55	C	57	SER	0	-0.021	-0.004	13.371	-1.146	-1.146	0.000	0.000	0.000	0.000
57	C	59	ALA	0	0.022	-0.001	8.889	-2.535	-2.535	0.000	0.000	0.000	0.000
58	C	60	ALA	0	0.004	0.000	8.631	-1.463	-1.463	0.000	0.000	0.000	0.000
59	C	61	SER	0	0.010	0.014	7.982	-2.053	-2.053	0.000	0.000	0.000	0.000
62	C	65	ALA	0	0.051	0.023	5.458	1.136	1.136	0.000	0.000	0.000	0.000
65	C	69	VAL	0	0.038	0.013	6.098	1.992	1.992	0.000	0.000	0.000	0.000
67	C	71	ASN	0	-0.042	-0.035	7.830	1.980	1.980	0.000	0.000	0.000	0.000
68	C	72	TYR	0	0.022	0.017	10.810	1.951	1.951	0.000	0.000	0.000	0.000
69	C	73	MET	0	-0.053	-0.010	10.273	2.086	2.086	0.000	0.000	0.000	0.000
70	C	74	LYS	1	0.927	0.961	11.972	21.564	21.564	0.000	0.000	0.000	0.000
71	C	75	ARG	1	0.827	0.938	13.784	16.160	16.160	0.000	0.000	0.000	0.000
72	C	76	TYR	0	-0.023	-0.044	15.746	1.217	1.217	0.000	0.000	0.000	0.000
73	C	77	ALA	0	0.060	0.029	14.797	0.734	0.734	0.000	0.000	0.000	0.000
74	C	78	LYS	1	0.938	0.975	16.797	14.660	14.660	0.000	0.000	0.000	0.000
75	C	79	TRP	0	0.029	0.005	19.035	0.855	0.855	0.000	0.000	0.000	0.000
76	C	80	ALA	0	0.009	0.003	19.736	0.739	0.739	0.000	0.000	0.000	0.000
77	C	81	GLY	0	0.004	0.009	21.438	0.554	0.554	0.000	0.000	0.000	0.000
78	C	82	CYS	0	-0.126	-0.040	17.815	0.898	0.898	0.000	0.000	0.000	0.000
79	C	83	PRO	0	0.020	0.020	18.144	-0.053	-0.053	0.000	0.000	0.000	0.000
80	C	84	LEU	0	-0.015	-0.017	15.074	-0.762	-0.762	0.000	0.000	0.000	0.000
81	C	85	ARG	1	0.957	0.970	12.779	15.217	15.217	0.000	0.000	0.000	0.000
82	C	87	GLU	-1	-0.866	-0.909	12.079	-14.444	-14.444	0.000	0.000	0.000	0.000
83	C	88	GLY	0	0.034	0.014	15.577	0.745	0.745	0.000	0.000	0.000	0.000
84	C	89	PHE	0	0.025	-0.017	10.614	0.107	0.107	0.000	0.000	0.000	0.000
85	C	90	ALA	0	0.042	0.009	11.707	-0.336	-0.336	0.000	0.000	0.000	0.000
86	C	91	ARG	1	0.795	0.888	13.016	14.580	14.580	0.000	0.000	0.000	0.000
87	C	92	GLU	-1	-0.819	-0.931	14.388	-14.874	-14.874	0.000	0.000	0.000	0.000
88	C	93	HIS	0	-0.032	-0.002	10.113	-0.241	-0.241	0.000	0.000	0.000	0.000
89	C	94	ASN	0	-0.012	-0.009	13.530	1.063	1.063	0.000	0.000	0.000	0.000
90	C	95	GLY	0	-0.013	-0.012	16.101	0.739	0.739	0.000	0.000	0.000	0.000
91	C	96	GLY	0	-0.007	0.015	17.506	0.779	0.779	0.000	0.000	0.000	0.000
92	C	97	PRO	0	0.015	-0.006	18.253	-0.082	-0.082	0.000	0.000	0.000	0.000
93	C	98	ARG	1	0.941	0.974	19.253	12.429	12.429	0.000	0.000	0.000	0.000
94	C	99	GLY	0	0.039	0.035	19.187	0.621	0.621	0.000	0.000	0.000	0.000
95	C	101	LYS	1	0.818	0.901	20.114	13.044	13.044	0.000	0.000	0.000	0.000
96	C	102	LYS	1	0.966	0.995	22.966	12.238	12.238	0.000	0.000	0.000	0.000
97	C	103	GLY	0	0.076	0.032	23.620	-0.380	-0.380	0.000	0.000	0.000	0.000
98	C	104	SER	0	-0.008	-0.009	23.306	-0.154	-0.154	0.000	0.000	0.000	0.000
99	C	105	THR	0	0.022	0.022	18.923	-0.129	-0.129	0.000	0.000	0.000	0.000
100	C	106	ILE	0	0.011	0.019	19.063	-0.706	-0.706	0.000	0.000	0.000	0.000
101	C	107	GLY	0	0.029	0.009	20.260	-0.237	-0.237	0.000	0.000	0.000	0.000
102	C	108	TYR	0	-0.097	-0.081	11.996	-0.095	-0.095	0.000	0.000	0.000	0.000
103	C	109	TRP	0	0.078	0.028	12.559	-0.912	-0.912	0.000	0.000	0.000	0.000
104	C	110	ASN	0	0.004	-0.010	16.023	-0.759	-0.759	0.000	0.000	0.000	0.000
105	C	111	ARG	1	0.930	0.970	16.334	14.452	14.452	0.000	0.000	0.000	0.000
106	C	112	LEU	0	0.046	0.023	10.183	-0.257	-0.257	0.000	0.000	0.000	0.000
107	C	113	GLN	0	-0.032	-0.020	12.397	-0.815	-0.815	0.000	0.000	0.000	0.000
108	C	114	LYS	1	0.930	0.966	14.440	13.613	13.613	0.000	0.000	0.000	0.000
109	C	115	ILE	0	-0.011	0.016	9.175	0.134	0.134	0.000	0.000	0.000	0.000
110	C	116	SER	0	0.049	0.009	11.599	-0.049	-0.049	0.000	0.000	0.000	0.000
111	C	117	GLY	0	-0.002	-0.005	9.875	-1.704	-1.704	0.000	0.000	0.000	0.000
112	C	119	HIS	0	0.073	0.042	10.943	-0.053	-0.053	0.000	0.000	0.000	0.000
113	C	120	GLY	0	0.012	0.013	14.518	-0.224	-0.224	0.000	0.000	0.000	0.000
114	C	121	VAL	0	-0.062	-0.017	8.655	-0.484	-0.484	0.000	0.000	0.000	0.000
115	C	122	GLN	-1	-0.762	-0.858	9.935	-24.919	-24.919	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:PHE)