FMO DATABASE

FMODB ID: RMLZ8

Calculation Name: 4JDE-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | chloride ion

Ligand 3-letter code: GOL | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JDE

Chain ID: A

ChEMBL ID:

UniProt ID: G5EET8

Base Structure: X-ray

Registration Date: 2025-10-04

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1311300.397501
FMO2-HF: Nuclear repulsion	1253845.0601
FMO2-HF: Total energy	-57455.337401
FMO2-MP2: Total energy	-57624.412423

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:8:SER)

Summations of interaction energy for fragment #1(A:8:SER)

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.
11.054	17.374	6.961	-6.218	-7.064	-0.045

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.908

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	10	LEU	0	0.029	0.016	2.645	1.219	3.779	0.736	-1.451	-1.845	0.006
4	A	11	THR	0	-0.034	-0.014	1.992	-27.100	-24.311	6.215	-4.382	-4.622	-0.050
5	A	12	ARG	1	1.001	1.012	3.821	24.594	24.749	0.001	-0.074	-0.082	0.000
58	A	65	GLY	0	0.020	-0.009	3.649	-8.787	-8.456	0.009	-0.133	-0.207	-0.001
59	A	66	PHE	0	0.001	0.007	3.949	8.420	8.905	0.000	-0.178	-0.308	0.000
6	A	13	ARG	1	0.796	0.896	5.139	38.897	38.897	0.000	0.000	0.000	0.000
7	A	14	THR	0	-0.023	-0.020	10.036	1.600	1.600	0.000	0.000	0.000	0.000
8	A	15	ALA	0	0.019	0.039	13.849	-0.084	-0.084	0.000	0.000	0.000	0.000
9	A	16	LYS	1	0.930	0.972	16.266	14.743	14.743	0.000	0.000	0.000	0.000
10	A	17	VAL	0	-0.001	-0.006	20.034	-0.255	-0.255	0.000	0.000	0.000	0.000
11	A	18	SER	0	0.002	0.002	22.663	0.534	0.534	0.000	0.000	0.000	0.000
12	A	19	ILE	0	-0.010	0.012	26.219	-0.280	-0.280	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.768	-0.872	29.079	-9.842	-9.842	0.000	0.000	0.000	0.000
14	A	21	ASN	0	-0.005	-0.004	31.380	-0.107	-0.107	0.000	0.000	0.000	0.000
15	A	22	GLN	0	-0.034	-0.031	34.059	0.446	0.446	0.000	0.000	0.000	0.000
16	A	23	THR	0	-0.041	-0.050	36.254	0.240	0.240	0.000	0.000	0.000	0.000
17	A	24	GLY	0	0.021	0.014	38.494	0.196	0.196	0.000	0.000	0.000	0.000
18	A	25	SER	0	-0.041	-0.027	40.631	0.284	0.284	0.000	0.000	0.000	0.000
19	A	26	HIS	0	0.010	0.003	40.328	-0.341	-0.341	0.000	0.000	0.000	0.000
20	A	27	PHE	0	0.001	-0.002	37.093	0.075	0.075	0.000	0.000	0.000	0.000
21	A	28	LYS	1	0.841	0.921	37.242	7.590	7.590	0.000	0.000	0.000	0.000
22	A	29	PHE	0	0.022	0.002	32.029	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.053	-0.032	30.481	0.135	0.135	0.000	0.000	0.000	0.000
24	A	31	VAL	0	0.016	0.012	25.084	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.023	-0.012	24.690	0.053	0.053	0.000	0.000	0.000	0.000
26	A	33	HIS	1	0.759	0.850	16.584	16.825	16.825	0.000	0.000	0.000	0.000
27	A	34	LYS	1	0.902	0.932	20.142	14.013	14.013	0.000	0.000	0.000	0.000
28	A	35	TYR	0	0.084	0.056	10.900	-0.474	-0.474	0.000	0.000	0.000	0.000
29	A	36	THR	0	0.013	0.003	15.995	0.660	0.660	0.000	0.000	0.000	0.000
30	A	37	GLY	0	-0.012	-0.004	16.065	-0.835	-0.835	0.000	0.000	0.000	0.000
31	A	38	TRP	0	-0.046	-0.012	10.783	-0.180	-0.180	0.000	0.000	0.000	0.000
32	A	39	ASP	-1	-0.871	-0.928	18.052	-12.615	-12.615	0.000	0.000	0.000	0.000
33	A	40	ALA	0	-0.073	-0.046	20.018	-0.570	-0.570	0.000	0.000	0.000	0.000
34	A	41	ASP	-1	-0.780	-0.855	18.926	-15.331	-15.331	0.000	0.000	0.000	0.000
35	A	42	LYS	1	0.901	0.938	22.256	10.184	10.184	0.000	0.000	0.000	0.000
36	A	43	SER	0	-0.005	0.011	26.001	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	44	ASP	-1	-0.846	-0.919	27.696	-9.741	-9.741	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.035	-0.022	31.121	-0.133	-0.133	0.000	0.000	0.000	0.000
39	A	46	VAL	0	-0.009	0.005	31.199	0.228	0.228	0.000	0.000	0.000	0.000
40	A	47	MET	0	0.007	0.004	34.281	0.077	0.077	0.000	0.000	0.000	0.000
41	A	48	PHE	0	-0.021	-0.017	31.233	-0.183	-0.183	0.000	0.000	0.000	0.000
42	A	49	GLN	0	0.014	0.001	37.455	0.383	0.383	0.000	0.000	0.000	0.000
43	A	50	PRO	0	-0.017	-0.015	38.555	-0.251	-0.251	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.874	-0.919	37.374	-8.372	-8.372	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.792	-0.853	35.417	-8.633	-8.633	0.000	0.000	0.000	0.000
46	A	53	VAL	0	0.002	-0.015	30.038	-0.240	-0.240	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.784	0.879	30.848	8.973	8.973	0.000	0.000	0.000	0.000
48	A	55	GLU	-1	-0.920	-0.967	24.471	-12.779	-12.779	0.000	0.000	0.000	0.000
49	A	56	ILE	0	-0.041	-0.030	25.598	0.321	0.321	0.000	0.000	0.000	0.000
50	A	57	PHE	0	0.010	-0.005	21.954	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	58	LYS	1	0.968	0.987	22.334	11.325	11.325	0.000	0.000	0.000	0.000
52	A	59	SER	0	-0.033	-0.027	17.003	-0.792	-0.792	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.004	0.034	17.062	0.633	0.633	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.013	-0.010	13.711	-1.189	-1.189	0.000	0.000	0.000	0.000
55	A	62	TYR	0	-0.004	-0.026	10.385	1.000	1.000	0.000	0.000	0.000	0.000
56	A	63	ASN	0	-0.018	-0.015	7.657	-2.280	-2.280	0.000	0.000	0.000	0.000
57	A	64	THR	0	0.012	0.025	5.626	0.166	0.166	0.000	0.000	0.000	0.000
60	A	67	LEU	0	0.005	0.010	5.809	5.175	5.175	0.000	0.000	0.000	0.000
61	A	68	THR	0	-0.104	-0.053	6.185	3.576	3.576	0.000	0.000	0.000	0.000
62	A	69	THR	0	0.048	0.014	8.885	0.406	0.406	0.000	0.000	0.000	0.000
63	A	70	GLY	0	-0.032	-0.009	12.145	1.770	1.770	0.000	0.000	0.000	0.000
64	A	71	VAL	0	-0.001	-0.020	13.191	-1.188	-1.188	0.000	0.000	0.000	0.000
65	A	72	ASP	-1	-0.768	-0.878	14.397	-19.863	-19.863	0.000	0.000	0.000	0.000
66	A	73	ASN	0	-0.003	-0.009	17.226	0.979	0.979	0.000	0.000	0.000	0.000
67	A	74	TRP	0	-0.015	-0.029	18.599	0.088	0.088	0.000	0.000	0.000	0.000
68	A	75	LEU	0	-0.020	0.009	23.611	0.313	0.313	0.000	0.000	0.000	0.000
69	A	76	VAL	0	0.012	-0.006	27.338	-0.190	-0.190	0.000	0.000	0.000	0.000
70	A	77	ASP	-1	-0.799	-0.870	29.625	-8.692	-8.692	0.000	0.000	0.000	0.000
71	A	78	GLY	0	0.045	0.013	32.960	-0.142	-0.142	0.000	0.000	0.000	0.000
72	A	79	THR	0	-0.066	-0.030	35.723	0.219	0.219	0.000	0.000	0.000	0.000
73	A	80	MET	0	0.050	0.051	39.443	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	81	VAL	0	-0.028	-0.032	41.520	0.163	0.163	0.000	0.000	0.000	0.000
75	A	82	GLN	0	0.013	0.007	43.931	0.062	0.062	0.000	0.000	0.000	0.000
76	A	83	GLU	-1	-0.754	-0.863	47.313	-6.617	-6.617	0.000	0.000	0.000	0.000
77	A	84	ARG	1	0.809	0.900	49.185	5.739	5.739	0.000	0.000	0.000	0.000
78	A	85	THR	0	0.010	-0.004	52.814	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.801	-0.865	55.047	-5.360	-5.360	0.000	0.000	0.000	0.000
80	A	87	VAL	0	0.005	-0.010	58.479	-0.047	-0.047	0.000	0.000	0.000	0.000
81	A	88	ASP	-1	-0.794	-0.891	61.128	-4.933	-4.933	0.000	0.000	0.000	0.000
82	A	89	ASN	0	-0.009	-0.021	64.477	-0.060	-0.060	0.000	0.000	0.000	0.000
83	A	90	LYS	1	0.881	0.951	65.571	4.807	4.807	0.000	0.000	0.000	0.000
84	A	91	GLY	0	0.010	0.016	61.632	-0.056	-0.056	0.000	0.000	0.000	0.000
85	A	92	HIS	0	-0.056	-0.032	60.054	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	93	GLN	0	-0.004	-0.019	54.333	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	94	ILE	0	0.000	0.003	59.089	0.051	0.051	0.000	0.000	0.000	0.000
88	A	95	GLY	0	0.011	0.011	58.960	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	96	LYS	1	0.887	0.939	51.458	6.031	6.031	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.903	0.955	50.245	6.278	6.278	0.000	0.000	0.000	0.000
91	A	98	SER	0	-0.072	-0.042	51.104	0.015	0.015	0.000	0.000	0.000	0.000
92	A	99	TYR	0	-0.016	-0.035	46.436	0.009	0.009	0.000	0.000	0.000	0.000
93	A	100	ILE	0	0.006	0.010	47.911	0.051	0.051	0.000	0.000	0.000	0.000
94	A	101	GLU	-1	-0.852	-0.904	42.979	-7.501	-7.501	0.000	0.000	0.000	0.000
95	A	102	HIS	0	-0.076	-0.041	44.769	0.224	0.224	0.000	0.000	0.000	0.000
96	A	103	ALA	0	0.006	-0.013	43.446	0.081	0.081	0.000	0.000	0.000	0.000
97	A	104	LYS	1	0.901	0.975	37.823	8.085	8.085	0.000	0.000	0.000	0.000
98	A	105	PHE	0	0.014	-0.012	36.842	0.193	0.193	0.000	0.000	0.000	0.000
99	A	106	ILE	0	-0.007	0.008	32.133	-0.160	-0.160	0.000	0.000	0.000	0.000
100	A	107	SER	0	0.029	0.008	29.334	0.043	0.043	0.000	0.000	0.000	0.000
101	A	108	ASP	-1	-0.804	-0.903	28.523	-10.862	-10.862	0.000	0.000	0.000	0.000
102	A	109	SER	0	-0.005	0.014	31.258	0.095	0.095	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.850	0.931	33.854	8.300	8.300	0.000	0.000	0.000	0.000
104	A	111	SER	0	-0.042	-0.018	29.910	-0.123	-0.123	0.000	0.000	0.000	0.000
105	A	112	TRP	0	0.007	-0.013	23.826	-0.208	-0.208	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.929	0.989	24.114	12.135	12.135	0.000	0.000	0.000	0.000
107	A	114	GLN	0	0.028	0.001	17.982	0.057	0.057	0.000	0.000	0.000	0.000
108	A	115	HIS	1	0.799	0.870	19.010	16.328	16.328	0.000	0.000	0.000	0.000
109	A	116	MET	0	-0.019	0.014	13.225	0.520	0.520	0.000	0.000	0.000	0.000
110	A	117	LEU	0	-0.013	0.025	13.605	0.808	0.808	0.000	0.000	0.000	0.000
111	A	118	THR	0	0.010	-0.027	10.422	-2.449	-2.449	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.021	-0.027	7.463	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.886	-0.933	9.385	-21.040	-21.040	0.000	0.000	0.000	0.000
114	A	121	ASP	-1	-0.749	-0.850	13.079	-19.309	-19.309	0.000	0.000	0.000	0.000
115	A	122	ASP	-1	-0.771	-0.868	10.036	-26.394	-26.394	0.000	0.000	0.000	0.000
116	A	123	GLY	0	-0.002	-0.004	13.061	0.650	0.650	0.000	0.000	0.000	0.000
117	A	124	LYS	1	0.811	0.907	14.983	21.495	21.495	0.000	0.000	0.000	0.000
118	A	125	THR	0	-0.008	-0.008	18.440	-0.357	-0.357	0.000	0.000	0.000	0.000
119	A	126	THR	0	0.019	0.037	18.656	-0.190	-0.190	0.000	0.000	0.000	0.000
120	A	127	THR	0	-0.025	-0.018	21.171	0.580	0.580	0.000	0.000	0.000	0.000
121	A	128	ILE	0	-0.008	-0.004	24.070	-0.184	-0.184	0.000	0.000	0.000	0.000
122	A	129	ARG	1	0.869	0.924	26.704	10.905	10.905	0.000	0.000	0.000	0.000
123	A	130	VAL	0	-0.030	-0.009	29.868	-0.106	-0.106	0.000	0.000	0.000	0.000
124	A	131	PHE	0	0.045	0.017	32.277	0.160	0.160	0.000	0.000	0.000	0.000
125	A	132	PRO	0	-0.022	-0.026	35.738	-0.072	-0.072	0.000	0.000	0.000	0.000
126	A	133	THR	0	0.033	0.022	37.576	0.137	0.137	0.000	0.000	0.000	0.000
127	A	134	GLU	-1	-0.906	-0.936	32.810	-9.675	-9.675	0.000	0.000	0.000	0.000
128	A	135	ILE	0	-0.015	0.002	27.720	0.045	0.045	0.000	0.000	0.000	0.000
129	A	136	HIS	1	0.845	0.909	27.533	10.521	10.521	0.000	0.000	0.000	0.000
130	A	137	PHE	0	0.012	0.004	22.524	0.090	0.090	0.000	0.000	0.000	0.000
131	A	138	ILE	0	0.006	-0.001	23.094	-0.178	-0.178	0.000	0.000	0.000	0.000
132	A	139	SER	0	0.007	-0.006	17.799	0.231	0.231	0.000	0.000	0.000	0.000
133	A	140	PRO	0	-0.028	-0.019	16.831	0.208	0.208	0.000	0.000	0.000	0.000
134	A	141	SER	0	0.006	-0.008	14.733	0.590	0.590	0.000	0.000	0.000	0.000
135	A	142	GLY	0	0.016	0.015	16.631	0.040	0.040	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.937	-0.968	19.851	-12.326	-12.326	0.000	0.000	0.000	0.000
137	A	144	SER	0	-0.058	-0.033	22.094	-0.535	-0.535	0.000	0.000	0.000	0.000
138	A	145	THR	0	0.021	0.025	24.297	0.056	0.056	0.000	0.000	0.000	0.000
139	A	146	THR	0	-0.100	-0.073	27.742	-0.119	-0.119	0.000	0.000	0.000	0.000
140	A	147	THR	0	0.066	0.043	29.802	0.083	0.083	0.000	0.000	0.000	0.000
141	A	148	PHE	0	-0.014	-0.015	32.328	-0.265	-0.265	0.000	0.000	0.000	0.000
142	A	149	THR	0	0.002	-0.008	34.632	0.282	0.282	0.000	0.000	0.000	0.000
143	A	150	LYS	1	0.960	0.985	37.766	7.089	7.089	0.000	0.000	0.000	0.000
144	A	151	TYR	-1	-0.961	-0.996	35.915	-7.638	-7.638	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)