FMO DATABASE

FMODB ID: LQR79

Calculation Name: 1E6C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | (4s)-2-methyl-2,4-pentanediol | (4r)-2-methylpentane-2,4-diol | chloride ion

Ligand 3-letter code: PO4 | MPD | MRD | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E6C

Chain ID: A

ChEMBL ID:

UniProt ID: P10880

Base Structure: X-ray

Registration Date: 2025-09-02

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1640965.417753
FMO2-HF: Nuclear repulsion	1573375.517204
FMO2-HF: Total energy	-67589.900549
FMO2-MP2: Total energy	-67780.201423

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:1:MET)

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

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.
-110.043	-104.831	2.073	-3.009	-4.274	-0.022

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.896

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	3	GLU	-1	-0.809	-0.881	3.845	-35.243	-30.253	-0.037	-2.498	-2.455	-0.013
169	A	169	ARG	1	0.823	0.920	4.616	26.630	26.807	-0.001	-0.017	-0.158	0.000
170	A	170	LEU	-1	-0.902	-0.956	2.250	-36.680	-36.635	2.111	-0.494	-1.661	-0.009
4	A	4	PRO	0	-0.028	0.005	5.953	-0.823	-0.823	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.030	0.009	7.069	0.118	0.118	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.008	-0.005	10.155	2.140	2.140	0.000	0.000	0.000	0.000
7	A	7	MET	0	0.016	0.016	13.692	-0.202	-0.202	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.024	0.019	16.287	0.924	0.924	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.080	0.024	19.294	-0.088	-0.088	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.027	0.002	22.453	0.182	0.182	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.803	0.837	22.825	12.902	12.902	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.017	0.005	26.108	0.380	0.380	0.000	0.000	0.000	0.000
13	A	13	CYS	0	-0.027	0.003	23.619	0.370	0.370	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.060	0.022	22.282	-0.506	-0.506	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.018	0.014	19.467	-0.437	-0.437	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.004	0.002	19.099	-0.591	-0.591	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.033	-0.020	19.697	-0.484	-0.484	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.043	0.025	15.579	-0.402	-0.402	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.051	0.027	15.163	-1.082	-1.082	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.880	0.935	14.983	13.297	13.297	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.895	-0.932	14.923	-17.095	-17.095	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.026	0.013	9.113	-0.665	-0.665	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.029	-0.022	10.818	-1.862	-1.862	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.886	0.934	11.646	15.131	15.131	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.016	-0.011	10.866	-0.175	-0.175	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.007	0.008	5.562	-1.452	-1.452	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.042	-0.006	8.043	-2.420	-2.420	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.055	-0.025	5.334	-3.609	-3.609	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.843	-0.892	10.612	-17.180	-17.180	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.014	-0.021	13.628	-0.457	-0.457	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.003	0.002	15.504	0.959	0.959	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.772	-0.870	18.038	-14.120	-14.120	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.057	0.022	19.675	0.312	0.312	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.856	-0.926	22.073	-11.800	-11.800	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.039	-0.016	23.857	0.430	0.430	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.038	0.019	22.505	0.289	0.289	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.003	0.021	24.862	0.267	0.267	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.017	-0.009	27.581	0.231	0.231	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.009	-0.014	26.292	0.584	0.584	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.049	-0.031	26.862	0.270	0.270	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.047	-0.021	29.833	0.230	0.230	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.023	0.036	32.283	0.328	0.328	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.024	-0.026	32.859	-0.266	-0.266	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.055	-0.035	34.971	0.038	0.038	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.031	0.014	33.349	-0.131	-0.131	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.007	-0.001	35.701	0.043	0.043	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.826	-0.901	38.167	-7.909	-7.909	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.016	0.009	33.153	0.038	0.038	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.052	-0.028	36.003	0.036	0.036	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.025	-0.011	38.135	0.146	0.146	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.026	-0.002	38.907	0.154	0.154	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.840	-0.886	34.360	-9.288	-9.288	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.026	0.018	37.089	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.021	-0.007	33.179	-0.331	-0.331	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.012	-0.013	33.275	-0.310	-0.310	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.047	0.035	32.293	-0.324	-0.324	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.025	0.000	29.712	-0.328	-0.328	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.861	0.896	28.149	10.282	10.282	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.920	0.986	27.575	9.671	9.671	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.866	0.892	27.041	9.364	9.364	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.844	-0.913	24.633	-12.141	-12.141	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.020	-0.026	23.003	-0.451	-0.451	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.901	-0.964	22.173	-12.039	-12.039	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.021	-0.008	22.495	-0.545	-0.545	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.047	-0.033	17.455	-0.758	-0.758	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.054	-0.038	17.820	-0.626	-0.626	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.026	0.000	17.780	-0.835	-0.835	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.021	-0.013	16.848	-0.462	-0.462	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.012	0.016	13.767	-1.137	-1.137	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.002	-0.007	12.533	-0.307	-0.307	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.012	-0.025	7.271	-0.114	-0.114	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.012	0.015	6.655	-2.848	-2.848	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.847	0.914	8.670	23.187	23.187	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.015	0.007	10.490	-1.555	-1.555	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.004	-0.007	12.682	1.547	1.547	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.008	0.003	15.318	0.155	0.155	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.017	-0.025	17.720	0.405	0.405	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.092	0.054	20.422	0.420	0.420	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.024	-0.015	23.928	-0.122	-0.122	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.014	-0.017	26.174	0.184	0.184	0.000	0.000	0.000	0.000
81	A	81	MET	0	0.019	0.036	20.626	0.124	0.124	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.018	0.000	21.130	-0.113	-0.113	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.006	0.015	23.570	0.142	0.142	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.002	0.004	25.832	0.299	0.299	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.857	-0.925	24.229	-12.407	-12.407	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.010	-0.016	22.757	-0.413	-0.413	0.000	0.000	0.000	0.000
87	A	87	ASN	0	0.025	0.019	20.967	-0.785	-0.785	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.875	0.938	19.239	11.663	11.663	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.042	-0.031	18.207	-1.091	-1.091	0.000	0.000	0.000	0.000
90	A	90	PHE	0	-0.015	-0.005	16.067	-1.005	-1.005	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.003	0.005	14.884	-1.213	-1.213	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.888	0.926	13.355	15.943	15.943	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.048	-0.006	13.147	-1.029	-1.029	0.000	0.000	0.000	0.000
94	A	94	HIS	1	0.780	0.872	11.540	19.984	19.984	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.030	0.018	8.518	-2.342	-2.342	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.029	-0.007	7.038	2.940	2.940	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.017	-0.010	9.469	0.466	0.466	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.018	0.000	11.672	0.166	0.166	0.000	0.000	0.000	0.000
99	A	99	TYR	0	-0.009	-0.003	14.284	0.759	0.759	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.021	-0.014	16.876	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.003	-0.006	19.545	0.562	0.562	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.033	0.005	22.271	0.102	0.102	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.016	0.017	25.854	0.024	0.024	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.031	0.008	28.852	0.161	0.161	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.840	-0.902	31.430	-8.523	-8.523	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.798	-0.873	29.640	-9.241	-9.241	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.059	-0.041	27.955	0.039	0.039	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.030	0.016	32.104	0.154	0.154	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.020	-0.006	35.213	0.234	0.234	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.811	0.882	27.707	10.323	10.323	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.005	0.004	34.805	0.133	0.133	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.008	0.005	37.210	0.244	0.244	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.009	0.003	37.790	0.174	0.174	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.098	-0.047	37.494	0.034	0.034	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.039	-0.020	39.604	0.109	0.109	0.000	0.000	0.000	0.000
116	A	116	GLN	0	-0.041	-0.020	42.858	0.133	0.133	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.007	0.014	44.054	-0.083	-0.083	0.000	0.000	0.000	0.000
118	A	118	HIS	0	-0.017	-0.019	45.879	-0.074	-0.074	0.000	0.000	0.000	0.000
119	A	119	GLN	0	0.032	0.020	43.563	0.026	0.026	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.928	0.976	46.751	5.763	5.763	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.037	0.006	49.825	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.018	-0.018	50.567	0.124	0.124	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.006	-0.002	51.140	-0.082	-0.082	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.032	0.009	50.337	-0.038	-0.038	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.028	0.028	47.622	-0.119	-0.119	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.874	0.925	43.715	6.744	6.744	0.000	0.000	0.000	0.000
127	A	127	PRO	0	0.022	-0.001	44.744	-0.141	-0.141	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.015	0.008	44.536	-0.114	-0.114	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.009	0.014	41.358	-0.182	-0.182	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.843	-0.915	40.024	-7.297	-7.297	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.921	-0.953	39.896	-7.600	-7.600	0.000	0.000	0.000	0.000
132	A	132	MET	0	-0.050	-0.027	36.771	-0.211	-0.211	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.863	-0.945	35.691	-8.606	-8.606	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.013	0.005	35.006	-0.285	-0.285	0.000	0.000	0.000	0.000
135	A	135	VAL	0	0.049	0.021	34.011	-0.291	-0.291	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.075	-0.036	31.476	-0.430	-0.430	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.826	0.892	30.452	8.571	8.571	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.930	-0.953	30.233	-9.276	-9.276	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.881	0.936	27.099	10.516	10.516	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.888	-0.945	26.388	-10.974	-10.974	0.000	0.000	0.000	0.000
141	A	141	ALA	0	0.017	0.002	25.300	-0.518	-0.518	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.010	-0.009	25.086	-0.456	-0.456	0.000	0.000	0.000	0.000
143	A	143	TYR	0	-0.050	-0.032	22.064	-0.423	-0.423	0.000	0.000	0.000	0.000
144	A	144	GLN	0	0.013	0.003	20.646	-1.199	-1.199	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.905	-0.938	20.303	-13.700	-13.700	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.021	-0.010	17.430	-0.538	-0.538	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.004	0.026	16.380	-1.186	-1.186	0.000	0.000	0.000	0.000
148	A	148	HIS	0	-0.018	0.009	11.707	0.405	0.405	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.011	-0.001	7.221	0.325	0.325	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.002	-0.002	13.556	0.158	0.158	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.006	0.019	15.538	-0.157	-0.157	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.821	-0.878	17.519	-11.464	-11.464	0.000	0.000	0.000	0.000
153	A	153	ALA	0	-0.021	-0.029	20.628	-0.259	-0.259	0.000	0.000	0.000	0.000
154	A	154	THR	0	-0.099	-0.072	22.036	0.438	0.438	0.000	0.000	0.000	0.000
155	A	155	GLN	0	-0.063	-0.028	19.316	0.573	0.573	0.000	0.000	0.000	0.000
156	A	156	PRO	0	0.008	-0.011	23.167	-0.142	-0.142	0.000	0.000	0.000	0.000
157	A	157	PRO	0	0.015	-0.014	20.126	-0.422	-0.422	0.000	0.000	0.000	0.000
158	A	158	ALA	0	0.044	0.025	18.306	-0.698	-0.698	0.000	0.000	0.000	0.000
159	A	159	ALA	0	0.010	0.020	17.518	-0.619	-0.619	0.000	0.000	0.000	0.000
160	A	160	ILE	0	0.035	0.030	16.134	-0.654	-0.654	0.000	0.000	0.000	0.000
161	A	161	VAL	0	0.005	-0.005	12.631	-0.910	-0.910	0.000	0.000	0.000	0.000
162	A	162	CYS	0	-0.048	-0.021	12.639	-1.209	-1.209	0.000	0.000	0.000	0.000
163	A	163	GLU	-1	-0.816	-0.905	12.791	-15.871	-15.871	0.000	0.000	0.000	0.000
164	A	164	LEU	0	-0.005	-0.007	10.925	-0.840	-0.840	0.000	0.000	0.000	0.000
165	A	165	MET	0	-0.023	0.006	7.894	-2.153	-2.153	0.000	0.000	0.000	0.000
166	A	166	GLN	0	-0.018	-0.010	7.818	-1.322	-1.322	0.000	0.000	0.000	0.000
167	A	167	THR	0	-0.058	-0.030	9.383	-0.254	-0.254	0.000	0.000	0.000	0.000
168	A	168	MET	0	-0.084	-0.041	4.946	-0.949	-0.949	0.000	0.000	0.000	0.000

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