FMO DATABASE

FMODB ID: 3GQML

Calculation Name: 6SSC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | glycerol | zinc ion

Ligand 3-letter code: PO4 | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SSC

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1541884.171532
FMO2-HF: Nuclear repulsion	1481614.872685
FMO2-HF: Total energy	-60269.298848
FMO2-MP2: Total energy	-60445.537294

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:24:THR)

Summations of interaction energy for fragment #1(A:24:THR)

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.
55.648	59.463	0.694	-1.764	-2.745	-0.013

Interaction energy analysis for fragmet #1(A:24:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.918

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	26	LYS	1	0.958	0.978	2.710	28.095	30.572	0.480	-1.328	-1.629	-0.013
4	A	27	ILE	0	0.011	0.015	4.336	5.410	5.602	-0.001	-0.011	-0.180	0.000
111	A	134	TYR	0	-0.084	-0.068	3.313	-3.361	-2.215	0.215	-0.425	-0.936	0.000
5	A	28	VAL	0	-0.058	-0.022	6.419	-0.440	-0.440	0.000	0.000	0.000	0.000
6	A	29	GLU	-1	-0.783	-0.864	8.426	-26.478	-26.478	0.000	0.000	0.000	0.000
7	A	30	VAL	0	-0.024	-0.020	11.297	0.862	0.862	0.000	0.000	0.000	0.000
8	A	31	ASN	0	-0.004	0.004	15.061	-0.415	-0.415	0.000	0.000	0.000	0.000
9	A	32	TYR	0	-0.029	-0.038	15.699	1.020	1.020	0.000	0.000	0.000	0.000
10	A	33	THR	0	0.007	0.006	20.261	0.113	0.113	0.000	0.000	0.000	0.000
11	A	34	TRP	0	-0.024	-0.018	17.299	0.268	0.268	0.000	0.000	0.000	0.000
12	A	35	ALA	0	0.032	0.018	23.579	0.275	0.275	0.000	0.000	0.000	0.000
13	A	36	THR	0	0.006	-0.001	26.240	0.248	0.248	0.000	0.000	0.000	0.000
14	A	37	PRO	0	0.036	0.021	25.416	-0.499	-0.499	0.000	0.000	0.000	0.000
15	A	38	LEU	0	0.004	0.019	19.112	0.020	0.020	0.000	0.000	0.000	0.000
16	A	39	SER	0	0.010	0.008	22.937	0.086	0.086	0.000	0.000	0.000	0.000
17	A	40	TYR	0	0.044	0.002	17.036	-0.321	-0.321	0.000	0.000	0.000	0.000
18	A	41	ASN	0	-0.018	0.012	20.205	-0.459	-0.459	0.000	0.000	0.000	0.000
19	A	42	PHE	0	-0.049	-0.022	14.478	0.378	0.378	0.000	0.000	0.000	0.000
20	A	43	ASN	0	-0.017	-0.015	18.376	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	44	PRO	0	-0.051	-0.004	14.500	0.501	0.501	0.000	0.000	0.000	0.000
22	A	45	ASN	0	0.059	0.021	16.872	-0.272	-0.272	0.000	0.000	0.000	0.000
23	A	46	MET	0	-0.008	0.008	17.749	0.440	0.440	0.000	0.000	0.000	0.000
24	A	47	ILE	0	-0.006	0.005	12.520	-0.725	-0.725	0.000	0.000	0.000	0.000
25	A	48	VAL	0	-0.026	-0.014	16.680	0.740	0.740	0.000	0.000	0.000	0.000
26	A	49	TYR	0	-0.001	-0.023	13.765	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	50	HIS	1	0.763	0.820	18.992	14.610	14.610	0.000	0.000	0.000	0.000
28	A	51	HIS	0	0.065	0.023	20.259	-0.924	-0.924	0.000	0.000	0.000	0.000
29	A	52	THR	0	-0.022	-0.042	21.225	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	53	VAL	0	-0.033	0.010	23.930	0.422	0.422	0.000	0.000	0.000	0.000
31	A	54	ASP	-1	-0.860	-0.926	26.921	-10.401	-10.401	0.000	0.000	0.000	0.000
32	A	55	ASN	0	0.018	-0.011	24.918	-1.143	-1.143	0.000	0.000	0.000	0.000
33	A	56	ASN	0	0.013	-0.004	24.402	0.032	0.032	0.000	0.000	0.000	0.000
34	A	57	MET	0	-0.020	0.017	22.976	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	58	THR	0	0.040	0.027	20.218	-0.615	-0.615	0.000	0.000	0.000	0.000
36	A	59	PRO	0	0.046	0.014	16.337	0.443	0.443	0.000	0.000	0.000	0.000
37	A	60	GLN	0	0.062	0.016	18.636	0.414	0.414	0.000	0.000	0.000	0.000
38	A	61	LYS	1	0.855	0.929	21.812	10.902	10.902	0.000	0.000	0.000	0.000
39	A	62	ILE	0	0.043	0.016	19.737	0.383	0.383	0.000	0.000	0.000	0.000
40	A	63	ASP	-1	-0.847	-0.905	21.298	-12.508	-12.508	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.836	-0.897	23.175	-9.952	-9.952	0.000	0.000	0.000	0.000
42	A	65	ILE	0	0.036	0.014	26.458	0.346	0.346	0.000	0.000	0.000	0.000
43	A	66	HIS	0	-0.021	-0.018	22.732	0.089	0.089	0.000	0.000	0.000	0.000
44	A	67	LYS	1	0.812	0.883	23.872	12.230	12.230	0.000	0.000	0.000	0.000
45	A	68	GLN	0	-0.016	-0.003	28.121	0.353	0.353	0.000	0.000	0.000	0.000
46	A	69	ARG	1	0.898	0.955	27.573	10.816	10.816	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.036	0.035	30.568	0.068	0.068	0.000	0.000	0.000	0.000
48	A	71	TRP	0	-0.064	-0.033	25.014	-0.027	-0.027	0.000	0.000	0.000	0.000
49	A	72	SER	0	0.004	-0.006	23.597	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	73	GLY	0	0.062	0.007	22.535	0.003	0.003	0.000	0.000	0.000	0.000
51	A	74	ILE	0	-0.029	0.012	17.630	0.124	0.124	0.000	0.000	0.000	0.000
52	A	75	GLY	0	0.017	0.005	19.846	-0.329	-0.329	0.000	0.000	0.000	0.000
53	A	76	TYR	0	-0.011	-0.008	17.131	0.023	0.023	0.000	0.000	0.000	0.000
54	A	77	HIS	0	0.036	0.026	12.808	-0.091	-0.091	0.000	0.000	0.000	0.000
55	A	78	PHE	0	-0.012	-0.007	8.326	-1.367	-1.367	0.000	0.000	0.000	0.000
56	A	79	TYR	0	-0.042	-0.030	13.290	1.175	1.175	0.000	0.000	0.000	0.000
57	A	80	ILE	0	-0.005	0.007	12.249	-1.027	-1.027	0.000	0.000	0.000	0.000
58	A	81	ARG	1	0.872	0.913	14.617	16.145	16.145	0.000	0.000	0.000	0.000
59	A	82	LYS	1	0.832	0.893	16.522	12.400	12.400	0.000	0.000	0.000	0.000
60	A	83	ASP	-1	-0.825	-0.879	16.080	-19.044	-19.044	0.000	0.000	0.000	0.000
61	A	84	GLY	0	0.013	0.005	13.833	-0.779	-0.779	0.000	0.000	0.000	0.000
62	A	85	THR	0	-0.066	-0.036	11.641	-3.139	-3.139	0.000	0.000	0.000	0.000
63	A	86	ILE	0	-0.026	-0.007	7.377	1.361	1.361	0.000	0.000	0.000	0.000
64	A	87	TYR	0	0.036	0.007	9.895	-1.076	-1.076	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.800	0.856	6.564	27.992	27.992	0.000	0.000	0.000	0.000
66	A	89	GLY	0	-0.013	0.009	12.018	1.239	1.239	0.000	0.000	0.000	0.000
67	A	90	ARG	1	0.787	0.856	15.225	13.677	13.677	0.000	0.000	0.000	0.000
68	A	91	PRO	0	0.019	0.008	13.163	-1.301	-1.301	0.000	0.000	0.000	0.000
69	A	92	GLU	-1	-0.720	-0.801	7.225	-29.889	-29.889	0.000	0.000	0.000	0.000
70	A	93	ASN	0	0.041	0.013	11.727	-0.291	-0.291	0.000	0.000	0.000	0.000
71	A	94	ALA	0	0.020	0.019	14.639	0.948	0.948	0.000	0.000	0.000	0.000
72	A	95	VAL	0	-0.014	-0.001	17.276	-0.420	-0.420	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.004	0.022	19.526	-0.063	-0.063	0.000	0.000	0.000	0.000
74	A	97	SER	0	-0.074	-0.054	20.040	0.571	0.571	0.000	0.000	0.000	0.000
75	A	98	HIS	0	0.030	0.022	18.904	0.462	0.462	0.000	0.000	0.000	0.000
76	A	99	ALA	0	0.054	0.025	22.500	0.227	0.227	0.000	0.000	0.000	0.000
77	A	100	PRO	0	-0.020	-0.012	24.593	-0.068	-0.068	0.000	0.000	0.000	0.000
78	A	101	GLY	0	0.037	0.024	27.177	0.264	0.264	0.000	0.000	0.000	0.000
79	A	102	VAL	0	0.024	-0.001	22.793	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	103	ASN	0	0.012	0.017	21.647	-0.801	-0.801	0.000	0.000	0.000	0.000
81	A	104	ALA	0	0.047	0.020	20.688	-0.518	-0.518	0.000	0.000	0.000	0.000
82	A	105	ARG	1	0.919	0.953	20.262	12.342	12.342	0.000	0.000	0.000	0.000
83	A	106	ALA	0	0.028	0.019	18.271	-0.333	-0.333	0.000	0.000	0.000	0.000
84	A	107	PHE	0	0.030	0.019	11.878	0.033	0.033	0.000	0.000	0.000	0.000
85	A	108	GLY	0	-0.019	-0.001	15.591	0.384	0.384	0.000	0.000	0.000	0.000
86	A	109	ILE	0	-0.013	-0.014	12.066	-0.686	-0.686	0.000	0.000	0.000	0.000
87	A	110	ALA	0	0.006	0.003	15.522	0.850	0.850	0.000	0.000	0.000	0.000
88	A	111	SER	0	-0.024	-0.020	16.417	-1.393	-1.393	0.000	0.000	0.000	0.000
89	A	112	GLU	-1	-0.782	-0.867	18.506	-13.873	-13.873	0.000	0.000	0.000	0.000
90	A	113	GLY	0	0.067	0.017	20.767	-0.209	-0.209	0.000	0.000	0.000	0.000
91	A	114	ASN	0	0.023	0.040	24.188	-0.193	-0.193	0.000	0.000	0.000	0.000
92	A	115	PHE	0	-0.047	-0.019	21.295	0.126	0.126	0.000	0.000	0.000	0.000
93	A	116	ASN	0	-0.035	-0.031	26.491	-0.203	-0.203	0.000	0.000	0.000	0.000
94	A	117	GLU	-1	-0.938	-0.966	29.766	-9.347	-9.347	0.000	0.000	0.000	0.000
95	A	118	GLU	-1	-0.769	-0.859	25.818	-12.327	-12.327	0.000	0.000	0.000	0.000
96	A	119	TYR	0	0.024	-0.009	24.312	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	120	VAL	0	-0.036	-0.006	18.152	-0.195	-0.195	0.000	0.000	0.000	0.000
98	A	121	THR	0	0.015	0.000	18.790	-0.116	-0.116	0.000	0.000	0.000	0.000
99	A	122	PRO	0	0.056	0.015	18.059	-0.849	-0.849	0.000	0.000	0.000	0.000
100	A	123	GLN	0	0.049	0.037	14.640	-1.023	-1.023	0.000	0.000	0.000	0.000
101	A	124	GLN	0	-0.027	-0.012	13.810	-1.419	-1.419	0.000	0.000	0.000	0.000
102	A	125	MET	0	0.005	0.014	14.102	-1.551	-1.551	0.000	0.000	0.000	0.000
103	A	126	THR	0	-0.027	-0.023	10.176	-1.126	-1.126	0.000	0.000	0.000	0.000
104	A	127	SER	0	-0.033	-0.045	9.524	-3.559	-3.559	0.000	0.000	0.000	0.000
105	A	128	LEU	0	-0.011	0.008	9.623	-2.014	-2.014	0.000	0.000	0.000	0.000
106	A	129	ILE	0	0.004	0.030	10.135	-0.618	-0.618	0.000	0.000	0.000	0.000
107	A	130	ALA	0	0.007	0.001	5.844	-1.675	-1.675	0.000	0.000	0.000	0.000
108	A	131	LEU	0	-0.024	-0.015	5.867	-4.141	-4.141	0.000	0.000	0.000	0.000
109	A	132	SER	0	0.010	-0.003	7.608	1.086	1.086	0.000	0.000	0.000	0.000
110	A	133	ARG	1	0.915	0.945	7.532	24.770	24.770	0.000	0.000	0.000	0.000
112	A	135	LEU	0	-0.014	-0.004	5.839	1.444	1.444	0.000	0.000	0.000	0.000
113	A	136	MET	0	-0.037	-0.009	8.971	1.151	1.151	0.000	0.000	0.000	0.000
114	A	137	ASN	0	0.001	0.002	7.731	3.379	3.379	0.000	0.000	0.000	0.000
115	A	138	LYS	1	0.792	0.902	5.821	31.928	31.928	0.000	0.000	0.000	0.000
116	A	139	TYR	0	-0.041	-0.062	9.152	1.391	1.391	0.000	0.000	0.000	0.000
117	A	140	ASN	0	-0.019	0.004	12.620	1.008	1.008	0.000	0.000	0.000	0.000
118	A	141	ILE	0	-0.033	0.001	13.314	1.135	1.135	0.000	0.000	0.000	0.000
119	A	142	THR	0	0.025	-0.003	14.835	-0.706	-0.706	0.000	0.000	0.000	0.000
120	A	143	ASP	-1	-0.848	-0.904	17.587	-13.087	-13.087	0.000	0.000	0.000	0.000
121	A	144	LEU	0	0.012	0.004	14.806	-0.702	-0.702	0.000	0.000	0.000	0.000
122	A	145	LYS	1	0.861	0.908	18.760	13.403	13.403	0.000	0.000	0.000	0.000
123	A	146	ARG	1	0.903	0.933	20.380	10.975	10.975	0.000	0.000	0.000	0.000
124	A	147	HIS	0	0.012	-0.057	22.902	0.480	0.480	0.000	0.000	0.000	0.000
125	A	148	LYS	1	0.903	0.956	24.600	11.045	11.045	0.000	0.000	0.000	0.000
126	A	149	ASP	-1	-0.798	-0.858	24.671	-11.642	-11.642	0.000	0.000	0.000	0.000
127	A	150	VAL	0	-0.069	-0.036	24.211	0.108	0.108	0.000	0.000	0.000	0.000
128	A	151	ARG	1	0.869	0.933	27.339	10.326	10.326	0.000	0.000	0.000	0.000
129	A	152	GLN	0	0.052	0.034	29.593	-0.068	-0.068	0.000	0.000	0.000	0.000
130	A	153	THR	0	-0.027	-0.018	27.749	0.113	0.113	0.000	0.000	0.000	0.000
131	A	154	GLU	-1	-0.807	-0.899	30.217	-9.512	-9.512	0.000	0.000	0.000	0.000
132	A	155	CYS	-1	-0.879	-0.810	24.586	-13.032	-13.032	0.000	0.000	0.000	0.000
133	A	156	PRO	0	-0.012	-0.023	21.993	0.176	0.176	0.000	0.000	0.000	0.000
134	A	157	GLY	0	0.068	0.018	24.088	-0.291	-0.291	0.000	0.000	0.000	0.000
135	A	158	ASN	0	-0.051	-0.044	26.495	-0.301	-0.301	0.000	0.000	0.000	0.000
136	A	159	ASN	0	-0.030	-0.009	26.757	0.152	0.152	0.000	0.000	0.000	0.000
137	A	160	PHE	0	-0.016	-0.003	17.798	-0.572	-0.572	0.000	0.000	0.000	0.000
138	A	161	PRO	0	0.051	0.034	19.382	0.294	0.294	0.000	0.000	0.000	0.000
139	A	162	PHE	0	-0.025	-0.032	20.116	-0.707	-0.707	0.000	0.000	0.000	0.000
140	A	163	GLU	-1	-0.797	-0.907	20.288	-12.950	-12.950	0.000	0.000	0.000	0.000
141	A	164	GLU	-1	-0.836	-0.901	19.509	-15.765	-15.765	0.000	0.000	0.000	0.000
142	A	165	ILE	0	-0.016	-0.015	15.068	-0.858	-0.858	0.000	0.000	0.000	0.000
143	A	166	LYS	1	0.813	0.906	16.266	11.969	11.969	0.000	0.000	0.000	0.000
144	A	167	ALA	0	0.022	0.016	17.909	-0.471	-0.471	0.000	0.000	0.000	0.000
145	A	168	LYS	1	0.834	0.896	14.770	17.390	17.390	0.000	0.000	0.000	0.000
146	A	169	LEU	0	-0.080	-0.025	11.304	-1.719	-1.719	0.000	0.000	0.000	0.000
147	A	170	ASN	0	-0.056	-0.026	14.538	0.268	0.268	0.000	0.000	0.000	0.000
148	A	171	VAL	0	-0.031	-0.014	16.453	0.138	0.138	0.000	0.000	0.000	0.000
149	A	172	LYS	0	0.114	0.063	19.185	-0.108	-0.108	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:THR)