FMO DATABASE

FMODB ID: MLM7Z

Calculation Name: 1OGD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-ribopyranose | chloride ion

Ligand 3-letter code: RIP | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1OGD

Chain ID: A

ChEMBL ID:

UniProt ID: P36946

Base Structure: X-ray

Registration Date: 2025-10-05

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1098220.955452
FMO2-HF: Nuclear repulsion	1048827.19858
FMO2-HF: Total energy	-49393.756872
FMO2-MP2: Total energy	-49539.26343

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.
-80.663	-78.841	0.017	-0.693	-1.144	-0.001

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 : 0.867 / q_NPA : 0.921

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	A	3	LYS	1	0.938	0.965	3.581	36.913	38.530	0.011	-0.662	-0.965	-0.001
7	A	7	LEU	0	-0.007	0.001	3.833	-3.412	-3.207	0.006	-0.031	-0.179	0.000
4	A	4	HIS	0	0.064	0.037	5.689	1.135	1.135	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.097	0.058	8.305	-1.880	-1.880	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.010	0.020	8.354	-3.687	-3.687	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.028	0.018	6.453	-2.359	-2.359	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.017	-0.008	7.949	0.248	0.248	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.021	-0.014	9.332	-0.277	-0.277	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.066	0.026	12.564	0.638	0.638	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.002	-0.005	9.871	0.495	0.495	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.866	0.948	11.058	23.719	23.719	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.044	0.018	13.972	0.695	0.695	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.007	-0.009	14.213	0.609	0.609	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.066	-0.023	13.887	0.305	0.305	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.943	-0.966	16.022	-16.387	-16.387	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.082	-0.030	19.260	0.933	0.933	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.016	0.015	21.500	-0.112	-0.112	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.051	-0.043	24.703	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.075	-0.033	27.200	0.419	0.419	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.793	-0.884	24.808	-12.009	-12.009	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.892	0.945	26.036	10.273	10.273	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.013	0.003	19.991	-0.316	-0.316	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.008	0.003	23.698	0.437	0.437	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.013	0.011	20.700	-0.616	-0.616	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.051	0.010	23.137	0.551	0.551	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.778	-0.867	24.012	-10.311	-10.311	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.012	-0.016	25.487	-0.102	-0.102	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.027	-0.011	26.409	0.047	0.047	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.025	0.007	27.601	0.299	0.299	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.062	-0.024	28.420	-0.259	-0.259	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.003	-0.014	25.231	-0.115	-0.115	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.008	-0.002	28.590	0.193	0.193	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.900	-0.953	29.482	-9.599	-9.599	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.052	-0.026	29.004	0.125	0.125	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.006	0.015	25.489	-0.377	-0.377	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.015	0.001	18.808	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.953	0.982	22.015	11.842	11.842	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.027	-0.015	15.708	-0.565	-0.565	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.801	-0.883	18.622	-12.577	-12.577	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.026	-0.015	13.903	-0.961	-0.961	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.092	-0.043	16.942	0.050	0.050	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.012	-0.006	15.955	-0.176	-0.176	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.908	0.945	19.418	11.910	11.910	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.000	0.002	22.784	-0.231	-0.231	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.001	0.006	24.148	0.061	0.061	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.054	0.002	17.126	-0.259	-0.259	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.053	-0.007	16.228	0.041	0.041	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.067	0.040	18.886	0.424	0.424	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.009	-0.010	20.805	-0.628	-0.628	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.016	0.009	22.385	-0.107	-0.107	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.875	-0.942	17.694	-13.726	-13.726	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.062	-0.046	17.463	-0.899	-0.899	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.011	-0.006	18.487	-0.496	-0.496	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.018	0.011	19.196	-0.085	-0.085	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.001	-0.003	13.153	-0.454	-0.454	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.043	-0.042	15.741	-0.817	-0.817	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.001	0.008	17.792	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.977	-0.975	15.029	-17.625	-17.625	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.875	-0.947	11.958	-23.933	-23.933	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.069	-0.023	15.773	-0.452	-0.452	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.033	0.025	19.088	0.532	0.532	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.030	-0.011	22.227	0.261	0.261	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.784	-0.876	24.858	-10.273	-10.273	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.756	0.870	28.525	9.210	9.210	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.004	0.004	27.212	-0.392	-0.392	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.008	0.009	29.497	0.377	0.377	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.030	0.005	30.448	-0.342	-0.342	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.026	0.026	32.539	0.255	0.255	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.028	0.002	35.220	-0.059	-0.059	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.837	-0.920	37.322	-7.811	-7.811	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.000	0.011	30.696	0.110	0.110	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.879	0.952	35.253	8.035	8.035	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.049	-0.013	37.589	0.109	0.109	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.036	-0.025	36.591	0.145	0.145	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.044	-0.026	30.582	-0.055	-0.055	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.025	0.007	33.492	-0.259	-0.259	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.942	-0.958	30.035	-9.363	-9.363	0.000	0.000	0.000	0.000
80	A	80	ASN	0	0.046	-0.009	27.430	-0.485	-0.485	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.012	0.002	29.912	-0.173	-0.173	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.908	0.943	32.118	8.074	8.074	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.011	0.010	22.930	-0.082	-0.082	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.006	0.000	26.641	-0.292	-0.292	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.860	-0.910	28.902	-8.852	-8.852	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.042	-0.021	29.218	0.181	0.181	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.051	-0.002	22.303	-0.114	-0.114	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.009	-0.016	23.131	-0.383	-0.383	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.005	-0.009	27.835	0.362	0.362	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.996	-0.988	28.449	-10.262	-10.262	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.033	-0.010	27.102	0.154	0.154	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.849	-0.910	30.586	-8.494	-8.494	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.007	0.005	30.981	-0.277	-0.277	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.886	-0.938	33.289	-8.271	-8.271	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.065	-0.095	34.047	-0.136	-0.136	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.015	0.027	36.166	0.222	0.222	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.034	-0.052	38.175	-0.056	-0.056	0.000	0.000	0.000	0.000
98	A	98	HIS	0	0.048	-0.014	32.765	-0.211	-0.211	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.879	-0.913	36.226	-8.028	-8.028	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.821	-0.879	37.800	-7.706	-7.706	0.000	0.000	0.000	0.000
101	A	101	PHE	0	-0.008	0.006	28.981	-0.188	-0.188	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.857	0.895	33.115	7.907	7.907	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.066	-0.015	33.596	-0.188	-0.188	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.058	0.022	32.624	-0.120	-0.120	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.069	-0.045	29.079	-0.347	-0.347	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.891	0.941	29.187	8.327	8.327	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.909	-0.940	30.788	-9.529	-9.529	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.071	-0.022	25.639	-0.279	-0.279	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.849	0.923	22.593	12.161	12.161	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.017	-0.023	20.653	-0.324	-0.324	0.000	0.000	0.000	0.000
111	A	111	VAL	0	0.005	0.012	22.582	0.243	0.243	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.008	-0.009	17.755	-0.497	-0.497	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.761	0.869	20.406	12.044	12.044	0.000	0.000	0.000	0.000
114	A	114	THR	0	0.000	-0.015	19.934	-0.545	-0.545	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.021	-0.002	20.975	0.338	0.338	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.808	-0.873	22.525	-10.323	-10.323	0.000	0.000	0.000	0.000
117	A	117	PHE	0	-0.001	-0.033	25.217	0.181	0.181	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.040	-0.013	28.733	0.399	0.399	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.016	-0.008	30.715	-0.141	-0.141	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.009	-0.005	32.532	0.033	0.033	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.012	0.025	27.790	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.041	-0.037	27.219	-0.616	-0.616	0.000	0.000	0.000	0.000
123	A	123	CYS	0	-0.032	-0.008	25.860	0.151	0.151	0.000	0.000	0.000	0.000
124	A	124	ILE	0	-0.008	0.000	26.411	-0.401	-0.401	0.000	0.000	0.000	0.000
125	A	125	LEU	0	0.016	0.009	21.832	0.201	0.201	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.052	-0.049	25.489	-0.116	-0.116	0.000	0.000	0.000	0.000
127	A	127	ALA	0	0.030	0.007	23.577	-0.043	-0.043	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.042	0.021	24.984	0.520	0.520	0.000	0.000	0.000	0.000
129	A	129	VAL	0	-0.029	-0.023	25.453	-0.321	-0.321	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.049	-0.034	20.157	-0.145	-0.145	0.000	0.000	0.000	0.000
131	A	131	PHE	-1	-0.939	-0.956	24.689	-11.075	-11.075	0.000	0.000	0.000	0.000

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