FMO DATABASE

FMODB ID: LQ3G9

Calculation Name: 1R8S-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | sulfate ion | sulfite ion | beta-mercaptoethanol | formic acid

Ligand 3-letter code: GDP | SO4 | SO3 | BME | FMT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1R8S

Chain ID: A

ChEMBL ID:

UniProt ID: P84080

Base Structure: X-ray

Registration Date: 2025-10-03

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1649963.268456
FMO2-HF: Nuclear repulsion	1585706.897542
FMO2-HF: Total energy	-64256.370914
FMO2-MP2: Total energy	-64443.197036

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:18:MET)

Summations of interaction energy for fragment #1(A:18: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.
-233.039	-224.789	21.018	-11.024	-18.243	-0.1

Interaction energy analysis for fragmet #1(A:18:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.917

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	20	ILE	0	0.034	0.019	2.708	-1.595	1.363	0.715	-1.170	-2.503	-0.002
4	A	21	LEU	0	-0.011	0.012	5.115	2.339	2.376	-0.001	-0.004	-0.032	0.000
44	A	61	ILE	0	0.039	0.036	2.329	-4.499	-3.844	1.112	-0.280	-1.486	-0.002
45	A	62	SER	0	0.056	0.028	3.446	5.588	6.494	0.011	-0.344	-0.573	-0.001
46	A	63	PHE	0	-0.020	-0.008	1.788	-50.271	-50.316	12.882	-6.409	-6.427	-0.071
47	A	64	THR	0	-0.021	-0.017	3.606	5.615	6.427	0.001	-0.309	-0.504	0.000
68	A	85	THR	0	-0.042	-0.006	5.091	-4.787	-4.697	-0.001	-0.004	-0.085	0.000
69	A	86	GLN	0	0.054	0.015	2.607	-6.468	-4.731	2.986	-1.478	-3.245	-0.010
70	A	87	GLY	0	0.046	0.023	5.161	1.914	2.028	-0.001	-0.012	-0.102	0.000
71	A	88	LEU	0	-0.059	-0.023	6.041	-1.720	-1.732	-0.001	-0.002	0.016	0.000
156	A	173	LEU	0	-0.015	-0.016	5.399	-0.246	-0.128	-0.001	-0.009	-0.109	0.000
160	A	177	LEU	-1	-0.977	-0.973	2.178	-45.393	-44.513	3.316	-1.003	-3.193	-0.014
5	A	22	MET	0	-0.003	0.009	8.898	0.631	0.631	0.000	0.000	0.000	0.000
6	A	23	VAL	0	-0.012	-0.016	11.363	1.089	1.089	0.000	0.000	0.000	0.000
7	A	24	GLY	0	0.074	0.040	14.870	-0.126	-0.126	0.000	0.000	0.000	0.000
8	A	25	LEU	0	-0.015	0.012	18.183	-0.260	-0.260	0.000	0.000	0.000	0.000
9	A	26	ASP	-1	-0.849	-0.913	20.952	-12.316	-12.316	0.000	0.000	0.000	0.000
10	A	27	ALA	0	0.053	0.018	23.273	0.119	0.119	0.000	0.000	0.000	0.000
11	A	28	ALA	0	-0.003	0.009	20.164	0.098	0.098	0.000	0.000	0.000	0.000
12	A	29	GLY	0	0.036	0.013	20.356	-0.162	-0.162	0.000	0.000	0.000	0.000
13	A	30	LYS	1	0.875	0.939	15.580	15.614	15.614	0.000	0.000	0.000	0.000
14	A	31	THR	0	0.046	0.016	15.985	-0.666	-0.666	0.000	0.000	0.000	0.000
15	A	32	THR	0	-0.036	-0.015	18.089	-0.197	-0.197	0.000	0.000	0.000	0.000
16	A	33	ILE	0	0.025	0.017	13.428	0.050	0.050	0.000	0.000	0.000	0.000
17	A	34	LEU	0	-0.002	0.003	11.502	-0.453	-0.453	0.000	0.000	0.000	0.000
18	A	35	TYR	0	-0.001	-0.008	14.626	-0.422	-0.422	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.815	0.894	17.248	14.703	14.703	0.000	0.000	0.000	0.000
20	A	37	LEU	0	0.003	0.010	10.537	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	38	LYS	1	0.836	0.908	14.120	19.116	19.116	0.000	0.000	0.000	0.000
22	A	39	LEU	0	-0.071	-0.037	15.234	0.484	0.484	0.000	0.000	0.000	0.000
23	A	40	GLY	0	-0.002	0.020	15.847	0.865	0.865	0.000	0.000	0.000	0.000
24	A	41	GLU	-1	-0.854	-0.923	11.028	-27.695	-27.695	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.005	-0.010	14.373	1.273	1.273	0.000	0.000	0.000	0.000
26	A	43	VAL	0	-0.021	-0.003	12.100	1.252	1.252	0.000	0.000	0.000	0.000
27	A	44	THR	0	0.002	-0.001	14.563	-0.192	-0.192	0.000	0.000	0.000	0.000
28	A	45	THR	0	-0.024	-0.009	13.590	-0.294	-0.294	0.000	0.000	0.000	0.000
29	A	46	ILE	0	-0.023	-0.013	16.138	0.813	0.813	0.000	0.000	0.000	0.000
30	A	47	PRO	0	-0.005	-0.011	17.757	-0.734	-0.734	0.000	0.000	0.000	0.000
31	A	48	THR	0	0.007	0.006	16.209	0.252	0.252	0.000	0.000	0.000	0.000
32	A	49	ILE	0	-0.027	-0.011	18.869	0.027	0.027	0.000	0.000	0.000	0.000
33	A	50	GLY	0	0.012	-0.005	17.535	-0.328	-0.328	0.000	0.000	0.000	0.000
34	A	51	PHE	0	-0.020	-0.002	15.292	0.634	0.634	0.000	0.000	0.000	0.000
35	A	52	ASN	0	0.008	0.009	15.528	-0.398	-0.398	0.000	0.000	0.000	0.000
36	A	53	VAL	0	-0.007	-0.009	9.427	-0.837	-0.837	0.000	0.000	0.000	0.000
37	A	54	GLU	-1	-0.822	-0.891	10.552	-20.396	-20.396	0.000	0.000	0.000	0.000
38	A	55	THR	0	-0.045	-0.029	5.183	-5.803	-5.803	0.000	0.000	0.000	0.000
39	A	56	VAL	0	0.004	0.029	7.088	2.878	2.878	0.000	0.000	0.000	0.000
40	A	57	GLU	-1	-0.976	-0.998	6.315	-38.845	-38.845	0.000	0.000	0.000	0.000
41	A	58	TYR	0	0.035	0.018	7.266	5.884	5.884	0.000	0.000	0.000	0.000
42	A	59	LYS	1	0.904	0.943	8.683	19.030	19.030	0.000	0.000	0.000	0.000
43	A	60	ASN	0	-0.022	-0.022	8.160	2.108	2.108	0.000	0.000	0.000	0.000
48	A	65	VAL	0	0.016	0.004	5.467	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	66	TRP	0	0.009	-0.007	7.783	4.451	4.451	0.000	0.000	0.000	0.000
50	A	67	ASP	-1	-0.910	-0.957	10.728	-17.249	-17.249	0.000	0.000	0.000	0.000
51	A	68	VAL	0	-0.005	-0.016	12.663	0.641	0.641	0.000	0.000	0.000	0.000
52	A	69	GLY	0	0.037	0.018	15.345	0.355	0.355	0.000	0.000	0.000	0.000
53	A	70	GLY	0	0.012	0.004	16.814	0.460	0.460	0.000	0.000	0.000	0.000
54	A	71	GLN	0	-0.021	-0.021	20.254	1.093	1.093	0.000	0.000	0.000	0.000
55	A	72	ASP	-1	-0.752	-0.863	21.804	-12.830	-12.830	0.000	0.000	0.000	0.000
56	A	73	LYS	1	0.906	0.942	23.002	10.253	10.253	0.000	0.000	0.000	0.000
57	A	74	ILE	0	-0.003	0.005	18.534	0.092	0.092	0.000	0.000	0.000	0.000
58	A	75	ARG	1	0.839	0.930	18.155	13.681	13.681	0.000	0.000	0.000	0.000
59	A	76	PRO	0	0.007	-0.005	17.180	-0.777	-0.777	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.012	0.009	16.845	-0.628	-0.628	0.000	0.000	0.000	0.000
61	A	78	TRP	0	0.030	0.014	12.930	-1.305	-1.305	0.000	0.000	0.000	0.000
62	A	79	ARG	1	0.814	0.881	12.269	13.788	13.788	0.000	0.000	0.000	0.000
63	A	80	HIS	0	0.006	-0.008	12.878	-0.158	-0.158	0.000	0.000	0.000	0.000
64	A	81	TYR	0	-0.027	-0.007	8.306	-2.295	-2.295	0.000	0.000	0.000	0.000
65	A	82	PHE	0	-0.064	-0.049	6.840	-3.058	-3.058	0.000	0.000	0.000	0.000
66	A	83	GLN	0	0.040	0.029	8.971	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	84	ASN	0	-0.059	-0.032	9.030	-0.117	-0.117	0.000	0.000	0.000	0.000
72	A	89	ILE	0	0.026	0.013	7.924	1.039	1.039	0.000	0.000	0.000	0.000
73	A	90	PHE	0	0.005	-0.001	10.882	0.548	0.548	0.000	0.000	0.000	0.000
74	A	91	VAL	0	-0.031	-0.013	14.687	0.319	0.319	0.000	0.000	0.000	0.000
75	A	92	VAL	0	-0.002	-0.009	17.109	0.478	0.478	0.000	0.000	0.000	0.000
76	A	93	ASP	-1	-0.794	-0.891	20.826	-11.577	-11.577	0.000	0.000	0.000	0.000
77	A	94	SER	0	0.036	-0.005	23.492	0.210	0.210	0.000	0.000	0.000	0.000
78	A	95	ASN	0	-0.004	-0.002	25.514	0.574	0.574	0.000	0.000	0.000	0.000
79	A	96	ASP	-1	-0.845	-0.909	26.839	-10.057	-10.057	0.000	0.000	0.000	0.000
80	A	97	ARG	1	0.781	0.850	28.335	9.246	9.246	0.000	0.000	0.000	0.000
81	A	98	GLU	-1	-0.998	-0.970	30.872	-8.891	-8.891	0.000	0.000	0.000	0.000
82	A	99	ARG	1	0.789	0.847	26.166	11.068	11.068	0.000	0.000	0.000	0.000
83	A	100	VAL	0	-0.008	0.000	25.279	-0.400	-0.400	0.000	0.000	0.000	0.000
84	A	101	ASN	0	0.015	-0.004	25.905	-0.409	-0.409	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.771	-0.859	25.804	-11.135	-11.135	0.000	0.000	0.000	0.000
86	A	103	ALA	0	-0.021	-0.014	22.202	-0.429	-0.429	0.000	0.000	0.000	0.000
87	A	104	ARG	1	0.856	0.918	21.859	10.122	10.122	0.000	0.000	0.000	0.000
88	A	105	GLU	-1	-0.894	-0.925	23.026	-10.555	-10.555	0.000	0.000	0.000	0.000
89	A	106	GLU	-1	-0.806	-0.904	20.712	-13.216	-13.216	0.000	0.000	0.000	0.000
90	A	107	LEU	0	-0.020	0.000	16.620	-0.703	-0.703	0.000	0.000	0.000	0.000
91	A	108	MET	0	-0.020	-0.021	18.716	-0.631	-0.631	0.000	0.000	0.000	0.000
92	A	109	ARG	1	0.751	0.840	20.880	12.305	12.305	0.000	0.000	0.000	0.000
93	A	110	MET	0	-0.058	-0.027	14.317	-0.119	-0.119	0.000	0.000	0.000	0.000
94	A	111	LEU	0	-0.031	-0.019	14.623	-0.803	-0.803	0.000	0.000	0.000	0.000
95	A	112	ALA	0	-0.020	-0.004	16.975	0.048	0.048	0.000	0.000	0.000	0.000
96	A	113	GLU	-1	-0.821	-0.899	15.620	-14.701	-14.701	0.000	0.000	0.000	0.000
97	A	114	ASP	-1	-0.913	-0.963	15.743	-16.214	-16.214	0.000	0.000	0.000	0.000
98	A	115	GLU	-1	-0.806	-0.877	12.985	-17.061	-17.061	0.000	0.000	0.000	0.000
99	A	116	LEU	0	0.004	-0.005	10.301	-1.984	-1.984	0.000	0.000	0.000	0.000
100	A	117	ARG	1	0.911	0.976	12.187	14.723	14.723	0.000	0.000	0.000	0.000
101	A	118	ASP	-1	-0.906	-0.957	10.503	-19.302	-19.302	0.000	0.000	0.000	0.000
102	A	119	ALA	0	-0.073	-0.004	8.097	-1.139	-1.139	0.000	0.000	0.000	0.000
103	A	120	VAL	0	0.000	0.002	6.789	2.349	2.349	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.028	-0.020	9.005	-1.104	-1.104	0.000	0.000	0.000	0.000
105	A	122	LEU	0	0.006	0.014	10.321	0.774	0.774	0.000	0.000	0.000	0.000
106	A	123	VAL	0	-0.004	-0.010	12.107	-0.087	-0.087	0.000	0.000	0.000	0.000
107	A	124	PHE	0	0.040	0.006	12.162	0.245	0.245	0.000	0.000	0.000	0.000
108	A	125	ALA	0	0.010	0.001	16.622	0.484	0.484	0.000	0.000	0.000	0.000
109	A	126	ASN	0	0.041	0.020	19.208	0.264	0.264	0.000	0.000	0.000	0.000
110	A	127	LYS	1	0.805	0.898	21.098	12.426	12.426	0.000	0.000	0.000	0.000
111	A	128	GLN	0	-0.064	-0.049	23.360	0.703	0.703	0.000	0.000	0.000	0.000
112	A	129	ASP	-1	-0.842	-0.907	25.829	-11.209	-11.209	0.000	0.000	0.000	0.000
113	A	130	LEU	0	-0.018	-0.005	28.070	0.462	0.462	0.000	0.000	0.000	0.000
114	A	131	PRO	0	0.008	-0.007	30.249	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	132	ASN	0	-0.024	-0.010	32.665	0.303	0.303	0.000	0.000	0.000	0.000
116	A	133	ALA	0	0.006	0.011	27.634	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	134	MET	0	-0.088	-0.027	27.179	0.299	0.299	0.000	0.000	0.000	0.000
118	A	135	ASN	0	0.072	0.035	26.893	-0.629	-0.629	0.000	0.000	0.000	0.000
119	A	136	ALA	0	0.089	0.026	22.895	-0.075	-0.075	0.000	0.000	0.000	0.000
120	A	137	ALA	0	0.007	0.026	24.202	-0.259	-0.259	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.818	-0.908	26.643	-9.543	-9.543	0.000	0.000	0.000	0.000
122	A	139	ILE	0	0.002	0.001	22.020	0.015	0.015	0.000	0.000	0.000	0.000
123	A	140	THR	0	-0.021	-0.033	22.407	-0.373	-0.373	0.000	0.000	0.000	0.000
124	A	141	ASP	-1	-0.950	-0.968	23.767	-9.881	-9.881	0.000	0.000	0.000	0.000
125	A	142	LYS	1	0.916	0.961	26.967	9.590	9.590	0.000	0.000	0.000	0.000
126	A	143	LEU	0	-0.004	-0.005	20.291	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	144	GLY	0	0.025	0.014	22.800	-0.294	-0.294	0.000	0.000	0.000	0.000
128	A	145	LEU	0	-0.008	0.013	18.835	-0.050	-0.050	0.000	0.000	0.000	0.000
129	A	146	HIS	0	0.039	0.004	21.290	-0.426	-0.426	0.000	0.000	0.000	0.000
130	A	147	SER	0	-0.088	-0.045	23.587	0.203	0.203	0.000	0.000	0.000	0.000
131	A	148	LEU	0	-0.031	-0.012	17.407	0.008	0.008	0.000	0.000	0.000	0.000
132	A	149	ARG	1	0.912	0.956	20.713	10.955	10.955	0.000	0.000	0.000	0.000
133	A	150	HIS	0	-0.017	-0.013	18.116	-0.101	-0.101	0.000	0.000	0.000	0.000
134	A	151	ARG	1	0.851	0.912	12.163	18.110	18.110	0.000	0.000	0.000	0.000
135	A	152	ASN	0	0.007	0.001	10.393	1.502	1.502	0.000	0.000	0.000	0.000
136	A	153	TRP	0	0.013	-0.006	12.564	-0.983	-0.983	0.000	0.000	0.000	0.000
137	A	154	TYR	0	0.019	0.024	13.531	0.845	0.845	0.000	0.000	0.000	0.000
138	A	155	ILE	0	-0.049	-0.020	15.292	-0.398	-0.398	0.000	0.000	0.000	0.000
139	A	156	GLN	0	-0.014	-0.005	15.738	0.074	0.074	0.000	0.000	0.000	0.000
140	A	157	ALA	0	0.003	0.004	17.837	0.018	0.018	0.000	0.000	0.000	0.000
141	A	158	THR	0	0.005	-0.002	16.769	-0.527	-0.527	0.000	0.000	0.000	0.000
142	A	159	CYS	0	-0.043	-0.008	20.186	0.671	0.671	0.000	0.000	0.000	0.000
143	A	160	ALA	0	0.034	0.019	19.247	-0.188	-0.188	0.000	0.000	0.000	0.000
144	A	161	THR	0	-0.003	-0.012	20.444	-0.323	-0.323	0.000	0.000	0.000	0.000
145	A	162	SER	0	0.008	-0.025	23.603	-0.023	-0.023	0.000	0.000	0.000	0.000
146	A	163	GLY	0	-0.006	-0.015	19.328	-0.185	-0.185	0.000	0.000	0.000	0.000
147	A	164	ASP	-1	-0.843	-0.881	18.616	-13.930	-13.930	0.000	0.000	0.000	0.000
148	A	165	GLY	0	0.023	-0.006	18.190	0.115	0.115	0.000	0.000	0.000	0.000
149	A	166	LEU	0	-0.038	-0.028	14.513	-0.831	-0.831	0.000	0.000	0.000	0.000
150	A	167	TYR	0	0.050	0.013	12.418	-0.931	-0.931	0.000	0.000	0.000	0.000
151	A	168	GLU	-1	-0.866	-0.921	13.189	-17.944	-17.944	0.000	0.000	0.000	0.000
152	A	169	GLY	0	0.018	0.002	13.125	-0.307	-0.307	0.000	0.000	0.000	0.000
153	A	170	LEU	0	-0.024	-0.018	7.488	-1.541	-1.541	0.000	0.000	0.000	0.000
154	A	171	ASP	-1	-0.883	-0.918	9.003	-23.375	-23.375	0.000	0.000	0.000	0.000
155	A	172	TRP	0	0.020	0.003	9.899	-1.286	-1.286	0.000	0.000	0.000	0.000
157	A	174	SER	0	-0.036	-0.039	5.819	-3.729	-3.729	0.000	0.000	0.000	0.000
158	A	175	ASN	0	-0.080	-0.030	6.906	-0.564	-0.564	0.000	0.000	0.000	0.000
159	A	176	GLN	0	-0.100	-0.040	7.068	3.033	3.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:MET)