FMO DATABASE

FMODB ID: VZMK1

Calculation Name: 1RYA-A-Xray549

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | 2-amino-2-hydroxymethyl-propane-1,3-diol | magnesium ion | chloride ion

Ligand 3-letter code: GDP | TRS | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RYA

Chain ID: A

ChEMBL ID:

UniProt ID: P32056

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-1661681.274685
FMO2-HF: Nuclear repulsion	1597787.830621
FMO2-HF: Total energy	-63893.444064
FMO2-MP2: Total energy	-64082.581704

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.
-181.304	-173.332	12.872	-10.511	-10.334	-0.122

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 : 0.779 / q_NPA : 0.891

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	PHE	0	0.032	0.031	3.712	3.489	5.072	-0.020	-0.619	-0.944	-0.001
54	A	54	GLN	0	-0.017	-0.011	2.771	-13.211	-10.527	1.069	-1.607	-2.147	-0.018
55	A	55	LYS	1	0.900	0.927	4.196	42.677	43.268	-0.001	-0.257	-0.333	-0.001
56	A	56	ASP	-1	-0.809	-0.902	1.818	-89.532	-89.849	8.750	-5.007	-3.425	-0.070
57	A	57	GLU	-1	-0.825	-0.876	2.501	-85.753	-82.809	3.047	-2.921	-3.071	-0.031
58	A	58	THR	0	-0.004	-0.004	3.557	7.366	7.529	0.022	-0.059	-0.126	-0.001
65	A	65	ARG	1	0.727	0.815	3.465	44.194	44.518	0.005	-0.041	-0.288	0.000
4	A	4	LEU	0	-0.040	-0.016	5.759	0.504	0.504	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.864	0.911	9.090	21.026	21.026	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.021	-0.008	12.186	-0.374	-0.374	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.805	-0.903	15.291	-17.360	-17.360	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.810	-0.873	12.848	-21.101	-21.101	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.015	-0.013	12.265	-0.962	-0.962	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.070	0.034	13.712	0.292	0.292	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.057	-0.040	16.715	1.067	1.067	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.040	-0.007	11.739	0.331	0.331	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.017	0.005	14.851	0.502	0.502	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.897	0.961	17.007	15.835	15.835	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.074	-0.047	17.798	1.124	1.124	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.060	-0.027	14.062	0.420	0.420	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.012	0.016	16.326	-0.216	-0.216	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.037	-0.017	11.919	-1.995	-1.995	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.024	0.004	10.346	1.224	1.224	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.001	-0.009	11.219	-2.467	-2.467	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.041	0.002	11.077	0.648	0.648	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.723	-0.837	14.179	-17.007	-17.007	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.038	-0.027	12.837	0.265	0.265	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.007	-0.007	18.945	0.687	0.687	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.008	-0.001	19.764	0.316	0.316	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.896	-0.958	22.755	-10.134	-10.134	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.031	0.003	25.576	-0.145	-0.145	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.041	-0.048	27.772	0.136	0.136	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.742	0.848	30.867	9.667	9.667	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.004	0.022	31.625	0.241	0.241	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.872	-0.907	30.550	-9.237	-9.237	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.016	-0.039	26.798	-0.291	-0.291	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.021	0.005	20.972	0.252	0.252	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.029	-0.024	23.975	-0.332	-0.332	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.086	0.036	22.603	0.285	0.285	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.767	0.870	23.621	10.644	10.644	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.907	0.960	17.934	15.329	15.329	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.010	0.002	20.082	0.422	0.422	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.019	-0.005	17.174	0.730	0.730	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.892	0.955	20.471	12.302	12.302	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.016	-0.005	18.388	-0.836	-0.836	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.010	-0.017	21.547	-0.190	-0.190	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.008	-0.011	23.913	0.238	0.238	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.032	-0.014	24.759	0.434	0.434	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.045	-0.022	26.159	0.405	0.405	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.046	-0.018	25.708	-0.351	-0.351	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.017	-0.028	20.555	0.366	0.366	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.005	0.011	20.255	0.179	0.179	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.046	0.027	17.724	-0.392	-0.392	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.011	0.010	15.390	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.041	0.034	12.340	0.331	0.331	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.872	0.936	7.640	33.486	33.486	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.028	0.025	6.337	-2.502	-2.502	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.063	0.024	7.027	-1.645	-1.645	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.818	-0.911	9.860	-26.854	-26.854	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.001	0.003	5.394	0.569	0.569	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.000	0.004	6.923	-0.280	-0.280	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.051	0.024	7.714	2.047	2.047	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.909	-0.938	8.689	-23.234	-23.234	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.018	-0.014	6.949	1.414	1.414	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.027	0.008	10.037	1.790	1.790	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.036	-0.019	9.115	1.374	1.374	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.040	-0.019	9.206	0.987	0.987	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.818	-0.912	11.208	-18.336	-18.336	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.024	-0.024	14.368	1.226	1.226	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.047	0.038	14.516	0.882	0.882	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.032	-0.014	14.886	0.233	0.233	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.873	0.938	9.346	21.087	21.087	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.007	0.009	12.647	1.064	1.064	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.028	0.012	13.129	-1.472	-1.472	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.032	0.002	13.113	0.959	0.959	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.055	-0.031	15.413	0.672	0.672	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.011	0.003	17.922	0.942	0.942	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.015	-0.001	18.840	0.578	0.578	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.032	-0.015	19.853	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.006	0.001	18.910	-0.152	-0.152	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.031	-0.040	21.131	1.003	1.003	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.079	0.056	22.551	0.290	0.290	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.054	-0.036	18.849	-0.828	-0.828	0.000	0.000	0.000	0.000
86	A	86	TRP	0	0.009	-0.013	20.665	1.008	1.008	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.049	-0.034	20.597	-0.830	-0.830	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.016	0.014	19.744	0.978	0.978	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.002	-0.016	21.207	-0.634	-0.634	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.010	-0.001	20.274	0.226	0.226	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.867	-0.937	24.083	-11.464	-11.464	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.860	-0.915	24.252	-12.737	-12.737	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.028	-0.016	19.842	-0.975	-0.975	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.006	-0.011	16.555	0.280	0.280	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.048	-0.017	18.966	-0.107	-0.107	0.000	0.000	0.000	0.000
96	A	96	GLY	0	-0.012	-0.002	20.967	0.600	0.600	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.068	-0.043	24.346	0.028	0.028	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.826	-0.906	24.795	-12.470	-12.470	0.000	0.000	0.000	0.000
99	A	99	PHE	0	-0.039	-0.023	19.340	0.011	0.011	0.000	0.000	0.000	0.000
100	A	100	THR	0	0.047	0.041	23.606	-0.270	-0.270	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.000	-0.027	17.684	-0.958	-0.958	0.000	0.000	0.000	0.000
102	A	102	HIS	0	-0.037	-0.017	18.998	0.594	0.594	0.000	0.000	0.000	0.000
103	A	103	TYR	0	0.010	-0.002	14.406	-0.868	-0.868	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.002	0.001	16.377	1.194	1.194	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.010	-0.008	15.796	-1.581	-1.581	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.029	-0.009	14.089	0.947	0.947	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.057	0.032	17.135	-0.483	-0.483	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.000	-0.018	15.729	-0.144	-0.144	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.913	0.980	19.882	11.957	11.957	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.027	0.009	17.133	-0.215	-0.215	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.898	0.972	22.723	10.235	10.235	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.012	0.013	20.765	-0.216	-0.216	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.012	0.006	24.162	0.595	0.595	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.807	-0.919	24.248	-10.516	-10.516	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.956	-0.977	24.455	-10.412	-10.412	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.989	-0.987	21.477	-12.031	-12.031	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.063	-0.026	18.801	-0.740	-0.740	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.052	-0.021	17.690	0.552	0.552	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.027	-0.015	18.105	-0.568	-0.568	0.000	0.000	0.000	0.000
120	A	120	PRO	0	0.013	0.036	15.181	0.658	0.658	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.891	-0.942	18.236	-13.117	-13.117	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.917	-0.956	15.381	-16.131	-16.131	0.000	0.000	0.000	0.000
123	A	123	GLN	0	-0.124	-0.081	13.683	-0.939	-0.939	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.039	-0.030	18.157	0.336	0.336	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.784	-0.871	21.630	-11.163	-11.163	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.867	-0.935	24.710	-9.607	-9.607	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.007	-0.016	19.158	-0.432	-0.432	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.818	0.910	25.659	10.079	10.079	0.000	0.000	0.000	0.000
129	A	129	TRP	0	0.053	0.030	23.594	-0.501	-0.501	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.028	-0.009	28.836	0.433	0.433	0.000	0.000	0.000	0.000
131	A	131	THR	0	0.085	0.034	31.092	-0.235	-0.235	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.057	0.013	32.707	-0.189	-0.189	0.000	0.000	0.000	0.000
133	A	133	ASP	-1	-0.913	-0.960	33.708	-8.400	-8.400	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.031	-0.010	34.718	0.056	0.056	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.024	-0.012	29.138	-0.019	-0.019	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.044	-0.027	32.040	-0.141	-0.141	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.020	-0.007	34.147	0.067	0.067	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.009	0.010	33.516	0.207	0.207	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.811	-0.921	33.179	-9.191	-9.191	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.045	-0.017	32.049	-0.170	-0.170	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.013	0.009	27.962	-0.394	-0.394	0.000	0.000	0.000	0.000
142	A	142	HIS	0	0.061	0.044	25.921	0.073	0.073	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.031	0.011	27.706	-0.141	-0.141	0.000	0.000	0.000	0.000
144	A	144	ASN	0	-0.011	-0.018	23.286	0.501	0.501	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.022	0.025	23.614	-0.469	-0.469	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.796	0.897	25.472	9.770	9.770	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.003	-0.006	26.640	0.283	0.283	0.000	0.000	0.000	0.000
148	A	148	TYR	0	-0.038	-0.036	20.437	0.300	0.300	0.000	0.000	0.000	0.000
149	A	149	PHE	0	0.016	0.012	26.753	0.142	0.142	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.014	0.003	30.521	0.409	0.409	0.000	0.000	0.000	0.000
151	A	151	ALA	0	0.008	-0.008	31.891	-0.203	-0.203	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.861	-0.922	33.611	-9.230	-9.230	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.863	0.919	29.560	9.677	9.677	0.000	0.000	0.000	0.000
154	A	154	ARG	1	0.904	0.963	29.047	10.086	10.086	0.000	0.000	0.000	0.000
155	A	155	THR	0	-0.063	-0.029	30.035	-0.094	-0.094	0.000	0.000	0.000	0.000
156	A	156	GLY	0	-0.002	0.000	30.348	0.018	0.018	0.000	0.000	0.000	0.000
157	A	157	VAL	0	-0.017	0.013	24.586	-0.302	-0.302	0.000	0.000	0.000	0.000
158	A	158	PRO	0	-0.035	-0.024	23.231	0.099	0.099	0.000	0.000	0.000	0.000
159	A	159	GLY	0	-0.013	-0.023	23.602	-0.708	-0.708	0.000	0.000	0.000	0.000
160	A	160	LEU	-1	-0.956	-0.952	25.061	-11.067	-11.067	0.000	0.000	0.000	0.000

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