FMO DATABASE

FMODB ID: 5531Z

Calculation Name: 1RRP-B-Xray547

Preferred Name: GTP-binding nuclear protein Ran

Target Type: SINGLE PROTEIN

Ligand Name: phosphoaminophosphonic acid-guanylate ester | magnesium ion

Ligand 3-letter code: GNP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RRP

Chain ID: B

ChEMBL ID: CHEMBL1741190

UniProt ID: P62826

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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1210462.98805
FMO2-HF: Nuclear repulsion	1155518.992524
FMO2-HF: Total energy	-54943.995526
FMO2-MP2: Total energy	-55104.19035

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:17:HIS)

Summations of interaction energy for fragment #1(A:17:HIS)

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.
-35.527	-31.964	1.469	-1.421	-3.61	-0.008

Interaction energy analysis for fragmet #1(A:17:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.909

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	19	GLU	-1	-0.885	-0.930	2.278	-37.316	-33.998	1.455	-1.403	-3.369	-0.008
4	A	20	PRO	0	-0.036	-0.011	3.833	0.972	1.217	0.014	-0.018	-0.241	0.000
5	A	21	VAL	0	0.035	0.006	7.241	1.377	1.377	0.000	0.000	0.000	0.000
6	A	22	VAL	0	-0.035	-0.001	10.053	1.662	1.662	0.000	0.000	0.000	0.000
7	A	23	PRO	0	0.001	0.000	11.510	-0.896	-0.896	0.000	0.000	0.000	0.000
8	A	24	LEU	0	0.001	-0.015	9.850	0.117	0.117	0.000	0.000	0.000	0.000
9	A	25	PRO	0	-0.012	-0.003	13.007	0.802	0.802	0.000	0.000	0.000	0.000
10	A	26	ASP	-1	-0.879	-0.925	16.220	-13.799	-13.799	0.000	0.000	0.000	0.000
11	A	27	LYS	1	0.884	0.930	16.441	14.865	14.865	0.000	0.000	0.000	0.000
12	A	28	ILE	0	0.020	0.010	19.885	0.388	0.388	0.000	0.000	0.000	0.000
13	A	29	GLU	-1	-0.948	-0.969	23.198	-9.746	-9.746	0.000	0.000	0.000	0.000
14	A	30	VAL	0	-0.055	-0.040	23.302	0.144	0.144	0.000	0.000	0.000	0.000
15	A	31	LYS	1	0.999	1.000	26.177	9.601	9.601	0.000	0.000	0.000	0.000
16	A	32	THR	0	-0.058	-0.021	28.455	-0.402	-0.402	0.000	0.000	0.000	0.000
17	A	33	GLY	0	-0.043	-0.011	30.730	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	34	GLU	-1	-0.802	-0.872	33.623	-8.808	-8.808	0.000	0.000	0.000	0.000
19	A	35	GLU	-1	-0.756	-0.911	33.585	-9.013	-9.013	0.000	0.000	0.000	0.000
20	A	36	ASP	-1	-0.886	-0.937	37.286	-7.664	-7.664	0.000	0.000	0.000	0.000
21	A	37	GLU	-1	-0.865	-0.905	39.685	-7.544	-7.544	0.000	0.000	0.000	0.000
22	A	38	GLU	-1	-0.899	-0.949	41.740	-6.820	-6.820	0.000	0.000	0.000	0.000
23	A	39	GLU	-1	-0.820	-0.910	37.987	-8.125	-8.125	0.000	0.000	0.000	0.000
24	A	40	PHE	0	0.009	0.014	42.747	0.064	0.064	0.000	0.000	0.000	0.000
25	A	41	PHE	0	0.006	-0.012	42.867	0.134	0.134	0.000	0.000	0.000	0.000
26	A	42	CYS	0	-0.051	-0.023	38.626	-0.224	-0.224	0.000	0.000	0.000	0.000
27	A	43	ASN	0	-0.006	-0.002	40.402	-0.070	-0.070	0.000	0.000	0.000	0.000
28	A	44	ARG	1	0.842	0.915	33.405	8.952	8.952	0.000	0.000	0.000	0.000
29	A	45	ALA	0	-0.010	-0.005	37.910	0.189	0.189	0.000	0.000	0.000	0.000
30	A	46	LYS	1	0.783	0.871	35.904	8.300	8.300	0.000	0.000	0.000	0.000
31	A	47	LEU	0	0.028	0.023	37.265	0.256	0.256	0.000	0.000	0.000	0.000
32	A	48	PHE	0	-0.045	-0.028	37.786	-0.271	-0.271	0.000	0.000	0.000	0.000
33	A	49	ARG	1	0.868	0.925	35.843	8.566	8.566	0.000	0.000	0.000	0.000
34	A	50	PHE	0	-0.035	-0.019	40.518	-0.102	-0.102	0.000	0.000	0.000	0.000
35	A	51	ASP	-1	-0.784	-0.865	39.749	-8.099	-8.099	0.000	0.000	0.000	0.000
36	A	52	VAL	0	-0.043	-0.019	41.994	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	53	GLU	-1	-0.936	-0.960	40.183	-7.595	-7.595	0.000	0.000	0.000	0.000
38	A	54	SER	0	0.013	-0.023	41.928	0.069	0.069	0.000	0.000	0.000	0.000
39	A	55	LYS	1	0.888	0.940	44.383	6.476	6.476	0.000	0.000	0.000	0.000
40	A	56	GLU	-1	-0.916	-0.951	39.510	-7.930	-7.930	0.000	0.000	0.000	0.000
41	A	57	TRP	0	-0.018	-0.015	42.330	-0.080	-0.080	0.000	0.000	0.000	0.000
42	A	58	LYS	1	0.854	0.937	36.563	8.284	8.284	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.839	-0.909	34.080	-8.963	-8.963	0.000	0.000	0.000	0.000
44	A	60	ARG	1	0.818	0.910	33.661	8.774	8.774	0.000	0.000	0.000	0.000
45	A	61	GLY	0	0.047	0.007	33.020	-0.343	-0.343	0.000	0.000	0.000	0.000
46	A	62	ILE	0	-0.002	0.015	31.699	0.345	0.345	0.000	0.000	0.000	0.000
47	A	63	GLY	0	0.045	0.022	32.331	-0.401	-0.401	0.000	0.000	0.000	0.000
48	A	64	ASN	0	-0.001	-0.003	33.716	0.440	0.440	0.000	0.000	0.000	0.000
49	A	65	VAL	0	0.000	0.000	36.211	-0.121	-0.121	0.000	0.000	0.000	0.000
50	A	66	LYS	1	0.827	0.875	35.009	8.769	8.769	0.000	0.000	0.000	0.000
51	A	67	ILE	0	-0.023	-0.004	40.420	0.014	0.014	0.000	0.000	0.000	0.000
52	A	68	LEU	0	-0.012	0.008	38.159	0.053	0.053	0.000	0.000	0.000	0.000
53	A	69	ARG	1	0.913	0.970	42.895	6.455	6.455	0.000	0.000	0.000	0.000
54	A	70	HIS	0	0.074	0.034	41.988	0.123	0.123	0.000	0.000	0.000	0.000
55	A	71	LYS	1	0.871	0.916	42.145	7.311	7.311	0.000	0.000	0.000	0.000
56	A	72	THR	0	-0.042	-0.012	45.928	0.132	0.132	0.000	0.000	0.000	0.000
57	A	73	SER	0	-0.062	-0.037	45.538	0.135	0.135	0.000	0.000	0.000	0.000
58	A	74	GLY	0	0.035	0.022	48.157	0.090	0.090	0.000	0.000	0.000	0.000
59	A	75	LYS	1	0.951	0.973	46.367	6.588	6.588	0.000	0.000	0.000	0.000
60	A	76	ILE	0	0.053	0.033	46.008	-0.171	-0.171	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.779	0.858	36.956	8.176	8.176	0.000	0.000	0.000	0.000
62	A	78	LEU	0	-0.008	0.010	40.386	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	79	LEU	0	-0.038	0.004	35.044	-0.118	-0.118	0.000	0.000	0.000	0.000
64	A	80	MET	0	-0.030	-0.016	35.628	0.083	0.083	0.000	0.000	0.000	0.000
65	A	81	ARG	1	0.849	0.919	29.221	9.785	9.785	0.000	0.000	0.000	0.000
66	A	82	ARG	1	0.853	0.910	28.756	10.434	10.434	0.000	0.000	0.000	0.000
67	A	83	GLU	-1	-0.802	-0.898	29.234	-10.055	-10.055	0.000	0.000	0.000	0.000
68	A	84	GLN	0	-0.043	-0.020	24.464	-0.592	-0.592	0.000	0.000	0.000	0.000
69	A	85	VAL	0	-0.003	-0.011	22.573	-0.350	-0.350	0.000	0.000	0.000	0.000
70	A	86	LEU	0	-0.004	0.006	24.511	-0.079	-0.079	0.000	0.000	0.000	0.000
71	A	87	LYS	1	0.955	0.979	24.916	11.859	11.859	0.000	0.000	0.000	0.000
72	A	88	ILE	0	0.034	0.027	28.264	0.178	0.178	0.000	0.000	0.000	0.000
73	A	89	CYS	0	-0.109	-0.068	31.795	-0.222	-0.222	0.000	0.000	0.000	0.000
74	A	90	ALA	0	0.010	0.004	34.317	0.183	0.183	0.000	0.000	0.000	0.000
75	A	91	ASN	0	-0.009	-0.023	35.851	-0.055	-0.055	0.000	0.000	0.000	0.000
76	A	92	HIS	0	0.028	0.023	38.625	0.194	0.194	0.000	0.000	0.000	0.000
77	A	93	TYR	0	-0.001	-0.012	42.368	0.000	0.000	0.000	0.000	0.000	0.000
78	A	94	ILE	0	0.004	-0.008	45.171	0.008	0.008	0.000	0.000	0.000	0.000
79	A	95	SER	0	-0.018	-0.016	47.918	0.093	0.093	0.000	0.000	0.000	0.000
80	A	96	PRO	0	0.063	0.020	51.181	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.885	-0.923	52.992	-5.816	-5.816	0.000	0.000	0.000	0.000
82	A	98	MET	0	-0.120	-0.027	46.443	-0.055	-0.055	0.000	0.000	0.000	0.000
83	A	99	LYS	1	0.991	1.003	51.804	5.668	5.668	0.000	0.000	0.000	0.000
84	A	100	LEU	0	0.018	0.021	48.042	-0.059	-0.059	0.000	0.000	0.000	0.000
85	A	101	THR	0	-0.076	-0.041	51.898	0.178	0.178	0.000	0.000	0.000	0.000
86	A	102	PRO	0	0.029	0.008	51.581	-0.124	-0.124	0.000	0.000	0.000	0.000
87	A	103	ASN	0	0.017	-0.007	48.112	-0.033	-0.033	0.000	0.000	0.000	0.000
88	A	104	ALA	0	-0.002	0.000	51.436	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	105	GLY	0	0.016	0.014	53.411	0.032	0.032	0.000	0.000	0.000	0.000
90	A	106	SER	0	-0.068	-0.030	48.774	0.021	0.021	0.000	0.000	0.000	0.000
91	A	107	ASP	-1	-0.856	-0.941	50.925	-6.209	-6.209	0.000	0.000	0.000	0.000
92	A	108	ARG	1	0.883	0.947	44.966	6.805	6.805	0.000	0.000	0.000	0.000
93	A	109	SER	0	-0.054	-0.035	46.393	-0.227	-0.227	0.000	0.000	0.000	0.000
94	A	110	PHE	0	0.003	0.013	47.175	0.155	0.155	0.000	0.000	0.000	0.000
95	A	111	VAL	0	-0.018	-0.009	46.983	-0.198	-0.198	0.000	0.000	0.000	0.000
96	A	112	TRP	0	0.003	-0.006	43.082	0.147	0.147	0.000	0.000	0.000	0.000
97	A	113	HIS	0	0.020	0.002	46.952	-0.225	-0.225	0.000	0.000	0.000	0.000
98	A	114	ALA	0	0.019	0.009	44.170	0.095	0.095	0.000	0.000	0.000	0.000
99	A	115	LEU	0	-0.001	0.013	43.061	-0.089	-0.089	0.000	0.000	0.000	0.000
100	A	116	ASP	-1	-0.752	-0.859	38.366	-8.180	-8.180	0.000	0.000	0.000	0.000
101	A	117	TYR	0	0.036	-0.006	36.541	0.037	0.037	0.000	0.000	0.000	0.000
102	A	118	ALA	0	-0.025	-0.006	34.315	-0.202	-0.202	0.000	0.000	0.000	0.000
103	A	119	ASP	-1	-0.883	-0.920	32.211	-9.718	-9.718	0.000	0.000	0.000	0.000
104	A	120	GLU	-1	-0.922	-0.960	30.893	-10.255	-10.255	0.000	0.000	0.000	0.000
105	A	121	LEU	0	-0.025	-0.011	34.045	0.136	0.136	0.000	0.000	0.000	0.000
106	A	122	PRO	0	-0.014	0.000	36.903	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	123	LYS	1	0.868	0.914	34.908	8.923	8.923	0.000	0.000	0.000	0.000
108	A	124	PRO	0	-0.003	0.007	41.456	0.015	0.015	0.000	0.000	0.000	0.000
109	A	125	GLU	-1	-0.790	-0.884	38.642	-8.325	-8.325	0.000	0.000	0.000	0.000
110	A	126	GLN	0	0.002	-0.006	43.417	0.213	0.213	0.000	0.000	0.000	0.000
111	A	127	LEU	0	0.010	-0.003	40.659	-0.196	-0.196	0.000	0.000	0.000	0.000
112	A	128	ALA	0	0.039	0.013	42.979	0.212	0.212	0.000	0.000	0.000	0.000
113	A	129	ILE	0	-0.019	0.008	40.540	-0.248	-0.248	0.000	0.000	0.000	0.000
114	A	130	ARG	1	0.929	0.956	41.736	7.613	7.613	0.000	0.000	0.000	0.000
115	A	131	PHE	0	0.064	0.039	41.997	-0.235	-0.235	0.000	0.000	0.000	0.000
116	A	132	LYS	1	0.891	0.941	39.650	7.814	7.814	0.000	0.000	0.000	0.000
117	A	133	THR	0	-0.007	-0.024	44.154	0.110	0.110	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.056	0.027	47.861	-0.094	-0.094	0.000	0.000	0.000	0.000
119	A	135	GLU	-1	-0.849	-0.932	50.049	-6.152	-6.152	0.000	0.000	0.000	0.000
120	A	136	GLU	-1	-0.803	-0.873	43.564	-7.256	-7.256	0.000	0.000	0.000	0.000
121	A	137	ALA	0	-0.019	0.004	47.633	-0.041	-0.041	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.010	-0.001	48.732	0.031	0.031	0.000	0.000	0.000	0.000
123	A	139	LEU	0	0.009	0.007	47.405	0.058	0.058	0.000	0.000	0.000	0.000
124	A	140	PHE	0	0.012	-0.001	44.282	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	141	LYS	1	0.828	0.895	47.940	5.842	5.842	0.000	0.000	0.000	0.000
126	A	142	CYS	0	0.001	0.002	51.050	0.082	0.082	0.000	0.000	0.000	0.000
127	A	143	LYS	1	0.816	0.899	48.344	6.282	6.282	0.000	0.000	0.000	0.000
128	A	144	PHE	0	0.014	-0.003	46.460	-0.050	-0.050	0.000	0.000	0.000	0.000
129	A	145	GLU	-1	-0.833	-0.900	49.740	-5.771	-5.771	0.000	0.000	0.000	0.000
130	A	146	GLU	-1	-0.862	-0.918	52.425	-5.964	-5.964	0.000	0.000	0.000	0.000
131	A	147	ALA	0	-0.021	-0.015	49.198	0.041	0.041	0.000	0.000	0.000	0.000
132	A	148	GLN	0	-0.071	-0.055	51.185	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	149	SER	0	-0.107	-0.051	53.666	0.133	0.133	0.000	0.000	0.000	0.000
134	A	150	ILE	-1	-0.973	-0.975	52.291	-5.803	-5.803	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:17:HIS)