FMO DATABASE

FMODB ID: NL73Q

Calculation Name: 3CON-A-Xray547

Preferred Name: GTPase NRas

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | magnesium ion | unknown atom or ion

Ligand 3-letter code: GDP | MG | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3CON

Chain ID: A

ChEMBL ID: CHEMBL2079845

UniProt ID: P01111

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1575612.102811
FMO2-HF: Nuclear repulsion	1513661.027035
FMO2-HF: Total energy	-61951.075776
FMO2-MP2: Total energy	-62130.673144

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.
-129.915	-119.644	7.65	-5.72	-12.2	-0.072

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 : 0.769 / q_NPA : 0.897

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	GLU	-1	-0.903	-0.958	2.576	-46.855	-43.586	0.778	-1.851	-2.196	-0.019
4	A	4	TYR	0	0.001	-0.020	4.809	3.584	3.659	-0.001	-0.010	-0.064	0.000
43	A	43	GLN	0	0.019	0.020	2.550	-6.189	-4.583	2.054	-1.134	-2.525	-0.015
44	A	44	VAL	0	-0.011	-0.013	5.301	2.890	2.931	-0.001	-0.014	-0.026	0.000
45	A	45	VAL	0	-0.030	-0.019	6.000	-3.403	-3.252	-0.001	-0.005	-0.145	0.000
50	A	50	THR	0	-0.025	-0.012	3.004	1.024	1.714	0.802	-0.313	-1.179	0.001
51	A	51	CYS	0	-0.055	-0.021	2.478	-13.942	-10.991	2.262	-2.119	-3.093	-0.028
52	A	52	LEU	0	0.011	0.002	3.026	4.661	6.147	1.736	-0.313	-2.909	-0.011
53	A	53	LEU	0	0.013	0.010	4.324	0.262	0.264	0.021	0.039	-0.063	0.000
5	A	5	LYS	1	0.811	0.911	8.346	21.151	21.151	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.026	0.013	11.147	1.516	1.516	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.005	0.001	13.532	0.237	0.237	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.025	0.008	17.170	0.269	0.269	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.026	0.026	20.002	0.396	0.396	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.065	0.023	23.550	0.028	0.028	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.020	0.022	27.078	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.058	0.026	29.118	-0.275	-0.275	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.033	0.010	30.429	0.160	0.160	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.051	-0.018	26.682	0.120	0.120	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.025	0.010	26.396	-0.062	-0.062	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.843	0.948	22.688	11.047	11.047	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.087	0.026	21.374	-0.362	-0.362	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.023	-0.006	21.168	-0.380	-0.380	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.041	-0.026	20.306	-0.228	-0.228	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.040	0.014	16.130	-0.813	-0.813	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.013	0.002	16.635	-0.896	-0.896	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.017	0.011	17.969	-0.729	-0.729	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.018	-0.006	12.625	-0.234	-0.234	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.026	-0.019	11.982	-0.858	-0.858	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.007	0.002	13.726	-0.160	-0.160	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.056	-0.012	14.823	-0.174	-0.174	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.006	0.000	17.959	0.809	0.809	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.004	-0.006	21.488	-0.225	-0.225	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.016	0.004	23.596	0.174	0.174	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.928	-0.971	25.948	-9.431	-9.431	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.964	-0.980	29.565	-8.624	-8.624	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.032	-0.056	21.747	-0.323	-0.323	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.817	-0.877	27.648	-9.661	-9.661	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.051	-0.034	27.424	-0.332	-0.332	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.057	-0.056	28.858	-0.085	-0.085	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.038	-0.013	23.115	-0.174	-0.174	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.869	-0.920	21.907	-12.932	-12.932	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.873	-0.934	18.959	-15.142	-15.142	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.109	-0.071	14.463	-0.472	-0.472	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.036	0.035	14.469	-0.385	-0.385	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.854	0.905	9.257	20.725	20.725	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.833	0.913	8.593	20.856	20.856	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.029	0.025	8.123	2.441	2.441	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.762	-0.852	9.628	-21.327	-21.327	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.003	0.004	10.468	0.334	0.334	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.760	-0.837	4.996	-39.095	-39.095	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.739	-0.856	7.960	-21.241	-21.241	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.005	-0.012	10.309	0.581	0.581	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.070	-0.019	13.692	0.395	0.395	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.822	-0.904	16.919	-12.851	-12.851	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.011	-0.031	19.896	0.340	0.340	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.033	-0.018	23.095	0.238	0.238	0.000	0.000	0.000	0.000
60	A	60	GLY	-1	-0.983	-0.983	26.604	-9.639	-9.639	0.000	0.000	0.000	0.000
61	A	72	MET	0	0.059	0.031	19.203	-0.075	-0.075	0.000	0.000	0.000	0.000
62	A	73	ARG	1	1.016	1.001	19.492	12.888	12.888	0.000	0.000	0.000	0.000
63	A	74	THR	0	-0.031	-0.021	15.170	0.063	0.063	0.000	0.000	0.000	0.000
64	A	75	GLY	0	0.001	0.018	14.885	-1.252	-1.252	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.812	-0.893	10.510	-26.372	-26.372	0.000	0.000	0.000	0.000
66	A	77	GLY	0	0.051	0.021	14.671	0.338	0.338	0.000	0.000	0.000	0.000
67	A	78	PHE	0	-0.029	-0.030	16.240	-0.197	-0.197	0.000	0.000	0.000	0.000
68	A	79	LEU	0	-0.002	0.007	17.849	0.448	0.448	0.000	0.000	0.000	0.000
69	A	80	CYS	0	-0.016	-0.005	20.448	0.359	0.359	0.000	0.000	0.000	0.000
70	A	81	VAL	0	-0.007	-0.007	23.055	0.286	0.286	0.000	0.000	0.000	0.000
71	A	82	PHE	0	0.005	0.001	25.685	0.350	0.350	0.000	0.000	0.000	0.000
72	A	83	ALA	0	0.008	0.000	28.812	-0.229	-0.229	0.000	0.000	0.000	0.000
73	A	84	ILE	0	0.021	0.009	31.231	0.294	0.294	0.000	0.000	0.000	0.000
74	A	85	ASN	0	0.012	0.005	33.600	0.038	0.038	0.000	0.000	0.000	0.000
75	A	86	ASN	0	0.017	0.011	34.388	0.311	0.311	0.000	0.000	0.000	0.000
76	A	87	SER	0	0.049	0.036	35.205	-0.245	-0.245	0.000	0.000	0.000	0.000
77	A	88	LYS	1	0.856	0.915	36.755	8.175	8.175	0.000	0.000	0.000	0.000
78	A	89	SER	0	-0.026	-0.037	31.763	-0.215	-0.215	0.000	0.000	0.000	0.000
79	A	90	PHE	0	0.010	0.002	31.886	-0.246	-0.246	0.000	0.000	0.000	0.000
80	A	91	ALA	0	0.013	0.006	33.149	-0.107	-0.107	0.000	0.000	0.000	0.000
81	A	92	ASP	-1	-0.808	-0.895	32.535	-8.697	-8.697	0.000	0.000	0.000	0.000
82	A	93	ILE	0	-0.004	0.009	27.707	-0.228	-0.228	0.000	0.000	0.000	0.000
83	A	94	ASN	0	0.030	0.035	29.432	-0.333	-0.333	0.000	0.000	0.000	0.000
84	A	95	LEU	0	-0.029	-0.014	31.505	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	96	TYR	0	0.047	0.017	26.214	-0.050	-0.050	0.000	0.000	0.000	0.000
86	A	97	ARG	1	0.985	1.002	26.304	10.535	10.535	0.000	0.000	0.000	0.000
87	A	98	GLU	-1	-0.827	-0.917	27.185	-10.061	-10.061	0.000	0.000	0.000	0.000
88	A	99	GLN	0	-0.077	-0.040	26.859	-0.252	-0.252	0.000	0.000	0.000	0.000
89	A	100	ILE	0	-0.013	-0.006	22.001	-0.139	-0.139	0.000	0.000	0.000	0.000
90	A	101	LYS	1	0.857	0.930	24.184	9.886	9.886	0.000	0.000	0.000	0.000
91	A	102	ARG	1	0.941	0.971	26.433	9.807	9.807	0.000	0.000	0.000	0.000
92	A	103	VAL	0	-0.098	-0.042	22.581	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.791	0.875	17.617	15.944	15.944	0.000	0.000	0.000	0.000
94	A	105	ASP	-1	-0.962	-0.957	23.116	-11.363	-11.363	0.000	0.000	0.000	0.000
95	A	106	SER	0	-0.022	-0.023	23.555	-0.213	-0.213	0.000	0.000	0.000	0.000
96	A	107	ASP	-1	-0.896	-0.965	25.669	-10.425	-10.425	0.000	0.000	0.000	0.000
97	A	108	ASP	-1	-0.929	-0.946	23.171	-12.267	-12.267	0.000	0.000	0.000	0.000
98	A	109	VAL	0	-0.050	-0.016	19.576	-0.671	-0.671	0.000	0.000	0.000	0.000
99	A	110	PRO	0	0.051	0.027	16.550	0.461	0.461	0.000	0.000	0.000	0.000
100	A	111	MET	0	-0.006	-0.010	18.793	0.049	0.049	0.000	0.000	0.000	0.000
101	A	112	VAL	0	0.019	0.014	19.433	0.231	0.231	0.000	0.000	0.000	0.000
102	A	113	LEU	0	-0.031	0.003	21.961	0.109	0.109	0.000	0.000	0.000	0.000
103	A	114	VAL	0	0.025	-0.007	21.829	-0.080	-0.080	0.000	0.000	0.000	0.000
104	A	115	GLY	0	0.048	0.026	25.179	0.293	0.293	0.000	0.000	0.000	0.000
105	A	116	ASN	0	0.025	-0.004	25.914	-0.104	-0.104	0.000	0.000	0.000	0.000
106	A	117	LYS	1	0.871	0.926	27.812	9.820	9.820	0.000	0.000	0.000	0.000
107	A	118	CYS	0	-0.009	0.000	29.340	0.405	0.405	0.000	0.000	0.000	0.000
108	A	119	ASP	-1	-0.823	-0.873	30.529	-9.338	-9.338	0.000	0.000	0.000	0.000
109	A	120	LEU	0	-0.049	-0.019	32.471	0.291	0.291	0.000	0.000	0.000	0.000
110	A	121	PRO	0	0.030	0.010	35.342	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	122	THR	0	-0.043	-0.016	38.474	0.078	0.078	0.000	0.000	0.000	0.000
112	A	123	ARG	1	0.778	0.848	33.068	8.780	8.780	0.000	0.000	0.000	0.000
113	A	124	THR	0	-0.018	-0.025	37.823	0.186	0.186	0.000	0.000	0.000	0.000
114	A	125	VAL	0	-0.038	0.002	34.150	0.064	0.064	0.000	0.000	0.000	0.000
115	A	126	ASP	-1	-0.825	-0.908	35.993	-8.032	-8.032	0.000	0.000	0.000	0.000
116	A	127	THR	0	0.081	0.014	33.292	-0.164	-0.164	0.000	0.000	0.000	0.000
117	A	128	LYS	1	0.809	0.918	34.521	7.480	7.480	0.000	0.000	0.000	0.000
118	A	129	GLN	0	0.043	0.013	36.114	-0.121	-0.121	0.000	0.000	0.000	0.000
119	A	130	ALA	0	0.018	0.020	31.134	-0.116	-0.116	0.000	0.000	0.000	0.000
120	A	131	HIS	0	-0.019	-0.022	31.141	-0.457	-0.457	0.000	0.000	0.000	0.000
121	A	132	GLU	-1	-0.867	-0.932	32.649	-8.002	-8.002	0.000	0.000	0.000	0.000
122	A	133	LEU	0	0.006	0.022	31.096	-0.027	-0.027	0.000	0.000	0.000	0.000
123	A	134	ALA	0	0.006	0.006	28.273	-0.138	-0.138	0.000	0.000	0.000	0.000
124	A	135	LYS	1	0.945	0.967	29.354	8.752	8.752	0.000	0.000	0.000	0.000
125	A	136	SER	0	-0.053	-0.040	31.818	0.061	0.061	0.000	0.000	0.000	0.000
126	A	137	TYR	0	-0.069	-0.066	27.912	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	138	GLY	0	0.004	0.021	28.046	-0.252	-0.252	0.000	0.000	0.000	0.000
128	A	139	ILE	0	-0.028	0.001	23.954	-0.319	-0.319	0.000	0.000	0.000	0.000
129	A	140	PRO	0	0.032	0.010	21.322	0.509	0.509	0.000	0.000	0.000	0.000
130	A	141	PHE	0	-0.026	-0.031	24.410	0.085	0.085	0.000	0.000	0.000	0.000
131	A	142	ILE	0	-0.009	0.005	21.680	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	143	GLU	-1	-0.798	-0.871	25.144	-9.232	-9.232	0.000	0.000	0.000	0.000
133	A	144	THR	0	-0.001	-0.013	22.718	-0.204	-0.204	0.000	0.000	0.000	0.000
134	A	145	SER	0	-0.079	-0.071	25.270	0.388	0.388	0.000	0.000	0.000	0.000
135	A	146	ALA	0	0.024	0.016	23.250	-0.259	-0.259	0.000	0.000	0.000	0.000
136	A	147	LYS	1	0.865	0.947	24.155	8.851	8.851	0.000	0.000	0.000	0.000
137	A	148	THR	0	-0.010	-0.037	26.809	-0.055	-0.055	0.000	0.000	0.000	0.000
138	A	149	ARG	1	0.771	0.883	15.767	15.076	15.076	0.000	0.000	0.000	0.000
139	A	150	GLN	0	0.037	0.041	22.095	-0.356	-0.356	0.000	0.000	0.000	0.000
140	A	151	GLY	0	0.071	0.013	22.399	0.110	0.110	0.000	0.000	0.000	0.000
141	A	152	VAL	0	-0.032	-0.005	18.223	-0.343	-0.343	0.000	0.000	0.000	0.000
142	A	153	GLU	-1	-0.795	-0.892	14.918	-17.390	-17.390	0.000	0.000	0.000	0.000
143	A	154	ASP	-1	-0.866	-0.935	16.381	-15.099	-15.099	0.000	0.000	0.000	0.000
144	A	155	ALA	0	0.024	0.018	18.380	-0.241	-0.241	0.000	0.000	0.000	0.000
145	A	156	PHE	0	0.017	-0.002	13.898	-0.327	-0.327	0.000	0.000	0.000	0.000
146	A	157	TYR	0	-0.009	-0.015	11.883	-1.523	-1.523	0.000	0.000	0.000	0.000
147	A	158	THR	0	0.016	0.007	14.270	-0.719	-0.719	0.000	0.000	0.000	0.000
148	A	159	LEU	0	-0.026	0.004	15.001	-0.116	-0.116	0.000	0.000	0.000	0.000
149	A	160	VAL	0	-0.012	-0.008	9.627	-0.381	-0.381	0.000	0.000	0.000	0.000
150	A	161	ARG	1	0.762	0.860	12.552	16.837	16.837	0.000	0.000	0.000	0.000
151	A	162	GLU	-1	-0.916	-0.961	14.465	-15.069	-15.069	0.000	0.000	0.000	0.000
152	A	163	ILE	0	-0.029	-0.022	11.810	-0.053	-0.053	0.000	0.000	0.000	0.000
153	A	164	ARG	1	0.697	0.810	8.306	26.368	26.368	0.000	0.000	0.000	0.000
154	A	165	GLN	0	-0.039	-0.006	13.121	0.268	0.268	0.000	0.000	0.000	0.000
155	A	166	TYR	0	-0.054	-0.022	16.308	0.651	0.651	0.000	0.000	0.000	0.000
156	A	167	ARG	0	-0.140	-0.066	8.053	9.646	9.646	0.000	0.000	0.000	0.000

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