FMO DATABASE

FMODB ID: 8212Y

Calculation Name: 1FT0-A-Xray372

Preferred Name: Rho GDP-dissociation inhibitor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1FT0

Chain ID: A

ChEMBL ID: CHEMBL3638327

UniProt ID: P52565

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1133408.727897
FMO2-HF: Nuclear repulsion	1081517.943432
FMO2-HF: Total energy	-51890.784465
FMO2-MP2: Total energy	-52041.734663

3D Structure

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:66:MET)

Summations of interaction energy for fragment #1(A:66: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.
-0.057	1.352	-0.013	-0.531	-0.864	0.001

Interaction energy analysis for fragmet #1(A:66:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.012

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	68	PRO	0	0.043	0.016	3.839	0.732	2.062	-0.012	-0.527	-0.790	0.001
4	A	69	ASN	0	0.012	0.026	6.047	0.708	0.708	0.000	0.000	0.000	0.000
5	A	70	VAL	0	0.053	0.027	8.400	0.162	0.162	0.000	0.000	0.000	0.000
6	A	71	VAL	0	-0.031	-0.010	8.523	-0.226	-0.226	0.000	0.000	0.000	0.000
7	A	72	VAL	0	0.002	0.000	11.735	0.141	0.141	0.000	0.000	0.000	0.000
8	A	73	THR	0	-0.030	-0.073	13.041	-0.075	-0.075	0.000	0.000	0.000	0.000
9	A	74	GLY	0	0.072	0.036	15.054	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	75	LEU	0	-0.057	0.003	18.474	0.013	0.013	0.000	0.000	0.000	0.000
11	A	76	THR	0	0.052	0.020	22.002	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	77	LEU	0	-0.020	0.011	24.989	0.004	0.004	0.000	0.000	0.000	0.000
13	A	78	VAL	0	-0.003	-0.009	28.135	0.007	0.007	0.000	0.000	0.000	0.000
14	A	79	CYS	0	-0.027	-0.031	30.283	0.002	0.002	0.000	0.000	0.000	0.000
15	A	80	SER	0	0.025	0.016	33.621	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	81	SER	0	-0.009	-0.009	35.817	0.003	0.003	0.000	0.000	0.000	0.000
17	A	82	ALA	0	-0.008	-0.019	33.244	0.000	0.000	0.000	0.000	0.000	0.000
18	A	83	PRO	0	-0.027	-0.011	34.814	0.002	0.002	0.000	0.000	0.000	0.000
19	A	84	GLY	0	-0.022	-0.011	31.789	0.004	0.004	0.000	0.000	0.000	0.000
20	A	85	PRO	0	0.033	0.026	26.247	0.000	0.000	0.000	0.000	0.000	0.000
21	A	86	LEU	0	-0.071	-0.046	27.421	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	87	GLU	-1	-0.908	-0.953	22.193	-0.091	-0.091	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.057	-0.033	19.281	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	89	ASP	-1	-0.837	-0.894	14.829	-0.351	-0.351	0.000	0.000	0.000	0.000
25	A	90	LEU	0	-0.069	-0.050	15.584	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	91	THR	0	-0.111	-0.055	10.642	-0.254	-0.254	0.000	0.000	0.000	0.000
27	A	101	SER	0	-0.048	-0.038	27.309	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	102	PHE	0	0.051	0.036	23.944	0.012	0.012	0.000	0.000	0.000	0.000
29	A	103	VAL	0	-0.082	-0.043	29.618	0.005	0.005	0.000	0.000	0.000	0.000
30	A	104	LEU	0	0.055	0.026	32.907	0.005	0.005	0.000	0.000	0.000	0.000
31	A	105	LYS	1	0.808	0.905	35.166	0.052	0.052	0.000	0.000	0.000	0.000
32	A	106	GLU	-1	-0.739	-0.883	38.916	-0.063	-0.063	0.000	0.000	0.000	0.000
33	A	107	GLY	0	-0.070	-0.050	41.014	0.005	0.005	0.000	0.000	0.000	0.000
34	A	108	VAL	0	-0.049	-0.006	36.870	0.002	0.002	0.000	0.000	0.000	0.000
35	A	109	GLU	-1	-0.844	-0.920	37.874	-0.048	-0.048	0.000	0.000	0.000	0.000
36	A	110	TYR	0	-0.069	-0.044	31.433	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	111	ARG	1	0.966	1.000	30.515	0.052	0.052	0.000	0.000	0.000	0.000
38	A	112	ILE	0	-0.006	0.001	25.792	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	113	ALA	0	0.019	0.005	24.931	0.006	0.006	0.000	0.000	0.000	0.000
40	A	114	ILE	0	-0.017	-0.007	19.939	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	115	SER	0	0.029	0.018	18.746	0.020	0.020	0.000	0.000	0.000	0.000
42	A	116	PHE	0	0.010	0.001	15.722	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	117	ARG	1	0.845	0.923	12.295	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	118	VAL	0	0.017	0.031	12.406	-0.096	-0.096	0.000	0.000	0.000	0.000
45	A	119	ASN	0	-0.068	-0.055	8.278	0.149	0.149	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.821	0.885	4.408	-0.513	-0.434	-0.001	-0.004	-0.074	0.000
47	A	121	GLU	-1	-0.833	-0.916	9.220	0.066	0.066	0.000	0.000	0.000	0.000
48	A	122	ILE	0	-0.002	0.000	12.683	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	123	VAL	0	0.014	0.018	14.040	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	124	SER	0	0.029	-0.019	16.800	0.032	0.032	0.000	0.000	0.000	0.000
51	A	125	GLY	0	0.040	0.028	20.194	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	126	MET	0	-0.076	-0.018	16.443	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	127	LYS	1	0.859	0.911	20.899	0.175	0.175	0.000	0.000	0.000	0.000
54	A	128	TYR	0	-0.015	-0.002	22.033	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	129	ILE	0	-0.023	-0.009	24.039	0.017	0.017	0.000	0.000	0.000	0.000
56	A	130	GLN	0	0.058	0.045	25.389	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	131	HIS	0	-0.015	-0.011	27.282	0.025	0.025	0.000	0.000	0.000	0.000
58	A	132	THR	0	0.037	-0.005	29.599	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	133	TYR	0	-0.031	-0.020	29.675	0.006	0.006	0.000	0.000	0.000	0.000
60	A	134	ARG	1	0.883	0.927	33.760	0.100	0.100	0.000	0.000	0.000	0.000
61	A	135	LYS	1	0.932	0.954	36.012	0.128	0.128	0.000	0.000	0.000	0.000
62	A	136	GLY	0	0.054	0.032	34.297	0.003	0.003	0.000	0.000	0.000	0.000
63	A	137	VAL	0	0.003	0.018	35.370	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	138	LYS	1	0.901	0.943	31.793	0.179	0.179	0.000	0.000	0.000	0.000
65	A	139	ILE	0	-0.034	-0.031	35.498	0.007	0.007	0.000	0.000	0.000	0.000
66	A	140	ASP	-1	-0.795	-0.876	33.933	-0.121	-0.121	0.000	0.000	0.000	0.000
67	A	141	LYS	1	0.886	0.975	32.056	0.141	0.141	0.000	0.000	0.000	0.000
68	A	142	THR	0	0.020	0.015	31.195	0.012	0.012	0.000	0.000	0.000	0.000
69	A	143	ASP	-1	-0.843	-0.916	28.620	-0.173	-0.173	0.000	0.000	0.000	0.000
70	A	144	TYR	0	-0.007	-0.012	27.080	0.012	0.012	0.000	0.000	0.000	0.000
71	A	145	MET	0	-0.015	-0.011	25.405	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	146	VAL	0	-0.017	-0.007	21.511	0.010	0.010	0.000	0.000	0.000	0.000
73	A	147	GLY	0	0.016	0.013	23.591	0.020	0.020	0.000	0.000	0.000	0.000
74	A	148	SER	0	-0.010	-0.002	20.755	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	149	TYR	0	-0.038	-0.010	18.074	0.017	0.017	0.000	0.000	0.000	0.000
76	A	150	GLY	0	0.053	0.022	16.961	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	151	PRO	0	-0.005	0.013	12.858	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	152	ARG	1	0.824	0.885	14.236	-0.149	-0.149	0.000	0.000	0.000	0.000
79	A	153	ALA	0	0.000	0.026	14.428	0.011	0.011	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.871	-0.953	15.339	0.247	0.247	0.000	0.000	0.000	0.000
81	A	155	GLU	-1	-0.781	-0.840	16.220	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	156	TYR	0	-0.081	-0.051	16.740	0.009	0.009	0.000	0.000	0.000	0.000
83	A	157	GLU	-1	-0.910	-0.969	19.988	-0.076	-0.076	0.000	0.000	0.000	0.000
84	A	158	PHE	0	-0.025	-0.002	22.759	0.009	0.009	0.000	0.000	0.000	0.000
85	A	159	LEU	0	0.009	0.003	24.492	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	160	THR	0	0.001	0.017	27.822	0.003	0.003	0.000	0.000	0.000	0.000
87	A	161	PRO	0	-0.001	-0.018	30.003	0.008	0.008	0.000	0.000	0.000	0.000
88	A	162	VAL	0	-0.046	-0.026	33.544	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	163	GLU	-1	-0.910	-0.947	33.640	-0.087	-0.087	0.000	0.000	0.000	0.000
90	A	164	GLU	-1	-0.912	-0.951	36.363	-0.051	-0.051	0.000	0.000	0.000	0.000
91	A	165	ALA	0	-0.053	-0.023	37.028	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	166	PRO	0	0.048	0.029	38.030	0.005	0.005	0.000	0.000	0.000	0.000
93	A	167	LYS	1	0.993	0.988	41.259	0.051	0.051	0.000	0.000	0.000	0.000
94	A	168	GLY	0	0.032	0.013	44.232	0.002	0.002	0.000	0.000	0.000	0.000
95	A	169	MET	0	-0.060	-0.030	44.814	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	170	LEU	0	0.063	0.025	45.388	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	171	ALA	0	0.025	0.019	41.942	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	172	ARG	1	0.837	0.919	40.682	0.061	0.061	0.000	0.000	0.000	0.000
99	A	173	GLY	0	0.016	0.007	38.764	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	174	SER	0	-0.038	-0.029	33.347	0.003	0.003	0.000	0.000	0.000	0.000
101	A	175	TYR	0	-0.063	-0.035	33.574	0.003	0.003	0.000	0.000	0.000	0.000
102	A	176	SER	0	-0.036	-0.028	29.635	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	177	ILE	0	0.001	0.005	26.899	0.009	0.009	0.000	0.000	0.000	0.000
104	A	178	LYS	1	0.806	0.887	25.242	0.232	0.232	0.000	0.000	0.000	0.000
105	A	179	SER	0	0.010	0.000	22.668	0.024	0.024	0.000	0.000	0.000	0.000
106	A	180	ARG	1	0.831	0.891	19.626	0.324	0.324	0.000	0.000	0.000	0.000
107	A	181	PHE	0	0.016	0.016	16.688	0.039	0.039	0.000	0.000	0.000	0.000
108	A	182	THR	0	-0.035	-0.033	18.241	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	183	ASP	-1	-0.682	-0.847	15.935	-0.276	-0.276	0.000	0.000	0.000	0.000
110	A	184	ASP	-1	-0.880	-0.919	19.394	-0.145	-0.145	0.000	0.000	0.000	0.000
111	A	185	ASP	-1	-0.904	-0.950	15.821	-0.254	-0.254	0.000	0.000	0.000	0.000
112	A	186	LYS	1	0.656	0.820	18.588	0.184	0.184	0.000	0.000	0.000	0.000
113	A	187	THR	0	0.040	0.033	12.835	-0.044	-0.044	0.000	0.000	0.000	0.000
114	A	188	ASP	-1	-0.826	-0.862	15.983	-0.452	-0.452	0.000	0.000	0.000	0.000
115	A	189	HIS	0	-0.040	-0.047	12.729	-0.155	-0.155	0.000	0.000	0.000	0.000
116	A	190	LEU	0	0.011	0.005	13.439	-0.095	-0.095	0.000	0.000	0.000	0.000
117	A	191	SER	0	-0.022	-0.033	16.068	0.110	0.110	0.000	0.000	0.000	0.000
118	A	192	TRP	0	0.003	0.006	18.356	-0.041	-0.041	0.000	0.000	0.000	0.000
119	A	193	GLU	-1	-0.823	-0.905	20.139	-0.223	-0.223	0.000	0.000	0.000	0.000
120	A	194	TRP	0	0.005	-0.002	22.891	0.002	0.002	0.000	0.000	0.000	0.000
121	A	195	ASN	0	0.003	0.000	25.272	0.019	0.019	0.000	0.000	0.000	0.000
122	A	196	LEU	0	0.083	0.065	28.793	0.003	0.003	0.000	0.000	0.000	0.000
123	A	197	THR	0	-0.072	-0.062	31.370	0.002	0.002	0.000	0.000	0.000	0.000
124	A	198	ILE	0	0.053	0.043	34.241	0.005	0.005	0.000	0.000	0.000	0.000
125	A	199	LYS	1	0.926	0.960	36.343	0.095	0.095	0.000	0.000	0.000	0.000
126	A	200	LYS	1	0.924	0.971	39.952	0.054	0.054	0.000	0.000	0.000	0.000
127	A	201	ASP	-1	-0.841	-0.922	41.883	-0.049	-0.049	0.000	0.000	0.000	0.000
128	A	202	TRP	0	0.064	0.040	34.569	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	203	LYS	1	0.949	0.989	33.146	0.085	0.085	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:66:MET)