FMO DATABASE

FMODB ID: N1R1Q

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1131839.929472
FMO2-HF: Nuclear repulsion	1079948.506007
FMO2-HF: Total energy	-51891.423464
FMO2-MP2: Total energy	-52042.290571

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.
-0.298	1.128	-0.014	-0.591	-0.82	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 : -0.013

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	0.058	0.027	3.869	-0.028	1.306	-0.013	-0.586	-0.735	0.001
4	A	69	ASN	0	0.013	0.025	6.531	0.760	0.760	0.000	0.000	0.000	0.000
5	A	70	VAL	0	0.024	0.014	8.654	0.178	0.178	0.000	0.000	0.000	0.000
6	A	71	VAL	0	-0.015	-0.013	8.584	-0.221	-0.221	0.000	0.000	0.000	0.000
7	A	72	VAL	0	0.001	0.001	11.768	0.133	0.133	0.000	0.000	0.000	0.000
8	A	73	THR	0	-0.037	-0.057	13.089	-0.072	-0.072	0.000	0.000	0.000	0.000
9	A	74	GLY	0	0.057	0.016	15.104	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	75	LEU	0	-0.066	-0.012	18.521	0.004	0.004	0.000	0.000	0.000	0.000
11	A	76	THR	0	0.044	0.005	22.048	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	77	LEU	0	-0.039	-0.011	25.136	0.005	0.005	0.000	0.000	0.000	0.000
13	A	78	VAL	0	0.028	0.012	27.962	0.008	0.008	0.000	0.000	0.000	0.000
14	A	79	CYS	0	-0.029	-0.019	30.312	0.001	0.001	0.000	0.000	0.000	0.000
15	A	80	SER	0	0.018	0.008	33.836	0.000	0.000	0.000	0.000	0.000	0.000
16	A	81	SER	0	0.005	-0.005	36.109	0.003	0.003	0.000	0.000	0.000	0.000
17	A	82	ALA	0	-0.006	-0.007	33.201	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	83	PRO	0	-0.059	-0.028	34.880	0.004	0.004	0.000	0.000	0.000	0.000
19	A	84	GLY	0	-0.006	-0.013	32.049	0.003	0.003	0.000	0.000	0.000	0.000
20	A	85	PRO	0	0.025	0.029	26.480	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	86	LEU	0	-0.084	-0.055	27.720	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	87	GLU	-1	-0.883	-0.938	22.640	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.056	-0.032	19.278	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	89	ASP	-1	-0.803	-0.858	14.491	-0.257	-0.257	0.000	0.000	0.000	0.000
25	A	90	LEU	0	-0.076	-0.043	15.505	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	91	THR	0	-0.122	-0.072	10.557	-0.208	-0.208	0.000	0.000	0.000	0.000
27	A	101	SER	0	-0.032	-0.031	27.399	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	102	PHE	0	0.059	0.041	24.007	0.014	0.014	0.000	0.000	0.000	0.000
29	A	103	VAL	0	-0.068	-0.032	29.727	0.003	0.003	0.000	0.000	0.000	0.000
30	A	104	LEU	0	0.067	0.041	32.991	0.006	0.006	0.000	0.000	0.000	0.000
31	A	105	LYS	1	0.853	0.927	35.214	0.036	0.036	0.000	0.000	0.000	0.000
32	A	106	GLU	-1	-0.728	-0.855	38.985	-0.050	-0.050	0.000	0.000	0.000	0.000
33	A	107	GLY	0	-0.013	-0.011	41.279	0.005	0.005	0.000	0.000	0.000	0.000
34	A	108	VAL	0	-0.071	-0.019	36.988	0.004	0.004	0.000	0.000	0.000	0.000
35	A	109	GLU	-1	-0.839	-0.922	37.909	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	110	TYR	0	-0.068	-0.039	31.436	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	111	ARG	1	0.925	0.964	30.520	0.031	0.031	0.000	0.000	0.000	0.000
38	A	112	ILE	0	-0.016	-0.014	25.759	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	113	ALA	0	0.035	0.025	24.554	0.001	0.001	0.000	0.000	0.000	0.000
40	A	114	ILE	0	-0.031	-0.023	20.218	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	115	SER	0	0.018	0.010	19.009	0.008	0.008	0.000	0.000	0.000	0.000
42	A	116	PHE	0	-0.005	-0.006	15.891	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	117	ARG	1	0.817	0.904	11.900	-0.222	-0.222	0.000	0.000	0.000	0.000
44	A	118	VAL	0	0.017	0.004	12.382	-0.115	-0.115	0.000	0.000	0.000	0.000
45	A	119	ASN	0	-0.045	-0.023	8.274	0.166	0.166	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.775	0.861	4.583	-0.176	-0.084	-0.001	-0.005	-0.085	0.000
47	A	121	GLU	-1	-0.813	-0.908	8.936	0.016	0.016	0.000	0.000	0.000	0.000
48	A	122	ILE	0	-0.012	-0.008	12.465	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	123	VAL	0	0.028	0.023	14.212	-0.044	-0.044	0.000	0.000	0.000	0.000
50	A	124	SER	0	-0.015	-0.037	16.975	0.039	0.039	0.000	0.000	0.000	0.000
51	A	125	GLY	0	0.078	0.045	20.298	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	126	MET	0	-0.082	-0.016	16.576	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	127	LYS	1	0.860	0.905	21.255	0.174	0.174	0.000	0.000	0.000	0.000
54	A	128	TYR	0	0.004	0.001	22.049	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	129	ILE	0	-0.043	-0.016	24.178	0.017	0.017	0.000	0.000	0.000	0.000
56	A	130	GLN	0	0.063	0.042	25.278	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	131	HIS	0	0.003	-0.004	27.476	0.020	0.020	0.000	0.000	0.000	0.000
58	A	132	THR	0	0.011	-0.008	29.913	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	133	TYR	0	-0.018	-0.009	29.859	0.002	0.002	0.000	0.000	0.000	0.000
60	A	134	ARG	1	0.871	0.916	33.814	0.089	0.089	0.000	0.000	0.000	0.000
61	A	135	LYS	1	0.925	0.950	35.766	0.114	0.114	0.000	0.000	0.000	0.000
62	A	136	GLY	0	0.065	0.046	34.422	0.001	0.001	0.000	0.000	0.000	0.000
63	A	137	VAL	0	-0.014	0.009	35.138	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	138	LYS	1	0.907	0.936	31.937	0.170	0.170	0.000	0.000	0.000	0.000
65	A	139	ILE	0	-0.039	-0.033	35.600	0.007	0.007	0.000	0.000	0.000	0.000
66	A	140	ASP	-1	-0.761	-0.849	33.067	-0.116	-0.116	0.000	0.000	0.000	0.000
67	A	141	LYS	1	0.868	0.944	32.169	0.138	0.138	0.000	0.000	0.000	0.000
68	A	142	THR	0	0.018	0.008	31.337	0.011	0.011	0.000	0.000	0.000	0.000
69	A	143	ASP	-1	-0.854	-0.923	28.364	-0.161	-0.161	0.000	0.000	0.000	0.000
70	A	144	TYR	0	-0.022	-0.013	27.422	0.008	0.008	0.000	0.000	0.000	0.000
71	A	145	MET	0	-0.013	-0.010	25.537	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	146	VAL	0	-0.019	-0.006	22.020	0.010	0.010	0.000	0.000	0.000	0.000
73	A	147	GLY	0	0.006	0.018	24.047	0.020	0.020	0.000	0.000	0.000	0.000
74	A	148	SER	0	-0.020	-0.019	21.023	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	149	TYR	0	-0.038	-0.017	18.070	0.018	0.018	0.000	0.000	0.000	0.000
76	A	150	GLY	0	0.037	0.010	16.290	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	151	PRO	0	-0.018	0.019	12.520	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	152	ARG	1	0.822	0.895	14.177	-0.185	-0.185	0.000	0.000	0.000	0.000
79	A	153	ALA	0	0.031	0.038	14.052	0.013	0.013	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.863	-0.941	14.952	0.332	0.332	0.000	0.000	0.000	0.000
81	A	155	GLU	-1	-0.775	-0.854	16.073	0.096	0.096	0.000	0.000	0.000	0.000
82	A	156	TYR	0	-0.078	-0.045	16.577	0.001	0.001	0.000	0.000	0.000	0.000
83	A	157	GLU	-1	-0.854	-0.936	20.020	-0.035	-0.035	0.000	0.000	0.000	0.000
84	A	158	PHE	0	-0.029	0.001	22.600	0.006	0.006	0.000	0.000	0.000	0.000
85	A	159	LEU	0	0.010	-0.006	24.646	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	160	THR	0	0.004	0.028	27.909	0.001	0.001	0.000	0.000	0.000	0.000
87	A	161	PRO	0	0.012	-0.002	30.256	0.011	0.011	0.000	0.000	0.000	0.000
88	A	162	VAL	0	-0.026	-0.006	33.461	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	163	GLU	-1	-0.835	-0.892	33.100	-0.075	-0.075	0.000	0.000	0.000	0.000
90	A	164	GLU	-1	-0.897	-0.963	36.139	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	165	ALA	0	-0.056	-0.021	37.320	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	166	PRO	0	0.037	0.022	38.158	0.005	0.005	0.000	0.000	0.000	0.000
93	A	167	LYS	1	0.888	0.925	41.377	0.040	0.040	0.000	0.000	0.000	0.000
94	A	168	GLY	0	0.026	0.021	44.214	0.001	0.001	0.000	0.000	0.000	0.000
95	A	169	MET	0	-0.039	-0.041	45.012	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	170	LEU	0	0.080	0.039	45.055	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	171	ALA	0	0.008	0.019	42.046	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	172	ARG	1	0.834	0.907	40.542	0.049	0.049	0.000	0.000	0.000	0.000
99	A	173	GLY	0	0.003	0.002	38.708	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	174	SER	0	-0.042	-0.029	33.299	0.003	0.003	0.000	0.000	0.000	0.000
101	A	175	TYR	0	-0.070	-0.038	33.572	0.001	0.001	0.000	0.000	0.000	0.000
102	A	176	SER	0	-0.029	-0.024	29.443	0.000	0.000	0.000	0.000	0.000	0.000
103	A	177	ILE	0	-0.020	-0.008	27.325	0.007	0.007	0.000	0.000	0.000	0.000
104	A	178	LYS	1	0.813	0.888	25.361	0.214	0.214	0.000	0.000	0.000	0.000
105	A	179	SER	0	0.016	0.001	22.796	0.025	0.025	0.000	0.000	0.000	0.000
106	A	180	ARG	1	0.815	0.890	19.786	0.330	0.330	0.000	0.000	0.000	0.000
107	A	181	PHE	0	0.012	0.012	16.964	0.039	0.039	0.000	0.000	0.000	0.000
108	A	182	THR	0	-0.041	-0.038	18.337	-0.043	-0.043	0.000	0.000	0.000	0.000
109	A	183	ASP	-1	-0.731	-0.865	16.067	-0.297	-0.297	0.000	0.000	0.000	0.000
110	A	184	ASP	-1	-0.851	-0.934	19.478	-0.143	-0.143	0.000	0.000	0.000	0.000
111	A	185	ASP	-1	-0.911	-0.930	16.484	-0.285	-0.285	0.000	0.000	0.000	0.000
112	A	186	LYS	1	0.696	0.844	18.612	0.177	0.177	0.000	0.000	0.000	0.000
113	A	187	THR	0	0.032	0.012	13.314	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	188	ASP	-1	-0.820	-0.864	16.144	-0.435	-0.435	0.000	0.000	0.000	0.000
115	A	189	HIS	0	-0.040	-0.037	12.682	-0.157	-0.157	0.000	0.000	0.000	0.000
116	A	190	LEU	0	0.016	0.015	13.629	-0.061	-0.061	0.000	0.000	0.000	0.000
117	A	191	SER	0	-0.015	-0.028	15.982	0.108	0.108	0.000	0.000	0.000	0.000
118	A	192	TRP	0	-0.001	-0.011	18.086	-0.042	-0.042	0.000	0.000	0.000	0.000
119	A	193	GLU	-1	-0.829	-0.903	20.227	-0.203	-0.203	0.000	0.000	0.000	0.000
120	A	194	TRP	0	0.017	0.013	22.633	0.004	0.004	0.000	0.000	0.000	0.000
121	A	195	ASN	0	0.005	0.000	25.119	0.015	0.015	0.000	0.000	0.000	0.000
122	A	196	LEU	0	0.051	0.049	28.771	0.003	0.003	0.000	0.000	0.000	0.000
123	A	197	THR	0	-0.046	-0.053	31.479	0.000	0.000	0.000	0.000	0.000	0.000
124	A	198	ILE	0	0.077	0.057	34.449	0.006	0.006	0.000	0.000	0.000	0.000
125	A	199	LYS	1	0.931	0.966	36.554	0.073	0.073	0.000	0.000	0.000	0.000
126	A	200	LYS	1	0.915	0.959	40.178	0.040	0.040	0.000	0.000	0.000	0.000
127	A	201	ASP	-1	-0.854	-0.925	41.991	-0.035	-0.035	0.000	0.000	0.000	0.000
128	A	202	TRP	0	0.060	0.040	34.357	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	203	LYS	1	0.913	0.959	32.744	0.058	0.058	0.000	0.000	0.000	0.000

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