FMO DATABASE

FMODB ID: GNMN1

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	OptH
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	-1134053.647696
FMO2-HF: Nuclear repulsion	1082164.044124
FMO2-HF: Total energy	-51889.603572
FMO2-MP2: Total energy	-52040.621575

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.
-0.291	1.09	-0.013	-0.531	-0.836	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 : 0.005 / q_NPA : -0.007

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	0.048	0.023	3.839	1.148	2.458	-0.012	-0.528	-0.770	0.001
4	A	69	ASN	0	0.050	0.040	6.123	0.683	0.683	0.000	0.000	0.000	0.000
5	A	70	VAL	0	0.046	0.033	8.481	0.130	0.130	0.000	0.000	0.000	0.000
6	A	71	VAL	0	-0.027	-0.007	8.868	-0.215	-0.215	0.000	0.000	0.000	0.000
7	A	72	VAL	0	-0.001	-0.002	11.827	0.130	0.130	0.000	0.000	0.000	0.000
8	A	73	THR	0	-0.043	-0.072	13.452	-0.079	-0.079	0.000	0.000	0.000	0.000
9	A	74	GLY	0	0.077	0.040	15.357	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	75	LEU	0	-0.065	0.005	18.714	0.021	0.021	0.000	0.000	0.000	0.000
11	A	76	THR	0	0.061	0.022	22.264	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	77	LEU	0	-0.032	0.004	25.123	0.008	0.008	0.000	0.000	0.000	0.000
13	A	78	VAL	0	0.000	-0.008	28.360	0.005	0.005	0.000	0.000	0.000	0.000
14	A	79	CYS	0	-0.013	-0.014	30.428	0.005	0.005	0.000	0.000	0.000	0.000
15	A	80	SER	0	0.042	0.019	33.628	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	81	SER	0	-0.032	-0.018	35.743	0.002	0.002	0.000	0.000	0.000	0.000
17	A	82	ALA	0	0.000	-0.015	33.296	0.001	0.001	0.000	0.000	0.000	0.000
18	A	83	PRO	0	-0.031	-0.012	34.796	0.001	0.001	0.000	0.000	0.000	0.000
19	A	84	GLY	0	-0.016	-0.007	31.829	0.003	0.003	0.000	0.000	0.000	0.000
20	A	85	PRO	0	0.021	0.019	26.284	0.002	0.002	0.000	0.000	0.000	0.000
21	A	86	LEU	0	-0.053	-0.036	27.475	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	87	GLU	-1	-0.906	-0.950	22.307	-0.156	-0.156	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.062	-0.038	19.564	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	89	ASP	-1	-0.843	-0.907	14.966	-0.468	-0.468	0.000	0.000	0.000	0.000
25	A	90	LEU	0	-0.078	-0.051	15.832	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	91	THR	0	-0.095	-0.038	10.654	-0.203	-0.203	0.000	0.000	0.000	0.000
27	A	101	SER	0	-0.004	-0.008	26.812	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	102	PHE	0	0.012	0.006	24.348	0.010	0.010	0.000	0.000	0.000	0.000
29	A	103	VAL	0	-0.072	-0.037	29.900	0.007	0.007	0.000	0.000	0.000	0.000
30	A	104	LEU	0	0.047	0.024	32.841	0.003	0.003	0.000	0.000	0.000	0.000
31	A	105	LYS	1	0.875	0.951	35.374	0.067	0.067	0.000	0.000	0.000	0.000
32	A	106	GLU	-1	-0.768	-0.914	39.109	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	107	GLY	0	-0.060	-0.048	41.232	0.004	0.004	0.000	0.000	0.000	0.000
34	A	108	VAL	0	-0.052	-0.004	36.953	0.002	0.002	0.000	0.000	0.000	0.000
35	A	109	GLU	-1	-0.834	-0.922	38.317	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	110	TYR	0	-0.082	-0.055	31.790	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	111	ARG	1	0.973	1.005	30.818	0.073	0.073	0.000	0.000	0.000	0.000
38	A	112	ILE	0	-0.006	0.004	25.988	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	113	ALA	0	0.032	0.002	25.327	0.008	0.008	0.000	0.000	0.000	0.000
40	A	114	ILE	0	-0.031	-0.013	20.217	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	115	SER	0	0.037	0.025	18.931	0.034	0.034	0.000	0.000	0.000	0.000
42	A	116	PHE	0	0.011	0.000	15.812	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	117	ARG	1	0.915	0.984	12.204	0.087	0.087	0.000	0.000	0.000	0.000
44	A	118	VAL	0	0.035	0.043	12.518	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	119	ASN	0	-0.066	-0.058	8.433	0.116	0.116	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.857	0.899	4.655	-1.038	-0.967	-0.001	-0.003	-0.066	0.000
47	A	121	GLU	-1	-0.929	-0.964	10.259	0.034	0.034	0.000	0.000	0.000	0.000
48	A	122	ILE	0	-0.013	0.011	12.749	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	123	VAL	0	0.002	0.012	14.258	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	124	SER	0	0.036	-0.028	16.869	0.024	0.024	0.000	0.000	0.000	0.000
51	A	125	GLY	0	0.067	0.041	20.256	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	126	MET	0	-0.065	-0.011	16.251	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	127	LYS	1	0.909	0.946	20.972	0.169	0.169	0.000	0.000	0.000	0.000
54	A	128	TYR	0	0.016	0.036	22.102	-0.034	-0.034	0.000	0.000	0.000	0.000
55	A	129	ILE	0	-0.042	-0.018	23.960	0.017	0.017	0.000	0.000	0.000	0.000
56	A	130	GLN	0	0.078	0.047	25.528	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	131	HIS	0	0.007	-0.006	27.772	0.023	0.023	0.000	0.000	0.000	0.000
58	A	132	THR	0	0.088	0.039	29.725	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	133	TYR	0	-0.070	-0.038	29.757	0.008	0.008	0.000	0.000	0.000	0.000
60	A	134	ARG	1	0.917	0.951	33.855	0.104	0.104	0.000	0.000	0.000	0.000
61	A	135	LYS	1	0.940	0.955	36.284	0.136	0.136	0.000	0.000	0.000	0.000
62	A	136	GLY	0	0.045	0.030	34.427	0.004	0.004	0.000	0.000	0.000	0.000
63	A	137	VAL	0	0.007	0.022	35.407	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	138	LYS	1	0.911	0.951	31.565	0.169	0.169	0.000	0.000	0.000	0.000
65	A	139	ILE	0	-0.041	-0.033	35.578	0.007	0.007	0.000	0.000	0.000	0.000
66	A	140	ASP	-1	-0.833	-0.917	35.228	-0.114	-0.114	0.000	0.000	0.000	0.000
67	A	141	LYS	1	0.862	0.953	32.069	0.135	0.135	0.000	0.000	0.000	0.000
68	A	142	THR	0	0.025	0.028	31.225	0.012	0.012	0.000	0.000	0.000	0.000
69	A	143	ASP	-1	-0.879	-0.951	28.694	-0.169	-0.169	0.000	0.000	0.000	0.000
70	A	144	TYR	0	-0.013	-0.013	27.105	0.011	0.011	0.000	0.000	0.000	0.000
71	A	145	MET	0	-0.021	-0.016	25.194	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	146	VAL	0	-0.042	-0.007	21.500	0.008	0.008	0.000	0.000	0.000	0.000
73	A	147	GLY	0	0.018	0.003	23.659	0.017	0.017	0.000	0.000	0.000	0.000
74	A	148	SER	0	-0.007	0.011	20.823	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	149	TYR	0	-0.037	-0.002	18.157	0.011	0.011	0.000	0.000	0.000	0.000
76	A	150	GLY	0	0.071	0.011	16.998	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	151	PRO	0	-0.019	0.007	12.936	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	152	ARG	1	0.864	0.931	14.337	-0.088	-0.088	0.000	0.000	0.000	0.000
79	A	153	ALA	0	-0.013	0.018	14.408	0.006	0.006	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.908	-0.978	15.279	0.157	0.157	0.000	0.000	0.000	0.000
81	A	155	GLU	-1	-0.808	-0.901	16.227	-0.157	-0.157	0.000	0.000	0.000	0.000
82	A	156	TYR	0	-0.107	-0.076	16.934	0.021	0.021	0.000	0.000	0.000	0.000
83	A	157	GLU	-1	-0.905	-0.965	20.084	-0.125	-0.125	0.000	0.000	0.000	0.000
84	A	158	PHE	0	-0.025	-0.005	22.892	0.014	0.014	0.000	0.000	0.000	0.000
85	A	159	LEU	0	0.008	0.002	24.582	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	160	THR	0	-0.003	0.014	28.066	0.004	0.004	0.000	0.000	0.000	0.000
87	A	161	PRO	0	-0.020	-0.033	30.154	0.007	0.007	0.000	0.000	0.000	0.000
88	A	162	VAL	0	-0.049	-0.021	33.832	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	163	GLU	-1	-0.883	-0.928	34.254	-0.092	-0.092	0.000	0.000	0.000	0.000
90	A	164	GLU	-1	-0.917	-0.958	36.634	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	165	ALA	0	-0.074	-0.028	37.217	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	166	PRO	0	0.041	0.031	38.226	0.006	0.006	0.000	0.000	0.000	0.000
93	A	167	LYS	1	1.008	0.985	41.471	0.060	0.060	0.000	0.000	0.000	0.000
94	A	168	GLY	0	0.009	-0.003	44.461	0.002	0.002	0.000	0.000	0.000	0.000
95	A	169	MET	0	-0.081	-0.035	45.154	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	170	LEU	0	0.050	0.012	45.788	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	171	ALA	0	0.030	0.014	42.052	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	172	ARG	1	0.886	0.972	40.965	0.071	0.071	0.000	0.000	0.000	0.000
99	A	173	GLY	0	0.014	0.005	39.181	0.000	0.000	0.000	0.000	0.000	0.000
100	A	174	SER	0	-0.032	-0.021	33.843	0.002	0.002	0.000	0.000	0.000	0.000
101	A	175	TYR	0	-0.077	-0.039	33.706	0.005	0.005	0.000	0.000	0.000	0.000
102	A	176	SER	0	0.002	-0.004	30.051	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	177	ILE	0	-0.015	0.000	26.936	0.012	0.012	0.000	0.000	0.000	0.000
104	A	178	LYS	1	0.944	0.973	25.346	0.226	0.226	0.000	0.000	0.000	0.000
105	A	179	SER	0	0.000	-0.017	22.848	0.024	0.024	0.000	0.000	0.000	0.000
106	A	180	ARG	1	0.925	0.961	20.129	0.293	0.293	0.000	0.000	0.000	0.000
107	A	181	PHE	0	0.029	0.024	16.972	0.037	0.037	0.000	0.000	0.000	0.000
108	A	182	THR	0	-0.068	-0.039	18.301	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	183	ASP	-1	-0.691	-0.856	15.965	-0.233	-0.233	0.000	0.000	0.000	0.000
110	A	184	ASP	-1	-0.935	-0.952	19.454	-0.117	-0.117	0.000	0.000	0.000	0.000
111	A	185	ASP	-1	-0.911	-0.935	16.050	-0.194	-0.194	0.000	0.000	0.000	0.000
112	A	186	LYS	1	0.782	0.878	18.624	0.171	0.171	0.000	0.000	0.000	0.000
113	A	187	THR	0	0.022	0.015	12.890	-0.035	-0.035	0.000	0.000	0.000	0.000
114	A	188	ASP	-1	-0.925	-0.930	15.928	-0.462	-0.462	0.000	0.000	0.000	0.000
115	A	189	HIS	0	-0.061	-0.064	13.184	-0.146	-0.146	0.000	0.000	0.000	0.000
116	A	190	LEU	0	0.003	-0.001	13.695	-0.097	-0.097	0.000	0.000	0.000	0.000
117	A	191	SER	0	-0.020	-0.037	16.199	0.108	0.108	0.000	0.000	0.000	0.000
118	A	192	TRP	0	-0.005	0.002	18.480	-0.042	-0.042	0.000	0.000	0.000	0.000
119	A	193	GLU	-1	-0.956	-0.990	20.242	-0.219	-0.219	0.000	0.000	0.000	0.000
120	A	194	TRP	0	-0.010	-0.013	23.251	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	195	ASN	0	0.008	0.003	25.629	0.019	0.019	0.000	0.000	0.000	0.000
122	A	196	LEU	0	0.080	0.058	29.215	0.000	0.000	0.000	0.000	0.000	0.000
123	A	197	THR	0	-0.073	-0.069	31.718	0.004	0.004	0.000	0.000	0.000	0.000
124	A	198	ILE	0	0.046	0.040	34.597	0.003	0.003	0.000	0.000	0.000	0.000
125	A	199	LYS	1	0.921	0.951	36.909	0.111	0.111	0.000	0.000	0.000	0.000
126	A	200	LYS	1	0.955	0.987	40.246	0.065	0.065	0.000	0.000	0.000	0.000
127	A	201	ASP	-1	-0.917	-0.961	42.105	-0.064	-0.064	0.000	0.000	0.000	0.000
128	A	202	TRP	0	0.030	0.014	34.859	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	203	LYS	1	0.955	0.985	33.693	0.105	0.105	0.000	0.000	0.000	0.000

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