FMO DATABASE

FMODB ID: QVMQY

Calculation Name: 2ANC-F-Xray372

Preferred Name: Guanylate kinase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2ANC

Chain ID: F

ChEMBL ID: CHEMBL3309016

UniProt ID: P60546

Base Structure: X-ray

Registration Date: 2023-09-23

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1392642.959607
FMO2-HF: Nuclear repulsion	1332345.115065
FMO2-HF: Total energy	-60297.844542
FMO2-MP2: Total energy	-60474.628812

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(F:2:ALA)

Summations of interaction energy for fragment #1(F:2:ALA)

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.
-7.575	-3.514	2.827	-2.446	-4.441	-0.003

Interaction energy analysis for fragmet #1(F:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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

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	F	4	GLY	0	-0.009	0.018	3.870	0.955	2.475	-0.018	-0.790	-0.711	0.001
4	F	5	THR	0	-0.090	-0.063	6.447	0.316	0.316	0.000	0.000	0.000	0.000
5	F	6	LEU	0	0.040	0.025	10.026	-0.090	-0.090	0.000	0.000	0.000	0.000
6	F	7	TYR	0	0.021	-0.003	11.505	0.087	0.087	0.000	0.000	0.000	0.000
7	F	8	ILE	0	0.028	0.020	15.773	-0.035	-0.035	0.000	0.000	0.000	0.000
8	F	9	VAL	0	-0.034	-0.020	19.195	0.026	0.026	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.019	0.007	21.849	-0.012	-0.012	0.000	0.000	0.000	0.000
10	F	11	ALA	0	-0.013	-0.010	25.626	0.009	0.009	0.000	0.000	0.000	0.000
11	F	12	PRO	0	-0.034	0.003	28.830	-0.008	-0.008	0.000	0.000	0.000	0.000
12	F	13	SER	0	0.015	-0.002	31.486	0.000	0.000	0.000	0.000	0.000	0.000
13	F	14	GLY	0	0.042	0.006	33.552	0.003	0.003	0.000	0.000	0.000	0.000
14	F	15	ALA	0	0.021	0.006	29.911	0.003	0.003	0.000	0.000	0.000	0.000
15	F	16	GLY	0	0.021	0.017	29.603	0.005	0.005	0.000	0.000	0.000	0.000
16	F	17	LYS	1	0.838	0.923	24.498	0.019	0.019	0.000	0.000	0.000	0.000
17	F	18	SER	0	0.058	0.026	24.580	0.002	0.002	0.000	0.000	0.000	0.000
18	F	19	SER	0	-0.013	-0.014	24.796	-0.007	-0.007	0.000	0.000	0.000	0.000
19	F	20	LEU	0	0.034	0.026	23.567	-0.003	-0.003	0.000	0.000	0.000	0.000
20	F	21	ILE	0	0.018	0.013	19.178	0.001	0.001	0.000	0.000	0.000	0.000
21	F	22	GLN	0	-0.007	-0.014	20.478	-0.009	-0.009	0.000	0.000	0.000	0.000
22	F	23	ALA	0	0.011	0.007	22.330	-0.008	-0.008	0.000	0.000	0.000	0.000
23	F	24	LEU	0	-0.016	-0.005	16.009	0.006	0.006	0.000	0.000	0.000	0.000
24	F	25	LEU	0	0.006	0.000	16.011	-0.003	-0.003	0.000	0.000	0.000	0.000
25	F	26	LYS	1	0.892	0.957	18.439	0.050	0.050	0.000	0.000	0.000	0.000
26	F	27	THR	0	-0.053	-0.017	19.492	0.012	0.012	0.000	0.000	0.000	0.000
27	F	28	GLN	0	0.025	0.024	13.168	0.029	0.029	0.000	0.000	0.000	0.000
28	F	29	PRO	0	0.022	0.039	12.282	-0.015	-0.015	0.000	0.000	0.000	0.000
29	F	30	LEU	0	0.069	0.017	12.532	-0.016	-0.016	0.000	0.000	0.000	0.000
30	F	31	TYR	0	0.009	0.013	8.958	-0.073	-0.073	0.000	0.000	0.000	0.000
31	F	32	ASP	-1	-0.867	-0.909	7.731	-0.182	-0.182	0.000	0.000	0.000	0.000
32	F	33	THR	0	-0.032	-0.053	8.944	0.027	0.027	0.000	0.000	0.000	0.000
33	F	34	GLN	0	-0.017	0.005	11.570	0.050	0.050	0.000	0.000	0.000	0.000
34	F	87	GLU	-1	-0.909	-0.960	16.082	-0.363	-0.363	0.000	0.000	0.000	0.000
35	F	88	ALA	0	0.033	0.010	14.543	-0.073	-0.073	0.000	0.000	0.000	0.000
36	F	89	ILE	0	-0.024	-0.011	13.823	-0.043	-0.043	0.000	0.000	0.000	0.000
37	F	90	GLU	-1	-0.818	-0.920	11.311	-0.440	-0.440	0.000	0.000	0.000	0.000
38	F	91	GLN	0	-0.083	-0.051	9.768	-0.265	-0.265	0.000	0.000	0.000	0.000
39	F	92	VAL	0	0.008	0.016	9.123	-0.221	-0.221	0.000	0.000	0.000	0.000
40	F	93	LEU	0	-0.006	0.012	7.693	-0.314	-0.314	0.000	0.000	0.000	0.000
41	F	94	ALA	0	0.007	0.005	5.592	-0.718	-0.718	0.000	0.000	0.000	0.000
42	F	95	THR	0	-0.048	-0.035	4.361	-0.725	-0.530	-0.001	-0.025	-0.169	0.000
43	F	96	GLY	0	-0.060	-0.022	2.793	-1.594	-0.941	0.160	-0.287	-0.526	-0.001
44	F	97	VAL	0	-0.024	-0.002	3.444	1.467	1.663	0.009	0.036	-0.242	-0.001
45	F	98	ASP	-1	-0.759	-0.860	7.104	0.428	0.428	0.000	0.000	0.000	0.000
46	F	99	VAL	0	0.009	0.002	9.547	-0.045	-0.045	0.000	0.000	0.000	0.000
47	F	100	PHE	0	0.002	-0.015	12.734	0.073	0.073	0.000	0.000	0.000	0.000
48	F	101	LEU	0	-0.010	-0.007	16.230	-0.028	-0.028	0.000	0.000	0.000	0.000
49	F	102	ASP	-1	-0.861	-0.907	19.085	-0.013	-0.013	0.000	0.000	0.000	0.000
50	F	103	ILE	0	0.010	0.002	22.100	-0.013	-0.013	0.000	0.000	0.000	0.000
51	F	104	ASP	-1	-0.779	-0.867	25.087	-0.015	-0.015	0.000	0.000	0.000	0.000
52	F	105	TRP	0	0.046	0.014	26.813	0.000	0.000	0.000	0.000	0.000	0.000
53	F	106	GLN	0	-0.079	-0.037	27.975	0.002	0.002	0.000	0.000	0.000	0.000
54	F	107	GLY	0	0.010	-0.003	25.854	-0.003	-0.003	0.000	0.000	0.000	0.000
55	F	108	ALA	0	-0.001	-0.007	23.189	-0.004	-0.004	0.000	0.000	0.000	0.000
56	F	109	GLN	0	-0.028	-0.031	23.448	0.000	0.000	0.000	0.000	0.000	0.000
57	F	110	GLN	0	0.011	0.002	24.859	-0.006	-0.006	0.000	0.000	0.000	0.000
58	F	111	ILE	0	-0.003	0.002	18.775	-0.010	-0.010	0.000	0.000	0.000	0.000
59	F	112	ARG	1	0.883	0.935	20.087	-0.054	-0.054	0.000	0.000	0.000	0.000
60	F	113	GLN	0	-0.060	-0.019	20.847	0.013	0.013	0.000	0.000	0.000	0.000
61	F	114	LYS	1	0.852	0.921	20.277	0.070	0.070	0.000	0.000	0.000	0.000
62	F	115	MET	0	0.013	0.021	14.841	-0.018	-0.018	0.000	0.000	0.000	0.000
63	F	116	PRO	0	0.051	0.030	16.585	0.023	0.023	0.000	0.000	0.000	0.000
64	F	117	HIS	0	-0.081	-0.049	11.548	0.065	0.065	0.000	0.000	0.000	0.000
65	F	118	ALA	0	-0.020	0.005	13.728	0.044	0.044	0.000	0.000	0.000	0.000
66	F	119	ARG	1	0.738	0.853	14.693	-0.256	-0.256	0.000	0.000	0.000	0.000
67	F	120	SER	0	-0.023	-0.029	17.110	-0.036	-0.036	0.000	0.000	0.000	0.000
68	F	121	ILE	0	-0.021	-0.013	17.790	0.016	0.016	0.000	0.000	0.000	0.000
69	F	122	PHE	0	0.036	0.014	21.816	-0.019	-0.019	0.000	0.000	0.000	0.000
70	F	123	ILE	0	-0.014	-0.011	23.761	0.007	0.007	0.000	0.000	0.000	0.000
71	F	124	LEU	0	0.016	-0.001	27.644	-0.008	-0.008	0.000	0.000	0.000	0.000
72	F	125	PRO	0	-0.018	-0.008	31.416	0.001	0.001	0.000	0.000	0.000	0.000
73	F	126	PRO	0	0.034	0.024	34.300	0.003	0.003	0.000	0.000	0.000	0.000
74	F	127	SER	0	0.031	0.006	36.065	0.000	0.000	0.000	0.000	0.000	0.000
75	F	128	LYS	1	0.975	0.974	39.054	-0.016	-0.016	0.000	0.000	0.000	0.000
76	F	129	ILE	0	0.050	0.028	40.999	-0.003	-0.003	0.000	0.000	0.000	0.000
77	F	130	GLU	-1	-0.721	-0.816	37.455	0.011	0.011	0.000	0.000	0.000	0.000
78	F	131	LEU	0	-0.026	-0.010	36.040	-0.002	-0.002	0.000	0.000	0.000	0.000
79	F	132	ASP	-1	-0.839	-0.904	38.793	0.001	0.001	0.000	0.000	0.000	0.000
80	F	133	ARG	1	0.889	0.913	39.133	-0.011	-0.011	0.000	0.000	0.000	0.000
81	F	134	ARG	1	0.738	0.858	33.110	-0.020	-0.020	0.000	0.000	0.000	0.000
82	F	135	LEU	0	-0.042	-0.015	36.973	-0.004	-0.004	0.000	0.000	0.000	0.000
83	F	136	ARG	1	0.778	0.832	39.520	-0.004	-0.004	0.000	0.000	0.000	0.000
84	F	137	GLY	0	-0.002	0.012	39.736	-0.002	-0.002	0.000	0.000	0.000	0.000
85	F	138	ARG	1	0.899	0.957	40.568	0.014	0.014	0.000	0.000	0.000	0.000
86	F	139	GLY	0	0.009	0.004	43.445	0.001	0.001	0.000	0.000	0.000	0.000
87	F	140	GLN	0	-0.065	-0.041	45.898	0.000	0.000	0.000	0.000	0.000	0.000
88	F	141	ASP	-1	-0.774	-0.848	44.286	-0.015	-0.015	0.000	0.000	0.000	0.000
89	F	142	SER	0	-0.011	-0.022	47.565	0.001	0.001	0.000	0.000	0.000	0.000
90	F	143	GLU	-1	-0.749	-0.864	48.284	-0.001	-0.001	0.000	0.000	0.000	0.000
91	F	144	GLU	-1	-0.844	-0.903	48.370	-0.006	-0.006	0.000	0.000	0.000	0.000
92	F	145	VAL	0	-0.041	-0.015	44.139	0.000	0.000	0.000	0.000	0.000	0.000
93	F	146	ILE	0	0.015	0.015	43.711	0.000	0.000	0.000	0.000	0.000	0.000
94	F	147	ALA	0	0.019	0.010	43.623	0.001	0.001	0.000	0.000	0.000	0.000
95	F	148	LYS	1	0.958	0.981	42.546	0.017	0.017	0.000	0.000	0.000	0.000
96	F	149	ARG	1	0.753	0.834	39.141	0.012	0.012	0.000	0.000	0.000	0.000
97	F	150	MET	0	-0.006	0.003	39.245	0.002	0.002	0.000	0.000	0.000	0.000
98	F	151	ALA	0	-0.018	-0.012	40.276	0.002	0.002	0.000	0.000	0.000	0.000
99	F	152	GLN	0	-0.008	-0.005	35.655	0.002	0.002	0.000	0.000	0.000	0.000
100	F	153	ALA	0	0.012	0.000	35.663	0.001	0.001	0.000	0.000	0.000	0.000
101	F	154	VAL	0	-0.009	-0.014	35.714	0.003	0.003	0.000	0.000	0.000	0.000
102	F	155	ALA	0	0.004	0.018	36.967	0.003	0.003	0.000	0.000	0.000	0.000
103	F	156	GLU	-1	-0.812	-0.917	29.322	0.002	0.002	0.000	0.000	0.000	0.000
104	F	157	MET	0	-0.033	-0.035	32.328	0.005	0.005	0.000	0.000	0.000	0.000
105	F	158	SER	0	-0.052	-0.034	33.278	0.006	0.006	0.000	0.000	0.000	0.000
106	F	159	HIS	1	0.839	0.920	30.067	-0.014	-0.014	0.000	0.000	0.000	0.000
107	F	160	TYR	0	0.009	0.010	28.980	0.006	0.006	0.000	0.000	0.000	0.000
108	F	161	ALA	0	-0.007	-0.007	28.317	0.008	0.008	0.000	0.000	0.000	0.000
109	F	162	GLU	-1	-0.844	-0.894	27.236	0.035	0.035	0.000	0.000	0.000	0.000
110	F	163	TYR	0	-0.057	-0.046	23.406	0.001	0.001	0.000	0.000	0.000	0.000
111	F	164	ASP	-1	-0.788	-0.839	19.671	0.174	0.174	0.000	0.000	0.000	0.000
112	F	165	TYR	0	-0.041	-0.049	17.293	0.012	0.012	0.000	0.000	0.000	0.000
113	F	166	LEU	0	-0.003	-0.002	22.889	-0.017	-0.017	0.000	0.000	0.000	0.000
114	F	167	ILE	0	0.000	0.012	22.283	0.007	0.007	0.000	0.000	0.000	0.000
115	F	168	VAL	0	0.020	0.004	26.790	-0.009	-0.009	0.000	0.000	0.000	0.000
116	F	169	ASN	0	-0.014	-0.015	28.909	0.004	0.004	0.000	0.000	0.000	0.000
117	F	170	ASP	-1	-0.900	-0.957	30.504	0.029	0.029	0.000	0.000	0.000	0.000
118	F	171	ASP	-1	-0.774	-0.868	31.350	0.033	0.033	0.000	0.000	0.000	0.000
119	F	172	PHE	0	-0.029	-0.012	26.579	0.003	0.003	0.000	0.000	0.000	0.000
120	F	173	ASP	-1	-0.871	-0.947	27.415	0.029	0.029	0.000	0.000	0.000	0.000
121	F	174	THR	0	-0.045	-0.028	26.550	0.010	0.010	0.000	0.000	0.000	0.000
122	F	175	ALA	0	0.034	0.023	26.120	0.010	0.010	0.000	0.000	0.000	0.000
123	F	176	LEU	0	-0.041	-0.027	21.847	0.006	0.006	0.000	0.000	0.000	0.000
124	F	177	THR	0	-0.025	-0.024	21.917	0.010	0.010	0.000	0.000	0.000	0.000
125	F	178	ASP	-1	-0.864	-0.924	21.797	0.118	0.118	0.000	0.000	0.000	0.000
126	F	179	LEU	0	-0.028	-0.020	18.975	0.023	0.023	0.000	0.000	0.000	0.000
127	F	180	LYS	1	0.895	0.934	17.567	-0.016	-0.016	0.000	0.000	0.000	0.000
128	F	181	THR	0	-0.047	-0.027	17.048	0.041	0.041	0.000	0.000	0.000	0.000
129	F	182	ILE	0	-0.004	0.002	16.265	0.049	0.049	0.000	0.000	0.000	0.000
130	F	183	ILE	0	-0.013	0.004	12.117	0.066	0.066	0.000	0.000	0.000	0.000
131	F	184	ARG	1	0.955	0.972	12.561	-0.150	-0.150	0.000	0.000	0.000	0.000
132	F	185	ALA	0	0.030	0.011	13.624	0.097	0.097	0.000	0.000	0.000	0.000
133	F	186	GLU	-1	-0.755	-0.836	11.800	0.503	0.503	0.000	0.000	0.000	0.000
134	F	187	ARG	1	0.736	0.843	8.364	0.002	0.002	0.000	0.000	0.000	0.000
135	F	188	LEU	0	-0.032	-0.016	9.939	0.189	0.189	0.000	0.000	0.000	0.000
136	F	189	ARG	1	0.822	0.910	11.134	-0.604	-0.604	0.000	0.000	0.000	0.000
137	F	190	MET	0	0.023	0.005	10.782	0.209	0.209	0.000	0.000	0.000	0.000
138	F	191	SER	0	0.002	-0.005	8.397	0.020	0.020	0.000	0.000	0.000	0.000
139	F	192	ARG	1	0.895	0.944	5.304	-0.946	-0.946	0.000	0.000	0.000	0.000
140	F	193	GLN	0	0.049	0.027	6.482	0.429	0.429	0.000	0.000	0.000	0.000
141	F	194	LYS	1	0.952	0.968	8.793	-1.016	-1.016	0.000	0.000	0.000	0.000
142	F	195	GLN	0	-0.014	-0.009	2.605	-2.789	-1.415	2.678	-1.376	-2.675	-0.002
143	F	196	ARG	1	0.918	0.971	4.922	-1.601	-1.478	-0.001	-0.004	-0.118	0.000
144	F	197	HIS	0	-0.027	-0.019	6.136	-0.493	-0.493	0.000	0.000	0.000	0.000
145	F	198	ASP	-1	-0.885	-0.930	8.268	0.363	0.363	0.000	0.000	0.000	0.000
146	F	199	ALA	0	0.068	0.033	10.080	-0.091	-0.091	0.000	0.000	0.000	0.000
147	F	200	LEU	0	-0.023	-0.009	12.430	-0.050	-0.050	0.000	0.000	0.000	0.000
148	F	201	ILE	0	-0.013	-0.018	11.220	-0.027	-0.027	0.000	0.000	0.000	0.000
149	F	202	SER	0	0.023	0.003	13.303	-0.052	-0.052	0.000	0.000	0.000	0.000
150	F	203	LYS	1	0.834	0.908	15.976	-0.193	-0.193	0.000	0.000	0.000	0.000
151	F	204	LEU	0	-0.020	0.001	16.951	-0.028	-0.028	0.000	0.000	0.000	0.000
152	F	205	LEU	0	-0.016	0.000	17.049	-0.012	-0.012	0.000	0.000	0.000	0.000
153	F	206	ALA	0	-0.030	0.005	20.621	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:ALA)