FMO DATABASE

FMODB ID: R8MR8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1388354.48721
FMO2-HF: Nuclear repulsion	1328057.102202
FMO2-HF: Total energy	-60297.385008
FMO2-MP2: Total energy	-60474.233249

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.
-7.375	-3.54	2.658	-2.449	-4.041	-0.008

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 : -0.008 / q_NPA : -0.022

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	-0.019	0.010	3.827	1.021	2.394	-0.019	-0.624	-0.729	0.000
4	F	5	THR	0	-0.080	-0.058	6.228	0.174	0.174	0.000	0.000	0.000	0.000
5	F	6	LEU	0	0.040	0.023	9.911	-0.082	-0.082	0.000	0.000	0.000	0.000
6	F	7	TYR	0	0.018	-0.012	11.423	0.093	0.093	0.000	0.000	0.000	0.000
7	F	8	ILE	0	0.004	0.007	15.823	-0.031	-0.031	0.000	0.000	0.000	0.000
8	F	9	VAL	0	-0.010	-0.002	19.119	0.028	0.028	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.012	-0.001	21.676	-0.013	-0.013	0.000	0.000	0.000	0.000
10	F	11	ALA	0	-0.001	-0.007	25.432	0.011	0.011	0.000	0.000	0.000	0.000
11	F	12	PRO	0	-0.013	0.022	28.617	-0.008	-0.008	0.000	0.000	0.000	0.000
12	F	13	SER	0	-0.012	-0.017	31.562	0.000	0.000	0.000	0.000	0.000	0.000
13	F	14	GLY	0	0.059	0.018	33.116	0.003	0.003	0.000	0.000	0.000	0.000
14	F	15	ALA	0	0.001	0.003	30.056	0.004	0.004	0.000	0.000	0.000	0.000
15	F	16	GLY	0	0.047	0.023	29.420	0.006	0.006	0.000	0.000	0.000	0.000
16	F	17	LYS	1	0.837	0.917	24.494	0.031	0.031	0.000	0.000	0.000	0.000
17	F	18	SER	0	0.074	0.045	24.436	0.001	0.001	0.000	0.000	0.000	0.000
18	F	19	SER	0	-0.009	-0.027	24.699	-0.004	-0.004	0.000	0.000	0.000	0.000
19	F	20	LEU	0	0.027	0.018	23.648	-0.001	-0.001	0.000	0.000	0.000	0.000
20	F	21	ILE	0	0.014	0.010	19.149	0.005	0.005	0.000	0.000	0.000	0.000
21	F	22	GLN	0	-0.037	-0.020	20.315	-0.010	-0.010	0.000	0.000	0.000	0.000
22	F	23	ALA	0	0.006	0.002	21.604	-0.005	-0.005	0.000	0.000	0.000	0.000
23	F	24	LEU	0	-0.026	-0.009	16.501	0.008	0.008	0.000	0.000	0.000	0.000
24	F	25	LEU	0	0.000	-0.003	15.964	0.003	0.003	0.000	0.000	0.000	0.000
25	F	26	LYS	1	0.904	0.964	18.487	0.035	0.035	0.000	0.000	0.000	0.000
26	F	27	THR	0	-0.053	-0.020	19.452	0.007	0.007	0.000	0.000	0.000	0.000
27	F	28	GLN	0	0.016	0.010	13.143	0.049	0.049	0.000	0.000	0.000	0.000
28	F	29	PRO	0	0.027	0.045	12.021	-0.025	-0.025	0.000	0.000	0.000	0.000
29	F	30	LEU	0	0.103	0.028	12.286	-0.004	-0.004	0.000	0.000	0.000	0.000
30	F	31	TYR	0	-0.031	-0.007	8.244	-0.083	-0.083	0.000	0.000	0.000	0.000
31	F	32	ASP	-1	-0.845	-0.897	7.250	0.057	0.057	0.000	0.000	0.000	0.000
32	F	33	THR	0	-0.054	-0.060	9.074	0.050	0.050	0.000	0.000	0.000	0.000
33	F	34	GLN	0	-0.004	0.007	11.102	0.021	0.021	0.000	0.000	0.000	0.000
34	F	87	GLU	-1	-0.944	-0.976	15.907	-0.340	-0.340	0.000	0.000	0.000	0.000
35	F	88	ALA	0	0.008	-0.011	14.419	-0.078	-0.078	0.000	0.000	0.000	0.000
36	F	89	ILE	0	-0.010	-0.012	13.692	-0.049	-0.049	0.000	0.000	0.000	0.000
37	F	90	GLU	-1	-0.860	-0.940	11.389	-0.494	-0.494	0.000	0.000	0.000	0.000
38	F	91	GLN	0	-0.017	-0.009	9.694	-0.223	-0.223	0.000	0.000	0.000	0.000
39	F	92	VAL	0	0.030	0.021	8.758	-0.277	-0.277	0.000	0.000	0.000	0.000
40	F	93	LEU	0	-0.027	0.006	7.539	-0.362	-0.362	0.000	0.000	0.000	0.000
41	F	94	ALA	0	0.034	0.026	5.537	-0.723	-0.723	0.000	0.000	0.000	0.000
42	F	95	THR	0	-0.113	-0.068	4.006	-1.190	-0.956	0.001	-0.070	-0.164	0.000
43	F	96	GLY	0	-0.022	-0.003	2.410	-1.341	-0.772	0.457	-0.478	-0.548	-0.001
44	F	97	VAL	0	-0.056	-0.011	3.240	1.698	1.854	0.008	0.126	-0.290	-0.001
45	F	98	ASP	-1	-0.767	-0.861	6.833	0.506	0.506	0.000	0.000	0.000	0.000
46	F	99	VAL	0	0.022	0.006	9.542	-0.022	-0.022	0.000	0.000	0.000	0.000
47	F	100	PHE	0	0.002	-0.010	12.659	0.077	0.077	0.000	0.000	0.000	0.000
48	F	101	LEU	0	-0.003	-0.003	16.208	-0.022	-0.022	0.000	0.000	0.000	0.000
49	F	102	ASP	-1	-0.860	-0.911	18.850	-0.023	-0.023	0.000	0.000	0.000	0.000
50	F	103	ILE	0	0.001	0.004	22.230	-0.011	-0.011	0.000	0.000	0.000	0.000
51	F	104	ASP	-1	-0.804	-0.894	24.884	-0.031	-0.031	0.000	0.000	0.000	0.000
52	F	105	TRP	0	0.027	-0.013	26.774	-0.004	-0.004	0.000	0.000	0.000	0.000
53	F	106	GLN	0	-0.072	-0.025	28.101	0.001	0.001	0.000	0.000	0.000	0.000
54	F	107	GLY	0	0.031	0.008	25.598	-0.002	-0.002	0.000	0.000	0.000	0.000
55	F	108	ALA	0	0.002	-0.002	23.293	-0.007	-0.007	0.000	0.000	0.000	0.000
56	F	109	GLN	0	-0.014	-0.017	23.343	-0.004	-0.004	0.000	0.000	0.000	0.000
57	F	110	GLN	0	-0.014	-0.010	24.945	-0.009	-0.009	0.000	0.000	0.000	0.000
58	F	111	ILE	0	-0.035	-0.026	18.773	-0.012	-0.012	0.000	0.000	0.000	0.000
59	F	112	ARG	1	0.902	0.946	19.863	-0.036	-0.036	0.000	0.000	0.000	0.000
60	F	113	GLN	0	-0.044	0.001	20.955	0.015	0.015	0.000	0.000	0.000	0.000
61	F	114	LYS	1	0.895	0.952	19.839	0.109	0.109	0.000	0.000	0.000	0.000
62	F	115	MET	0	-0.003	-0.005	14.524	-0.031	-0.031	0.000	0.000	0.000	0.000
63	F	116	PRO	0	0.041	0.031	16.466	0.024	0.024	0.000	0.000	0.000	0.000
64	F	117	HIS	0	-0.063	-0.034	11.013	0.054	0.054	0.000	0.000	0.000	0.000
65	F	118	ALA	0	-0.037	-0.004	13.882	0.048	0.048	0.000	0.000	0.000	0.000
66	F	119	ARG	1	0.800	0.901	14.633	-0.220	-0.220	0.000	0.000	0.000	0.000
67	F	120	SER	0	-0.016	-0.030	17.117	-0.038	-0.038	0.000	0.000	0.000	0.000
68	F	121	ILE	0	-0.022	-0.013	17.874	0.020	0.020	0.000	0.000	0.000	0.000
69	F	122	PHE	0	0.041	0.014	21.916	-0.019	-0.019	0.000	0.000	0.000	0.000
70	F	123	ILE	0	-0.017	-0.010	23.629	0.008	0.008	0.000	0.000	0.000	0.000
71	F	124	LEU	0	0.022	-0.005	27.511	-0.009	-0.009	0.000	0.000	0.000	0.000
72	F	125	PRO	0	-0.027	-0.007	31.273	0.002	0.002	0.000	0.000	0.000	0.000
73	F	126	PRO	0	0.021	0.018	34.201	0.002	0.002	0.000	0.000	0.000	0.000
74	F	127	SER	0	0.026	0.007	35.915	0.000	0.000	0.000	0.000	0.000	0.000
75	F	128	LYS	1	0.976	0.978	38.960	-0.014	-0.014	0.000	0.000	0.000	0.000
76	F	129	ILE	0	0.048	0.022	41.191	-0.003	-0.003	0.000	0.000	0.000	0.000
77	F	130	GLU	-1	-0.723	-0.816	37.620	0.014	0.014	0.000	0.000	0.000	0.000
78	F	131	LEU	0	-0.016	-0.001	35.992	-0.002	-0.002	0.000	0.000	0.000	0.000
79	F	132	ASP	-1	-0.863	-0.927	38.702	0.001	0.001	0.000	0.000	0.000	0.000
80	F	133	ARG	1	0.891	0.911	39.160	-0.014	-0.014	0.000	0.000	0.000	0.000
81	F	134	ARG	1	0.767	0.864	33.281	-0.023	-0.023	0.000	0.000	0.000	0.000
82	F	135	LEU	0	-0.020	-0.006	37.182	-0.004	-0.004	0.000	0.000	0.000	0.000
83	F	136	ARG	1	0.740	0.833	39.410	-0.004	-0.004	0.000	0.000	0.000	0.000
84	F	137	GLY	0	0.003	0.017	39.931	-0.002	-0.002	0.000	0.000	0.000	0.000
85	F	138	ARG	1	0.904	0.948	40.840	0.013	0.013	0.000	0.000	0.000	0.000
86	F	139	GLY	0	0.024	0.014	43.586	0.001	0.001	0.000	0.000	0.000	0.000
87	F	140	GLN	0	-0.085	-0.045	46.054	0.001	0.001	0.000	0.000	0.000	0.000
88	F	141	ASP	-1	-0.778	-0.885	43.971	-0.017	-0.017	0.000	0.000	0.000	0.000
89	F	142	SER	0	-0.006	0.017	47.629	0.001	0.001	0.000	0.000	0.000	0.000
90	F	143	GLU	-1	-0.739	-0.853	48.265	-0.002	-0.002	0.000	0.000	0.000	0.000
91	F	144	GLU	-1	-0.883	-0.952	48.821	-0.007	-0.007	0.000	0.000	0.000	0.000
92	F	145	VAL	0	-0.067	-0.037	44.124	-0.001	-0.001	0.000	0.000	0.000	0.000
93	F	146	ILE	0	0.002	0.014	43.858	-0.001	-0.001	0.000	0.000	0.000	0.000
94	F	147	ALA	0	0.042	0.024	43.416	0.001	0.001	0.000	0.000	0.000	0.000
95	F	148	LYS	1	0.978	0.991	42.574	0.021	0.021	0.000	0.000	0.000	0.000
96	F	149	ARG	1	0.808	0.881	38.973	0.013	0.013	0.000	0.000	0.000	0.000
97	F	150	MET	0	-0.011	-0.005	39.223	0.002	0.002	0.000	0.000	0.000	0.000
98	F	151	ALA	0	-0.031	-0.016	40.342	0.002	0.002	0.000	0.000	0.000	0.000
99	F	152	GLN	0	0.003	-0.001	35.595	0.002	0.002	0.000	0.000	0.000	0.000
100	F	153	ALA	0	0.020	0.014	35.547	0.000	0.000	0.000	0.000	0.000	0.000
101	F	154	VAL	0	-0.010	-0.015	35.647	0.003	0.003	0.000	0.000	0.000	0.000
102	F	155	ALA	0	-0.002	0.005	37.141	0.003	0.003	0.000	0.000	0.000	0.000
103	F	156	GLU	-1	-0.851	-0.923	29.922	-0.011	-0.011	0.000	0.000	0.000	0.000
104	F	157	MET	0	-0.040	-0.035	32.551	0.004	0.004	0.000	0.000	0.000	0.000
105	F	158	SER	0	-0.022	-0.008	33.332	0.006	0.006	0.000	0.000	0.000	0.000
106	F	159	HIS	1	0.834	0.920	30.329	-0.001	-0.001	0.000	0.000	0.000	0.000
107	F	160	TYR	0	0.001	0.005	29.185	0.004	0.004	0.000	0.000	0.000	0.000
108	F	161	ALA	0	0.002	-0.001	28.449	0.007	0.007	0.000	0.000	0.000	0.000
109	F	162	GLU	-1	-0.857	-0.903	27.260	0.019	0.019	0.000	0.000	0.000	0.000
110	F	163	TYR	0	-0.053	-0.051	23.487	-0.002	-0.002	0.000	0.000	0.000	0.000
111	F	164	ASP	-1	-0.798	-0.840	19.901	0.140	0.140	0.000	0.000	0.000	0.000
112	F	165	TYR	0	-0.070	-0.064	17.478	0.012	0.012	0.000	0.000	0.000	0.000
113	F	166	LEU	0	-0.007	-0.010	23.215	-0.017	-0.017	0.000	0.000	0.000	0.000
114	F	167	ILE	0	0.002	0.011	22.275	0.007	0.007	0.000	0.000	0.000	0.000
115	F	168	VAL	0	0.016	0.009	26.746	-0.011	-0.011	0.000	0.000	0.000	0.000
116	F	169	ASN	0	-0.021	-0.035	28.893	0.007	0.007	0.000	0.000	0.000	0.000
117	F	170	ASP	-1	-0.906	-0.947	30.521	0.033	0.033	0.000	0.000	0.000	0.000
118	F	171	ASP	-1	-0.784	-0.869	31.593	0.043	0.043	0.000	0.000	0.000	0.000
119	F	172	PHE	0	-0.016	-0.019	26.821	0.003	0.003	0.000	0.000	0.000	0.000
120	F	173	ASP	-1	-0.884	-0.949	27.966	0.045	0.045	0.000	0.000	0.000	0.000
121	F	174	THR	0	-0.037	-0.040	26.840	0.010	0.010	0.000	0.000	0.000	0.000
122	F	175	ALA	0	0.014	0.014	26.317	0.011	0.011	0.000	0.000	0.000	0.000
123	F	176	LEU	0	-0.032	-0.020	22.065	0.006	0.006	0.000	0.000	0.000	0.000
124	F	177	THR	0	-0.024	-0.016	22.120	0.013	0.013	0.000	0.000	0.000	0.000
125	F	178	ASP	-1	-0.867	-0.914	21.771	0.133	0.133	0.000	0.000	0.000	0.000
126	F	179	LEU	0	-0.031	-0.019	19.079	0.023	0.023	0.000	0.000	0.000	0.000
127	F	180	LYS	1	0.918	0.955	17.662	-0.047	-0.047	0.000	0.000	0.000	0.000
128	F	181	THR	0	-0.042	-0.032	17.096	0.051	0.051	0.000	0.000	0.000	0.000
129	F	182	ILE	0	-0.006	0.002	16.606	0.053	0.053	0.000	0.000	0.000	0.000
130	F	183	ILE	0	0.004	0.013	12.323	0.067	0.067	0.000	0.000	0.000	0.000
131	F	184	ARG	1	0.955	0.969	12.883	-0.194	-0.194	0.000	0.000	0.000	0.000
132	F	185	ALA	0	0.005	-0.008	13.836	0.104	0.104	0.000	0.000	0.000	0.000
133	F	186	GLU	-1	-0.747	-0.849	12.152	0.509	0.509	0.000	0.000	0.000	0.000
134	F	187	ARG	1	0.749	0.861	8.689	-0.186	-0.186	0.000	0.000	0.000	0.000
135	F	188	LEU	0	-0.044	-0.022	10.443	0.193	0.193	0.000	0.000	0.000	0.000
136	F	189	ARG	1	0.851	0.926	11.055	-0.580	-0.580	0.000	0.000	0.000	0.000
137	F	190	MET	0	0.013	-0.002	10.865	0.176	0.176	0.000	0.000	0.000	0.000
138	F	191	SER	0	-0.005	-0.015	8.028	0.079	0.079	0.000	0.000	0.000	0.000
139	F	192	ARG	1	0.928	0.946	5.889	-1.215	-1.215	0.000	0.000	0.000	0.000
140	F	193	GLN	0	0.026	0.026	6.775	0.726	0.726	0.000	0.000	0.000	0.000
141	F	194	LYS	1	0.966	0.978	8.456	-0.942	-0.942	0.000	0.000	0.000	0.000
142	F	195	GLN	0	0.009	0.013	2.487	-2.582	-1.079	2.211	-1.403	-2.310	-0.006
143	F	196	ARG	1	0.932	0.964	5.731	-1.659	-1.659	0.000	0.000	0.000	0.000
144	F	197	HIS	0	-0.052	-0.026	6.490	-0.535	-0.535	0.000	0.000	0.000	0.000
145	F	198	ASP	-1	-0.894	-0.929	7.935	0.395	0.395	0.000	0.000	0.000	0.000
146	F	199	ALA	0	0.053	0.015	9.944	-0.124	-0.124	0.000	0.000	0.000	0.000
147	F	200	LEU	0	-0.032	-0.024	12.626	-0.060	-0.060	0.000	0.000	0.000	0.000
148	F	201	ILE	0	0.014	-0.010	11.646	-0.053	-0.053	0.000	0.000	0.000	0.000
149	F	202	SER	0	0.024	0.023	13.494	-0.059	-0.059	0.000	0.000	0.000	0.000
150	F	203	LYS	1	0.854	0.926	16.076	-0.224	-0.224	0.000	0.000	0.000	0.000
151	F	204	LEU	0	-0.034	-0.017	17.438	-0.029	-0.029	0.000	0.000	0.000	0.000
152	F	205	LEU	0	-0.003	0.007	17.085	-0.016	-0.016	0.000	0.000	0.000	0.000
153	F	206	ALA	0	-0.037	0.009	20.740	-0.019	-0.019	0.000	0.000	0.000	0.000

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