FMO DATABASE

FMODB ID: ZVL3N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1387684.261574
FMO2-HF: Nuclear repulsion	1327387.794081
FMO2-HF: Total energy	-60296.467493
FMO2-MP2: Total energy	-60473.421097

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.
-3.039	0.413	4.108	-2.823	-4.737	-0.01

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 : -0.023 / q_NPA : -0.024

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	-0.012	0.008	3.827	0.036	1.472	-0.018	-0.647	-0.771	0.000
4	F	5	THR	0	-0.079	-0.055	6.332	-0.272	-0.272	0.000	0.000	0.000	0.000
5	F	6	LEU	0	0.031	0.020	9.785	0.087	0.087	0.000	0.000	0.000	0.000
6	F	7	TYR	0	0.015	-0.021	11.710	-0.013	-0.013	0.000	0.000	0.000	0.000
7	F	8	ILE	0	0.003	0.007	15.882	0.013	0.013	0.000	0.000	0.000	0.000
8	F	9	VAL	0	-0.002	0.004	19.382	0.003	0.003	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.015	0.019	21.831	-0.005	-0.005	0.000	0.000	0.000	0.000
10	F	11	ALA	0	-0.008	-0.015	25.561	0.004	0.004	0.000	0.000	0.000	0.000
11	F	12	PRO	0	-0.006	0.029	28.757	-0.001	-0.001	0.000	0.000	0.000	0.000
12	F	13	SER	0	-0.012	-0.017	31.822	0.005	0.005	0.000	0.000	0.000	0.000
13	F	14	GLY	0	0.065	0.021	33.520	-0.002	-0.002	0.000	0.000	0.000	0.000
14	F	15	ALA	0	0.005	0.001	29.911	0.000	0.000	0.000	0.000	0.000	0.000
15	F	16	GLY	0	0.043	0.020	29.793	0.003	0.003	0.000	0.000	0.000	0.000
16	F	17	LYS	1	0.865	0.936	24.847	-0.031	-0.031	0.000	0.000	0.000	0.000
17	F	18	SER	0	0.092	0.051	24.890	0.007	0.007	0.000	0.000	0.000	0.000
18	F	19	SER	0	-0.024	-0.034	25.342	0.010	0.010	0.000	0.000	0.000	0.000
19	F	20	LEU	0	0.040	0.022	23.783	0.009	0.009	0.000	0.000	0.000	0.000
20	F	21	ILE	0	0.008	0.010	19.651	0.014	0.014	0.000	0.000	0.000	0.000
21	F	22	GLN	0	-0.036	-0.016	21.010	0.028	0.028	0.000	0.000	0.000	0.000
22	F	23	ALA	0	-0.008	-0.005	22.397	0.017	0.017	0.000	0.000	0.000	0.000
23	F	24	LEU	0	-0.027	-0.011	16.900	0.010	0.010	0.000	0.000	0.000	0.000
24	F	25	LEU	0	0.009	-0.003	16.569	0.029	0.029	0.000	0.000	0.000	0.000
25	F	26	LYS	1	0.901	0.966	19.345	-0.109	-0.109	0.000	0.000	0.000	0.000
26	F	27	THR	0	-0.067	-0.027	20.235	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	28	GLN	0	0.031	-0.002	13.844	0.058	0.058	0.000	0.000	0.000	0.000
28	F	29	PRO	0	0.030	0.050	12.890	-0.042	-0.042	0.000	0.000	0.000	0.000
29	F	30	LEU	0	0.078	0.013	13.273	0.061	0.061	0.000	0.000	0.000	0.000
30	F	31	TYR	0	-0.044	-0.019	9.099	-0.098	-0.098	0.000	0.000	0.000	0.000
31	F	32	ASP	-1	-0.896	-0.926	8.234	1.459	1.459	0.000	0.000	0.000	0.000
32	F	33	THR	0	-0.055	-0.054	9.868	0.016	0.016	0.000	0.000	0.000	0.000
33	F	34	GLN	0	0.006	0.013	12.238	-0.121	-0.121	0.000	0.000	0.000	0.000
34	F	87	GLU	-1	-0.930	-0.965	15.892	-0.078	-0.078	0.000	0.000	0.000	0.000
35	F	88	ALA	0	0.036	0.001	14.415	-0.022	-0.022	0.000	0.000	0.000	0.000
36	F	89	ILE	0	-0.011	-0.012	13.459	0.025	0.025	0.000	0.000	0.000	0.000
37	F	90	GLU	-1	-0.905	-0.962	11.380	-0.270	-0.270	0.000	0.000	0.000	0.000
38	F	91	GLN	0	-0.013	-0.010	9.688	-0.104	-0.104	0.000	0.000	0.000	0.000
39	F	92	VAL	0	0.022	0.021	8.760	-0.042	-0.042	0.000	0.000	0.000	0.000
40	F	93	LEU	0	-0.029	-0.008	7.616	0.197	0.197	0.000	0.000	0.000	0.000
41	F	94	ALA	0	0.038	0.032	5.528	-0.474	-0.474	0.000	0.000	0.000	0.000
42	F	95	THR	0	-0.129	-0.069	4.000	-1.061	-0.837	0.001	-0.068	-0.157	0.000
43	F	96	GLY	0	0.003	0.009	3.371	1.165	1.788	0.139	-0.314	-0.448	0.002
44	F	97	VAL	0	-0.062	-0.011	4.108	-0.409	-0.168	0.004	-0.010	-0.236	0.000
45	F	98	ASP	-1	-0.795	-0.902	7.758	0.147	0.147	0.000	0.000	0.000	0.000
46	F	99	VAL	0	0.018	0.003	10.060	0.004	0.004	0.000	0.000	0.000	0.000
47	F	100	PHE	0	-0.017	-0.019	13.278	-0.042	-0.042	0.000	0.000	0.000	0.000
48	F	101	LEU	0	-0.002	-0.001	16.730	-0.003	-0.003	0.000	0.000	0.000	0.000
49	F	102	ASP	-1	-0.876	-0.924	19.333	0.041	0.041	0.000	0.000	0.000	0.000
50	F	103	ILE	0	-0.010	-0.001	22.604	-0.007	-0.007	0.000	0.000	0.000	0.000
51	F	104	ASP	-1	-0.843	-0.927	25.261	0.000	0.000	0.000	0.000	0.000	0.000
52	F	105	TRP	0	0.020	-0.020	26.940	-0.006	-0.006	0.000	0.000	0.000	0.000
53	F	106	GLN	0	-0.034	0.003	28.086	-0.009	-0.009	0.000	0.000	0.000	0.000
54	F	107	GLY	0	0.036	0.013	25.671	-0.006	-0.006	0.000	0.000	0.000	0.000
55	F	108	ALA	0	0.009	0.001	23.336	-0.010	-0.010	0.000	0.000	0.000	0.000
56	F	109	GLN	0	0.014	0.005	23.343	-0.009	-0.009	0.000	0.000	0.000	0.000
57	F	110	GLN	0	-0.023	-0.006	24.925	-0.012	-0.012	0.000	0.000	0.000	0.000
58	F	111	ILE	0	-0.032	-0.023	18.737	-0.013	-0.013	0.000	0.000	0.000	0.000
59	F	112	ARG	1	0.947	0.959	19.811	0.016	0.016	0.000	0.000	0.000	0.000
60	F	113	GLN	0	-0.042	0.006	20.888	-0.008	-0.008	0.000	0.000	0.000	0.000
61	F	114	LYS	1	0.913	0.951	19.762	0.072	0.072	0.000	0.000	0.000	0.000
62	F	115	MET	0	-0.010	-0.003	14.225	-0.036	-0.036	0.000	0.000	0.000	0.000
63	F	116	PRO	0	0.042	0.033	16.171	0.012	0.012	0.000	0.000	0.000	0.000
64	F	117	HIS	0	-0.050	-0.031	10.778	-0.016	-0.016	0.000	0.000	0.000	0.000
65	F	118	ALA	0	-0.045	-0.009	13.814	0.004	0.004	0.000	0.000	0.000	0.000
66	F	119	ARG	1	0.891	0.971	14.076	0.039	0.039	0.000	0.000	0.000	0.000
67	F	120	SER	0	-0.036	-0.024	16.714	0.015	0.015	0.000	0.000	0.000	0.000
68	F	121	ILE	0	-0.021	-0.016	17.771	0.002	0.002	0.000	0.000	0.000	0.000
69	F	122	PHE	0	0.038	0.013	21.742	0.001	0.001	0.000	0.000	0.000	0.000
70	F	123	ILE	0	-0.010	-0.008	23.753	0.003	0.003	0.000	0.000	0.000	0.000
71	F	124	LEU	0	0.007	-0.018	27.503	-0.004	-0.004	0.000	0.000	0.000	0.000
72	F	125	PRO	0	-0.019	-0.002	31.230	0.004	0.004	0.000	0.000	0.000	0.000
73	F	126	PRO	0	0.030	0.022	34.234	-0.002	-0.002	0.000	0.000	0.000	0.000
74	F	127	SER	0	0.026	0.006	35.848	-0.002	-0.002	0.000	0.000	0.000	0.000
75	F	128	LYS	1	0.978	0.981	38.971	-0.010	-0.010	0.000	0.000	0.000	0.000
76	F	129	ILE	0	0.051	0.023	41.181	0.000	0.000	0.000	0.000	0.000	0.000
77	F	130	GLU	-1	-0.736	-0.833	37.782	0.034	0.034	0.000	0.000	0.000	0.000
78	F	131	LEU	0	-0.024	-0.009	36.070	0.001	0.001	0.000	0.000	0.000	0.000
79	F	132	ASP	-1	-0.903	-0.963	38.865	0.019	0.019	0.000	0.000	0.000	0.000
80	F	133	ARG	1	0.888	0.919	39.310	-0.033	-0.033	0.000	0.000	0.000	0.000
81	F	134	ARG	1	0.790	0.890	33.210	-0.040	-0.040	0.000	0.000	0.000	0.000
82	F	135	LEU	0	-0.038	-0.020	37.608	0.001	0.001	0.000	0.000	0.000	0.000
83	F	136	ARG	1	0.851	0.946	39.794	-0.018	-0.018	0.000	0.000	0.000	0.000
84	F	137	GLY	0	0.011	0.021	40.467	0.000	0.000	0.000	0.000	0.000	0.000
85	F	138	ARG	1	0.889	0.943	41.381	-0.031	-0.031	0.000	0.000	0.000	0.000
86	F	139	GLY	0	0.025	0.015	44.204	0.000	0.000	0.000	0.000	0.000	0.000
87	F	140	GLN	0	-0.076	-0.041	46.651	0.000	0.000	0.000	0.000	0.000	0.000
88	F	141	ASP	-1	-0.854	-0.938	44.875	0.021	0.021	0.000	0.000	0.000	0.000
89	F	142	SER	0	0.003	0.011	48.198	0.000	0.000	0.000	0.000	0.000	0.000
90	F	143	GLU	-1	-0.828	-0.936	48.729	0.014	0.014	0.000	0.000	0.000	0.000
91	F	144	GLU	-1	-0.897	-0.953	49.164	0.009	0.009	0.000	0.000	0.000	0.000
92	F	145	VAL	0	-0.074	-0.038	44.539	-0.001	-0.001	0.000	0.000	0.000	0.000
93	F	146	ILE	0	-0.012	0.000	44.129	0.001	0.001	0.000	0.000	0.000	0.000
94	F	147	ALA	0	0.054	0.030	43.734	0.000	0.000	0.000	0.000	0.000	0.000
95	F	148	LYS	1	0.974	0.991	42.978	-0.007	-0.007	0.000	0.000	0.000	0.000
96	F	149	ARG	1	0.928	0.969	39.561	-0.021	-0.021	0.000	0.000	0.000	0.000
97	F	150	MET	0	-0.010	-0.006	39.496	0.000	0.000	0.000	0.000	0.000	0.000
98	F	151	ALA	0	-0.027	-0.014	40.477	0.000	0.000	0.000	0.000	0.000	0.000
99	F	152	GLN	0	0.008	0.002	36.110	0.000	0.000	0.000	0.000	0.000	0.000
100	F	153	ALA	0	0.019	0.011	35.719	0.000	0.000	0.000	0.000	0.000	0.000
101	F	154	VAL	0	-0.015	-0.014	35.709	0.000	0.000	0.000	0.000	0.000	0.000
102	F	155	ALA	0	0.004	0.007	37.083	-0.001	-0.001	0.000	0.000	0.000	0.000
103	F	156	GLU	-1	-0.874	-0.931	30.289	0.003	0.003	0.000	0.000	0.000	0.000
104	F	157	MET	0	-0.046	-0.042	32.488	-0.001	-0.001	0.000	0.000	0.000	0.000
105	F	158	SER	0	-0.015	-0.005	33.136	-0.001	-0.001	0.000	0.000	0.000	0.000
106	F	159	HIS	1	0.849	0.933	30.262	0.009	0.009	0.000	0.000	0.000	0.000
107	F	160	TYR	0	-0.001	0.006	28.940	-0.003	-0.003	0.000	0.000	0.000	0.000
108	F	161	ALA	0	0.002	-0.001	28.072	0.000	0.000	0.000	0.000	0.000	0.000
109	F	162	GLU	-1	-0.903	-0.947	27.095	-0.023	-0.023	0.000	0.000	0.000	0.000
110	F	163	TYR	0	-0.098	-0.077	23.259	-0.008	-0.008	0.000	0.000	0.000	0.000
111	F	164	ASP	-1	-0.837	-0.889	19.545	-0.037	-0.037	0.000	0.000	0.000	0.000
112	F	165	TYR	0	-0.090	-0.069	16.459	0.004	0.004	0.000	0.000	0.000	0.000
113	F	166	LEU	0	-0.002	-0.011	22.754	-0.002	-0.002	0.000	0.000	0.000	0.000
114	F	167	ILE	0	0.002	0.011	22.226	0.003	0.003	0.000	0.000	0.000	0.000
115	F	168	VAL	0	0.016	0.009	26.552	-0.004	-0.004	0.000	0.000	0.000	0.000
116	F	169	ASN	0	-0.042	-0.040	29.064	0.004	0.004	0.000	0.000	0.000	0.000
117	F	170	ASP	-1	-0.919	-0.962	30.557	0.036	0.036	0.000	0.000	0.000	0.000
118	F	171	ASP	-1	-0.831	-0.919	32.155	0.062	0.062	0.000	0.000	0.000	0.000
119	F	172	PHE	0	-0.008	-0.023	27.401	0.004	0.004	0.000	0.000	0.000	0.000
120	F	173	ASP	-1	-0.891	-0.949	28.195	0.095	0.095	0.000	0.000	0.000	0.000
121	F	174	THR	0	-0.017	-0.001	26.980	0.008	0.008	0.000	0.000	0.000	0.000
122	F	175	ALA	0	0.041	0.024	26.284	0.005	0.005	0.000	0.000	0.000	0.000
123	F	176	LEU	0	-0.028	-0.018	22.409	0.008	0.008	0.000	0.000	0.000	0.000
124	F	177	THR	0	-0.026	-0.016	22.263	0.020	0.020	0.000	0.000	0.000	0.000
125	F	178	ASP	-1	-0.875	-0.931	21.676	0.081	0.081	0.000	0.000	0.000	0.000
126	F	179	LEU	0	-0.016	-0.011	19.211	0.003	0.003	0.000	0.000	0.000	0.000
127	F	180	LYS	1	0.935	0.963	17.742	-0.154	-0.154	0.000	0.000	0.000	0.000
128	F	181	THR	0	-0.033	-0.016	16.964	0.023	0.023	0.000	0.000	0.000	0.000
129	F	182	ILE	0	-0.011	-0.002	16.218	0.005	0.005	0.000	0.000	0.000	0.000
130	F	183	ILE	0	0.003	0.019	12.462	-0.003	-0.003	0.000	0.000	0.000	0.000
131	F	184	ARG	1	0.941	0.959	12.541	-0.166	-0.166	0.000	0.000	0.000	0.000
132	F	185	ALA	0	0.010	-0.006	13.240	0.004	0.004	0.000	0.000	0.000	0.000
133	F	186	GLU	-1	-0.826	-0.910	11.356	-0.023	-0.023	0.000	0.000	0.000	0.000
134	F	187	ARG	1	0.804	0.909	8.244	-0.636	-0.636	0.000	0.000	0.000	0.000
135	F	188	LEU	0	-0.047	-0.024	9.537	0.005	0.005	0.000	0.000	0.000	0.000
136	F	189	ARG	1	0.931	0.983	10.505	-0.009	-0.009	0.000	0.000	0.000	0.000
137	F	190	MET	0	0.015	0.001	10.369	0.004	0.004	0.000	0.000	0.000	0.000
138	F	191	SER	0	-0.005	-0.017	8.101	0.021	0.021	0.000	0.000	0.000	0.000
139	F	192	ARG	1	0.962	0.985	4.524	-0.516	-0.420	-0.001	-0.007	-0.087	0.000
140	F	193	GLN	0	0.012	0.015	6.009	0.109	0.109	0.000	0.000	0.000	0.000
141	F	194	LYS	1	0.955	0.973	8.406	0.180	0.180	0.000	0.000	0.000	0.000
142	F	195	GLN	0	0.016	0.018	2.596	-1.685	-0.853	3.983	-1.777	-3.038	-0.012
143	F	196	ARG	1	0.951	0.974	5.702	-0.541	-0.541	0.000	0.000	0.000	0.000
144	F	197	HIS	0	-0.042	-0.019	6.433	0.045	0.045	0.000	0.000	0.000	0.000
145	F	198	ASP	-1	-0.899	-0.927	7.972	-0.156	-0.156	0.000	0.000	0.000	0.000
146	F	199	ALA	0	0.059	0.014	10.014	0.007	0.007	0.000	0.000	0.000	0.000
147	F	200	LEU	0	-0.032	-0.023	12.596	-0.002	-0.002	0.000	0.000	0.000	0.000
148	F	201	ILE	0	0.019	-0.010	11.828	-0.005	-0.005	0.000	0.000	0.000	0.000
149	F	202	SER	0	0.017	0.019	13.563	-0.009	-0.009	0.000	0.000	0.000	0.000
150	F	203	LYS	1	0.868	0.929	16.135	-0.016	-0.016	0.000	0.000	0.000	0.000
151	F	204	LEU	0	-0.044	-0.018	17.536	0.002	0.002	0.000	0.000	0.000	0.000
152	F	205	LEU	0	-0.007	0.005	17.096	-0.001	-0.001	0.000	0.000	0.000	0.000
153	F	206	ALA	0	-0.038	0.009	20.789	-0.001	-0.001	0.000	0.000	0.000	0.000

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