FMO DATABASE

FMODB ID: R86V8

Calculation Name: 1F46-A-Xray372

Preferred Name: Cell division protein zipA

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1F46

Chain ID: A

ChEMBL ID: CHEMBL3954

UniProt ID: P77173

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1246180.56555
FMO2-HF: Nuclear repulsion	1190734.594812
FMO2-HF: Total energy	-55445.970739
FMO2-MP2: Total energy	-55604.160279

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:6:ARG)

Summations of interaction energy for fragment #1(A:6:ARG)

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.
-223.047	-217.192	26.202	-14.955	-17.099	-0.156

Interaction energy analysis for fragmet #1(A:6:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.906

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	A	8	GLU	-1	-0.887	-0.937	3.050	-32.942	-30.396	0.023	-1.172	-1.396	0.002
4	A	9	ALA	0	0.020	0.011	2.560	-13.428	-10.904	1.011	-1.469	-2.067	-0.021
5	A	10	VAL	0	0.015	0.017	4.779	4.679	4.731	-0.001	-0.014	-0.037	0.000
6	A	11	ILE	0	-0.028	-0.008	6.807	-2.051	-2.051	0.000	0.000	0.000	0.000
7	A	12	ILE	0	0.015	-0.003	9.033	2.677	2.677	0.000	0.000	0.000	0.000
8	A	13	MET	0	-0.031	0.007	11.842	-0.834	-0.834	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.011	-0.013	14.951	1.147	1.147	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.024	0.031	18.440	-0.092	-0.092	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.007	0.002	22.164	0.159	0.159	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.065	0.038	24.229	0.223	0.223	0.000	0.000	0.000	0.000
13	A	18	HIS	0	-0.031	-0.007	26.166	-0.592	-0.592	0.000	0.000	0.000	0.000
14	A	19	HIS	0	0.002	-0.005	26.203	0.074	0.074	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.011	-0.003	27.947	0.289	0.289	0.000	0.000	0.000	0.000
16	A	21	SER	0	-0.081	-0.045	30.310	0.398	0.398	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.857	-0.935	29.935	-10.561	-10.561	0.000	0.000	0.000	0.000
18	A	23	LEU	0	-0.011	0.007	26.656	0.254	0.254	0.000	0.000	0.000	0.000
19	A	24	ASN	0	0.043	0.011	31.126	0.060	0.060	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.068	0.020	31.796	-0.220	-0.220	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.790	-0.892	32.416	-8.369	-8.369	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.026	0.001	33.019	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	28	LEU	0	0.021	0.010	26.367	-0.218	-0.218	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.017	0.000	29.629	-0.291	-0.291	0.000	0.000	0.000	0.000
25	A	30	ASN	0	-0.041	-0.025	31.064	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	31	SER	0	0.048	0.026	29.019	-0.200	-0.200	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.050	-0.027	25.664	-0.368	-0.368	0.000	0.000	0.000	0.000
28	A	33	GLN	0	0.063	0.037	27.677	-0.471	-0.471	0.000	0.000	0.000	0.000
29	A	34	GLN	0	-0.066	-0.019	30.432	0.157	0.157	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.028	-0.011	25.122	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	36	GLY	0	-0.024	-0.006	26.066	-0.415	-0.415	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.072	-0.049	20.717	-0.410	-0.410	0.000	0.000	0.000	0.000
33	A	38	ILE	0	0.017	0.009	26.011	0.474	0.474	0.000	0.000	0.000	0.000
34	A	39	PHE	0	0.000	-0.001	26.225	-0.503	-0.503	0.000	0.000	0.000	0.000
35	A	40	GLY	0	0.042	0.007	26.787	0.313	0.313	0.000	0.000	0.000	0.000
36	A	41	ASP	-1	-0.912	-0.951	23.364	-11.857	-11.857	0.000	0.000	0.000	0.000
37	A	42	MET	0	-0.039	-0.037	21.835	-0.263	-0.263	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.004	0.011	24.808	0.047	0.047	0.000	0.000	0.000	0.000
39	A	44	ILE	0	-0.007	0.001	20.417	-0.065	-0.065	0.000	0.000	0.000	0.000
40	A	45	TYR	0	-0.001	-0.016	23.496	0.237	0.237	0.000	0.000	0.000	0.000
41	A	46	HIS	1	0.847	0.912	20.576	12.545	12.545	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.874	0.956	21.086	12.948	12.948	0.000	0.000	0.000	0.000
43	A	48	HIS	0	0.028	0.005	21.697	-0.752	-0.752	0.000	0.000	0.000	0.000
44	A	49	LEU	0	-0.002	-0.006	23.071	0.034	0.034	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.043	-0.040	24.710	0.031	0.031	0.000	0.000	0.000	0.000
46	A	51	PRO	0	0.004	-0.009	28.486	-0.129	-0.129	0.000	0.000	0.000	0.000
47	A	52	ASP	-1	-0.817	-0.867	30.791	-9.857	-9.857	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.005	0.005	27.919	0.107	0.107	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.058	-0.028	27.445	-0.267	-0.267	0.000	0.000	0.000	0.000
50	A	55	GLY	0	0.005	-0.005	25.015	-0.297	-0.297	0.000	0.000	0.000	0.000
51	A	56	PRO	0	-0.025	-0.016	19.304	0.000	0.000	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.030	0.016	19.620	0.131	0.131	0.000	0.000	0.000	0.000
53	A	58	LEU	0	-0.066	-0.031	17.969	-0.859	-0.859	0.000	0.000	0.000	0.000
54	A	59	PHE	0	0.013	-0.004	16.070	-1.237	-1.237	0.000	0.000	0.000	0.000
55	A	60	SER	0	-0.025	0.005	16.982	1.377	1.377	0.000	0.000	0.000	0.000
56	A	61	LEU	0	0.003	0.005	18.068	-0.887	-0.887	0.000	0.000	0.000	0.000
57	A	62	ALA	0	0.029	0.015	19.584	0.589	0.589	0.000	0.000	0.000	0.000
58	A	63	ASN	0	0.054	0.030	21.435	-0.366	-0.366	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.049	-0.006	20.479	-0.432	-0.432	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.021	0.005	23.508	0.011	0.011	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.952	0.974	23.830	11.847	11.847	0.000	0.000	0.000	0.000
62	A	67	PRO	0	-0.013	-0.013	25.323	0.403	0.403	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.028	0.013	22.777	-0.483	-0.483	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.020	0.001	23.688	-0.287	-0.287	0.000	0.000	0.000	0.000
65	A	70	PHE	0	-0.034	-0.026	23.985	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.834	-0.925	28.821	-8.830	-8.830	0.000	0.000	0.000	0.000
67	A	72	PRO	0	-0.033	-0.024	31.347	0.070	0.070	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.904	-0.944	33.570	-8.016	-8.016	0.000	0.000	0.000	0.000
69	A	74	MET	0	-0.086	-0.023	34.234	0.174	0.174	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.799	0.891	36.700	8.186	8.186	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.945	-0.980	38.246	-7.890	-7.890	0.000	0.000	0.000	0.000
72	A	77	PHE	0	-0.027	0.010	30.864	-0.109	-0.109	0.000	0.000	0.000	0.000
73	A	78	THR	0	-0.053	-0.049	33.017	0.098	0.098	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.033	-0.006	26.844	-0.189	-0.189	0.000	0.000	0.000	0.000
75	A	80	PRO	0	0.003	0.011	25.535	-0.072	-0.072	0.000	0.000	0.000	0.000
76	A	81	GLY	0	0.036	0.005	24.292	-0.238	-0.238	0.000	0.000	0.000	0.000
77	A	82	VAL	0	-0.033	-0.001	22.006	0.192	0.192	0.000	0.000	0.000	0.000
78	A	83	THR	0	-0.046	-0.039	16.150	-0.322	-0.322	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.003	-0.005	16.973	0.489	0.489	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.011	-0.017	12.930	-1.341	-1.341	0.000	0.000	0.000	0.000
81	A	86	MET	0	0.010	-0.001	11.286	1.773	1.773	0.000	0.000	0.000	0.000
82	A	87	GLN	0	-0.042	-0.010	7.646	-0.622	-0.622	0.000	0.000	0.000	0.000
83	A	88	VAL	0	-0.028	-0.006	5.961	1.485	1.485	0.000	0.000	0.000	0.000
84	A	89	PRO	0	0.041	0.004	6.496	-2.789	-2.789	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.060	-0.030	9.050	1.112	1.112	0.000	0.000	0.000	0.000
86	A	91	TYR	0	0.011	-0.011	12.738	0.927	0.927	0.000	0.000	0.000	0.000
87	A	92	GLY	0	0.004	0.014	13.999	0.766	0.766	0.000	0.000	0.000	0.000
88	A	93	ASP	-1	-0.832	-0.903	14.868	-16.261	-16.261	0.000	0.000	0.000	0.000
89	A	94	GLU	-1	-0.727	-0.860	10.188	-21.838	-21.838	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.003	-0.004	11.452	-0.291	-0.291	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.080	-0.049	14.043	0.906	0.906	0.000	0.000	0.000	0.000
92	A	97	LEU	0	0.025	0.015	15.319	0.644	0.644	0.000	0.000	0.000	0.000
93	A	98	PHE	0	0.025	0.013	12.632	0.199	0.199	0.000	0.000	0.000	0.000
94	A	99	LYS	1	0.921	0.967	14.772	14.843	14.843	0.000	0.000	0.000	0.000
95	A	100	LEU	0	0.019	0.010	17.776	0.560	0.560	0.000	0.000	0.000	0.000
96	A	101	MET	0	-0.003	0.026	13.122	0.519	0.519	0.000	0.000	0.000	0.000
97	A	102	LEU	0	0.020	-0.001	16.687	0.455	0.455	0.000	0.000	0.000	0.000
98	A	103	GLN	0	-0.036	-0.029	18.784	0.392	0.392	0.000	0.000	0.000	0.000
99	A	104	SER	0	-0.006	-0.010	21.342	0.772	0.772	0.000	0.000	0.000	0.000
100	A	105	ALA	0	-0.024	-0.014	19.570	0.459	0.459	0.000	0.000	0.000	0.000
101	A	106	GLN	0	-0.063	-0.050	21.724	-0.220	-0.220	0.000	0.000	0.000	0.000
102	A	107	HIS	0	0.020	0.009	24.173	0.453	0.453	0.000	0.000	0.000	0.000
103	A	108	ILE	0	0.035	0.020	23.641	0.328	0.328	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.022	-0.018	24.525	0.323	0.323	0.000	0.000	0.000	0.000
105	A	110	ASP	-1	-0.875	-0.927	26.554	-11.126	-11.126	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.909	-0.969	29.751	-9.791	-9.791	0.000	0.000	0.000	0.000
107	A	112	VAL	0	-0.075	-0.039	27.800	0.332	0.332	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.002	0.017	31.020	0.157	0.157	0.000	0.000	0.000	0.000
109	A	114	GLY	0	-0.018	0.000	27.510	0.082	0.082	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.034	-0.032	22.667	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.029	0.023	19.192	-0.365	-0.365	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.049	-0.028	18.136	-0.085	-0.085	0.000	0.000	0.000	0.000
113	A	118	ASP	-1	-0.708	-0.860	12.288	-24.404	-24.404	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.825	-0.883	9.376	-29.534	-29.534	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.096	-0.052	9.151	1.716	1.716	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.867	0.929	12.764	18.111	18.111	0.000	0.000	0.000	0.000
117	A	122	ARG	1	0.845	0.929	10.773	25.459	25.459	0.000	0.000	0.000	0.000
118	A	123	MET	0	0.038	0.017	16.836	-0.058	-0.058	0.000	0.000	0.000	0.000
119	A	124	MET	0	-0.014	0.009	15.538	-1.271	-1.271	0.000	0.000	0.000	0.000
120	A	125	THR	0	0.034	0.016	15.695	0.498	0.498	0.000	0.000	0.000	0.000
121	A	126	PRO	0	0.033	-0.001	16.356	-0.965	-0.965	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.043	-0.018	11.378	0.889	0.889	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.826	0.903	9.186	28.336	28.336	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.005	0.001	11.963	-1.676	-1.676	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.782	0.850	11.539	23.363	23.363	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.823	-0.914	8.123	-30.712	-30.712	0.000	0.000	0.000	0.000
127	A	132	TYR	0	0.016	-0.022	7.525	-3.957	-3.957	0.000	0.000	0.000	0.000
128	A	133	GLN	0	0.022	0.014	8.799	-1.480	-1.480	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.748	-0.841	7.532	-27.741	-27.741	0.000	0.000	0.000	0.000
130	A	135	ILE	0	0.011	0.015	2.679	-4.963	-3.472	1.552	-0.533	-2.509	0.002
131	A	136	ILE	0	0.008	0.004	4.764	-2.406	-2.278	-0.001	-0.004	-0.123	0.000
132	A	137	ARG	1	0.847	0.902	7.380	27.951	27.951	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.845	-0.896	1.705	-131.454	-133.430	22.785	-11.269	-9.540	-0.137
134	A	139	VAL	0	0.014	0.011	2.559	1.104	1.886	0.826	-0.417	-1.191	-0.002
135	A	140	LYS	1	0.778	0.886	4.310	27.946	27.993	0.000	-0.013	-0.032	0.000
136	A	141	ASP	-1	-0.924	-0.957	7.164	-24.188	-24.188	0.000	0.000	0.000	0.000
137	A	142	ALA	0	0.010	0.014	3.496	2.596	2.857	0.007	-0.064	-0.204	0.000
138	A	143	ASN	0	-0.130	-0.079	5.503	4.146	4.146	0.000	0.000	0.000	0.000
139	A	144	ALA	0	-0.010	0.019	8.625	2.265	2.265	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:ARG)