FMO DATABASE

FMODB ID: ZVK1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1245501.112622
FMO2-HF: Nuclear repulsion	1190055.286464
FMO2-HF: Total energy	-55445.826159
FMO2-MP2: Total energy	-55604.05071

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.
-218.91	-213.199	22.869	-13.641	-14.938	-0.14

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 : 0.853 / q_NPA : 0.899

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	-0.880	-0.932	3.257	-30.761	-28.049	0.000	-1.281	-1.430	0.003
4	A	9	ALA	0	0.001	0.011	2.995	-8.217	-7.115	0.059	-0.425	-0.737	-0.003
5	A	10	VAL	0	0.015	0.015	5.059	4.424	4.466	-0.001	-0.005	-0.035	0.000
6	A	11	ILE	0	-0.043	-0.020	7.039	-2.226	-2.226	0.000	0.000	0.000	0.000
7	A	12	ILE	0	0.018	-0.002	9.397	2.676	2.676	0.000	0.000	0.000	0.000
8	A	13	MET	0	-0.014	0.020	12.214	-0.740	-0.740	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.003	-0.008	15.350	0.944	0.944	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.047	0.052	18.659	-0.138	-0.138	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.021	-0.015	21.893	0.155	0.155	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.080	0.047	23.741	0.203	0.203	0.000	0.000	0.000	0.000
13	A	18	HIS	0	-0.006	0.005	26.014	-0.511	-0.511	0.000	0.000	0.000	0.000
14	A	19	HIS	0	0.019	0.000	25.944	0.032	0.032	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.022	-0.009	27.648	0.291	0.291	0.000	0.000	0.000	0.000
16	A	21	SER	0	-0.095	-0.044	30.144	0.407	0.407	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.860	-0.930	29.752	-10.528	-10.528	0.000	0.000	0.000	0.000
18	A	23	LEU	0	-0.020	-0.003	26.685	0.239	0.239	0.000	0.000	0.000	0.000
19	A	24	ASN	0	0.038	0.012	31.026	0.100	0.100	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.077	0.024	32.344	-0.199	-0.199	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.829	-0.921	32.978	-8.247	-8.247	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.031	-0.010	33.408	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	28	LEU	0	0.026	0.010	26.805	-0.209	-0.209	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.011	0.005	30.054	-0.299	-0.299	0.000	0.000	0.000	0.000
25	A	30	ASN	0	-0.008	-0.003	31.490	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	31	SER	0	0.038	0.015	29.476	-0.192	-0.192	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.036	-0.022	26.076	-0.369	-0.369	0.000	0.000	0.000	0.000
28	A	33	GLN	0	0.051	0.013	27.968	-0.496	-0.496	0.000	0.000	0.000	0.000
29	A	34	GLN	0	-0.060	-0.015	30.613	0.155	0.155	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.039	-0.014	25.684	-0.078	-0.078	0.000	0.000	0.000	0.000
31	A	36	GLY	0	-0.042	-0.022	26.300	-0.430	-0.430	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.087	-0.047	21.074	-0.368	-0.368	0.000	0.000	0.000	0.000
33	A	38	ILE	0	0.022	0.007	26.259	0.474	0.474	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.006	-0.005	26.675	-0.462	-0.462	0.000	0.000	0.000	0.000
35	A	40	GLY	0	0.036	0.007	26.986	0.264	0.264	0.000	0.000	0.000	0.000
36	A	41	ASP	-1	-0.902	-0.945	23.642	-11.697	-11.697	0.000	0.000	0.000	0.000
37	A	42	MET	0	-0.044	-0.040	21.989	-0.259	-0.259	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.001	0.015	24.996	0.069	0.069	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.001	0.006	20.548	-0.081	-0.081	0.000	0.000	0.000	0.000
40	A	45	TYR	0	0.002	0.000	23.885	0.280	0.280	0.000	0.000	0.000	0.000
41	A	46	HIS	1	0.841	0.903	20.689	12.481	12.481	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.935	1.000	21.412	12.893	12.893	0.000	0.000	0.000	0.000
43	A	48	HIS	0	0.045	0.019	21.856	-0.693	-0.693	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.003	0.002	23.025	0.167	0.167	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.041	-0.041	24.715	0.018	0.018	0.000	0.000	0.000	0.000
46	A	51	PRO	0	0.021	0.004	28.330	-0.163	-0.163	0.000	0.000	0.000	0.000
47	A	52	ASP	-1	-0.849	-0.880	31.024	-9.720	-9.720	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.009	-0.001	28.065	0.060	0.060	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.043	-0.021	28.081	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	55	GLY	0	-0.003	-0.004	25.294	-0.234	-0.234	0.000	0.000	0.000	0.000
51	A	56	PRO	0	-0.022	-0.019	19.600	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.003	0.007	19.757	0.114	0.114	0.000	0.000	0.000	0.000
53	A	58	LEU	0	-0.064	-0.044	18.034	-0.756	-0.756	0.000	0.000	0.000	0.000
54	A	59	PHE	0	0.020	-0.012	16.201	-1.250	-1.250	0.000	0.000	0.000	0.000
55	A	60	SER	0	-0.025	-0.005	17.133	1.348	1.348	0.000	0.000	0.000	0.000
56	A	61	LEU	0	0.004	0.007	18.386	-0.853	-0.853	0.000	0.000	0.000	0.000
57	A	62	ALA	0	0.037	0.019	19.857	0.619	0.619	0.000	0.000	0.000	0.000
58	A	63	ASN	0	0.049	0.021	21.636	-0.326	-0.326	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.058	-0.014	20.141	-0.360	-0.360	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.035	0.006	23.423	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.961	0.983	24.136	11.588	11.588	0.000	0.000	0.000	0.000
62	A	67	PRO	0	-0.018	-0.023	25.590	0.378	0.378	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.032	0.007	23.123	-0.395	-0.395	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.022	0.001	23.940	-0.296	-0.296	0.000	0.000	0.000	0.000
65	A	70	PHE	0	-0.023	-0.021	24.286	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.844	-0.921	29.103	-8.812	-8.812	0.000	0.000	0.000	0.000
67	A	72	PRO	0	-0.051	-0.036	31.454	0.088	0.088	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.931	-0.957	33.703	-8.000	-8.000	0.000	0.000	0.000	0.000
69	A	74	MET	0	-0.093	-0.027	34.659	0.174	0.174	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.854	0.919	36.888	8.006	8.006	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.969	-0.986	38.865	-7.728	-7.728	0.000	0.000	0.000	0.000
72	A	77	PHE	0	0.002	0.027	31.200	-0.090	-0.090	0.000	0.000	0.000	0.000
73	A	78	THR	0	-0.043	-0.052	32.910	0.093	0.093	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.030	0.001	27.229	-0.175	-0.175	0.000	0.000	0.000	0.000
75	A	80	PRO	0	0.016	0.013	25.314	-0.057	-0.057	0.000	0.000	0.000	0.000
76	A	81	GLY	0	0.048	0.015	24.033	-0.287	-0.287	0.000	0.000	0.000	0.000
77	A	82	VAL	0	-0.030	0.001	22.385	0.158	0.158	0.000	0.000	0.000	0.000
78	A	83	THR	0	-0.048	-0.040	16.434	-0.316	-0.316	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.008	-0.005	17.368	0.405	0.405	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.012	-0.015	13.087	-1.320	-1.320	0.000	0.000	0.000	0.000
81	A	86	MET	0	0.016	0.002	11.702	1.746	1.746	0.000	0.000	0.000	0.000
82	A	87	GLN	0	-0.035	-0.001	8.188	-0.893	-0.893	0.000	0.000	0.000	0.000
83	A	88	VAL	0	-0.044	-0.005	6.289	1.429	1.429	0.000	0.000	0.000	0.000
84	A	89	PRO	0	0.030	-0.009	6.805	-2.730	-2.730	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.015	-0.022	9.366	1.178	1.178	0.000	0.000	0.000	0.000
86	A	91	TYR	0	0.005	-0.012	13.072	0.373	0.373	0.000	0.000	0.000	0.000
87	A	92	GLY	0	0.015	0.014	13.756	0.746	0.746	0.000	0.000	0.000	0.000
88	A	93	ASP	-1	-0.842	-0.905	14.800	-15.694	-15.694	0.000	0.000	0.000	0.000
89	A	94	GLU	-1	-0.737	-0.864	10.085	-21.750	-21.750	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.014	-0.011	11.478	-0.072	-0.072	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.082	-0.047	14.182	0.871	0.871	0.000	0.000	0.000	0.000
92	A	97	LEU	0	0.037	0.022	15.456	0.625	0.625	0.000	0.000	0.000	0.000
93	A	98	PHE	0	0.013	0.010	12.898	0.179	0.179	0.000	0.000	0.000	0.000
94	A	99	LYS	1	0.932	0.970	15.023	14.839	14.839	0.000	0.000	0.000	0.000
95	A	100	LEU	0	0.014	0.008	18.044	0.599	0.599	0.000	0.000	0.000	0.000
96	A	101	MET	0	-0.008	0.022	13.092	0.481	0.481	0.000	0.000	0.000	0.000
97	A	102	LEU	0	0.021	-0.003	17.095	0.432	0.432	0.000	0.000	0.000	0.000
98	A	103	GLN	0	-0.040	-0.025	18.958	0.505	0.505	0.000	0.000	0.000	0.000
99	A	104	SER	0	0.000	-0.007	21.535	0.769	0.769	0.000	0.000	0.000	0.000
100	A	105	ALA	0	-0.015	-0.009	19.815	0.468	0.468	0.000	0.000	0.000	0.000
101	A	106	GLN	0	-0.075	-0.053	21.968	-0.224	-0.224	0.000	0.000	0.000	0.000
102	A	107	HIS	0	0.025	0.013	24.273	0.464	0.464	0.000	0.000	0.000	0.000
103	A	108	ILE	0	0.024	0.015	24.010	0.325	0.325	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.032	-0.024	24.532	0.354	0.354	0.000	0.000	0.000	0.000
105	A	110	ASP	-1	-0.861	-0.924	26.659	-11.186	-11.186	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.950	-0.975	29.657	-9.805	-9.805	0.000	0.000	0.000	0.000
107	A	112	VAL	0	-0.077	-0.043	28.079	0.344	0.344	0.000	0.000	0.000	0.000
108	A	113	GLY	0	-0.004	0.014	30.812	0.167	0.167	0.000	0.000	0.000	0.000
109	A	114	GLY	0	-0.036	-0.020	26.957	0.035	0.035	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.041	-0.030	22.447	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.028	0.020	18.814	-0.379	-0.379	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.065	-0.034	17.803	-0.102	-0.102	0.000	0.000	0.000	0.000
113	A	118	ASP	-1	-0.721	-0.870	12.664	-23.605	-23.605	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.826	-0.893	8.870	-30.184	-30.184	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.114	-0.059	9.037	1.566	1.566	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.873	0.936	12.827	18.098	18.098	0.000	0.000	0.000	0.000
117	A	122	ARG	1	0.887	0.938	10.946	24.736	24.736	0.000	0.000	0.000	0.000
118	A	123	MET	0	0.034	0.020	16.889	-0.197	-0.197	0.000	0.000	0.000	0.000
119	A	124	MET	0	-0.005	0.012	15.191	-1.265	-1.265	0.000	0.000	0.000	0.000
120	A	125	THR	0	0.038	0.019	15.398	0.561	0.561	0.000	0.000	0.000	0.000
121	A	126	PRO	0	0.042	0.002	16.042	-0.949	-0.949	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.047	-0.027	11.073	0.988	0.988	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.872	0.939	8.449	29.923	29.923	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.013	0.010	11.577	-1.773	-1.773	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.773	0.838	11.405	23.454	23.454	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.846	-0.919	7.828	-31.718	-31.718	0.000	0.000	0.000	0.000
127	A	132	TYR	0	-0.023	-0.033	7.384	-4.217	-4.217	0.000	0.000	0.000	0.000
128	A	133	GLN	0	0.012	0.001	8.750	-1.689	-1.689	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.743	-0.842	7.306	-28.493	-28.493	0.000	0.000	0.000	0.000
130	A	135	ILE	0	0.033	0.035	2.724	-4.597	-3.056	1.085	-0.460	-2.166	0.001
131	A	136	ILE	0	0.004	0.002	4.808	-2.132	-2.014	-0.001	-0.003	-0.114	0.000
132	A	137	ARG	1	0.845	0.896	7.423	27.860	27.860	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.844	-0.894	1.718	-131.310	-132.037	21.473	-11.217	-9.529	-0.140
134	A	139	VAL	0	0.004	0.006	2.722	0.880	1.576	0.254	-0.200	-0.750	-0.001
135	A	140	LYS	1	0.785	0.880	4.783	26.668	26.696	-0.001	-0.005	-0.022	0.000
136	A	141	ASP	-1	-0.936	-0.963	7.528	-24.864	-24.864	0.000	0.000	0.000	0.000
137	A	142	ALA	0	0.015	0.020	3.805	2.372	2.571	0.001	-0.045	-0.155	0.000
138	A	143	ASN	0	-0.146	-0.085	5.747	4.190	4.190	0.000	0.000	0.000	0.000
139	A	144	ALA	0	-0.004	0.022	8.690	2.071	2.071	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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