FMO DATABASE

FMODB ID: JVM29

Calculation Name: 1L1D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cacodylate ion

Ligand 3-letter code: CAC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1L1D

Chain ID: A

ChEMBL ID:

UniProt ID: P14930

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1346688.469157
FMO2-HF: Nuclear repulsion	1290006.385355
FMO2-HF: Total energy	-56682.083801
FMO2-MP2: Total energy	-56847.757442

3D Structure Molmil

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:378:TYR)

Summations of interaction energy for fragment #1(A:378:TYR)

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.
-152.5	-136.681	14.227	-9.045	-21	-0.069

Interaction energy analysis for fragmet #1(A:378:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.939

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	380	LYS	1	0.999	1.020	3.874	23.452	25.274	-0.019	-0.854	-0.948	0.000
48	A	425	SER	0	-0.054	-0.035	2.580	-6.275	-4.946	0.326	-0.722	-0.933	-0.003
49	A	426	GLY	0	0.011	0.007	2.432	-24.756	-19.474	2.543	-3.627	-4.198	-0.045
50	A	427	GLU	-1	-0.799	-0.898	2.398	-56.373	-51.362	6.780	-3.947	-7.845	-0.016
51	A	428	PRO	0	0.002	-0.002	2.682	4.755	4.174	3.090	1.635	-4.143	0.000
96	A	473	ALA	0	-0.085	-0.063	2.565	-0.546	-0.066	1.114	-0.560	-1.034	-0.002
97	A	474	ALA	0	-0.080	-0.059	4.367	-1.616	-1.570	-0.001	-0.024	-0.022	0.000
137	A	514	TYR	0	-0.049	-0.052	2.704	-4.456	-2.135	0.395	-0.944	-1.772	-0.003
140	A	517	LEU	0	0.022	0.005	4.781	0.495	0.604	-0.001	-0.002	-0.105	0.000
4	A	381	PRO	0	0.014	0.024	6.691	1.724	1.724	0.000	0.000	0.000	0.000
5	A	382	SER	0	-0.036	-0.056	9.533	1.455	1.455	0.000	0.000	0.000	0.000
6	A	383	ASP	-1	-0.750	-0.863	13.162	-16.915	-16.915	0.000	0.000	0.000	0.000
7	A	384	ALA	0	-0.018	-0.010	15.625	0.547	0.547	0.000	0.000	0.000	0.000
8	A	385	GLU	-1	-0.837	-0.886	12.412	-23.142	-23.142	0.000	0.000	0.000	0.000
9	A	386	LEU	0	0.007	0.021	10.077	0.171	0.171	0.000	0.000	0.000	0.000
10	A	387	LYS	1	0.872	0.926	14.038	15.667	15.667	0.000	0.000	0.000	0.000
11	A	388	ARG	1	0.877	0.944	16.606	15.644	15.644	0.000	0.000	0.000	0.000
12	A	389	THR	0	-0.053	-0.034	13.116	-0.414	-0.414	0.000	0.000	0.000	0.000
13	A	390	LEU	0	-0.035	0.005	11.176	-0.289	-0.289	0.000	0.000	0.000	0.000
14	A	391	THR	0	-0.016	-0.030	15.122	1.246	1.246	0.000	0.000	0.000	0.000
15	A	392	GLU	-1	-0.825	-0.915	17.666	-14.116	-14.116	0.000	0.000	0.000	0.000
16	A	393	GLU	-1	-0.879	-0.938	19.350	-13.817	-13.817	0.000	0.000	0.000	0.000
17	A	394	GLN	0	0.044	0.034	14.080	0.119	0.119	0.000	0.000	0.000	0.000
18	A	395	TYR	0	-0.058	-0.038	14.682	-0.868	-0.868	0.000	0.000	0.000	0.000
19	A	396	GLN	0	-0.002	-0.014	16.203	-0.584	-0.584	0.000	0.000	0.000	0.000
20	A	397	VAL	0	-0.028	0.002	15.154	-0.054	-0.054	0.000	0.000	0.000	0.000
21	A	398	THR	0	-0.024	-0.028	11.308	-0.657	-0.657	0.000	0.000	0.000	0.000
22	A	399	GLN	0	-0.041	-0.032	11.036	-1.119	-1.119	0.000	0.000	0.000	0.000
23	A	400	ASN	0	-0.054	-0.037	14.972	0.065	0.065	0.000	0.000	0.000	0.000
24	A	401	SER	0	-0.016	-0.012	17.017	0.500	0.500	0.000	0.000	0.000	0.000
25	A	402	ALA	0	-0.015	0.013	18.328	0.749	0.749	0.000	0.000	0.000	0.000
26	A	403	THR	0	-0.062	-0.044	19.306	-0.419	-0.419	0.000	0.000	0.000	0.000
27	A	404	GLU	-1	-0.705	-0.833	18.977	-14.812	-14.812	0.000	0.000	0.000	0.000
28	A	405	TYR	0	-0.006	-0.014	22.078	0.366	0.366	0.000	0.000	0.000	0.000
29	A	406	ALA	0	0.037	0.039	24.873	-0.243	-0.243	0.000	0.000	0.000	0.000
30	A	407	PHE	0	-0.079	-0.050	25.651	0.361	0.361	0.000	0.000	0.000	0.000
31	A	408	SER	0	-0.095	-0.046	24.458	0.010	0.010	0.000	0.000	0.000	0.000
32	A	409	HIS	0	0.081	0.065	18.033	-0.112	-0.112	0.000	0.000	0.000	0.000
33	A	410	GLU	-1	-0.866	-0.946	20.490	-13.561	-13.561	0.000	0.000	0.000	0.000
34	A	411	TYR	0	-0.046	-0.048	14.522	-0.317	-0.317	0.000	0.000	0.000	0.000
35	A	412	ASP	-1	-0.805	-0.891	19.535	-12.255	-12.255	0.000	0.000	0.000	0.000
36	A	413	HIS	1	0.862	0.902	22.341	11.328	11.328	0.000	0.000	0.000	0.000
37	A	414	LEU	0	-0.028	0.017	17.674	0.323	0.323	0.000	0.000	0.000	0.000
38	A	415	PHE	0	0.018	0.010	20.302	-0.458	-0.458	0.000	0.000	0.000	0.000
39	A	416	LYS	1	0.860	0.922	18.302	14.703	14.703	0.000	0.000	0.000	0.000
40	A	417	PRO	0	0.057	0.025	17.058	-0.566	-0.566	0.000	0.000	0.000	0.000
41	A	418	GLY	0	0.036	0.020	12.806	-0.061	-0.061	0.000	0.000	0.000	0.000
42	A	419	ILE	0	0.004	0.021	6.369	0.280	0.280	0.000	0.000	0.000	0.000
43	A	420	TYR	0	0.025	0.006	10.811	0.295	0.295	0.000	0.000	0.000	0.000
44	A	421	VAL	0	-0.014	-0.006	5.849	-0.724	-0.724	0.000	0.000	0.000	0.000
45	A	422	ASP	-1	-0.696	-0.831	4.909	-32.983	-32.983	0.000	0.000	0.000	0.000
46	A	423	VAL	0	-0.062	-0.024	6.364	-3.924	-3.924	0.000	0.000	0.000	0.000
47	A	424	VAL	0	-0.014	0.001	6.863	0.246	0.246	0.000	0.000	0.000	0.000
52	A	429	LEU	0	-0.018	0.008	5.753	-0.120	-0.120	0.000	0.000	0.000	0.000
53	A	430	PHE	0	0.029	0.013	8.896	1.441	1.441	0.000	0.000	0.000	0.000
54	A	431	SER	0	0.009	-0.021	11.322	-0.938	-0.938	0.000	0.000	0.000	0.000
55	A	432	SER	0	-0.041	-0.043	13.182	0.888	0.888	0.000	0.000	0.000	0.000
56	A	433	ALA	0	0.018	0.018	15.917	0.765	0.765	0.000	0.000	0.000	0.000
57	A	434	ASP	-1	-0.845	-0.913	14.977	-15.787	-15.787	0.000	0.000	0.000	0.000
58	A	435	LYS	1	0.757	0.891	17.622	14.322	14.322	0.000	0.000	0.000	0.000
59	A	436	TYR	0	-0.022	-0.030	19.331	0.477	0.477	0.000	0.000	0.000	0.000
60	A	437	ASP	-1	-0.875	-0.941	23.144	-11.017	-11.017	0.000	0.000	0.000	0.000
61	A	438	SER	0	-0.043	-0.042	24.589	0.378	0.378	0.000	0.000	0.000	0.000
62	A	439	GLY	0	-0.011	-0.003	27.110	0.271	0.271	0.000	0.000	0.000	0.000
63	A	440	CYS	0	-0.122	-0.051	24.719	0.029	0.029	0.000	0.000	0.000	0.000
64	A	441	GLY	0	0.045	0.026	26.123	0.055	0.055	0.000	0.000	0.000	0.000
65	A	442	TRP	0	0.016	-0.001	20.640	0.068	0.068	0.000	0.000	0.000	0.000
66	A	443	PRO	0	0.010	0.005	17.809	0.242	0.242	0.000	0.000	0.000	0.000
67	A	444	SER	0	-0.005	0.024	19.183	-0.201	-0.201	0.000	0.000	0.000	0.000
68	A	445	PHE	0	-0.004	-0.008	15.811	-0.045	-0.045	0.000	0.000	0.000	0.000
69	A	446	THR	0	0.005	0.000	18.709	0.019	0.019	0.000	0.000	0.000	0.000
70	A	447	ARG	1	0.834	0.914	12.762	17.722	17.722	0.000	0.000	0.000	0.000
71	A	448	PRO	0	0.015	0.011	11.164	-0.294	-0.294	0.000	0.000	0.000	0.000
72	A	449	ILE	0	-0.020	-0.015	7.785	0.611	0.611	0.000	0.000	0.000	0.000
73	A	450	ASP	-1	-0.763	-0.855	7.797	-23.064	-23.064	0.000	0.000	0.000	0.000
74	A	451	ALA	0	0.046	0.030	9.890	-0.897	-0.897	0.000	0.000	0.000	0.000
75	A	452	LYS	1	0.793	0.869	8.276	24.100	24.100	0.000	0.000	0.000	0.000
76	A	453	SER	0	-0.041	-0.028	6.311	-1.952	-1.952	0.000	0.000	0.000	0.000
77	A	454	VAL	0	0.022	0.015	7.358	-1.591	-1.591	0.000	0.000	0.000	0.000
78	A	455	THR	0	-0.058	-0.021	10.219	1.028	1.028	0.000	0.000	0.000	0.000
79	A	456	GLU	-1	-0.844	-0.922	12.764	-15.467	-15.467	0.000	0.000	0.000	0.000
80	A	457	HIS	1	0.848	0.912	13.584	18.500	18.500	0.000	0.000	0.000	0.000
81	A	458	ASP	-1	-0.794	-0.876	18.821	-11.796	-11.796	0.000	0.000	0.000	0.000
82	A	459	ASP	-1	-0.759	-0.830	21.616	-12.864	-12.864	0.000	0.000	0.000	0.000
83	A	460	PHE	0	-0.004	-0.020	23.494	0.430	0.430	0.000	0.000	0.000	0.000
84	A	461	SER	0	-0.056	-0.047	24.374	0.445	0.445	0.000	0.000	0.000	0.000
85	A	462	PHE	0	-0.001	-0.022	25.770	0.192	0.192	0.000	0.000	0.000	0.000
86	A	463	ASN	0	-0.037	-0.018	29.660	0.073	0.073	0.000	0.000	0.000	0.000
87	A	464	MET	0	0.005	0.019	28.016	0.206	0.206	0.000	0.000	0.000	0.000
88	A	465	ARG	1	0.832	0.912	26.821	10.661	10.661	0.000	0.000	0.000	0.000
89	A	466	ARG	1	0.855	0.925	23.752	12.370	12.370	0.000	0.000	0.000	0.000
90	A	467	THR	0	0.039	0.025	19.359	0.171	0.171	0.000	0.000	0.000	0.000
91	A	468	GLU	-1	-0.792	-0.876	16.755	-16.793	-16.793	0.000	0.000	0.000	0.000
92	A	469	VAL	0	-0.022	-0.027	13.389	-0.331	-0.331	0.000	0.000	0.000	0.000
93	A	470	ARG	1	0.810	0.886	11.885	19.644	19.644	0.000	0.000	0.000	0.000
94	A	471	SER	0	0.003	-0.018	6.456	0.584	0.584	0.000	0.000	0.000	0.000
95	A	472	ARG	1	0.838	0.919	6.025	27.856	27.856	0.000	0.000	0.000	0.000
98	A	475	ASP	-1	-0.870	-0.902	6.400	-19.457	-19.457	0.000	0.000	0.000	0.000
99	A	476	SER	0	-0.005	-0.008	7.786	2.437	2.437	0.000	0.000	0.000	0.000
100	A	477	HIS	0	-0.068	-0.043	10.080	0.198	0.198	0.000	0.000	0.000	0.000
101	A	478	LEU	0	-0.007	-0.010	9.472	-0.560	-0.560	0.000	0.000	0.000	0.000
102	A	479	GLY	0	0.041	0.024	13.588	0.831	0.831	0.000	0.000	0.000	0.000
103	A	480	HIS	0	-0.044	-0.019	17.270	-0.213	-0.213	0.000	0.000	0.000	0.000
104	A	481	VAL	0	-0.011	0.002	18.632	-0.155	-0.155	0.000	0.000	0.000	0.000
105	A	482	PHE	0	-0.019	-0.001	20.617	0.549	0.549	0.000	0.000	0.000	0.000
106	A	483	PRO	0	-0.002	-0.005	23.836	-0.204	-0.204	0.000	0.000	0.000	0.000
107	A	484	ASP	-1	-0.808	-0.881	26.134	-10.734	-10.734	0.000	0.000	0.000	0.000
108	A	485	GLY	0	0.046	0.041	24.669	0.114	0.114	0.000	0.000	0.000	0.000
109	A	486	PRO	0	0.024	-0.004	24.196	0.383	0.383	0.000	0.000	0.000	0.000
110	A	487	ARG	1	0.887	0.950	25.630	9.896	9.896	0.000	0.000	0.000	0.000
111	A	488	ASP	-1	-0.860	-0.916	26.997	-10.629	-10.629	0.000	0.000	0.000	0.000
112	A	489	LYS	1	0.839	0.900	22.067	11.090	11.090	0.000	0.000	0.000	0.000
113	A	490	GLY	0	0.037	0.025	21.887	-0.533	-0.533	0.000	0.000	0.000	0.000
114	A	491	GLY	0	-0.092	-0.039	23.501	0.056	0.056	0.000	0.000	0.000	0.000
115	A	492	LEU	0	0.006	0.005	19.961	0.292	0.292	0.000	0.000	0.000	0.000
116	A	493	ARG	1	0.845	0.886	21.909	11.615	11.615	0.000	0.000	0.000	0.000
117	A	494	TYR	0	-0.003	-0.009	16.043	-0.062	-0.062	0.000	0.000	0.000	0.000
118	A	495	CYS	0	-0.051	-0.019	18.983	0.270	0.270	0.000	0.000	0.000	0.000
119	A	496	ILE	0	0.000	-0.008	14.040	-0.281	-0.281	0.000	0.000	0.000	0.000
120	A	497	ASN	0	0.064	0.024	16.186	1.139	1.139	0.000	0.000	0.000	0.000
121	A	498	GLY	0	0.010	0.002	15.330	-1.322	-1.322	0.000	0.000	0.000	0.000
122	A	499	ALA	0	-0.002	-0.008	15.242	-1.035	-1.035	0.000	0.000	0.000	0.000
123	A	500	SER	0	-0.042	-0.043	11.937	-1.157	-1.157	0.000	0.000	0.000	0.000
124	A	501	LEU	0	-0.034	-0.012	10.520	-2.312	-2.312	0.000	0.000	0.000	0.000
125	A	502	LYS	1	0.884	0.937	9.467	21.647	21.647	0.000	0.000	0.000	0.000
126	A	503	PHE	0	0.006	0.004	10.421	-1.104	-1.104	0.000	0.000	0.000	0.000
127	A	504	ILE	0	-0.041	-0.014	7.560	-0.134	-0.134	0.000	0.000	0.000	0.000
128	A	505	PRO	0	0.006	0.011	10.969	0.421	0.421	0.000	0.000	0.000	0.000
129	A	506	LEU	0	0.086	0.019	12.736	-0.872	-0.872	0.000	0.000	0.000	0.000
130	A	507	GLU	-1	-0.860	-0.927	13.740	-15.225	-15.225	0.000	0.000	0.000	0.000
131	A	508	GLN	0	-0.026	-0.011	11.730	0.447	0.447	0.000	0.000	0.000	0.000
132	A	509	MET	0	-0.033	0.005	8.421	-0.804	-0.804	0.000	0.000	0.000	0.000
133	A	510	ASP	-1	-0.831	-0.906	8.363	-20.779	-20.779	0.000	0.000	0.000	0.000
134	A	511	ALA	0	-0.027	-0.007	9.801	-1.068	-1.068	0.000	0.000	0.000	0.000
135	A	512	ALA	0	-0.027	-0.010	7.798	-0.377	-0.377	0.000	0.000	0.000	0.000
136	A	513	GLY	0	-0.006	0.004	5.875	-3.936	-3.936	0.000	0.000	0.000	0.000
138	A	515	GLY	0	0.040	0.026	5.527	2.120	2.120	0.000	0.000	0.000	0.000
139	A	516	ALA	0	-0.021	-0.016	7.431	1.709	1.709	0.000	0.000	0.000	0.000
141	A	518	LYS	1	0.796	0.864	8.855	18.853	18.853	0.000	0.000	0.000	0.000
142	A	519	GLY	0	-0.024	0.000	12.052	0.952	0.952	0.000	0.000	0.000	0.000
143	A	520	GLU	-1	-0.944	-0.967	10.292	-18.111	-18.111	0.000	0.000	0.000	0.000
144	A	521	VAL	-1	-0.930	-0.931	12.418	-14.915	-14.915	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:378:TYR)