FMO DATABASE

FMODB ID: 3M9RL

Calculation Name: 1VCP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: mercury (ii) ion

Ligand 3-letter code: HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VCP

Chain ID: A

ChEMBL ID:

UniProt ID: P03315

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1364021.584654
FMO2-HF: Nuclear repulsion	1306682.344894
FMO2-HF: Total energy	-57339.23976
FMO2-MP2: Total energy	-57505.24495

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:119:CYS)

Summations of interaction energy for fragment #1(A:119:CYS)

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.
-22.572	-9.702	13.019	-11.949	-13.942	-0.113

Interaction energy analysis for fragmet #1(A:119:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.915

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	121	PHE	0	0.031	0.023	3.439	-6.845	-4.756	0.015	-0.962	-1.142	0.000
16	A	134	CYS	0	-0.043	-0.023	3.944	-7.896	-7.473	0.040	-0.121	-0.343	0.000
17	A	135	LEU	0	-0.025	0.017	1.980	5.235	6.263	4.403	-2.851	-2.581	-0.011
18	A	136	VAL	0	0.025	-0.005	2.654	-11.091	-9.195	0.689	-1.115	-1.470	-0.014
19	A	137	GLY	0	0.007	0.008	5.330	4.922	4.923	-0.001	-0.001	0.001	0.000
62	A	180	ASP	-1	-0.885	-0.911	2.786	-54.572	-53.896	0.075	-0.336	-0.415	-0.003
63	A	181	ALA	0	-0.009	-0.021	2.093	-47.025	-42.263	6.053	-5.481	-5.334	-0.076
64	A	182	SER	0	-0.008	-0.008	2.180	2.207	3.293	1.586	-0.897	-1.776	-0.009
65	A	183	LYS	1	0.977	0.980	3.961	34.700	34.818	0.005	-0.022	-0.101	0.000
104	A	222	PRO	0	-0.022	-0.011	4.536	1.742	1.903	0.003	-0.032	-0.132	0.000
106	A	224	PHE	0	-0.011	-0.012	3.010	-1.886	-1.256	0.151	-0.131	-0.649	0.000
4	A	122	GLU	-1	-0.814	-0.918	6.351	-21.594	-21.594	0.000	0.000	0.000	0.000
5	A	123	VAL	0	-0.062	-0.027	10.145	-0.124	-0.124	0.000	0.000	0.000	0.000
6	A	124	LYS	1	0.914	0.965	13.116	21.522	21.522	0.000	0.000	0.000	0.000
7	A	125	HIS	0	0.021	0.000	16.103	-0.255	-0.255	0.000	0.000	0.000	0.000
8	A	126	GLU	-1	-0.917	-0.964	19.771	-12.254	-12.254	0.000	0.000	0.000	0.000
9	A	127	GLY	0	0.012	0.006	19.662	0.389	0.389	0.000	0.000	0.000	0.000
10	A	128	LYS	1	0.887	0.957	19.307	12.693	12.693	0.000	0.000	0.000	0.000
11	A	129	VAL	0	-0.014	0.003	14.061	-0.201	-0.201	0.000	0.000	0.000	0.000
12	A	130	THR	0	-0.038	-0.039	16.177	0.587	0.587	0.000	0.000	0.000	0.000
13	A	131	GLY	0	0.024	0.013	14.106	0.804	0.804	0.000	0.000	0.000	0.000
14	A	132	TYR	0	-0.077	-0.025	8.629	-0.652	-0.652	0.000	0.000	0.000	0.000
15	A	133	ALA	0	0.021	0.003	7.945	2.503	2.503	0.000	0.000	0.000	0.000
20	A	138	ASP	-1	-0.804	-0.894	7.988	-25.646	-25.646	0.000	0.000	0.000	0.000
21	A	139	LYS	1	0.808	0.879	8.744	24.577	24.577	0.000	0.000	0.000	0.000
22	A	140	VAL	0	0.012	0.019	6.893	-4.955	-4.955	0.000	0.000	0.000	0.000
23	A	141	MET	0	-0.048	-0.020	7.268	4.662	4.662	0.000	0.000	0.000	0.000
24	A	142	LYS	1	0.906	0.937	8.406	17.041	17.041	0.000	0.000	0.000	0.000
25	A	143	PRO	0	0.054	0.025	11.115	1.222	1.222	0.000	0.000	0.000	0.000
26	A	144	ALA	0	-0.080	-0.041	14.201	0.077	0.077	0.000	0.000	0.000	0.000
27	A	145	HIS	1	0.758	0.863	17.242	16.645	16.645	0.000	0.000	0.000	0.000
28	A	146	VAL	0	0.010	0.017	14.728	0.724	0.724	0.000	0.000	0.000	0.000
29	A	147	LYS	1	0.935	0.964	17.482	13.749	13.749	0.000	0.000	0.000	0.000
30	A	148	GLY	0	0.055	0.038	17.927	-0.468	-0.468	0.000	0.000	0.000	0.000
31	A	149	VAL	0	-0.034	-0.022	15.213	-0.255	-0.255	0.000	0.000	0.000	0.000
32	A	150	ILE	0	0.006	-0.008	8.650	-0.360	-0.360	0.000	0.000	0.000	0.000
33	A	151	ASP	-1	-0.871	-0.934	10.993	-21.813	-21.813	0.000	0.000	0.000	0.000
34	A	152	ASN	0	0.013	-0.019	8.149	-0.551	-0.551	0.000	0.000	0.000	0.000
35	A	153	ALA	0	0.027	0.018	10.776	0.555	0.555	0.000	0.000	0.000	0.000
36	A	154	ASP	-1	-0.821	-0.899	10.359	-25.108	-25.108	0.000	0.000	0.000	0.000
37	A	155	LEU	0	-0.045	-0.037	6.582	1.081	1.081	0.000	0.000	0.000	0.000
38	A	156	ALA	0	-0.004	0.006	10.527	1.409	1.409	0.000	0.000	0.000	0.000
39	A	157	LYS	1	0.888	0.937	13.855	18.679	18.679	0.000	0.000	0.000	0.000
40	A	158	LEU	0	-0.024	0.016	10.404	0.917	0.917	0.000	0.000	0.000	0.000
41	A	159	ALA	0	0.005	0.005	14.805	0.684	0.684	0.000	0.000	0.000	0.000
42	A	160	PHE	0	-0.020	-0.014	10.873	-0.647	-0.647	0.000	0.000	0.000	0.000
43	A	161	LYS	1	0.942	0.972	16.076	16.217	16.217	0.000	0.000	0.000	0.000
44	A	162	LYS	1	0.907	0.945	16.929	14.546	14.546	0.000	0.000	0.000	0.000
45	A	163	SER	0	-0.022	-0.012	18.172	0.975	0.975	0.000	0.000	0.000	0.000
46	A	164	SER	0	0.062	0.011	19.473	-0.543	-0.543	0.000	0.000	0.000	0.000
47	A	165	LYS	1	0.974	0.994	21.879	12.206	12.206	0.000	0.000	0.000	0.000
48	A	166	TYR	0	0.006	-0.007	17.277	0.279	0.279	0.000	0.000	0.000	0.000
49	A	167	ASP	-1	-0.740	-0.842	17.302	-16.765	-16.765	0.000	0.000	0.000	0.000
50	A	168	LEU	0	0.014	0.027	11.574	-0.858	-0.858	0.000	0.000	0.000	0.000
51	A	169	GLU	-1	-0.812	-0.905	13.852	-16.475	-16.475	0.000	0.000	0.000	0.000
52	A	170	CYS	0	-0.031	-0.019	11.982	-1.237	-1.237	0.000	0.000	0.000	0.000
53	A	171	ALA	0	0.080	0.061	11.598	2.011	2.011	0.000	0.000	0.000	0.000
54	A	172	GLN	0	-0.038	-0.022	11.303	-1.879	-1.879	0.000	0.000	0.000	0.000
55	A	173	ILE	0	0.000	0.016	5.711	0.009	0.009	0.000	0.000	0.000	0.000
56	A	174	PRO	0	0.053	0.038	8.559	2.282	2.282	0.000	0.000	0.000	0.000
57	A	175	VAL	0	0.019	-0.023	10.095	-2.333	-2.333	0.000	0.000	0.000	0.000
58	A	176	HIS	0	-0.022	-0.017	10.842	-0.208	-0.208	0.000	0.000	0.000	0.000
59	A	177	MET	0	0.015	0.016	6.010	-2.486	-2.486	0.000	0.000	0.000	0.000
60	A	178	ARG	1	0.841	0.908	5.974	17.977	17.977	0.000	0.000	0.000	0.000
61	A	179	SER	0	-0.012	-0.009	7.132	1.616	1.616	0.000	0.000	0.000	0.000
66	A	184	TYR	0	0.039	0.030	7.307	-0.604	-0.604	0.000	0.000	0.000	0.000
67	A	185	THR	0	-0.051	-0.029	9.491	1.413	1.413	0.000	0.000	0.000	0.000
68	A	186	HIS	0	0.057	0.039	12.675	-0.744	-0.744	0.000	0.000	0.000	0.000
69	A	187	GLU	-1	-0.937	-0.954	16.000	-14.833	-14.833	0.000	0.000	0.000	0.000
70	A	188	LYS	1	0.866	0.922	15.344	15.301	15.301	0.000	0.000	0.000	0.000
71	A	189	PRO	0	0.026	0.030	17.409	0.604	0.604	0.000	0.000	0.000	0.000
72	A	190	GLU	-1	-0.837	-0.903	19.409	-11.888	-11.888	0.000	0.000	0.000	0.000
73	A	191	GLY	0	-0.003	0.001	20.337	0.198	0.198	0.000	0.000	0.000	0.000
74	A	192	HIS	0	-0.054	-0.029	17.809	0.023	0.023	0.000	0.000	0.000	0.000
75	A	193	TYR	0	-0.031	-0.031	12.796	-0.686	-0.686	0.000	0.000	0.000	0.000
76	A	194	ASN	0	-0.028	-0.016	10.201	1.361	1.361	0.000	0.000	0.000	0.000
77	A	195	TRP	0	0.051	0.008	9.682	-2.197	-2.197	0.000	0.000	0.000	0.000
78	A	196	HIS	0	0.011	-0.003	9.517	1.062	1.062	0.000	0.000	0.000	0.000
79	A	197	HIS	1	0.790	0.885	11.139	19.948	19.948	0.000	0.000	0.000	0.000
80	A	198	GLY	0	0.040	0.039	13.949	1.181	1.181	0.000	0.000	0.000	0.000
81	A	199	ALA	0	0.004	0.001	14.154	-1.020	-1.020	0.000	0.000	0.000	0.000
82	A	200	VAL	0	-0.032	-0.016	13.857	0.557	0.557	0.000	0.000	0.000	0.000
83	A	201	GLN	0	-0.004	0.001	16.517	-0.073	-0.073	0.000	0.000	0.000	0.000
84	A	202	TYR	0	-0.038	-0.031	17.633	-0.272	-0.272	0.000	0.000	0.000	0.000
85	A	203	SER	0	0.062	0.022	19.696	0.201	0.201	0.000	0.000	0.000	0.000
86	A	204	GLY	0	0.001	0.003	23.339	0.003	0.003	0.000	0.000	0.000	0.000
87	A	205	GLY	0	-0.037	-0.013	22.585	0.110	0.110	0.000	0.000	0.000	0.000
88	A	206	ARG	1	0.828	0.897	21.388	10.995	10.995	0.000	0.000	0.000	0.000
89	A	207	PHE	0	0.031	0.014	14.978	-0.082	-0.082	0.000	0.000	0.000	0.000
90	A	208	THR	0	0.039	0.025	18.960	0.415	0.415	0.000	0.000	0.000	0.000
91	A	209	ILE	0	-0.008	0.009	17.017	-0.494	-0.494	0.000	0.000	0.000	0.000
92	A	210	PRO	0	0.032	0.017	20.202	0.511	0.511	0.000	0.000	0.000	0.000
93	A	211	THR	0	0.056	0.014	22.223	-0.711	-0.711	0.000	0.000	0.000	0.000
94	A	212	GLY	0	0.027	0.030	23.615	0.227	0.227	0.000	0.000	0.000	0.000
95	A	213	ALA	0	-0.032	-0.015	19.306	-0.362	-0.362	0.000	0.000	0.000	0.000
96	A	214	GLY	0	-0.034	-0.026	17.745	-1.022	-1.022	0.000	0.000	0.000	0.000
97	A	215	LYS	1	0.853	0.932	18.033	15.578	15.578	0.000	0.000	0.000	0.000
98	A	216	PRO	0	0.060	0.013	18.143	-0.936	-0.936	0.000	0.000	0.000	0.000
99	A	217	GLY	0	0.029	0.030	16.831	0.241	0.241	0.000	0.000	0.000	0.000
100	A	218	ASP	-1	-0.820	-0.895	13.775	-20.497	-20.497	0.000	0.000	0.000	0.000
101	A	219	SER	0	-0.006	-0.028	13.055	-1.280	-1.280	0.000	0.000	0.000	0.000
102	A	220	GLY	0	-0.016	-0.021	10.567	-0.864	-0.864	0.000	0.000	0.000	0.000
103	A	221	ARG	1	0.829	0.927	8.458	20.402	20.402	0.000	0.000	0.000	0.000
105	A	223	ILE	0	-0.008	0.004	7.599	0.809	0.809	0.000	0.000	0.000	0.000
107	A	225	ASP	-1	-0.699	-0.847	8.410	-19.795	-19.795	0.000	0.000	0.000	0.000
108	A	226	ASN	0	0.020	-0.006	10.066	-1.972	-1.972	0.000	0.000	0.000	0.000
109	A	227	LYS	1	0.861	0.944	11.027	19.861	19.861	0.000	0.000	0.000	0.000
110	A	228	GLY	0	0.024	0.019	6.888	-1.115	-1.115	0.000	0.000	0.000	0.000
111	A	229	ARG	1	0.778	0.884	5.809	16.145	16.145	0.000	0.000	0.000	0.000
112	A	230	VAL	0	-0.035	-0.026	4.938	0.897	0.897	0.000	0.000	0.000	0.000
113	A	231	VAL	0	0.009	-0.003	7.494	1.335	1.335	0.000	0.000	0.000	0.000
114	A	232	ALA	0	-0.001	-0.006	10.281	1.349	1.349	0.000	0.000	0.000	0.000
115	A	233	ILE	0	-0.021	-0.017	7.354	-2.452	-2.452	0.000	0.000	0.000	0.000
116	A	234	VAL	0	0.000	0.012	10.830	1.615	1.615	0.000	0.000	0.000	0.000
117	A	235	LEU	0	-0.054	-0.022	13.410	-0.995	-0.995	0.000	0.000	0.000	0.000
118	A	236	GLY	0	0.072	0.022	16.223	0.478	0.478	0.000	0.000	0.000	0.000
119	A	237	GLY	0	-0.003	-0.003	18.824	-0.546	-0.546	0.000	0.000	0.000	0.000
120	A	238	ALA	0	0.019	0.050	21.368	0.261	0.261	0.000	0.000	0.000	0.000
121	A	239	ASN	0	-0.003	-0.013	24.971	-0.141	-0.141	0.000	0.000	0.000	0.000
122	A	240	GLU	-1	-0.809	-0.888	26.385	-10.770	-10.770	0.000	0.000	0.000	0.000
123	A	241	GLY	0	0.035	0.024	28.918	0.313	0.313	0.000	0.000	0.000	0.000
124	A	242	SER	0	-0.017	-0.019	28.626	-0.219	-0.219	0.000	0.000	0.000	0.000
125	A	243	ARG	1	0.865	0.933	21.313	12.033	12.033	0.000	0.000	0.000	0.000
126	A	244	THR	0	0.030	0.010	21.493	0.243	0.243	0.000	0.000	0.000	0.000
127	A	245	ALA	0	0.004	0.013	21.719	-0.577	-0.577	0.000	0.000	0.000	0.000
128	A	246	LEU	0	-0.023	-0.023	15.525	-0.072	-0.072	0.000	0.000	0.000	0.000
129	A	247	SER	0	0.003	0.016	19.235	0.290	0.290	0.000	0.000	0.000	0.000
130	A	248	VAL	0	-0.022	-0.020	14.898	-0.992	-0.992	0.000	0.000	0.000	0.000
131	A	249	VAL	0	0.044	0.028	12.504	0.943	0.943	0.000	0.000	0.000	0.000
132	A	250	THR	0	-0.015	-0.042	13.427	-0.786	-0.786	0.000	0.000	0.000	0.000
133	A	251	TRP	0	0.001	0.017	8.788	0.351	0.351	0.000	0.000	0.000	0.000
134	A	252	ASN	0	0.031	0.013	15.478	0.375	0.375	0.000	0.000	0.000	0.000
135	A	253	LYS	1	0.921	0.943	18.056	11.706	11.706	0.000	0.000	0.000	0.000
136	A	254	ASP	-1	-0.843	-0.933	17.808	-14.085	-14.085	0.000	0.000	0.000	0.000
137	A	255	MET	0	-0.040	0.003	16.599	-1.037	-1.037	0.000	0.000	0.000	0.000
138	A	256	VAL	0	0.005	-0.005	13.789	-0.136	-0.136	0.000	0.000	0.000	0.000
139	A	257	THR	0	-0.019	-0.005	16.440	1.244	1.244	0.000	0.000	0.000	0.000
140	A	258	ARG	1	0.864	0.918	16.919	13.208	13.208	0.000	0.000	0.000	0.000
141	A	259	VAL	0	0.012	0.018	18.789	0.756	0.756	0.000	0.000	0.000	0.000
142	A	260	THR	0	-0.013	-0.019	19.983	-0.674	-0.674	0.000	0.000	0.000	0.000
143	A	261	PRO	0	0.010	0.014	21.862	0.508	0.508	0.000	0.000	0.000	0.000
144	A	262	GLU	-1	-0.890	-0.930	25.036	-9.550	-9.550	0.000	0.000	0.000	0.000
145	A	263	GLY	0	0.039	0.017	28.035	-0.039	-0.039	0.000	0.000	0.000	0.000
146	A	264	SER	0	-0.093	-0.076	22.930	-0.348	-0.348	0.000	0.000	0.000	0.000
147	A	265	GLU	-1	-0.904	-0.944	23.888	-11.146	-11.146	0.000	0.000	0.000	0.000
148	A	266	GLU	-1	-0.953	-0.993	20.283	-14.667	-14.667	0.000	0.000	0.000	0.000
149	A	267	TRP	-1	-0.753	-0.845	17.000	-17.406	-17.406	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:119:CYS)