FMO DATABASE

FMODB ID: VNVR1

Calculation Name: 3RCC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RCC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DZY1

Base Structure: X-ray

Registration Date: 2025-10-04

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1164344.646799
FMO2-HF: Nuclear repulsion	1111897.774324
FMO2-HF: Total energy	-52446.872474
FMO2-MP2: Total energy	-52598.904918

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:66:HIS)

Summations of interaction energy for fragment #1(A:66:HIS)

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.
-102.003	-96.416	16.049	-9.378	-12.259	-0.083

Interaction energy analysis for fragmet #1(A:66:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.812 / q_NPA : 0.886

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	68	LEU	0	0.035	0.026	2.322	-7.426	-3.872	2.257	-1.919	-3.893	-0.008
4	A	69	PRO	0	-0.017	-0.002	4.394	4.557	4.723	0.000	-0.023	-0.143	0.000
25	A	90	GLY	0	0.040	0.036	4.515	1.002	1.033	-0.001	-0.005	-0.025	0.000
27	A	92	THR	0	-0.038	0.010	2.559	-0.601	1.428	2.778	-1.314	-3.492	0.005
28	A	93	GLU	-1	-0.804	-0.904	1.781	-78.633	-78.859	11.016	-6.116	-4.675	-0.080
29	A	94	LEU	0	-0.022	-0.001	5.389	3.361	3.394	-0.001	-0.001	-0.031	0.000
5	A	70	VAL	0	0.007	0.005	7.954	0.491	0.491	0.000	0.000	0.000	0.000
6	A	71	ILE	0	-0.060	-0.031	10.006	1.328	1.328	0.000	0.000	0.000	0.000
7	A	72	GLY	0	-0.007	-0.005	12.537	1.596	1.596	0.000	0.000	0.000	0.000
8	A	73	GLY	0	-0.012	0.007	13.647	-1.472	-1.472	0.000	0.000	0.000	0.000
9	A	74	ILE	0	0.010	0.002	15.346	0.901	0.901	0.000	0.000	0.000	0.000
10	A	75	ALA	0	0.016	0.013	17.647	-0.455	-0.455	0.000	0.000	0.000	0.000
11	A	76	ILE	0	0.009	-0.002	20.442	0.466	0.466	0.000	0.000	0.000	0.000
12	A	77	PRO	0	0.002	-0.004	23.191	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	78	ASP	-1	-0.875	-0.945	25.300	-10.197	-10.197	0.000	0.000	0.000	0.000
14	A	79	VAL	0	-0.057	-0.034	23.323	0.250	0.250	0.000	0.000	0.000	0.000
15	A	80	GLU	-1	-0.947	-0.972	22.983	-12.415	-12.415	0.000	0.000	0.000	0.000
16	A	81	ILE	0	-0.028	0.000	17.955	-0.727	-0.727	0.000	0.000	0.000	0.000
17	A	82	ASN	0	-0.007	-0.023	18.064	0.330	0.330	0.000	0.000	0.000	0.000
18	A	83	LEU	0	-0.010	0.011	13.169	-0.691	-0.691	0.000	0.000	0.000	0.000
19	A	84	PRO	0	0.003	0.011	9.731	0.896	0.896	0.000	0.000	0.000	0.000
20	A	85	ILE	0	-0.003	0.002	11.243	-0.418	-0.418	0.000	0.000	0.000	0.000
21	A	86	PHE	0	0.023	-0.002	6.440	-2.019	-2.019	0.000	0.000	0.000	0.000
22	A	87	LYS	1	0.979	0.982	7.903	22.203	22.203	0.000	0.000	0.000	0.000
23	A	88	GLY	0	0.005	0.013	7.104	-2.984	-2.984	0.000	0.000	0.000	0.000
24	A	89	LEU	0	0.012	-0.004	8.419	-0.410	-0.410	0.000	0.000	0.000	0.000
26	A	91	ASN	0	0.058	0.001	5.557	1.060	1.060	0.000	0.000	0.000	0.000
30	A	95	SER	0	0.002	-0.009	7.766	1.739	1.739	0.000	0.000	0.000	0.000
31	A	96	TYR	0	-0.045	-0.031	5.261	-0.587	-0.587	0.000	0.000	0.000	0.000
32	A	97	GLY	0	0.022	0.008	8.301	1.337	1.337	0.000	0.000	0.000	0.000
33	A	98	ALA	0	-0.003	0.027	10.506	0.698	0.698	0.000	0.000	0.000	0.000
34	A	99	GLY	0	0.029	0.019	9.401	-1.481	-1.481	0.000	0.000	0.000	0.000
35	A	100	THR	0	-0.021	-0.027	10.042	1.832	1.832	0.000	0.000	0.000	0.000
36	A	101	MET	0	-0.040	-0.017	12.088	-0.488	-0.488	0.000	0.000	0.000	0.000
37	A	102	LYS	1	0.808	0.902	14.561	13.290	13.290	0.000	0.000	0.000	0.000
38	A	103	GLU	-1	-0.961	-0.982	13.829	-17.170	-17.170	0.000	0.000	0.000	0.000
39	A	104	ASN	0	-0.067	-0.035	15.235	-0.541	-0.541	0.000	0.000	0.000	0.000
40	A	105	GLN	0	0.019	0.008	15.771	1.047	1.047	0.000	0.000	0.000	0.000
41	A	106	ILE	0	-0.003	0.000	18.653	-0.498	-0.498	0.000	0.000	0.000	0.000
42	A	107	MET	0	0.002	0.023	16.898	0.408	0.408	0.000	0.000	0.000	0.000
43	A	108	GLY	0	0.033	0.014	20.758	0.304	0.304	0.000	0.000	0.000	0.000
44	A	109	GLY	0	-0.019	0.000	23.625	0.477	0.477	0.000	0.000	0.000	0.000
45	A	110	PRO	0	-0.058	-0.033	25.413	0.015	0.015	0.000	0.000	0.000	0.000
46	A	111	ASN	0	-0.007	-0.008	22.695	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	112	ASN	0	0.001	0.009	23.123	-0.218	-0.218	0.000	0.000	0.000	0.000
48	A	113	TYR	0	-0.007	-0.008	15.378	-0.462	-0.462	0.000	0.000	0.000	0.000
49	A	114	ALA	0	0.066	0.032	18.309	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	115	LEU	0	-0.021	-0.021	13.671	-0.976	-0.976	0.000	0.000	0.000	0.000
51	A	116	ALA	0	0.030	0.008	12.928	0.996	0.996	0.000	0.000	0.000	0.000
52	A	117	SER	0	-0.069	-0.052	12.223	-1.057	-1.057	0.000	0.000	0.000	0.000
53	A	118	HIS	0	0.015	0.003	10.912	1.751	1.751	0.000	0.000	0.000	0.000
54	A	119	HIS	0	0.006	0.014	12.065	-1.250	-1.250	0.000	0.000	0.000	0.000
55	A	120	VAL	0	-0.002	0.004	11.814	1.442	1.442	0.000	0.000	0.000	0.000
56	A	121	PHE	0	0.010	-0.007	14.230	0.158	0.158	0.000	0.000	0.000	0.000
57	A	122	GLY	0	-0.025	-0.020	17.746	0.041	0.041	0.000	0.000	0.000	0.000
58	A	123	LEU	0	-0.007	0.014	21.346	0.090	0.090	0.000	0.000	0.000	0.000
59	A	124	THR	0	-0.008	-0.021	24.753	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	125	GLY	0	0.046	0.012	28.011	0.160	0.160	0.000	0.000	0.000	0.000
61	A	126	SER	0	-0.065	-0.011	31.602	0.152	0.152	0.000	0.000	0.000	0.000
62	A	127	SER	0	-0.003	-0.003	30.275	0.000	0.000	0.000	0.000	0.000	0.000
63	A	128	LYS	1	0.903	0.956	21.168	13.763	13.763	0.000	0.000	0.000	0.000
64	A	129	MET	0	-0.014	0.004	25.279	0.033	0.033	0.000	0.000	0.000	0.000
65	A	130	LEU	0	0.066	0.011	19.660	-0.392	-0.392	0.000	0.000	0.000	0.000
66	A	131	PHE	0	0.021	0.028	21.520	-0.309	-0.309	0.000	0.000	0.000	0.000
67	A	132	SER	0	0.108	0.046	20.669	-0.405	-0.405	0.000	0.000	0.000	0.000
68	A	133	PRO	0	0.038	0.015	20.187	0.620	0.620	0.000	0.000	0.000	0.000
69	A	134	LEU	0	-0.025	-0.024	20.434	0.621	0.621	0.000	0.000	0.000	0.000
70	A	135	GLU	-1	-0.873	-0.907	23.947	-10.968	-10.968	0.000	0.000	0.000	0.000
71	A	136	HIS	0	0.020	0.001	26.461	0.627	0.627	0.000	0.000	0.000	0.000
72	A	137	ALA	0	0.019	0.027	25.823	0.363	0.363	0.000	0.000	0.000	0.000
73	A	138	LYS	1	0.862	0.892	27.951	9.731	9.731	0.000	0.000	0.000	0.000
74	A	139	LYS	1	0.979	0.985	30.039	8.235	8.235	0.000	0.000	0.000	0.000
75	A	140	GLY	0	-0.049	-0.025	31.797	0.203	0.203	0.000	0.000	0.000	0.000
76	A	141	MET	0	0.003	0.060	28.260	-0.081	-0.081	0.000	0.000	0.000	0.000
77	A	142	LYS	1	0.859	0.927	28.159	9.352	9.352	0.000	0.000	0.000	0.000
78	A	143	VAL	0	0.003	-0.009	22.148	-0.350	-0.350	0.000	0.000	0.000	0.000
79	A	144	TYR	0	-0.020	-0.007	22.830	0.427	0.427	0.000	0.000	0.000	0.000
80	A	145	LEU	0	0.010	0.016	18.586	-0.707	-0.707	0.000	0.000	0.000	0.000
81	A	146	THR	0	0.019	-0.002	18.305	0.644	0.644	0.000	0.000	0.000	0.000
82	A	147	ASP	-1	-0.748	-0.876	17.988	-14.490	-14.490	0.000	0.000	0.000	0.000
83	A	148	LYS	1	0.902	0.961	18.813	14.504	14.504	0.000	0.000	0.000	0.000
84	A	149	SER	0	-0.027	-0.033	20.026	0.603	0.603	0.000	0.000	0.000	0.000
85	A	150	LYS	1	0.899	0.975	22.722	12.290	12.290	0.000	0.000	0.000	0.000
86	A	151	VAL	0	0.025	0.002	22.646	-0.665	-0.665	0.000	0.000	0.000	0.000
87	A	152	TYR	0	-0.036	-0.034	22.167	0.724	0.724	0.000	0.000	0.000	0.000
88	A	153	THR	0	0.008	0.004	24.733	-0.435	-0.435	0.000	0.000	0.000	0.000
89	A	154	TYR	0	0.026	0.000	23.518	0.173	0.173	0.000	0.000	0.000	0.000
90	A	155	THR	0	0.001	-0.009	27.246	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	156	ILE	0	-0.024	-0.007	25.636	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	157	THR	0	-0.073	-0.055	28.677	0.398	0.398	0.000	0.000	0.000	0.000
93	A	158	GLU	-1	-0.859	-0.941	29.068	-9.295	-9.295	0.000	0.000	0.000	0.000
94	A	159	ILE	0	-0.032	-0.002	25.924	-0.416	-0.416	0.000	0.000	0.000	0.000
95	A	160	SER	0	-0.016	-0.019	26.721	0.453	0.453	0.000	0.000	0.000	0.000
96	A	161	LYS	1	0.783	0.887	26.038	10.164	10.164	0.000	0.000	0.000	0.000
97	A	162	VAL	0	-0.031	-0.010	24.646	0.405	0.405	0.000	0.000	0.000	0.000
98	A	163	THR	0	0.075	0.026	26.113	-0.321	-0.321	0.000	0.000	0.000	0.000
99	A	164	PRO	0	0.029	-0.002	24.356	-0.201	-0.201	0.000	0.000	0.000	0.000
100	A	165	GLU	-1	-0.962	-0.981	24.863	-9.512	-9.512	0.000	0.000	0.000	0.000
101	A	166	HIS	0	-0.043	-0.010	24.781	0.350	0.350	0.000	0.000	0.000	0.000
102	A	167	VAL	0	0.007	0.007	23.889	-0.582	-0.582	0.000	0.000	0.000	0.000
103	A	168	GLU	-1	-0.801	-0.876	22.152	-10.903	-10.903	0.000	0.000	0.000	0.000
104	A	169	VAL	0	0.000	0.008	23.023	-0.378	-0.378	0.000	0.000	0.000	0.000
105	A	170	ILE	0	-0.012	-0.012	18.718	0.028	0.028	0.000	0.000	0.000	0.000
106	A	171	ASP	-1	-0.868	-0.932	22.536	-10.816	-10.816	0.000	0.000	0.000	0.000
107	A	172	ASP	-1	-0.821	-0.897	23.752	-11.950	-11.950	0.000	0.000	0.000	0.000
108	A	173	THR	0	-0.010	-0.013	26.321	0.390	0.390	0.000	0.000	0.000	0.000
109	A	174	PRO	0	0.005	-0.012	29.891	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	175	GLY	0	-0.016	-0.005	32.064	0.193	0.193	0.000	0.000	0.000	0.000
111	A	176	LYS	1	0.867	0.934	30.248	8.968	8.968	0.000	0.000	0.000	0.000
112	A	177	SER	0	0.018	0.025	27.278	-0.131	-0.131	0.000	0.000	0.000	0.000
113	A	178	GLN	0	0.008	0.000	25.625	0.043	0.043	0.000	0.000	0.000	0.000
114	A	179	LEU	0	-0.023	-0.002	19.828	-0.351	-0.351	0.000	0.000	0.000	0.000
115	A	180	THR	0	-0.005	-0.017	21.062	0.260	0.260	0.000	0.000	0.000	0.000
116	A	181	LEU	0	-0.010	0.002	16.330	-0.652	-0.652	0.000	0.000	0.000	0.000
117	A	182	VAL	0	0.001	0.005	17.427	0.587	0.587	0.000	0.000	0.000	0.000
118	A	183	THR	0	-0.006	-0.017	16.566	-1.191	-1.191	0.000	0.000	0.000	0.000
119	A	184	CYS	0	-0.018	-0.012	16.699	0.990	0.990	0.000	0.000	0.000	0.000
120	A	185	THR	0	0.012	0.008	16.577	-0.792	-0.792	0.000	0.000	0.000	0.000
121	A	186	ASP	-1	-0.890	-0.935	18.237	-13.937	-13.937	0.000	0.000	0.000	0.000
122	A	187	PRO	0	-0.045	-0.034	17.263	0.441	0.441	0.000	0.000	0.000	0.000
123	A	188	GLU	-1	-0.948	-0.974	19.683	-12.692	-12.692	0.000	0.000	0.000	0.000
124	A	189	ALA	0	0.002	-0.009	22.983	0.515	0.515	0.000	0.000	0.000	0.000
125	A	190	THR	0	-0.069	-0.028	22.509	0.596	0.596	0.000	0.000	0.000	0.000
126	A	191	GLU	-1	-0.921	-0.946	23.593	-11.445	-11.445	0.000	0.000	0.000	0.000
127	A	192	ARG	1	0.851	0.907	20.421	11.899	11.899	0.000	0.000	0.000	0.000
128	A	193	ILE	0	-0.002	0.005	21.583	0.554	0.554	0.000	0.000	0.000	0.000
129	A	194	ILE	0	-0.025	-0.018	21.279	-0.739	-0.739	0.000	0.000	0.000	0.000
130	A	195	VAL	0	-0.019	0.004	22.195	0.589	0.589	0.000	0.000	0.000	0.000
131	A	196	HIS	1	0.857	0.905	23.265	10.443	10.443	0.000	0.000	0.000	0.000
132	A	197	ALA	0	0.009	0.012	24.890	0.377	0.377	0.000	0.000	0.000	0.000
133	A	198	GLU	-1	-0.875	-0.931	26.548	-9.220	-9.220	0.000	0.000	0.000	0.000
134	A	199	LEU	0	-0.057	-0.022	26.230	-0.075	-0.075	0.000	0.000	0.000	0.000
135	A	200	GLU	-1	-0.851	-0.898	28.655	-8.895	-8.895	0.000	0.000	0.000	0.000
136	A	201	LYS	1	0.860	0.910	30.599	8.916	8.916	0.000	0.000	0.000	0.000
137	A	202	THR	-1	-0.872	-0.917	27.648	-10.136	-10.136	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:66:HIS)