FMO DATABASE

FMODB ID: QK6GY

Calculation Name: 1V4P-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V4P

Chain ID: A

ChEMBL ID:

UniProt ID: O58307

Base Structure: X-ray

Registration Date: 2025-10-03

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1538791.477731
FMO2-HF: Nuclear repulsion	1478115.497166
FMO2-HF: Total energy	-60675.980565
FMO2-MP2: Total energy	-60854.913453

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:1:MET)

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

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.
2.836	5.828	0.387	-1.577	-1.801	-0.012

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.916

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	3	SER	0	0.000	-0.016	2.818	-4.046	-1.211	0.388	-1.567	-1.656	-0.012
4	A	4	ILE	0	0.032	0.015	4.762	1.583	1.740	-0.001	-0.010	-0.145	0.000
5	A	5	GLU	-1	-0.816	-0.888	6.715	-27.551	-27.551	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.022	0.023	7.129	1.665	1.665	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.812	0.912	4.993	32.692	32.692	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.029	-0.037	8.804	2.783	2.783	0.000	0.000	0.000	0.000
9	A	9	HIS	0	-0.026	-0.027	11.928	1.826	1.826	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.038	0.007	10.888	1.254	1.254	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.007	-0.005	12.960	1.350	1.350	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.040	-0.015	14.628	1.438	1.438	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.038	0.025	16.035	0.343	0.343	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.015	0.019	15.615	0.786	0.786	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.008	0.004	18.173	0.932	0.932	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.839	0.907	20.499	12.783	12.783	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.064	0.033	21.909	0.595	0.595	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.013	-0.006	22.345	0.567	0.567	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.030	-0.030	24.168	0.542	0.542	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.010	-0.001	26.471	0.448	0.448	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.814	0.921	26.127	11.574	11.574	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.052	-0.009	27.987	0.309	0.309	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.081	-0.047	30.050	0.325	0.325	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.069	0.051	31.645	0.291	0.291	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.000	-0.021	32.121	-0.232	-0.232	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.916	-0.954	33.903	-8.327	-8.327	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.046	-0.018	30.077	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.781	0.879	29.600	9.137	9.137	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.012	0.018	29.124	-0.459	-0.459	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.012	-0.031	24.414	0.131	0.131	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.032	-0.015	27.848	0.255	0.255	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.006	-0.017	25.002	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.016	0.009	20.243	-0.229	-0.229	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.024	-0.010	19.087	0.061	0.061	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.045	0.022	12.759	0.029	0.029	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.921	0.960	14.494	15.715	15.715	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.027	0.017	10.434	0.552	0.552	0.000	0.000	0.000	0.000
38	A	38	ASN	0	0.011	-0.011	10.424	-0.259	-0.259	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.805	0.901	11.702	17.486	17.486	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.068	0.030	15.292	-0.699	-0.699	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.073	-0.030	17.129	0.762	0.762	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.062	0.040	20.841	-0.270	-0.270	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.050	-0.029	23.103	0.516	0.516	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.075	0.044	26.681	-0.147	-0.147	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.875	0.940	29.150	9.131	9.131	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.048	0.011	32.634	-0.142	-0.142	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.870	-0.944	34.655	-8.080	-8.080	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.861	0.908	35.299	8.845	8.845	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.895	0.943	31.974	8.950	8.950	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.020	-0.003	30.890	0.199	0.199	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.017	-0.006	33.807	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.909	-0.965	31.570	-9.544	-9.544	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.888	-0.956	30.734	-8.934	-8.934	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.739	-0.824	30.884	-9.169	-9.169	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.028	-0.017	26.856	-0.465	-0.465	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.878	0.919	25.280	10.490	10.490	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.742	-0.834	26.376	-10.990	-10.990	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.003	0.000	23.851	-0.419	-0.419	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.806	-0.882	21.536	-13.217	-13.217	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.748	0.843	21.656	10.531	10.531	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.040	0.018	22.462	-0.511	-0.511	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.015	-0.001	19.061	-0.479	-0.479	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.060	-0.057	17.464	-1.598	-1.598	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.859	-0.907	18.323	-12.447	-12.447	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.906	0.940	18.268	13.707	13.707	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.039	-0.002	13.138	-0.687	-0.687	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.899	0.947	15.133	14.287	14.287	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.841	-0.902	17.176	-14.123	-14.123	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.033	-0.011	12.424	-1.444	-1.444	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.055	0.045	15.073	-0.348	-0.348	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.016	0.001	14.628	-1.355	-1.355	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.036	-0.026	12.227	1.394	1.394	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.839	0.945	14.578	14.083	14.083	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.008	-0.006	14.806	0.203	0.203	0.000	0.000	0.000	0.000
75	A	75	TYR	0	0.001	0.001	17.851	0.042	0.042	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.921	-0.974	20.043	-15.705	-15.705	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.001	0.003	22.710	0.235	0.235	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.051	0.029	26.531	-0.142	-0.142	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.820	0.909	29.846	9.893	9.893	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.798	-0.898	30.832	-9.490	-9.490	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.979	-1.000	30.522	-9.997	-9.997	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.004	-0.005	27.669	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.839	-0.913	29.179	-9.539	-9.539	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.880	0.943	32.239	9.022	9.022	0.000	0.000	0.000	0.000
85	A	85	MET	0	-0.058	-0.005	27.361	-0.038	-0.038	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.002	-0.025	24.681	-0.214	-0.214	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.011	0.026	29.567	0.067	0.067	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.863	-0.944	31.305	-9.214	-9.214	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.843	-0.911	28.970	-10.215	-10.215	0.000	0.000	0.000	0.000
90	A	90	MET	0	-0.042	0.008	25.955	-0.589	-0.589	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.077	-0.067	26.249	-0.653	-0.653	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.818	-0.886	25.193	-12.697	-12.697	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.058	-0.049	28.512	0.346	0.346	0.000	0.000	0.000	0.000
94	A	94	PHE	0	-0.057	-0.031	29.962	0.428	0.428	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.031	0.022	30.039	-0.390	-0.390	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.024	0.022	26.763	0.067	0.067	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.014	0.013	29.566	0.278	0.278	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.793	-0.888	31.965	-9.418	-9.418	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.907	-0.939	32.392	-9.982	-9.982	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.040	-0.018	27.180	-0.208	-0.208	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.809	0.867	30.186	9.408	9.408	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.020	0.007	24.823	0.101	0.101	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.001	-0.003	25.284	-0.242	-0.242	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.924	0.979	16.930	17.652	17.652	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.023	-0.020	21.467	0.201	0.201	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.008	0.007	16.915	-0.483	-0.483	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.016	-0.004	18.987	0.841	0.841	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.015	0.000	16.527	-0.552	-0.552	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.881	-0.973	19.638	-12.887	-12.887	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.860	-0.934	22.589	-11.190	-11.190	0.000	0.000	0.000	0.000
111	A	111	TRP	0	-0.057	-0.036	20.617	0.191	0.191	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.012	-0.021	20.868	-0.308	-0.308	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.051	0.042	21.851	-0.503	-0.503	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.035	-0.033	21.414	-0.323	-0.323	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.049	0.030	21.826	-0.643	-0.643	0.000	0.000	0.000	0.000
116	A	116	CYS	0	-0.059	-0.007	18.690	-0.359	-0.359	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.002	-0.013	19.421	-0.831	-0.831	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.915	0.962	15.020	17.391	17.391	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.911	-0.953	10.719	-24.644	-24.644	0.000	0.000	0.000	0.000
120	A	120	HIS	0	-0.022	-0.020	11.045	-0.166	-0.166	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.084	-0.061	6.873	-2.612	-2.612	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.965	0.977	8.320	33.303	33.303	0.000	0.000	0.000	0.000
123	A	123	THR	0	-0.020	-0.018	9.710	1.746	1.746	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.012	-0.019	10.820	-1.896	-1.896	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.045	0.029	11.955	0.147	0.147	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.839	-0.907	6.462	-38.284	-38.284	0.000	0.000	0.000	0.000
127	A	127	ILE	0	-0.026	0.013	7.072	-2.825	-2.825	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.040	0.026	9.345	-0.925	-0.925	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.024	0.001	10.887	0.883	0.883	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.015	0.012	14.001	-0.553	-0.553	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.802	0.894	16.335	13.564	13.564	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.036	0.007	19.439	-0.267	-0.267	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.800	0.885	18.118	14.431	14.431	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.888	0.948	23.076	11.943	11.943	0.000	0.000	0.000	0.000
135	A	135	VAL	0	0.047	0.037	25.515	-0.305	-0.305	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.893	0.952	28.222	9.794	9.794	0.000	0.000	0.000	0.000
137	A	137	PHE	0	0.062	0.046	30.715	-0.118	-0.118	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.762	0.854	29.477	9.954	9.954	0.000	0.000	0.000	0.000
139	A	139	LYS	1	1.036	1.010	35.318	7.420	7.420	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.028	-0.011	38.813	0.016	0.016	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.979	0.981	34.915	8.459	8.459	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.037	0.040	36.688	-0.096	-0.096	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.026	-0.014	31.213	-0.148	-0.148	0.000	0.000	0.000	0.000
144	A	144	LEU	0	0.000	0.010	29.351	0.223	0.223	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.796	-0.863	26.503	-10.923	-10.923	0.000	0.000	0.000	0.000
146	A	146	ILE	0	0.051	0.015	23.096	0.306	0.306	0.000	0.000	0.000	0.000
147	A	147	HIS	0	-0.016	-0.028	21.821	-0.766	-0.766	0.000	0.000	0.000	0.000
148	A	148	PHE	0	0.021	0.001	15.754	0.537	0.537	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.783	-0.859	14.975	-16.195	-16.195	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.058	-0.011	9.674	0.467	0.467	0.000	0.000	0.000	0.000
151	A	151	LEU	-1	-0.838	-0.911	10.834	-23.224	-23.224	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:1:MET)