FMO DATABASE

FMODB ID: 3G5ZL

Calculation Name: 1ZD0-A-Xray549

Preferred Name:

Target Type:

Ligand Name: methanol | unknown atom or ion

Ligand 3-letter code: MOH | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ZD0

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3E5

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1260792.863907
FMO2-HF: Nuclear repulsion	1205994.542558
FMO2-HF: Total energy	-54798.321349
FMO2-MP2: Total energy	-54960.002615

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:4:HIS)

Summations of interaction energy for fragment #1(A:4: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.
-21.119	-16.347	0.563	-2.631	-2.703	-0.024

Interaction energy analysis for fragmet #1(A:4:HIS)

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 : 0.908

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	6	HIS	0	0.066	0.044	3.662	-15.100	-13.804	0.011	-0.647	-0.660	0.001
5	A	8	SER	0	-0.083	-0.044	2.483	-10.884	-7.539	0.554	-1.979	-1.920	-0.025
6	A	9	LEU	0	0.075	0.034	4.891	-1.630	-1.579	-0.001	-0.004	-0.046	0.000
7	A	10	GLU	-1	-0.964	-0.973	4.834	-33.659	-33.579	-0.001	-0.001	-0.077	0.000
4	A	7	GLY	0	0.033	0.021	6.119	2.416	2.416	0.000	0.000	0.000	0.000
8	A	11	ILE	0	-0.015	-0.011	5.825	4.156	4.156	0.000	0.000	0.000	0.000
9	A	12	ARG	1	0.958	0.971	8.372	19.017	19.017	0.000	0.000	0.000	0.000
10	A	13	THR	0	0.006	0.003	10.308	2.173	2.173	0.000	0.000	0.000	0.000
11	A	14	LYS	1	0.950	0.971	12.659	21.224	21.224	0.000	0.000	0.000	0.000
12	A	15	VAL	0	0.021	0.002	16.390	-0.395	-0.395	0.000	0.000	0.000	0.000
13	A	16	GLY	0	-0.005	0.010	18.947	0.248	0.248	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.843	-0.931	21.979	-10.995	-10.995	0.000	0.000	0.000	0.000
15	A	18	ILE	0	-0.038	-0.027	22.724	-0.161	-0.161	0.000	0.000	0.000	0.000
16	A	19	CYS	0	-0.044	0.012	26.560	0.098	0.098	0.000	0.000	0.000	0.000
17	A	20	ILE	0	-0.026	-0.025	30.132	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.017	-0.036	32.185	0.100	0.100	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.827	0.918	35.837	7.934	7.934	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.010	-0.020	37.892	0.162	0.162	0.000	0.000	0.000	0.000
21	A	24	TRP	0	0.033	0.025	41.033	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.059	-0.035	40.486	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	26	THR	0	0.050	0.020	44.829	-0.040	-0.040	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.824	-0.921	45.799	-7.076	-7.076	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.895	-0.948	46.622	-6.467	-6.467	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.073	-0.043	45.314	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	30	ILE	0	0.027	0.020	41.203	-0.158	-0.158	0.000	0.000	0.000	0.000
28	A	31	ASN	0	0.004	-0.001	42.702	-0.252	-0.252	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.916	0.959	44.412	6.487	6.487	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.010	0.019	38.156	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	34	PHE	0	0.028	0.001	36.572	-0.136	-0.136	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.898	-0.937	40.399	-7.252	-7.252	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.849	0.936	42.527	6.967	6.967	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.004	0.002	37.544	-0.067	-0.067	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.854	0.919	36.172	7.949	7.949	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.017	0.018	32.906	-0.152	-0.152	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.890	-0.949	28.732	-11.237	-11.237	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.037	-0.049	30.412	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	42	GLN	0	-0.060	-0.043	30.597	0.110	0.110	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.003	0.002	32.414	0.016	0.016	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.053	-0.033	31.388	-0.060	-0.060	0.000	0.000	0.000	0.000
42	A	45	ASN	0	0.024	0.023	34.865	0.218	0.218	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.027	-0.046	32.907	-0.264	-0.264	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.896	-0.943	34.587	-8.608	-8.608	0.000	0.000	0.000	0.000
45	A	48	CYS	0	-0.041	0.005	30.412	0.171	0.171	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.032	0.019	31.361	-0.301	-0.301	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.810	-0.883	27.237	-11.140	-11.140	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.943	0.984	26.511	10.671	10.671	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.032	0.023	26.777	-0.393	-0.393	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.009	0.020	23.993	-0.424	-0.424	0.000	0.000	0.000	0.000
51	A	54	PHE	0	-0.029	-0.019	22.365	-0.671	-0.671	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.028	0.019	21.981	-0.698	-0.698	0.000	0.000	0.000	0.000
53	A	56	THR	0	-0.008	-0.022	23.152	-0.268	-0.268	0.000	0.000	0.000	0.000
54	A	57	ILE	0	-0.027	-0.013	18.250	-0.581	-0.581	0.000	0.000	0.000	0.000
55	A	58	ILE	0	-0.014	-0.006	16.824	-1.040	-1.040	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.000	0.003	18.814	-0.526	-0.526	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.008	-0.011	19.587	-0.353	-0.353	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.870	0.932	13.454	20.403	20.403	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.005	0.004	16.204	-0.683	-0.683	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.012	-0.019	17.273	-0.163	-0.163	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.904	0.967	16.193	17.418	17.418	0.000	0.000	0.000	0.000
62	A	65	GLU	-1	-0.964	-0.985	11.675	-25.174	-25.174	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.007	0.016	14.026	-0.462	-0.462	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.895	0.951	12.307	22.735	22.735	0.000	0.000	0.000	0.000
65	A	68	SER	0	-0.019	-0.010	16.220	-0.099	-0.099	0.000	0.000	0.000	0.000
66	A	69	ILE	0	-0.059	-0.033	19.626	0.223	0.223	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.015	0.006	22.511	0.403	0.403	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.880	0.935	21.257	12.823	12.823	0.000	0.000	0.000	0.000
69	A	72	THR	0	0.047	0.031	25.062	-0.046	-0.046	0.000	0.000	0.000	0.000
70	A	73	VAL	0	0.051	0.028	23.056	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	74	PRO	0	0.083	0.041	25.447	-0.096	-0.096	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.013	0.023	28.247	0.246	0.246	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.771	-0.878	21.032	-13.825	-13.825	0.000	0.000	0.000	0.000
74	A	77	ILE	0	0.029	0.013	24.919	-0.209	-0.209	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.045	0.034	26.551	0.037	0.037	0.000	0.000	0.000	0.000
76	A	79	VAL	0	-0.036	-0.001	24.081	0.117	0.117	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.823	0.900	17.915	15.171	15.171	0.000	0.000	0.000	0.000
78	A	81	LEU	0	0.054	0.035	24.468	-0.078	-0.078	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.054	-0.038	27.736	0.228	0.228	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.055	0.035	25.785	0.243	0.243	0.000	0.000	0.000	0.000
81	A	84	ASN	0	-0.031	-0.023	26.863	-0.048	-0.048	0.000	0.000	0.000	0.000
82	A	85	ARG	1	1.014	0.995	20.642	12.792	12.792	0.000	0.000	0.000	0.000
83	A	86	GLN	0	0.001	0.007	26.847	0.186	0.186	0.000	0.000	0.000	0.000
84	A	87	ILE	0	0.084	0.027	28.314	0.150	0.150	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.889	0.947	31.104	8.632	8.632	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.811	-0.889	32.460	-8.257	-8.257	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.004	0.004	30.106	0.088	0.088	0.000	0.000	0.000	0.000
88	A	91	ILE	0	0.035	0.012	32.128	0.058	0.058	0.000	0.000	0.000	0.000
89	A	92	LYS	1	0.844	0.908	35.148	8.272	8.272	0.000	0.000	0.000	0.000
90	A	93	LYS	1	0.855	0.927	31.022	9.863	9.863	0.000	0.000	0.000	0.000
91	A	94	VAL	0	0.047	0.017	30.720	0.078	0.078	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.006	0.017	34.214	-0.124	-0.124	0.000	0.000	0.000	0.000
93	A	96	ALA	0	-0.006	0.009	35.642	0.129	0.129	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.805	0.894	38.393	8.167	8.167	0.000	0.000	0.000	0.000
95	A	98	GLU	-1	-0.843	-0.904	42.078	-6.611	-6.611	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.007	-0.004	44.395	0.013	0.013	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.889	-0.940	41.019	-7.699	-7.699	0.000	0.000	0.000	0.000
98	A	101	ASN	0	-0.053	-0.038	38.402	-0.232	-0.232	0.000	0.000	0.000	0.000
99	A	102	TYR	0	0.016	0.003	33.784	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	103	ILE	0	-0.018	0.000	34.998	-0.067	-0.067	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.014	-0.012	28.445	-0.107	-0.107	0.000	0.000	0.000	0.000
102	A	105	THR	0	-0.007	-0.028	30.581	0.067	0.067	0.000	0.000	0.000	0.000
103	A	106	PHE	0	-0.003	-0.018	25.407	-0.416	-0.416	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.028	0.016	25.568	0.284	0.284	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.950	-0.970	26.567	-10.806	-10.806	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.025	-0.023	27.926	0.280	0.280	0.000	0.000	0.000	0.000
107	A	110	ALA	0	0.000	0.022	28.314	0.356	0.356	0.000	0.000	0.000	0.000
108	A	111	SER	0	0.060	0.033	30.470	0.432	0.432	0.000	0.000	0.000	0.000
109	A	112	ALA	0	0.031	0.013	32.938	0.282	0.282	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.030	-0.009	32.583	0.325	0.325	0.000	0.000	0.000	0.000
111	A	114	LEU	0	0.021	0.012	33.650	0.225	0.225	0.000	0.000	0.000	0.000
112	A	115	GLN	0	0.047	0.026	35.894	0.171	0.171	0.000	0.000	0.000	0.000
113	A	116	LYS	1	0.915	0.985	38.461	7.919	7.919	0.000	0.000	0.000	0.000
114	A	117	ILE	0	-0.007	-0.002	36.059	0.234	0.234	0.000	0.000	0.000	0.000
115	A	118	LEU	0	0.016	0.010	38.425	0.199	0.199	0.000	0.000	0.000	0.000
116	A	119	SER	0	-0.035	-0.038	41.705	0.229	0.229	0.000	0.000	0.000	0.000
117	A	120	THR	0	-0.078	-0.064	43.244	0.184	0.184	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.074	-0.037	42.506	0.152	0.152	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.944	-0.962	46.022	-6.258	-6.258	0.000	0.000	0.000	0.000
120	A	123	ILE	0	-0.048	-0.009	41.581	0.058	0.058	0.000	0.000	0.000	0.000
121	A	124	LYS	1	0.899	0.957	44.597	6.913	6.913	0.000	0.000	0.000	0.000
122	A	125	GLU	-1	-0.803	-0.874	39.317	-8.158	-8.158	0.000	0.000	0.000	0.000
123	A	126	LEU	0	-0.071	-0.038	41.151	0.289	0.289	0.000	0.000	0.000	0.000
124	A	127	GLU	-1	-0.919	-0.955	39.943	-7.786	-7.786	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.021	-0.017	32.703	-0.106	-0.106	0.000	0.000	0.000	0.000
126	A	129	GLU	-1	-0.856	-0.907	36.390	-8.388	-8.388	0.000	0.000	0.000	0.000
127	A	130	ARG	1	0.838	0.880	28.477	10.277	10.277	0.000	0.000	0.000	0.000
128	A	132	ASP	-1	-0.771	-0.873	32.104	-9.410	-9.410	0.000	0.000	0.000	0.000
129	A	133	LEU	0	-0.001	-0.030	27.527	-0.315	-0.315	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.956	-0.959	29.582	-9.499	-9.499	0.000	0.000	0.000	0.000
131	A	135	TYR	0	0.039	-0.005	30.498	-0.361	-0.361	0.000	0.000	0.000	0.000
132	A	136	ALA	0	-0.012	-0.011	27.316	-0.352	-0.352	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.852	0.902	25.762	11.227	11.227	0.000	0.000	0.000	0.000
134	A	138	LYS	1	0.871	0.920	25.565	10.313	10.313	0.000	0.000	0.000	0.000
135	A	139	ALA	0	-0.036	-0.025	26.291	-0.256	-0.256	0.000	0.000	0.000	0.000
136	A	140	PHE	0	-0.003	-0.004	17.515	-0.433	-0.433	0.000	0.000	0.000	0.000
137	A	141	GLU	-1	-0.821	-0.888	21.495	-12.723	-12.723	0.000	0.000	0.000	0.000
138	A	142	ASP	-1	-0.875	-0.927	22.164	-11.423	-11.423	0.000	0.000	0.000	0.000
139	A	143	ILE	0	-0.139	-0.072	20.877	0.122	0.122	0.000	0.000	0.000	0.000
140	A	144	ALA	-1	-0.975	-0.972	16.544	-18.235	-18.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:HIS)