FMO DATABASE

FMODB ID: Y1ML2

Calculation Name: 4YGO-E-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion | methanol

Ligand 3-letter code: CA | MOH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YGO

Chain ID: E

ChEMBL ID:

UniProt ID: Q9KL03

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1865448.120228
FMO2-HF: Nuclear repulsion	1796357.038742
FMO2-HF: Total energy	-69091.081486
FMO2-MP2: Total energy	-69296.225314

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:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-58.541	-56.068	-0.016	-0.949	-1.511	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.914

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	THR	0	-0.004	-0.016	3.883	-4.301	-2.610	-0.018	-0.806	-0.868	-0.002
59	A	62	ASP	-1	-0.781	-0.877	4.328	-43.912	-43.737	-0.001	-0.032	-0.142	0.000
60	A	63	ALA	0	-0.051	-0.043	3.675	3.843	4.170	0.005	-0.078	-0.254	0.000
61	A	64	GLN	0	-0.048	-0.023	5.266	5.322	5.422	-0.001	-0.002	-0.098	0.000
102	A	105	ARG	1	0.889	0.936	3.668	50.929	51.109	-0.001	-0.031	-0.149	0.000
4	A	7	LEU	0	0.015	0.006	6.574	1.392	1.392	0.000	0.000	0.000	0.000
5	A	8	ARG	1	0.762	0.845	10.279	20.434	20.434	0.000	0.000	0.000	0.000
6	A	9	ALA	0	0.012	0.003	12.962	0.523	0.523	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.016	0.005	16.705	-0.170	-0.170	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.948	-0.976	18.937	-14.839	-14.839	0.000	0.000	0.000	0.000
9	A	12	ARG	1	0.895	0.941	21.413	10.963	10.963	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.020	0.012	21.751	0.252	0.252	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.753	-0.852	17.568	-18.070	-18.070	0.000	0.000	0.000	0.000
12	A	15	LEU	0	0.030	0.016	20.135	-0.235	-0.235	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.909	0.978	22.074	12.296	12.296	0.000	0.000	0.000	0.000
14	A	17	PHE	0	-0.016	-0.008	14.196	0.188	0.188	0.000	0.000	0.000	0.000
15	A	18	ILE	0	0.033	0.011	19.372	-0.092	-0.092	0.000	0.000	0.000	0.000
16	A	19	HIS	0	0.007	-0.002	21.397	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.014	-0.013	20.799	0.742	0.742	0.000	0.000	0.000	0.000
18	A	21	LEU	0	-0.016	-0.008	16.638	0.085	0.085	0.000	0.000	0.000	0.000
19	A	22	ASN	0	-0.002	0.021	20.792	0.162	0.162	0.000	0.000	0.000	0.000
20	A	23	ASN	0	0.026	0.004	24.399	0.441	0.441	0.000	0.000	0.000	0.000
21	A	24	ASN	0	-0.104	-0.068	21.437	0.312	0.312	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.897	0.950	20.910	12.923	12.923	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.061	-0.016	24.655	0.326	0.326	0.000	0.000	0.000	0.000
24	A	27	ILE	0	-0.016	-0.007	26.441	0.329	0.329	0.000	0.000	0.000	0.000
25	A	28	MET	0	0.021	0.034	28.967	-0.254	-0.254	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.016	-0.016	26.407	-0.435	-0.435	0.000	0.000	0.000	0.000
27	A	30	TYR	0	0.007	-0.010	27.512	0.346	0.346	0.000	0.000	0.000	0.000
28	A	31	TRP	0	-0.008	-0.020	23.409	-0.894	-0.894	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.044	-0.046	26.450	0.343	0.343	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.910	-0.949	29.942	-9.240	-9.240	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.826	-0.864	31.857	-8.764	-8.764	0.000	0.000	0.000	0.000
32	A	35	PRO	0	-0.020	-0.012	31.575	-0.370	-0.370	0.000	0.000	0.000	0.000
33	A	36	TYR	0	-0.015	-0.011	25.475	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.911	-0.951	30.980	-9.234	-9.234	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.082	-0.070	30.717	-0.316	-0.316	0.000	0.000	0.000	0.000
36	A	39	PHE	0	-0.035	-0.041	25.916	-0.382	-0.382	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.845	-0.929	29.788	-9.605	-9.605	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.771	-0.854	32.783	-9.287	-9.287	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.004	0.010	25.094	-0.087	-0.087	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.940	-0.978	29.127	-10.939	-10.939	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.936	-0.970	30.062	-8.916	-8.916	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.021	-0.018	30.815	0.069	0.069	0.000	0.000	0.000	0.000
43	A	46	TYR	0	-0.009	-0.011	23.991	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	47	ASN	0	0.030	0.000	28.949	-0.293	-0.293	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.789	0.883	31.608	8.930	8.930	0.000	0.000	0.000	0.000
46	A	49	HIS	1	0.758	0.855	30.038	10.210	10.210	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.012	0.008	28.001	-0.321	-0.321	0.000	0.000	0.000	0.000
48	A	51	HIS	0	-0.055	-0.030	28.271	-0.429	-0.429	0.000	0.000	0.000	0.000
49	A	52	ASP	-1	-0.804	-0.877	29.543	-10.037	-10.037	0.000	0.000	0.000	0.000
50	A	53	ASN	0	0.004	-0.006	27.438	-0.504	-0.504	0.000	0.000	0.000	0.000
51	A	54	ALA	0	0.041	0.033	27.190	-0.389	-0.389	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.776	-0.862	24.901	-12.088	-12.088	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.863	0.931	20.468	13.810	13.810	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.795	0.873	19.121	13.245	13.245	0.000	0.000	0.000	0.000
55	A	58	PHE	0	-0.031	-0.020	14.003	-0.103	-0.103	0.000	0.000	0.000	0.000
56	A	59	VAL	0	0.030	0.032	12.971	-0.352	-0.352	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.035	-0.019	8.334	-2.118	-2.118	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.750	-0.847	8.776	-24.415	-24.415	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.834	0.919	8.049	33.985	33.985	0.000	0.000	0.000	0.000
63	A	66	ASN	0	-0.034	-0.019	8.325	4.554	4.554	0.000	0.000	0.000	0.000
64	A	67	LEU	0	0.018	0.002	9.745	-2.506	-2.506	0.000	0.000	0.000	0.000
65	A	68	ILE	0	-0.045	-0.022	6.865	0.787	0.787	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.019	-0.008	10.344	1.337	1.337	0.000	0.000	0.000	0.000
67	A	70	LEU	0	-0.023	0.007	13.008	-0.750	-0.750	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.005	-0.008	12.902	-0.099	-0.099	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.828	-0.908	15.685	-14.096	-14.096	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.043	-0.021	19.124	-0.255	-0.255	0.000	0.000	0.000	0.000
71	A	74	ILE	0	0.073	0.028	21.582	0.159	0.159	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.850	-0.926	25.267	-10.415	-10.415	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.077	-0.029	23.525	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	77	ASN	0	0.016	0.013	27.329	0.437	0.437	0.000	0.000	0.000	0.000
75	A	78	TYR	0	-0.002	-0.041	25.702	-0.297	-0.297	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.050	-0.010	29.738	0.023	0.023	0.000	0.000	0.000	0.000
77	A	80	HIS	0	-0.018	-0.018	32.291	-0.058	-0.058	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.815	0.920	26.054	11.409	11.409	0.000	0.000	0.000	0.000
79	A	82	SER	0	0.013	-0.004	26.707	-0.337	-0.337	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.044	0.028	23.601	0.073	0.073	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.791	-0.879	24.108	-12.073	-12.073	0.000	0.000	0.000	0.000
82	A	85	PHE	0	-0.034	-0.031	15.400	-0.711	-0.711	0.000	0.000	0.000	0.000
83	A	86	GLN	0	-0.018	-0.015	19.787	0.125	0.125	0.000	0.000	0.000	0.000
84	A	87	ILE	0	-0.041	-0.027	12.334	-1.187	-1.187	0.000	0.000	0.000	0.000
85	A	88	ILE	0	0.012	0.018	16.095	0.809	0.809	0.000	0.000	0.000	0.000
86	A	89	ILE	0	-0.033	-0.016	11.600	-1.580	-1.580	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.059	0.037	13.574	1.347	1.347	0.000	0.000	0.000	0.000
88	A	91	PRO	0	0.044	0.011	14.573	-0.915	-0.915	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.858	-0.929	13.650	-18.970	-18.970	0.000	0.000	0.000	0.000
90	A	93	HIS	0	-0.032	-0.035	10.106	-2.434	-2.434	0.000	0.000	0.000	0.000
91	A	94	GLN	0	-0.034	-0.009	11.483	-0.958	-0.958	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.011	-0.002	14.063	0.073	0.073	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.840	0.930	9.136	23.616	23.616	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.007	0.010	8.700	-2.137	-2.137	0.000	0.000	0.000	0.000
95	A	98	PHE	0	-0.002	-0.011	5.662	-2.145	-2.145	0.000	0.000	0.000	0.000
96	A	99	ALA	0	0.057	0.021	8.185	-0.975	-0.975	0.000	0.000	0.000	0.000
97	A	100	ARG	1	0.885	0.921	10.961	18.958	18.958	0.000	0.000	0.000	0.000
98	A	101	THR	0	-0.022	-0.002	4.805	-1.276	-1.276	0.000	0.000	0.000	0.000
99	A	102	LEU	0	-0.034	-0.019	7.425	-0.406	-0.406	0.000	0.000	0.000	0.000
100	A	103	ILE	0	0.062	0.031	9.799	0.947	0.947	0.000	0.000	0.000	0.000
101	A	104	ASN	0	0.000	0.015	10.641	0.474	0.474	0.000	0.000	0.000	0.000
103	A	106	ALA	0	0.029	0.024	10.868	0.895	0.895	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.016	0.017	14.248	1.343	1.343	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.869	-0.919	12.472	-21.938	-21.938	0.000	0.000	0.000	0.000
106	A	109	TYR	0	0.030	0.013	13.883	1.478	1.478	0.000	0.000	0.000	0.000
107	A	110	SER	0	-0.005	-0.027	15.425	1.397	1.397	0.000	0.000	0.000	0.000
108	A	111	PHE	0	-0.053	-0.023	18.100	1.053	1.053	0.000	0.000	0.000	0.000
109	A	112	THR	0	-0.030	-0.023	15.502	0.990	0.990	0.000	0.000	0.000	0.000
110	A	113	ILE	0	-0.059	-0.021	14.542	0.451	0.451	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.031	-0.016	18.773	0.744	0.744	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.011	0.008	21.195	0.654	0.654	0.000	0.000	0.000	0.000
113	A	116	LEU	0	0.043	0.024	21.941	0.761	0.761	0.000	0.000	0.000	0.000
114	A	117	HIS	0	-0.020	-0.011	24.152	-0.379	-0.379	0.000	0.000	0.000	0.000
115	A	118	LYS	1	0.777	0.860	25.457	10.601	10.601	0.000	0.000	0.000	0.000
116	A	119	ILE	0	0.023	0.028	20.079	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.012	-0.006	23.357	0.228	0.228	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.003	0.012	20.352	-0.468	-0.468	0.000	0.000	0.000	0.000
119	A	122	HIS	0	0.012	-0.006	23.961	0.759	0.759	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.029	-0.012	23.162	-0.506	-0.506	0.000	0.000	0.000	0.000
121	A	124	ALA	0	0.061	0.039	25.588	0.405	0.405	0.000	0.000	0.000	0.000
122	A	125	VAL	0	0.008	-0.004	27.709	-0.284	-0.284	0.000	0.000	0.000	0.000
123	A	126	GLU	-1	-0.812	-0.859	30.009	-9.426	-9.426	0.000	0.000	0.000	0.000
124	A	127	ASN	0	-0.035	-0.016	22.405	-0.208	-0.208	0.000	0.000	0.000	0.000
125	A	128	PRO	0	0.065	0.023	25.223	-0.416	-0.416	0.000	0.000	0.000	0.000
126	A	129	LYS	1	0.844	0.910	22.363	12.316	12.316	0.000	0.000	0.000	0.000
127	A	130	ALA	0	0.019	0.014	20.473	-0.658	-0.658	0.000	0.000	0.000	0.000
128	A	131	VAL	0	0.015	0.012	21.175	-0.432	-0.432	0.000	0.000	0.000	0.000
129	A	132	HIS	0	0.078	0.051	22.848	-0.496	-0.496	0.000	0.000	0.000	0.000
130	A	133	LEU	0	-0.038	-0.007	15.274	-0.543	-0.543	0.000	0.000	0.000	0.000
131	A	134	TYR	0	0.057	0.013	17.343	-0.759	-0.759	0.000	0.000	0.000	0.000
132	A	135	GLU	-1	-0.886	-0.945	19.931	-12.127	-12.127	0.000	0.000	0.000	0.000
133	A	136	GLU	-1	-0.875	-0.918	18.877	-15.628	-15.628	0.000	0.000	0.000	0.000
134	A	137	CYS	0	-0.142	-0.061	15.706	-1.340	-1.340	0.000	0.000	0.000	0.000
135	A	138	GLY	0	0.024	0.014	17.691	-0.277	-0.277	0.000	0.000	0.000	0.000
136	A	139	PHE	0	-0.012	-0.004	18.111	0.483	0.483	0.000	0.000	0.000	0.000
137	A	140	VAL	0	-0.019	-0.014	22.797	0.209	0.209	0.000	0.000	0.000	0.000
138	A	141	GLU	-1	-0.820	-0.893	26.602	-10.078	-10.078	0.000	0.000	0.000	0.000
139	A	142	GLU	-1	-0.805	-0.886	29.066	-10.398	-10.398	0.000	0.000	0.000	0.000
140	A	143	GLY	0	0.000	0.001	31.340	0.327	0.327	0.000	0.000	0.000	0.000
141	A	144	HIS	0	-0.029	-0.008	31.806	-0.528	-0.528	0.000	0.000	0.000	0.000
142	A	145	LEU	0	-0.023	-0.003	31.657	0.281	0.281	0.000	0.000	0.000	0.000
143	A	146	VAL	0	0.002	-0.010	34.647	-0.156	-0.156	0.000	0.000	0.000	0.000
144	A	147	GLU	-1	-0.965	-1.003	37.196	-7.556	-7.556	0.000	0.000	0.000	0.000
145	A	148	GLU	-1	-0.926	-0.947	32.666	-9.088	-9.088	0.000	0.000	0.000	0.000
146	A	149	PHE	0	0.024	0.007	28.829	-0.085	-0.085	0.000	0.000	0.000	0.000
147	A	150	PHE	0	-0.026	-0.007	34.039	0.092	0.092	0.000	0.000	0.000	0.000
148	A	151	ILE	0	0.014	0.005	29.399	-0.218	-0.218	0.000	0.000	0.000	0.000
149	A	152	ASN	0	-0.041	-0.032	32.077	0.290	0.290	0.000	0.000	0.000	0.000
150	A	153	GLY	0	0.007	0.007	34.079	0.118	0.118	0.000	0.000	0.000	0.000
151	A	154	ARG	1	0.773	0.846	33.905	9.214	9.214	0.000	0.000	0.000	0.000
152	A	155	TYR	0	0.032	0.027	36.448	-0.245	-0.245	0.000	0.000	0.000	0.000
153	A	156	GLN	0	-0.064	-0.041	31.616	-0.179	-0.179	0.000	0.000	0.000	0.000
154	A	157	ASP	-1	-0.749	-0.851	33.959	-8.714	-8.714	0.000	0.000	0.000	0.000
155	A	158	VAL	0	-0.032	-0.025	29.010	-0.376	-0.376	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.785	0.882	27.561	10.109	10.109	0.000	0.000	0.000	0.000
157	A	160	ARG	1	0.881	0.947	27.613	10.189	10.189	0.000	0.000	0.000	0.000
158	A	161	MET	0	-0.041	-0.021	24.499	0.119	0.119	0.000	0.000	0.000	0.000
159	A	162	TYR	0	-0.016	-0.018	24.643	-0.328	-0.328	0.000	0.000	0.000	0.000
160	A	163	ILE	0	0.031	0.017	19.933	0.011	0.011	0.000	0.000	0.000	0.000
161	A	164	LEU	0	-0.003	-0.005	23.756	0.146	0.146	0.000	0.000	0.000	0.000
162	A	165	GLN	0	0.020	0.003	22.532	0.168	0.168	0.000	0.000	0.000	0.000
163	A	166	SER	0	-0.043	-0.036	23.180	-0.404	-0.404	0.000	0.000	0.000	0.000
164	A	167	LYS	1	0.868	0.932	23.048	13.197	13.197	0.000	0.000	0.000	0.000
165	A	168	TYR	0	0.016	-0.011	13.724	-0.060	-0.060	0.000	0.000	0.000	0.000
166	A	169	LEU	0	-0.060	-0.017	18.977	-0.724	-0.724	0.000	0.000	0.000	0.000
167	A	170	ASN	-1	-0.990	-0.981	20.593	-13.875	-13.875	0.000	0.000	0.000	0.000

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