FMO DATABASE

FMODB ID: 97G42

Calculation Name: 2Y1R-D-Xray547

Preferred Name:

Target Type:

Ligand Name: s,r meso-tartaric acid

Ligand 3-letter code: SRT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2Y1R

Chain ID: D

ChEMBL ID:

UniProt ID: P37571

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1288578.228821
FMO2-HF: Nuclear repulsion	1235460.797036
FMO2-HF: Total energy	-53117.431785
FMO2-MP2: Total energy	-53275.367579

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:3:PHE)

Summations of interaction energy for fragment #1(A:3:PHE)

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.
14.541	17.782	10.569	-3.148	-10.659	0.009

Interaction energy analysis for fragmet #1(A:3:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.921

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	5	ARG	1	0.865	0.928	3.381	20.715	22.353	0.005	-0.986	-0.656	0.000
4	A	6	PHE	0	0.042	0.018	3.746	1.893	2.266	0.001	-0.045	-0.329	0.000
84	A	86	LYS	1	0.897	0.944	4.549	21.813	21.961	-0.001	-0.010	-0.136	0.000
86	A	88	ILE	0	0.006	0.011	3.036	-1.290	-0.681	0.074	-0.155	-0.528	0.000
87	A	89	GLU	-1	-0.855	-0.905	2.258	-35.641	-35.030	2.747	-0.954	-2.403	-0.004
88	A	90	LEU	0	-0.030	-0.011	3.249	1.429	1.273	0.033	0.317	-0.194	-0.001
90	A	92	MET	0	-0.036	-0.006	2.355	-3.130	-3.112	7.710	-1.315	-6.413	0.014
5	A	7	THR	0	0.022	0.000	8.468	1.163	1.163	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.884	-0.937	11.813	-18.812	-18.812	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.917	0.946	13.826	14.672	14.672	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.004	0.002	10.689	0.265	0.265	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.044	-0.033	8.697	-1.282	-1.282	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.929	0.972	10.975	15.471	15.471	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.020	-0.014	12.426	0.499	0.499	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.020	-0.013	7.431	0.550	0.550	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.007	0.013	11.509	0.236	0.236	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.006	0.015	13.690	1.032	1.032	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.002	0.001	12.569	0.863	0.863	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.021	-0.015	12.793	-0.603	-0.603	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.842	-0.920	15.026	-14.721	-14.721	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.805	-0.899	17.931	-12.870	-12.870	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.003	-0.002	16.127	0.614	0.614	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.006	-0.007	17.785	0.549	0.549	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.823	0.916	20.503	13.217	13.217	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.033	-0.007	21.351	0.688	0.688	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.040	0.041	23.156	0.350	0.350	0.000	0.000	0.000	0.000
24	A	26	HIS	0	0.005	0.014	19.506	-0.368	-0.368	0.000	0.000	0.000	0.000
25	A	27	ASN	0	0.010	-0.008	18.701	-0.225	-0.225	0.000	0.000	0.000	0.000
26	A	28	ASN	0	-0.045	-0.045	14.333	-1.142	-1.142	0.000	0.000	0.000	0.000
27	A	29	ILE	0	0.024	0.033	10.917	0.679	0.679	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.051	0.010	12.208	-1.279	-1.279	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.060	-0.034	11.859	-0.506	-0.506	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.780	-0.910	13.621	-16.290	-16.290	0.000	0.000	0.000	0.000
31	A	33	HIS	0	0.048	0.030	14.855	-0.521	-0.521	0.000	0.000	0.000	0.000
32	A	34	ILE	0	0.002	0.006	9.457	-0.260	-0.260	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.023	-0.012	13.680	0.168	0.168	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.002	0.000	16.910	0.419	0.419	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.025	0.010	15.796	0.484	0.484	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.066	-0.048	13.747	0.101	0.101	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.046	-0.010	17.063	0.400	0.400	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.781	0.873	19.956	14.794	14.794	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.850	-0.912	16.806	-15.664	-15.664	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.060	0.041	19.446	0.304	0.304	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.926	-0.966	21.286	-12.814	-12.814	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.019	-0.019	18.893	0.213	0.213	0.000	0.000	0.000	0.000
43	A	45	ILE	0	0.030	0.017	19.286	0.417	0.417	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.000	-0.002	16.704	0.475	0.475	0.000	0.000	0.000	0.000
45	A	47	ALA	0	0.045	0.041	18.825	0.575	0.575	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.846	0.914	21.241	12.750	12.750	0.000	0.000	0.000	0.000
47	A	49	ALA	0	0.048	0.018	20.791	0.570	0.570	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.024	-0.013	18.768	0.500	0.500	0.000	0.000	0.000	0.000
49	A	51	GLN	0	0.025	0.010	23.027	0.725	0.725	0.000	0.000	0.000	0.000
50	A	52	ALA	0	0.026	0.015	26.077	0.457	0.457	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.090	-0.029	22.375	0.357	0.357	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.001	0.010	26.642	0.294	0.294	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.079	-0.049	23.051	0.203	0.203	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.089	0.047	25.299	-0.332	-0.332	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.025	-0.004	24.252	-0.438	-0.438	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.826	-0.928	25.257	-10.841	-10.841	0.000	0.000	0.000	0.000
57	A	59	LYS	1	0.840	0.923	27.601	10.123	10.123	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.009	0.008	21.078	0.048	0.048	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.011	-0.008	23.221	-0.166	-0.166	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.975	0.987	25.166	9.025	9.025	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.849	-0.905	24.907	-10.324	-10.324	0.000	0.000	0.000	0.000
62	A	64	VAL	0	0.008	-0.009	20.884	-0.079	-0.079	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.845	-0.937	23.705	-11.025	-11.025	0.000	0.000	0.000	0.000
64	A	66	SER	0	-0.054	-0.022	26.415	0.377	0.377	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.097	-0.040	23.151	0.148	0.148	0.000	0.000	0.000	0.000
66	A	68	ILE	0	-0.056	-0.036	21.009	-0.065	-0.065	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.014	0.030	24.298	0.053	0.053	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.771	0.882	25.846	10.942	10.942	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.056	0.008	25.802	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	72	GLN	0	-0.063	-0.014	24.391	0.471	0.471	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.809	-0.928	25.003	-12.018	-12.018	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.092	-0.033	23.348	-0.690	-0.690	0.000	0.000	0.000	0.000
73	A	75	SER	0	0.014	-0.002	22.305	0.149	0.149	0.000	0.000	0.000	0.000
74	A	76	GLN	0	0.003	0.014	19.984	-0.219	-0.219	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.015	-0.021	14.687	-0.139	-0.139	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.008	0.032	14.861	-0.435	-0.435	0.000	0.000	0.000	0.000
77	A	79	HIS	0	0.030	0.012	11.259	-3.127	-3.127	0.000	0.000	0.000	0.000
78	A	80	TYR	0	0.030	0.021	7.258	1.200	1.200	0.000	0.000	0.000	0.000
79	A	81	THR	0	0.034	0.017	9.947	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	82	PRO	0	0.010	-0.011	9.764	-1.616	-1.616	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.808	0.879	8.960	15.276	15.276	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.029	0.024	9.373	-0.633	-0.633	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.883	0.933	5.524	25.178	25.178	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.025	0.015	6.270	-0.840	-0.840	0.000	0.000	0.000	0.000
89	A	91	SER	0	-0.028	-0.025	5.861	1.113	1.113	0.000	0.000	0.000	0.000
91	A	93	ASP	-1	-0.767	-0.848	6.629	-20.498	-20.498	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.818	-0.890	8.018	-16.493	-16.493	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.013	0.010	9.845	1.155	1.155	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.855	0.917	8.549	23.096	23.096	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.786	0.873	11.296	19.281	19.281	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.016	0.003	13.782	1.128	1.128	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.013	0.019	15.009	0.535	0.535	0.000	0.000	0.000	0.000
98	A	100	HIS	0	-0.015	0.003	13.694	-0.799	-0.799	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.003	-0.006	10.952	-1.691	-1.691	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.044	-0.025	9.772	-3.306	-3.306	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.017	0.014	7.133	2.169	2.169	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.082	0.042	10.059	-0.102	-0.102	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.021	-0.021	12.689	-0.460	-0.460	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.782	-0.909	14.270	-18.288	-18.288	0.000	0.000	0.000	0.000
105	A	107	HIS	0	0.051	0.043	11.131	-0.981	-0.981	0.000	0.000	0.000	0.000
106	A	108	ILE	0	0.013	-0.002	9.215	-0.590	-0.590	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.003	0.013	10.949	0.358	0.358	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.013	0.001	13.623	0.539	0.539	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.019	0.004	9.729	0.462	0.462	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.016	-0.015	10.669	0.272	0.272	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.049	-0.036	12.613	0.856	0.856	0.000	0.000	0.000	0.000
112	A	114	ARG	1	0.756	0.855	9.887	20.484	20.484	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.811	-0.901	10.542	-18.722	-18.722	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.037	-0.016	12.651	0.603	0.603	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.852	-0.930	15.019	-13.003	-13.003	0.000	0.000	0.000	0.000
116	A	118	GLY	0	-0.010	-0.005	15.144	-0.895	-0.895	0.000	0.000	0.000	0.000
117	A	119	VAL	0	0.014	0.008	16.963	0.458	0.458	0.000	0.000	0.000	0.000
118	A	120	ALA	0	0.037	0.013	15.825	0.547	0.547	0.000	0.000	0.000	0.000
119	A	121	ALA	0	0.019	0.026	17.344	0.496	0.496	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.897	0.954	18.956	11.221	11.221	0.000	0.000	0.000	0.000
121	A	123	VAL	0	0.038	0.014	20.854	0.466	0.466	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.026	-0.016	18.504	0.444	0.444	0.000	0.000	0.000	0.000
123	A	125	ASN	0	-0.015	-0.002	22.611	0.620	0.620	0.000	0.000	0.000	0.000
124	A	126	ASN	0	-0.019	-0.027	24.775	0.426	0.426	0.000	0.000	0.000	0.000
125	A	127	LEU	0	-0.035	-0.007	24.722	0.402	0.402	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.012	0.011	27.633	0.137	0.137	0.000	0.000	0.000	0.000
127	A	129	VAL	0	-0.086	-0.042	23.047	0.129	0.129	0.000	0.000	0.000	0.000
128	A	130	SER	0	0.024	0.008	23.952	-0.380	-0.380	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.053	0.032	17.992	-0.037	-0.037	0.000	0.000	0.000	0.000
130	A	132	ASN	0	0.037	0.016	20.644	-0.641	-0.641	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.940	0.987	22.688	10.182	10.182	0.000	0.000	0.000	0.000
132	A	134	ALA	0	0.044	0.007	20.332	0.014	0.014	0.000	0.000	0.000	0.000
133	A	135	ARG	1	0.901	0.943	18.201	12.329	12.329	0.000	0.000	0.000	0.000
134	A	136	GLN	0	0.026	0.017	20.189	-0.466	-0.466	0.000	0.000	0.000	0.000
135	A	137	GLN	0	0.014	0.011	23.438	0.097	0.097	0.000	0.000	0.000	0.000
136	A	138	VAL	0	-0.009	-0.018	17.392	-0.066	-0.066	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.039	-0.029	18.749	-0.173	-0.173	0.000	0.000	0.000	0.000
138	A	140	GLN	0	-0.045	-0.008	21.805	0.377	0.377	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.048	-0.019	22.937	0.257	0.257	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.094	-0.046	18.293	-0.584	-0.584	0.000	0.000	0.000	0.000
141	A	143	GLY	-1	-0.916	-0.938	22.852	-11.339	-11.339	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:PHE)