FMO DATABASE

FMODB ID: 5RMVZ

Calculation Name: 2DB1-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DB1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Z2X1

Base Structure: SolutionNMR

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-878285.066186
FMO2-HF: Nuclear repulsion	832230.039575
FMO2-HF: Total energy	-46055.026611
FMO2-MP2: Total energy	-46186.14966

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:-6:GLY)

Summations of interaction energy for fragment #1(A:-6:GLY)

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.
-67.485	-66.506	-0.01	-0.364	-0.605	-0.002

Interaction energy analysis for fragmet #1(A:-6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.907

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	-4	SER	0	0.029	0.014	3.835	2.074	3.053	-0.010	-0.364	-0.605	-0.002
4	A	-3	GLY	0	0.062	0.040	6.256	-0.151	-0.151	0.000	0.000	0.000	0.000
5	A	-2	SER	0	-0.015	-0.006	9.955	-1.794	-1.794	0.000	0.000	0.000	0.000
6	A	-1	SER	0	0.000	-0.009	10.743	0.771	0.771	0.000	0.000	0.000	0.000
7	A	0	GLY	0	0.035	0.034	13.208	1.372	1.372	0.000	0.000	0.000	0.000
8	A	1	MET	0	-0.080	-0.047	15.730	-0.538	-0.538	0.000	0.000	0.000	0.000
9	A	2	MET	0	0.057	0.034	17.722	0.520	0.520	0.000	0.000	0.000	0.000
10	A	3	LEU	0	-0.021	-0.010	19.881	0.573	0.573	0.000	0.000	0.000	0.000
11	A	4	GLY	0	0.004	0.004	19.399	-0.836	-0.836	0.000	0.000	0.000	0.000
12	A	5	PRO	0	-0.048	-0.026	17.895	0.705	0.705	0.000	0.000	0.000	0.000
13	A	6	GLU	-1	-0.876	-0.948	19.515	-14.255	-14.255	0.000	0.000	0.000	0.000
14	A	7	GLY	0	-0.004	0.011	17.989	-0.158	-0.158	0.000	0.000	0.000	0.000
15	A	8	GLY	0	-0.042	-0.032	18.303	-0.607	-0.607	0.000	0.000	0.000	0.000
16	A	9	GLU	-1	-1.002	-0.989	15.424	-18.648	-18.648	0.000	0.000	0.000	0.000
17	A	10	GLY	0	0.031	0.002	18.693	-0.434	-0.434	0.000	0.000	0.000	0.000
18	A	11	TYR	0	0.002	-0.007	12.542	0.137	0.137	0.000	0.000	0.000	0.000
19	A	12	VAL	0	0.029	0.024	19.051	0.707	0.707	0.000	0.000	0.000	0.000
20	A	13	VAL	0	-0.028	-0.008	21.519	-0.442	-0.442	0.000	0.000	0.000	0.000
21	A	14	LYS	1	0.844	0.929	24.116	10.895	10.895	0.000	0.000	0.000	0.000
22	A	15	LEU	0	0.038	0.022	27.432	-0.122	-0.122	0.000	0.000	0.000	0.000
23	A	16	ARG	1	0.905	0.930	30.015	9.253	9.253	0.000	0.000	0.000	0.000
24	A	17	GLY	0	0.051	0.034	32.979	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	18	LEU	0	0.029	0.016	33.483	0.247	0.247	0.000	0.000	0.000	0.000
26	A	19	PRO	0	-0.016	-0.021	37.242	0.195	0.195	0.000	0.000	0.000	0.000
27	A	20	TRP	0	-0.025	-0.028	40.631	0.053	0.053	0.000	0.000	0.000	0.000
28	A	21	SER	0	-0.021	-0.010	42.955	0.140	0.140	0.000	0.000	0.000	0.000
29	A	22	CYS	0	-0.060	0.008	37.203	-0.082	-0.082	0.000	0.000	0.000	0.000
30	A	23	SER	0	0.049	0.029	39.170	0.100	0.100	0.000	0.000	0.000	0.000
31	A	24	ILE	0	-0.001	-0.008	34.117	-0.199	-0.199	0.000	0.000	0.000	0.000
32	A	25	GLU	-1	-0.837	-0.926	34.723	-8.473	-8.473	0.000	0.000	0.000	0.000
33	A	26	ASP	-1	-0.847	-0.916	35.678	-8.316	-8.316	0.000	0.000	0.000	0.000
34	A	27	VAL	0	-0.021	-0.016	30.869	-0.215	-0.215	0.000	0.000	0.000	0.000
35	A	28	GLN	0	-0.004	-0.018	30.958	-0.109	-0.109	0.000	0.000	0.000	0.000
36	A	29	ASN	0	-0.077	-0.047	31.193	-0.186	-0.186	0.000	0.000	0.000	0.000
37	A	30	PHE	0	-0.017	-0.015	29.270	-0.104	-0.104	0.000	0.000	0.000	0.000
38	A	31	LEU	0	-0.006	-0.015	25.888	-0.203	-0.203	0.000	0.000	0.000	0.000
39	A	32	SER	0	0.024	0.026	27.438	-0.410	-0.410	0.000	0.000	0.000	0.000
40	A	33	ASP	-1	-0.915	-0.964	24.888	-12.106	-12.106	0.000	0.000	0.000	0.000
41	A	34	CYS	0	-0.085	-0.034	23.141	-0.827	-0.827	0.000	0.000	0.000	0.000
42	A	35	THR	0	-0.016	-0.019	22.087	0.725	0.725	0.000	0.000	0.000	0.000
43	A	36	ILE	0	-0.042	-0.015	23.489	-0.404	-0.404	0.000	0.000	0.000	0.000
44	A	37	HIS	1	0.821	0.901	23.443	13.084	13.084	0.000	0.000	0.000	0.000
45	A	38	ASP	-1	-0.857	-0.926	25.444	-11.320	-11.320	0.000	0.000	0.000	0.000
46	A	39	GLY	0	0.001	0.001	28.555	0.496	0.496	0.000	0.000	0.000	0.000
47	A	40	VAL	0	0.010	-0.011	30.446	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	41	ALA	0	-0.024	-0.012	31.879	0.126	0.126	0.000	0.000	0.000	0.000
49	A	42	GLY	0	0.036	0.028	28.375	-0.204	-0.204	0.000	0.000	0.000	0.000
50	A	43	VAL	0	-0.043	-0.018	28.682	-0.254	-0.254	0.000	0.000	0.000	0.000
51	A	44	HIS	1	0.884	0.936	29.143	10.789	10.789	0.000	0.000	0.000	0.000
52	A	45	PHE	0	0.044	0.017	32.509	-0.190	-0.190	0.000	0.000	0.000	0.000
53	A	46	ILE	0	-0.025	0.002	32.127	0.014	0.014	0.000	0.000	0.000	0.000
54	A	47	TYR	0	0.013	0.001	35.937	0.178	0.178	0.000	0.000	0.000	0.000
55	A	48	THR	0	0.041	0.029	39.201	-0.097	-0.097	0.000	0.000	0.000	0.000
56	A	49	ARG	1	1.036	1.007	41.824	6.847	6.847	0.000	0.000	0.000	0.000
57	A	50	GLU	-1	-0.912	-0.954	43.813	-6.460	-6.460	0.000	0.000	0.000	0.000
58	A	51	GLY	0	-0.009	0.000	44.078	0.118	0.118	0.000	0.000	0.000	0.000
59	A	52	ARG	1	0.828	0.917	44.369	6.632	6.632	0.000	0.000	0.000	0.000
60	A	53	GLN	0	0.030	0.016	39.507	-0.276	-0.276	0.000	0.000	0.000	0.000
61	A	54	SER	0	-0.030	-0.020	36.517	0.124	0.124	0.000	0.000	0.000	0.000
62	A	55	GLY	0	0.013	0.010	37.700	0.047	0.047	0.000	0.000	0.000	0.000
63	A	56	GLU	-1	-0.882	-0.939	32.737	-9.696	-9.696	0.000	0.000	0.000	0.000
64	A	57	ALA	0	0.002	-0.001	32.180	0.245	0.245	0.000	0.000	0.000	0.000
65	A	58	PHE	0	-0.005	-0.004	26.605	-0.180	-0.180	0.000	0.000	0.000	0.000
66	A	59	VAL	0	-0.017	-0.012	26.355	0.371	0.371	0.000	0.000	0.000	0.000
67	A	60	GLU	-1	-0.853	-0.943	23.227	-13.935	-13.935	0.000	0.000	0.000	0.000
68	A	61	LEU	0	-0.064	-0.032	20.642	0.368	0.368	0.000	0.000	0.000	0.000
69	A	62	GLU	-1	-0.819	-0.901	20.563	-14.275	-14.275	0.000	0.000	0.000	0.000
70	A	63	SER	0	-0.070	-0.045	16.209	-1.234	-1.234	0.000	0.000	0.000	0.000
71	A	64	GLU	-1	-0.888	-0.948	11.080	-26.529	-26.529	0.000	0.000	0.000	0.000
72	A	65	ASP	-1	-0.872	-0.948	14.229	-21.205	-21.205	0.000	0.000	0.000	0.000
73	A	66	ASP	-1	-0.697	-0.837	16.311	-14.632	-14.632	0.000	0.000	0.000	0.000
74	A	67	VAL	0	0.009	-0.001	17.071	0.681	0.681	0.000	0.000	0.000	0.000
75	A	68	LYS	1	0.753	0.880	11.716	24.292	24.292	0.000	0.000	0.000	0.000
76	A	69	LEU	0	-0.065	-0.024	18.028	0.452	0.452	0.000	0.000	0.000	0.000
77	A	70	ALA	0	0.127	0.050	21.259	0.570	0.570	0.000	0.000	0.000	0.000
78	A	71	LEU	0	-0.060	-0.039	18.823	0.436	0.436	0.000	0.000	0.000	0.000
79	A	72	LYS	1	0.845	0.928	19.233	15.207	15.207	0.000	0.000	0.000	0.000
80	A	73	LYS	1	0.833	0.931	24.358	11.253	11.253	0.000	0.000	0.000	0.000
81	A	74	ASP	-1	-0.852	-0.945	26.567	-10.424	-10.424	0.000	0.000	0.000	0.000
82	A	75	ARG	1	0.850	0.929	28.188	10.506	10.506	0.000	0.000	0.000	0.000
83	A	76	GLU	-1	-0.824	-0.879	30.102	-9.771	-9.771	0.000	0.000	0.000	0.000
84	A	77	SER	0	-0.052	-0.024	32.786	0.228	0.228	0.000	0.000	0.000	0.000
85	A	78	MET	0	0.001	0.008	34.215	0.001	0.001	0.000	0.000	0.000	0.000
86	A	79	GLY	0	0.010	-0.001	37.255	0.166	0.166	0.000	0.000	0.000	0.000
87	A	80	HIS	0	-0.038	-0.020	40.947	0.091	0.091	0.000	0.000	0.000	0.000
88	A	81	ARG	1	0.853	0.933	39.297	7.907	7.907	0.000	0.000	0.000	0.000
89	A	82	TYR	0	0.012	0.012	35.326	0.044	0.044	0.000	0.000	0.000	0.000
90	A	83	ILE	0	-0.065	-0.024	31.419	0.109	0.109	0.000	0.000	0.000	0.000
91	A	84	GLU	-1	-0.875	-0.931	30.566	-9.553	-9.553	0.000	0.000	0.000	0.000
92	A	85	VAL	0	0.004	-0.004	24.708	0.022	0.022	0.000	0.000	0.000	0.000
93	A	86	PHE	0	-0.036	-0.017	24.877	-0.175	-0.175	0.000	0.000	0.000	0.000
94	A	87	LYS	1	0.955	0.982	15.410	18.088	18.088	0.000	0.000	0.000	0.000
95	A	88	SER	0	-0.043	-0.034	21.691	0.020	0.020	0.000	0.000	0.000	0.000
96	A	89	HIS	0	0.040	0.012	19.899	-0.905	-0.905	0.000	0.000	0.000	0.000
97	A	90	ARG	1	0.934	0.958	21.490	13.115	13.115	0.000	0.000	0.000	0.000
98	A	91	THR	0	0.043	0.009	22.090	0.546	0.546	0.000	0.000	0.000	0.000
99	A	92	GLU	-1	-0.912	-0.935	24.386	-11.641	-11.641	0.000	0.000	0.000	0.000
100	A	93	MET	0	-0.007	0.006	25.882	0.580	0.580	0.000	0.000	0.000	0.000
101	A	94	ASP	-1	-0.836	-0.908	27.067	-11.235	-11.235	0.000	0.000	0.000	0.000
102	A	95	TRP	0	-0.023	-0.018	28.381	0.675	0.675	0.000	0.000	0.000	0.000
103	A	96	VAL	0	-0.019	-0.008	29.842	0.427	0.427	0.000	0.000	0.000	0.000
104	A	97	LEU	0	0.005	0.000	31.147	0.383	0.383	0.000	0.000	0.000	0.000
105	A	98	LYS	1	0.930	0.966	32.280	10.147	10.147	0.000	0.000	0.000	0.000
106	A	99	HIS	0	-0.072	-0.038	34.256	0.356	0.356	0.000	0.000	0.000	0.000
107	A	100	SER	0	-0.036	-0.002	36.052	0.068	0.068	0.000	0.000	0.000	0.000
108	A	101	GLY	0	0.017	0.005	37.802	0.206	0.206	0.000	0.000	0.000	0.000
109	A	102	PRO	0	-0.034	-0.024	40.428	0.051	0.051	0.000	0.000	0.000	0.000
110	A	103	ASN	0	-0.066	-0.031	43.290	0.168	0.168	0.000	0.000	0.000	0.000
111	A	104	SER	0	0.067	0.038	40.229	-0.060	-0.060	0.000	0.000	0.000	0.000
112	A	105	ALA	0	-0.019	-0.013	41.517	-0.092	-0.092	0.000	0.000	0.000	0.000
113	A	106	SER	0	-0.030	-0.012	41.499	0.090	0.090	0.000	0.000	0.000	0.000
114	A	107	GLY	0	0.022	0.023	38.900	-0.139	-0.139	0.000	0.000	0.000	0.000
115	A	108	PRO	0	-0.058	-0.030	37.169	0.147	0.147	0.000	0.000	0.000	0.000
116	A	109	SER	0	0.008	-0.007	40.316	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	110	SER	0	-0.081	-0.037	39.162	0.090	0.090	0.000	0.000	0.000	0.000
118	A	111	GLY	-1	-0.897	-0.935	38.646	-8.294	-8.294	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-6:GLY)