FMO DATABASE

FMODB ID: J4JJ9

Calculation Name: 2DNP-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DNP

Chain ID: A

ChEMBL ID:

UniProt ID: Q96PK6

Base Structure: SolutionNMR

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-555271.308163
FMO2-HF: Nuclear repulsion	521240.379756
FMO2-HF: Total energy	-34030.928407
FMO2-MP2: Total energy	-34129.264569

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:70:GLY)

Summations of interaction energy for fragment #1(A:70: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.
64.083	64.67	0.004	-0.333	-0.257	-0.001

Interaction energy analysis for fragmet #1(A:70:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.926

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	72	SER	0	-0.011	-0.019	3.818	-3.523	-2.936	0.004	-0.333	-0.257	-0.001
4	A	73	GLY	0	0.039	0.018	6.604	1.974	1.974	0.000	0.000	0.000	0.000
5	A	74	SER	0	-0.051	-0.004	10.437	1.093	1.093	0.000	0.000	0.000	0.000
6	A	75	SER	0	0.052	0.007	12.647	1.382	1.382	0.000	0.000	0.000	0.000
7	A	76	GLY	0	-0.019	0.001	15.927	-0.247	-0.247	0.000	0.000	0.000	0.000
8	A	77	ASN	0	-0.005	-0.017	12.305	0.144	0.144	0.000	0.000	0.000	0.000
9	A	78	THR	0	0.001	0.021	13.964	-1.241	-1.241	0.000	0.000	0.000	0.000
10	A	79	TRP	0	0.002	0.012	14.470	0.564	0.564	0.000	0.000	0.000	0.000
11	A	80	LYS	1	0.977	0.987	18.078	15.907	15.907	0.000	0.000	0.000	0.000
12	A	81	ILE	0	-0.024	-0.009	21.258	-0.107	-0.107	0.000	0.000	0.000	0.000
13	A	82	PHE	0	0.011	0.012	24.385	0.254	0.254	0.000	0.000	0.000	0.000
14	A	83	VAL	0	0.004	-0.003	27.395	0.101	0.101	0.000	0.000	0.000	0.000
15	A	84	GLY	0	0.070	0.032	30.852	0.125	0.125	0.000	0.000	0.000	0.000
16	A	85	ASN	0	-0.025	-0.022	34.015	0.179	0.179	0.000	0.000	0.000	0.000
17	A	86	VAL	0	0.041	0.036	34.611	0.115	0.115	0.000	0.000	0.000	0.000
18	A	87	SER	0	-0.047	-0.023	37.526	0.246	0.246	0.000	0.000	0.000	0.000
19	A	88	ALA	0	0.051	0.010	40.711	-0.086	-0.086	0.000	0.000	0.000	0.000
20	A	89	ALA	0	-0.005	0.010	42.751	0.046	0.046	0.000	0.000	0.000	0.000
21	A	90	CYS	0	-0.034	-0.011	37.772	0.060	0.060	0.000	0.000	0.000	0.000
22	A	91	THR	0	0.081	0.040	38.595	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	92	SER	0	0.072	0.022	33.382	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	93	GLN	0	0.011	0.002	33.681	-0.199	-0.199	0.000	0.000	0.000	0.000
25	A	94	GLU	-1	-0.931	-0.942	34.984	-8.326	-8.326	0.000	0.000	0.000	0.000
26	A	95	LEU	0	0.011	0.003	30.901	-0.137	-0.137	0.000	0.000	0.000	0.000
27	A	96	ARG	1	1.003	0.977	26.732	10.921	10.921	0.000	0.000	0.000	0.000
28	A	97	SER	0	-0.029	-0.020	30.462	-0.260	-0.260	0.000	0.000	0.000	0.000
29	A	98	LEU	0	-0.062	-0.031	32.322	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	99	PHE	0	0.017	-0.008	26.430	-0.140	-0.140	0.000	0.000	0.000	0.000
31	A	100	GLU	-1	-0.769	-0.874	26.732	-12.115	-12.115	0.000	0.000	0.000	0.000
32	A	101	ARG	1	0.884	0.949	28.514	9.044	9.044	0.000	0.000	0.000	0.000
33	A	102	ARG	1	0.849	0.923	27.020	10.388	10.388	0.000	0.000	0.000	0.000
34	A	103	GLY	0	0.050	0.035	24.151	-0.270	-0.270	0.000	0.000	0.000	0.000
35	A	104	ARG	1	0.845	0.918	21.022	12.769	12.769	0.000	0.000	0.000	0.000
36	A	105	VAL	0	-0.027	-0.018	22.304	-0.592	-0.592	0.000	0.000	0.000	0.000
37	A	106	ILE	0	-0.033	-0.010	18.277	0.222	0.222	0.000	0.000	0.000	0.000
38	A	107	GLU	-1	-0.910	-0.963	21.509	-13.967	-13.967	0.000	0.000	0.000	0.000
39	A	108	CYS	0	-0.053	-0.041	24.625	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	109	ASP	-1	-0.886	-0.911	27.749	-10.727	-10.727	0.000	0.000	0.000	0.000
41	A	110	VAL	0	-0.031	-0.034	29.944	-0.122	-0.122	0.000	0.000	0.000	0.000
42	A	111	VAL	0	-0.035	-0.010	31.108	0.105	0.105	0.000	0.000	0.000	0.000
43	A	112	LYS	1	0.909	0.947	34.080	8.481	8.481	0.000	0.000	0.000	0.000
44	A	113	ASP	-1	-0.842	-0.913	36.958	-8.132	-8.132	0.000	0.000	0.000	0.000
45	A	114	TYR	0	-0.040	-0.025	31.061	0.062	0.062	0.000	0.000	0.000	0.000
46	A	115	ALA	0	-0.008	-0.008	31.043	0.096	0.096	0.000	0.000	0.000	0.000
47	A	116	PHE	0	-0.027	-0.011	25.186	-0.283	-0.283	0.000	0.000	0.000	0.000
48	A	117	VAL	0	0.009	0.004	25.290	0.152	0.152	0.000	0.000	0.000	0.000
49	A	118	HIS	0	0.025	0.014	20.690	-0.296	-0.296	0.000	0.000	0.000	0.000
50	A	119	MET	0	-0.013	0.006	20.980	0.289	0.289	0.000	0.000	0.000	0.000
51	A	120	GLU	-1	-0.901	-0.966	14.790	-20.513	-20.513	0.000	0.000	0.000	0.000
52	A	121	LYS	1	0.951	0.986	16.395	15.481	15.481	0.000	0.000	0.000	0.000
53	A	122	GLU	-1	-0.814	-0.890	14.777	-19.634	-19.634	0.000	0.000	0.000	0.000
54	A	123	ALA	0	-0.002	-0.009	17.475	0.744	0.744	0.000	0.000	0.000	0.000
55	A	124	ASP	-1	-0.810	-0.920	20.083	-13.630	-13.630	0.000	0.000	0.000	0.000
56	A	125	ALA	0	0.011	0.004	20.180	0.670	0.670	0.000	0.000	0.000	0.000
57	A	126	LYS	1	0.808	0.889	17.716	17.856	17.856	0.000	0.000	0.000	0.000
58	A	127	ALA	0	0.011	0.011	23.127	0.606	0.606	0.000	0.000	0.000	0.000
59	A	128	ALA	0	-0.013	-0.013	25.330	0.596	0.596	0.000	0.000	0.000	0.000
60	A	129	ILE	0	-0.024	-0.016	23.629	0.439	0.439	0.000	0.000	0.000	0.000
61	A	130	ALA	0	0.000	-0.006	27.333	0.471	0.471	0.000	0.000	0.000	0.000
62	A	131	GLN	0	-0.057	-0.021	29.275	0.631	0.631	0.000	0.000	0.000	0.000
63	A	132	LEU	0	-0.042	-0.025	29.150	0.376	0.376	0.000	0.000	0.000	0.000
64	A	133	ASN	0	0.003	0.011	30.715	0.402	0.402	0.000	0.000	0.000	0.000
65	A	134	GLY	0	0.013	0.013	32.631	0.135	0.135	0.000	0.000	0.000	0.000
66	A	135	LYS	1	0.918	0.962	35.318	8.935	8.935	0.000	0.000	0.000	0.000
67	A	136	GLU	-1	-0.940	-0.974	37.103	-7.411	-7.411	0.000	0.000	0.000	0.000
68	A	137	VAL	0	-0.010	-0.018	36.789	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	138	LYS	1	0.888	0.938	40.244	7.327	7.327	0.000	0.000	0.000	0.000
70	A	139	GLY	0	0.040	0.020	43.288	0.090	0.090	0.000	0.000	0.000	0.000
71	A	140	LYS	1	0.947	0.983	41.252	7.623	7.623	0.000	0.000	0.000	0.000
72	A	141	ARG	1	0.950	0.982	39.183	7.641	7.641	0.000	0.000	0.000	0.000
73	A	142	ILE	0	-0.004	0.019	33.335	-0.038	-0.038	0.000	0.000	0.000	0.000
74	A	143	ASN	0	-0.008	-0.004	33.827	0.115	0.115	0.000	0.000	0.000	0.000
75	A	144	VAL	0	-0.015	-0.009	28.131	-0.180	-0.180	0.000	0.000	0.000	0.000
76	A	145	GLU	-1	-0.896	-0.954	27.328	-11.131	-11.131	0.000	0.000	0.000	0.000
77	A	146	LEU	0	-0.023	-0.015	19.417	-0.323	-0.323	0.000	0.000	0.000	0.000
78	A	147	SER	0	-0.013	0.005	22.660	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	148	THR	0	-0.019	-0.017	16.556	0.325	0.325	0.000	0.000	0.000	0.000
80	A	149	LYS	1	1.030	1.021	19.949	14.722	14.722	0.000	0.000	0.000	0.000
81	A	150	GLY	0	-0.049	-0.022	17.108	0.176	0.176	0.000	0.000	0.000	0.000
82	A	151	GLN	0	0.054	0.010	14.320	-0.761	-0.761	0.000	0.000	0.000	0.000
83	A	152	LYS	1	0.963	0.983	6.945	38.780	38.780	0.000	0.000	0.000	0.000
84	A	153	LYS	1	0.977	0.983	9.579	17.548	17.548	0.000	0.000	0.000	0.000
85	A	154	SER	0	-0.045	-0.019	6.036	-0.963	-0.963	0.000	0.000	0.000	0.000
86	A	155	GLY	0	0.025	0.015	7.991	-2.233	-2.233	0.000	0.000	0.000	0.000
87	A	156	PRO	0	0.002	0.004	9.178	1.397	1.397	0.000	0.000	0.000	0.000
88	A	157	SER	0	-0.016	-0.010	12.906	-0.695	-0.695	0.000	0.000	0.000	0.000
89	A	158	SER	0	-0.062	-0.042	15.660	-0.496	-0.496	0.000	0.000	0.000	0.000
90	A	159	GLY	-1	-0.889	-0.925	16.937	-14.666	-14.666	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:70:GLY)