FMO DATABASE

FMODB ID: 7KM9K

Calculation Name: 2D2A-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D2A

Chain ID: B

ChEMBL ID:

UniProt ID: P77667

Base Structure: X-ray

Registration Date: 2025-10-05

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-744270.828013
FMO2-HF: Nuclear repulsion	703887.86661
FMO2-HF: Total energy	-40382.961403
FMO2-MP2: Total energy	-40501.317428

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-45.233	-43.336	0.006	-0.823	-1.081	-0.003

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.912

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	7	THR	0	-0.003	0.003	3.481	3.357	5.254	0.006	-0.823	-1.081	-0.003
4	A	8	PHE	0	0.002	0.000	5.615	-0.400	-0.400	0.000	0.000	0.000	0.000
5	A	9	ASN	0	0.022	-0.011	8.550	0.964	0.964	0.000	0.000	0.000	0.000
6	A	10	PRO	0	-0.001	0.000	12.162	0.355	0.355	0.000	0.000	0.000	0.000
7	A	11	GLN	0	-0.010	0.003	15.339	0.505	0.505	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.882	-0.929	13.164	-19.294	-19.294	0.000	0.000	0.000	0.000
9	A	13	PHE	0	-0.054	-0.026	11.762	-0.997	-0.997	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.024	-0.006	14.940	0.943	0.943	0.000	0.000	0.000	0.000
11	A	15	TRP	0	-0.012	-0.016	16.817	-0.183	-0.183	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.041	-0.018	19.782	-0.102	-0.102	0.000	0.000	0.000	0.000
13	A	17	GLY	0	-0.022	-0.017	22.288	0.355	0.355	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.061	-0.021	25.039	0.102	0.102	0.000	0.000	0.000	0.000
15	A	19	THR	0	0.008	0.002	28.557	0.040	0.040	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.009	-0.008	31.587	0.105	0.105	0.000	0.000	0.000	0.000
17	A	21	THR	0	0.034	-0.005	35.300	0.051	0.051	0.000	0.000	0.000	0.000
18	A	22	PRO	0	0.040	0.009	38.223	0.040	0.040	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.008	0.008	41.008	0.133	0.133	0.000	0.000	0.000	0.000
20	A	24	ALA	0	0.032	0.021	38.684	0.139	0.139	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.052	0.025	38.850	0.065	0.065	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.033	-0.029	40.292	0.075	0.075	0.000	0.000	0.000	0.000
23	A	27	HIS	1	0.826	0.917	43.503	6.866	6.866	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.019	0.019	38.443	0.075	0.075	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.901	0.952	41.762	7.221	7.221	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.921	-0.959	43.815	-6.355	-6.355	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.075	-0.035	42.858	0.159	0.159	0.000	0.000	0.000	0.000
28	A	32	VAL	0	0.026	0.008	40.913	0.091	0.091	0.000	0.000	0.000	0.000
29	A	33	ALA	0	0.000	-0.008	44.229	0.071	0.071	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.858	0.942	47.431	6.469	6.469	0.000	0.000	0.000	0.000
31	A	35	GLN	0	0.001	-0.001	46.076	0.134	0.134	0.000	0.000	0.000	0.000
32	A	36	PRO	0	0.006	0.011	46.514	-0.132	-0.132	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.041	0.011	44.655	0.012	0.012	0.000	0.000	0.000	0.000
34	A	38	MET	0	-0.077	-0.003	41.320	-0.120	-0.120	0.000	0.000	0.000	0.000
35	A	39	VAL	0	-0.011	-0.018	37.522	0.089	0.089	0.000	0.000	0.000	0.000
36	A	40	GLY	0	-0.004	-0.016	37.360	-0.115	-0.115	0.000	0.000	0.000	0.000
37	A	41	VAL	0	-0.021	0.004	36.380	0.156	0.156	0.000	0.000	0.000	0.000
38	A	42	ARG	1	0.844	0.916	32.032	9.110	9.110	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.011	-0.001	31.342	0.257	0.257	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.005	-0.008	31.498	-0.330	-0.330	0.000	0.000	0.000	0.000
41	A	45	VAL	0	0.001	0.005	30.142	0.232	0.232	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.930	0.964	32.932	8.743	8.743	0.000	0.000	0.000	0.000
43	A	47	GLN	0	0.004	-0.001	32.342	0.019	0.019	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.002	-0.007	35.525	0.293	0.293	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.003	-0.008	38.327	-0.142	-0.142	0.000	0.000	0.000	0.000
46	A	50	CYS	0	-0.026	-0.013	39.250	0.095	0.095	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.027	0.027	34.580	-0.142	-0.142	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.015	0.012	34.335	-0.313	-0.313	0.000	0.000	0.000	0.000
49	A	53	PHE	0	-0.012	-0.005	32.228	0.164	0.164	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.031	0.022	34.930	0.204	0.204	0.000	0.000	0.000	0.000
51	A	55	TYR	0	0.006	-0.009	31.007	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	56	VAL	0	-0.068	-0.036	35.593	0.280	0.280	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.014	0.007	35.973	-0.232	-0.232	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.874	-0.933	36.574	-8.144	-8.144	0.000	0.000	0.000	0.000
55	A	59	SER	0	-0.018	-0.016	38.310	0.009	0.009	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.030	-0.008	34.986	-0.090	-0.090	0.000	0.000	0.000	0.000
57	A	61	SER	0	-0.007	0.003	38.089	0.166	0.166	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.896	-0.958	36.425	-8.097	-8.097	0.000	0.000	0.000	0.000
59	A	63	PRO	0	-0.065	-0.033	31.816	-0.036	-0.036	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.860	-0.923	28.849	-10.516	-10.516	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.804	0.893	22.503	12.994	12.994	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.875	-0.946	22.918	-13.582	-13.582	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.823	-0.896	25.556	-10.393	-10.393	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.008	-0.001	22.237	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.034	-0.024	26.516	0.426	0.426	0.000	0.000	0.000	0.000
66	A	70	PHE	0	0.023	0.019	24.983	-0.311	-0.311	0.000	0.000	0.000	0.000
67	A	71	GLU	-1	-0.819	-0.908	30.319	-8.509	-8.509	0.000	0.000	0.000	0.000
68	A	72	HIS	0	-0.020	-0.020	33.263	-0.240	-0.240	0.000	0.000	0.000	0.000
69	A	73	ASP	-1	-0.883	-0.933	35.875	-7.604	-7.604	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.020	0.006	38.136	0.224	0.224	0.000	0.000	0.000	0.000
71	A	75	ALA	0	-0.063	-0.019	38.373	0.103	0.103	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.848	0.912	35.122	8.422	8.422	0.000	0.000	0.000	0.000
73	A	77	LEU	0	0.004	0.003	32.125	0.205	0.205	0.000	0.000	0.000	0.000
74	A	78	PHE	0	0.046	0.010	30.862	-0.266	-0.266	0.000	0.000	0.000	0.000
75	A	79	VAL	0	-0.002	-0.015	27.036	0.231	0.231	0.000	0.000	0.000	0.000
76	A	80	PRO	0	0.043	0.048	27.047	-0.340	-0.340	0.000	0.000	0.000	0.000
77	A	81	LEU	0	0.039	0.011	20.209	-0.151	-0.151	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.009	-0.016	22.510	-0.417	-0.417	0.000	0.000	0.000	0.000
79	A	83	ALA	0	-0.014	-0.009	23.909	0.065	0.065	0.000	0.000	0.000	0.000
80	A	84	MET	0	-0.002	0.028	21.998	0.259	0.259	0.000	0.000	0.000	0.000
81	A	85	PRO	0	-0.013	-0.005	19.553	0.004	0.004	0.000	0.000	0.000	0.000
82	A	86	PHE	0	-0.051	-0.019	21.353	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	87	ILE	0	0.010	0.000	24.824	0.181	0.181	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.751	-0.868	21.596	-12.838	-12.838	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.014	0.003	24.565	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	90	THR	0	-0.080	-0.059	26.027	0.396	0.396	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.888	-0.918	29.564	-8.608	-8.608	0.000	0.000	0.000	0.000
88	A	92	VAL	0	-0.032	-0.022	32.768	0.126	0.126	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.771	-0.876	35.528	-7.474	-7.474	0.000	0.000	0.000	0.000
90	A	94	PHE	0	-0.073	-0.051	39.043	0.068	0.068	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.037	0.028	42.660	0.115	0.115	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.907	0.959	45.778	6.062	6.062	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.870	-0.932	46.736	-6.645	-6.645	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.015	0.007	50.969	0.064	0.064	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.009	-0.022	53.779	-0.026	-0.026	0.000	0.000	0.000	0.000
96	A	100	ASN	0	-0.011	0.007	49.232	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.047	-0.034	47.920	0.017	0.017	0.000	0.000	0.000	0.000
98	A	102	ILE	0	-0.011	0.008	42.566	-0.064	-0.064	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.025	0.006	39.487	0.021	0.021	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.874	0.933	39.484	7.171	7.171	0.000	0.000	0.000	0.000
101	A	105	PHE	0	0.019	0.001	34.282	-0.079	-0.079	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.056	-0.034	34.212	0.184	0.184	0.000	0.000	0.000	0.000
103	A	107	ASN	0	0.054	0.033	28.520	-0.328	-0.328	0.000	0.000	0.000	0.000
104	A	108	PRO	0	0.002	0.001	26.244	0.143	0.143	0.000	0.000	0.000	0.000
105	A	109	LYS	1	0.806	0.906	22.270	12.603	12.603	0.000	0.000	0.000	0.000
106	A	110	ALA	-1	-0.933	-0.954	27.632	-9.672	-9.672	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)