FMO DATABASE

FMODB ID: 2R2ZR

Calculation Name: 3C0D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q87HB1

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-841796.02109
FMO2-HF: Nuclear repulsion	797875.332823
FMO2-HF: Total energy	-43920.688267
FMO2-MP2: Total energy	-44044.271571

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:LEU)

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

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.
-114.744	-110.741	5.616	-5.185	-4.434	-0.055

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.884

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	LYS	1	0.822	0.893	3.574	25.079	26.637	-0.006	-0.778	-0.774	-0.001
105	A	108	LEU	0	-0.060	-0.036	4.207	-3.144	-3.000	-0.001	-0.015	-0.127	0.000
106	A	109	ALA	0	0.025	0.016	3.542	5.997	6.331	-0.001	-0.115	-0.218	0.000
107	A	110	LYS	1	0.872	0.915	1.967	-0.596	0.872	5.624	-4.013	-3.080	-0.052
108	A	111	GLU	-1	-0.854	-0.921	3.753	-63.130	-62.631	0.000	-0.264	-0.235	-0.002
4	A	7	VAL	0	-0.002	0.006	6.393	2.872	2.872	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.971	0.969	9.261	21.424	21.424	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.060	-0.016	12.798	0.045	0.045	0.000	0.000	0.000	0.000
7	A	10	CYS	0	-0.048	-0.021	14.656	0.904	0.904	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.007	0.010	17.290	-1.840	-1.840	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.007	-0.004	19.051	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.913	-0.957	20.742	-12.991	-12.991	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.854	-0.917	21.657	-13.767	-13.767	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.084	-0.048	18.764	0.092	0.092	0.000	0.000	0.000	0.000
13	A	16	MET	0	0.010	0.000	23.490	0.309	0.309	0.000	0.000	0.000	0.000
14	A	17	PRO	0	-0.005	-0.009	25.333	-0.226	-0.226	0.000	0.000	0.000	0.000
15	A	18	PHE	0	-0.019	-0.019	25.376	0.422	0.422	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.057	-0.019	26.490	0.295	0.295	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.006	0.016	23.814	-0.434	-0.434	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.001	-0.007	22.130	0.520	0.520	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.048	-0.022	21.443	-0.474	-0.474	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.017	0.007	16.538	0.088	0.088	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.034	-0.025	17.896	0.351	0.351	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.002	0.003	11.273	-0.939	-0.939	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.916	-0.956	11.587	-22.656	-22.656	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.009	0.016	14.600	0.722	0.722	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.844	-0.902	15.035	-18.493	-18.493	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.843	0.923	18.056	13.762	13.762	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.017	0.017	15.107	0.004	0.004	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.001	0.005	18.439	0.530	0.530	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.005	-0.008	15.589	-0.802	-0.802	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.050	0.012	19.205	0.939	0.939	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.020	0.017	20.022	-0.885	-0.885	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.023	0.009	20.930	0.796	0.796	0.000	0.000	0.000	0.000
33	A	36	PRO	0	0.007	-0.004	21.634	-0.561	-0.561	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.884	-0.936	22.861	-12.168	-12.168	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.098	-0.057	19.683	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.001	0.022	17.101	-1.039	-1.039	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.009	-0.016	15.779	0.767	0.767	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.018	-0.001	15.293	-1.411	-1.411	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.000	-0.001	13.952	0.584	0.584	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.038	0.023	15.766	-0.769	-0.769	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.015	0.011	18.234	-0.538	-0.538	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.786	-0.928	19.649	-12.181	-12.181	0.000	0.000	0.000	0.000
43	A	46	TRP	0	-0.015	-0.009	22.573	0.751	0.751	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.716	-0.842	24.375	-11.136	-11.136	0.000	0.000	0.000	0.000
45	A	48	PRO	0	-0.035	0.002	24.992	0.294	0.294	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.005	0.005	27.261	0.335	0.335	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.045	0.004	30.784	0.238	0.238	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.754	0.885	29.179	10.855	10.855	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.063	0.029	29.382	0.245	0.245	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.059	-0.027	23.781	-0.260	-0.260	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.013	0.002	26.631	0.388	0.388	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.034	0.033	24.105	0.380	0.380	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.026	-0.009	24.147	0.210	0.210	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.882	0.935	25.574	10.612	10.612	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.007	0.010	28.063	0.441	0.441	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.042	-0.022	28.776	-0.158	-0.158	0.000	0.000	0.000	0.000
57	A	60	VAL	0	0.003	0.003	25.700	-0.126	-0.126	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.004	0.001	28.451	0.399	0.399	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.902	-0.954	28.758	-10.501	-10.501	0.000	0.000	0.000	0.000
60	A	63	ILE	0	-0.032	-0.018	29.108	0.467	0.467	0.000	0.000	0.000	0.000
61	A	64	ASN	0	-0.054	-0.028	28.227	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.006	0.012	28.229	-0.161	-0.161	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.880	-0.922	23.669	-12.770	-12.770	0.000	0.000	0.000	0.000
64	A	67	MET	0	0.038	0.022	24.501	0.269	0.269	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.019	0.013	24.233	-0.685	-0.685	0.000	0.000	0.000	0.000
66	A	69	VAL	0	-0.014	0.007	24.070	0.343	0.343	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.005	-0.003	26.712	0.008	0.008	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.004	-0.036	29.434	0.026	0.026	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.007	-0.004	29.788	0.381	0.381	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.039	-0.002	32.032	0.414	0.414	0.000	0.000	0.000	0.000
71	A	74	TYR	0	-0.018	-0.023	33.607	0.390	0.390	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.815	0.909	33.519	8.889	8.889	0.000	0.000	0.000	0.000
73	A	76	GLN	0	0.044	0.037	30.617	-0.151	-0.151	0.000	0.000	0.000	0.000
74	A	77	HIS	1	0.828	0.879	29.105	9.733	9.733	0.000	0.000	0.000	0.000
75	A	78	PHE	0	0.047	0.010	23.964	0.006	0.006	0.000	0.000	0.000	0.000
76	A	79	SER	0	0.018	-0.015	22.535	-0.448	-0.448	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.002	-0.011	20.737	-0.708	-0.708	0.000	0.000	0.000	0.000
78	A	81	LYS	1	0.912	0.970	13.656	19.379	19.379	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.053	-0.046	17.178	-1.045	-1.045	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.029	0.018	19.106	-0.423	-0.423	0.000	0.000	0.000	0.000
81	A	84	GLN	0	0.028	0.007	20.677	0.742	0.742	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.058	0.004	23.667	0.196	0.196	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.015	-0.001	27.151	0.094	0.094	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.783	-0.869	30.022	-9.635	-9.635	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.890	-0.979	30.994	-9.605	-9.605	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.915	-0.957	28.734	-10.451	-10.451	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.061	-0.010	27.896	-0.366	-0.366	0.000	0.000	0.000	0.000
88	A	91	HIS	0	-0.053	-0.025	26.277	-0.661	-0.661	0.000	0.000	0.000	0.000
89	A	92	CYS	0	-0.036	-0.023	20.171	-0.113	-0.113	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.074	-0.021	20.547	-0.167	-0.167	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.852	0.903	13.894	20.120	20.120	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.009	-0.003	14.835	-0.151	-0.151	0.000	0.000	0.000	0.000
93	A	96	TRP	0	0.001	-0.004	10.596	-0.904	-0.904	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.918	0.956	5.457	37.548	37.548	0.000	0.000	0.000	0.000
95	A	98	VAL	0	0.044	0.024	8.900	-2.679	-2.679	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.066	-0.030	8.300	-0.831	-0.831	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.039	0.004	11.037	0.241	0.241	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.873	-0.905	11.510	-27.319	-27.319	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.915	-0.955	14.280	-15.847	-15.847	0.000	0.000	0.000	0.000
100	A	103	ASN	0	-0.003	-0.006	18.050	0.715	0.715	0.000	0.000	0.000	0.000
101	A	104	GLN	0	-0.017	-0.003	14.159	-0.707	-0.707	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.050	0.022	14.323	-1.487	-1.487	0.000	0.000	0.000	0.000
103	A	106	CYS	0	-0.017	0.003	9.617	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	107	TYR	0	0.066	0.027	7.694	-1.103	-1.103	0.000	0.000	0.000	0.000
109	A	112	LEU	-1	-0.931	-0.943	5.849	-26.576	-26.576	0.000	0.000	0.000	0.000

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