FMO DATABASE

FMODB ID: 55Q3Z

Calculation Name: 3CPQ-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3CPQ

Chain ID: B

ChEMBL ID:

UniProt ID: P54061

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	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-743581.426865
FMO2-HF: Nuclear repulsion	705166.016715
FMO2-HF: Total energy	-38415.41015
FMO2-MP2: Total energy	-38528.159144

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:7:MET)

Summations of interaction energy for fragment #1(A:7:MET)

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.
84.65	87.626	0.031	-1.031	-1.977	-0.003

Interaction energy analysis for fragmet #1(A:7:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.910

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

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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	9	VAL	0	0.081	0.041	3.571	4.825	6.645	-0.006	-0.726	-1.089	-0.002
4	A	10	ASN	0	-0.012	-0.002	3.185	6.983	7.859	0.038	-0.228	-0.686	-0.001
5	A	11	LYS	1	1.006	1.004	4.328	41.155	41.435	-0.001	-0.077	-0.202	0.000
6	A	12	ALA	0	0.051	0.049	6.201	5.815	5.815	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.017	0.017	7.192	4.234	4.234	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.799	0.895	8.700	26.752	26.752	0.000	0.000	0.000	0.000
9	A	15	THR	0	-0.012	-0.024	9.996	2.524	2.524	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.033	0.043	12.163	1.968	1.968	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.124	-0.065	13.452	1.613	1.613	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.868	-0.925	14.325	-19.608	-19.608	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.059	-0.050	15.655	1.042	1.042	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.076	0.061	17.715	0.670	0.670	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.836	0.918	19.118	14.506	14.506	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.064	0.036	14.731	-0.130	-0.130	0.000	0.000	0.000	0.000
17	A	23	ILE	0	-0.051	-0.015	18.108	0.783	0.783	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.036	0.009	15.876	-0.697	-0.697	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.041	0.020	18.542	0.960	0.960	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.025	0.021	20.340	0.311	0.311	0.000	0.000	0.000	0.000
21	A	27	LYS	1	0.997	0.987	21.287	11.725	11.725	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.929	0.976	22.712	12.639	12.639	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.036	0.008	19.039	0.058	0.058	0.000	0.000	0.000	0.000
24	A	30	ILE	0	0.036	0.016	21.770	0.220	0.220	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.876	0.951	24.499	10.601	10.601	0.000	0.000	0.000	0.000
26	A	32	PHE	0	-0.006	-0.010	23.975	0.353	0.353	0.000	0.000	0.000	0.000
27	A	33	VAL	0	0.082	0.055	21.788	0.299	0.299	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.873	0.943	24.981	10.465	10.465	0.000	0.000	0.000	0.000
29	A	35	HIS	0	-0.088	-0.050	28.312	0.726	0.726	0.000	0.000	0.000	0.000
30	A	36	GLY	0	0.027	0.028	27.916	0.253	0.253	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.941	-0.965	25.593	-11.623	-11.623	0.000	0.000	0.000	0.000
32	A	38	GLY	0	-0.017	-0.041	21.865	-0.326	-0.326	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.823	0.927	18.986	15.612	15.612	0.000	0.000	0.000	0.000
34	A	40	LEU	0	0.018	0.006	12.346	-0.330	-0.330	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.032	0.003	16.572	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	42	VAL	0	-0.001	-0.003	10.238	-1.199	-1.199	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.023	-0.012	13.185	1.221	1.221	0.000	0.000	0.000	0.000
38	A	44	ALA	0	0.022	0.005	12.355	-1.923	-1.923	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.008	0.006	12.504	1.186	1.186	0.000	0.000	0.000	0.000
40	A	46	ASN	0	-0.014	-0.007	13.824	0.178	0.178	0.000	0.000	0.000	0.000
41	A	47	ILE	0	-0.024	-0.003	16.936	0.841	0.841	0.000	0.000	0.000	0.000
42	A	48	PRO	0	-0.019	-0.009	18.623	0.250	0.250	0.000	0.000	0.000	0.000
43	A	49	LYS	1	0.954	0.974	22.279	12.285	12.285	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.816	-0.907	23.408	-11.994	-11.994	0.000	0.000	0.000	0.000
45	A	51	LEU	0	-0.040	-0.031	22.471	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.879	-0.936	18.814	-15.501	-15.501	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.858	-0.938	21.317	-12.021	-12.021	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.899	-0.948	24.436	-11.094	-11.094	0.000	0.000	0.000	0.000
49	A	55	VAL	0	-0.084	-0.049	19.864	0.077	0.077	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.877	0.932	18.978	15.255	15.255	0.000	0.000	0.000	0.000
51	A	57	TYR	0	0.013	0.022	22.313	0.171	0.171	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.035	-0.014	25.650	0.394	0.394	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.010	0.004	21.334	0.169	0.169	0.000	0.000	0.000	0.000
54	A	60	LYS	1	0.923	0.972	23.417	12.049	12.049	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.048	-0.021	25.040	0.273	0.273	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.002	-0.005	25.531	0.441	0.441	0.000	0.000	0.000	0.000
57	A	63	ASN	0	-0.068	-0.029	24.577	-0.188	-0.188	0.000	0.000	0.000	0.000
58	A	64	ILE	0	0.013	0.027	19.790	-0.411	-0.411	0.000	0.000	0.000	0.000
59	A	65	PRO	0	0.006	0.012	16.736	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	66	VAL	0	0.017	-0.012	16.042	-0.253	-0.253	0.000	0.000	0.000	0.000
61	A	67	TYR	0	0.003	0.007	6.617	-0.493	-0.493	0.000	0.000	0.000	0.000
62	A	68	GLN	0	-0.035	-0.030	12.698	1.103	1.103	0.000	0.000	0.000	0.000
63	A	69	HIS	0	0.025	0.004	5.019	0.901	0.901	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.991	0.989	5.591	45.294	45.294	0.000	0.000	0.000	0.000
65	A	71	ILE	0	-0.068	-0.013	6.915	0.529	0.529	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.012	-0.024	9.812	2.295	2.295	0.000	0.000	0.000	0.000
67	A	73	SER	0	0.059	0.006	12.424	-1.310	-1.310	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.006	0.009	14.852	-0.056	-0.056	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.792	-0.861	9.611	-29.005	-29.005	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.006	0.002	9.579	-1.957	-1.957	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.037	0.020	11.258	-0.105	-0.105	0.000	0.000	0.000	0.000
72	A	78	ALA	0	0.034	0.020	11.409	0.150	0.150	0.000	0.000	0.000	0.000
73	A	79	VAL	0	-0.043	-0.014	6.614	-0.891	-0.891	0.000	0.000	0.000	0.000
74	A	80	CYS	0	-0.032	-0.019	9.245	0.250	0.250	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.020	0.019	12.254	1.644	1.644	0.000	0.000	0.000	0.000
76	A	82	LYS	1	0.796	0.885	14.017	19.939	19.939	0.000	0.000	0.000	0.000
77	A	83	PRO	0	0.028	0.017	15.945	-0.742	-0.742	0.000	0.000	0.000	0.000
78	A	84	PHE	0	0.007	0.010	18.521	0.361	0.361	0.000	0.000	0.000	0.000
79	A	85	PRO	0	0.001	-0.018	17.148	-0.958	-0.958	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.011	-0.005	14.724	1.018	1.018	0.000	0.000	0.000	0.000
81	A	87	ALA	0	-0.006	-0.019	15.202	-1.032	-1.032	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.013	0.004	15.643	-0.310	-0.310	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.044	-0.016	12.215	0.576	0.576	0.000	0.000	0.000	0.000
84	A	90	LEU	0	0.003	0.005	16.408	-0.323	-0.323	0.000	0.000	0.000	0.000
85	A	91	VAL	0	0.028	0.024	14.194	0.230	0.230	0.000	0.000	0.000	0.000
86	A	92	LEU	0	-0.019	-0.017	17.277	0.596	0.596	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.884	-0.965	19.615	-14.984	-14.984	0.000	0.000	0.000	0.000
88	A	94	GLU	-1	-0.772	-0.883	15.601	-17.175	-17.175	0.000	0.000	0.000	0.000
89	A	95	GLY	0	0.042	0.021	16.107	-1.146	-1.146	0.000	0.000	0.000	0.000
90	A	96	LEU	0	-0.071	-0.033	16.118	0.383	0.383	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.063	-0.053	11.606	-1.842	-1.842	0.000	0.000	0.000	0.000
92	A	98	ASN	0	0.044	0.029	9.394	0.109	0.109	0.000	0.000	0.000	0.000
93	A	99	ILE	0	-0.035	-0.035	8.907	-1.603	-1.603	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.007	0.001	11.394	-0.806	-0.806	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.790	-0.911	13.147	-21.736	-21.736	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.063	-0.035	6.941	-1.647	-1.647	0.000	0.000	0.000	0.000
97	A	103	VAL	0	-0.075	-0.035	9.986	-1.015	-1.015	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.985	-0.984	11.599	-16.844	-16.844	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.887	0.958	12.524	20.660	20.660	0.000	0.000	0.000	0.000
100	A	106	LYS	1	0.882	0.948	9.860	19.490	19.490	0.000	0.000	0.000	0.000
101	A	107	GLU	-2	-1.869	-1.934	9.119	-49.275	-49.275	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:MET)