FMO DATABASE

FMODB ID: 7KK9K

Calculation Name: 2RCD-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RCD

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D1E8

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1086772.148172
FMO2-HF: Nuclear repulsion	1036284.897366
FMO2-HF: Total energy	-50487.250806
FMO2-MP2: Total energy	-50633.501737

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-93.715	-92.746	-0.01	-0.36	-0.598	-0.002

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.893

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	2	LEU	0	0.001	-0.001	3.834	4.486	5.455	-0.010	-0.360	-0.598	-0.002
4	A	3	PRO	0	-0.010	-0.023	6.436	1.721	1.721	0.000	0.000	0.000	0.000
5	A	4	ASP	-1	-0.922	-0.958	10.088	-22.109	-22.109	0.000	0.000	0.000	0.000
6	A	5	ASP	-1	-0.814	-0.903	6.277	-46.398	-46.398	0.000	0.000	0.000	0.000
7	A	6	VAL	0	-0.045	-0.024	9.673	0.499	0.499	0.000	0.000	0.000	0.000
8	A	7	ASN	0	-0.017	-0.002	11.776	1.152	1.152	0.000	0.000	0.000	0.000
9	A	8	GLN	0	0.025	0.029	11.129	1.443	1.443	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.012	-0.012	15.571	0.365	0.365	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.948	-0.965	17.888	-16.610	-16.610	0.000	0.000	0.000	0.000
12	A	11	VAL	0	0.059	0.034	13.743	0.782	0.782	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.011	-0.004	16.962	0.414	0.414	0.000	0.000	0.000	0.000
14	A	13	ALA	0	-0.001	0.018	18.788	0.776	0.776	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.806	-0.904	19.179	-15.489	-15.489	0.000	0.000	0.000	0.000
16	A	15	VAL	0	-0.017	-0.007	16.620	0.559	0.559	0.000	0.000	0.000	0.000
17	A	16	THR	0	-0.058	-0.044	20.035	0.707	0.707	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.018	-0.009	23.138	0.657	0.657	0.000	0.000	0.000	0.000
19	A	18	ALA	0	-0.004	0.001	21.895	0.567	0.567	0.000	0.000	0.000	0.000
20	A	19	PHE	0	0.005	0.008	22.777	0.495	0.495	0.000	0.000	0.000	0.000
21	A	20	TYR	0	0.030	-0.004	24.506	0.579	0.579	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.772	0.855	27.284	11.680	11.680	0.000	0.000	0.000	0.000
23	A	22	TYR	0	0.072	0.027	26.055	0.417	0.417	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.767	-0.850	28.068	-10.309	-10.309	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.960	0.984	30.175	9.398	9.398	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.014	0.013	30.771	0.339	0.339	0.000	0.000	0.000	0.000
27	A	26	LEU	0	-0.057	-0.020	30.312	0.254	0.254	0.000	0.000	0.000	0.000
28	A	27	THR	0	-0.048	-0.038	32.924	0.336	0.336	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.019	-0.008	35.848	0.289	0.289	0.000	0.000	0.000	0.000
30	A	29	ASN	0	-0.046	-0.027	36.007	0.036	0.036	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.840	-0.917	34.283	-9.074	-9.074	0.000	0.000	0.000	0.000
32	A	31	VAL	0	0.005	-0.022	33.645	-0.351	-0.351	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.003	0.017	33.217	-0.220	-0.220	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.016	0.000	29.623	-0.359	-0.359	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.064	-0.040	29.050	-0.498	-0.498	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.849	-0.880	28.551	-10.900	-10.900	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.813	-0.855	27.296	-11.694	-11.694	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.012	-0.018	24.307	-0.473	-0.473	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.012	-0.016	23.364	-0.648	-0.648	0.000	0.000	0.000	0.000
40	A	39	TRP	0	0.054	0.030	17.616	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	40	HIS	0	0.030	0.016	22.137	0.707	0.707	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.783	-0.868	21.147	-14.748	-14.748	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.857	-0.945	23.699	-12.555	-12.555	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.763	0.863	19.083	15.004	15.004	0.000	0.000	0.000	0.000
45	A	44	THR	0	-0.048	-0.026	21.206	-0.579	-0.579	0.000	0.000	0.000	0.000
46	A	45	VAL	0	0.006	0.018	21.616	0.679	0.679	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.814	0.893	23.247	10.431	10.431	0.000	0.000	0.000	0.000
48	A	47	TYR	0	-0.019	-0.008	23.376	0.260	0.260	0.000	0.000	0.000	0.000
49	A	48	GLY	0	-0.004	-0.011	27.303	-0.220	-0.220	0.000	0.000	0.000	0.000
50	A	49	ALA	0	-0.069	-0.035	30.366	0.050	0.050	0.000	0.000	0.000	0.000
51	A	50	GLY	0	-0.004	-0.003	33.301	0.146	0.146	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.810	-0.885	32.252	-9.455	-9.455	0.000	0.000	0.000	0.000
53	A	52	ASN	0	-0.043	-0.033	29.381	-0.535	-0.535	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.024	-0.001	28.651	0.287	0.287	0.000	0.000	0.000	0.000
55	A	54	TYR	0	0.004	-0.011	25.005	-0.745	-0.745	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.084	0.052	25.546	0.362	0.362	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.050	-0.036	26.295	0.343	0.343	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.940	-0.959	27.815	-9.165	-9.165	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.815	-0.910	30.281	-9.947	-9.947	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.042	-0.017	25.998	0.269	0.269	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.817	0.875	30.370	10.528	10.528	0.000	0.000	0.000	0.000
62	A	61	ALA	0	0.011	0.012	32.959	0.285	0.285	0.000	0.000	0.000	0.000
63	A	62	PHE	0	-0.001	-0.014	32.131	0.220	0.220	0.000	0.000	0.000	0.000
64	A	63	ARG	1	0.839	0.915	28.103	10.943	10.943	0.000	0.000	0.000	0.000
65	A	64	LEU	0	-0.014	-0.006	34.867	0.195	0.195	0.000	0.000	0.000	0.000
66	A	65	ALA	0	-0.015	0.008	37.996	0.245	0.245	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.919	0.977	33.445	9.357	9.357	0.000	0.000	0.000	0.000
68	A	67	PRO	0	-0.013	-0.009	38.971	0.097	0.097	0.000	0.000	0.000	0.000
69	A	68	SER	0	0.052	0.014	40.107	-0.151	-0.151	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.013	-0.004	41.511	-0.035	-0.035	0.000	0.000	0.000	0.000
71	A	70	GLY	0	-0.001	-0.006	41.874	-0.079	-0.079	0.000	0.000	0.000	0.000
72	A	71	LEU	0	-0.006	0.005	36.274	-0.173	-0.173	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.850	-0.907	36.674	-8.695	-8.695	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.686	0.786	29.243	10.553	10.553	0.000	0.000	0.000	0.000
75	A	74	ALA	0	0.032	0.042	35.570	-0.110	-0.110	0.000	0.000	0.000	0.000
76	A	75	LEU	0	-0.012	-0.013	28.724	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.856	0.903	30.565	9.840	9.840	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.024	-0.039	27.408	-0.129	-0.129	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.014	-0.008	24.818	-0.233	-0.233	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.019	-0.002	19.599	0.041	0.041	0.000	0.000	0.000	0.000
81	A	80	ILE	0	0.025	0.012	18.859	-0.206	-0.206	0.000	0.000	0.000	0.000
82	A	81	THR	0	-0.080	-0.040	13.731	0.220	0.220	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.037	0.019	13.422	0.262	0.262	0.000	0.000	0.000	0.000
84	A	83	TYR	0	-0.018	-0.023	8.409	0.137	0.137	0.000	0.000	0.000	0.000
85	A	84	GLY	0	0.074	0.028	8.433	-2.489	-2.489	0.000	0.000	0.000	0.000
86	A	85	HIS	0	-0.025	-0.027	8.554	2.974	2.974	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.883	-0.944	9.432	-29.389	-29.389	0.000	0.000	0.000	0.000
88	A	87	MET	0	-0.010	0.001	7.390	0.345	0.345	0.000	0.000	0.000	0.000
89	A	88	ALA	0	0.013	0.003	11.630	-0.127	-0.127	0.000	0.000	0.000	0.000
90	A	89	VAL	0	-0.019	0.001	13.918	0.440	0.440	0.000	0.000	0.000	0.000
91	A	90	ALA	0	-0.001	0.015	16.415	0.250	0.250	0.000	0.000	0.000	0.000
92	A	91	SER	0	0.002	-0.012	19.877	0.247	0.247	0.000	0.000	0.000	0.000
93	A	92	THR	0	-0.001	-0.003	22.324	0.178	0.178	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.797	-0.858	26.051	-10.473	-10.473	0.000	0.000	0.000	0.000
95	A	94	PHE	0	-0.032	-0.006	29.199	0.053	0.053	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.010	-0.002	32.405	0.201	0.201	0.000	0.000	0.000	0.000
97	A	96	ARG	1	0.871	0.900	35.367	8.746	8.746	0.000	0.000	0.000	0.000
98	A	97	THR	0	0.035	0.017	39.400	0.019	0.019	0.000	0.000	0.000	0.000
99	A	98	GLY	0	0.022	0.024	42.917	0.152	0.152	0.000	0.000	0.000	0.000
100	A	99	SER	0	-0.086	-0.041	38.542	0.117	0.117	0.000	0.000	0.000	0.000
101	A	100	THR	0	0.040	0.013	41.163	-0.077	-0.077	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.812	0.898	36.830	8.383	8.383	0.000	0.000	0.000	0.000
103	A	102	ILE	0	0.027	0.020	32.154	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	103	GLY	0	0.017	0.009	32.418	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	104	ARG	1	0.884	0.926	26.904	10.729	10.729	0.000	0.000	0.000	0.000
106	A	105	GLN	0	0.031	0.018	25.249	0.543	0.543	0.000	0.000	0.000	0.000
107	A	106	MET	0	-0.006	0.004	19.735	-0.302	-0.302	0.000	0.000	0.000	0.000
108	A	107	GLN	0	0.030	0.019	20.693	0.149	0.149	0.000	0.000	0.000	0.000
109	A	108	THR	0	0.004	0.008	14.362	-0.846	-0.846	0.000	0.000	0.000	0.000
110	A	109	TRP	0	-0.028	-0.028	16.110	0.936	0.936	0.000	0.000	0.000	0.000
111	A	110	VAL	0	0.027	0.002	12.756	-1.635	-1.635	0.000	0.000	0.000	0.000
112	A	111	LYS	1	0.886	0.949	14.163	19.761	19.761	0.000	0.000	0.000	0.000
113	A	112	MET	0	-0.007	0.016	15.339	-1.252	-1.252	0.000	0.000	0.000	0.000
114	A	113	PRO	0	-0.006	-0.011	17.710	0.299	0.299	0.000	0.000	0.000	0.000
115	A	114	GLU	-1	-0.876	-0.940	20.103	-14.268	-14.268	0.000	0.000	0.000	0.000
116	A	115	GLY	0	-0.002	0.001	20.827	0.657	0.657	0.000	0.000	0.000	0.000
117	A	116	TRP	0	-0.057	-0.042	14.186	-0.469	-0.469	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.821	0.923	18.678	14.527	14.527	0.000	0.000	0.000	0.000
119	A	118	ILE	0	-0.025	-0.001	18.552	-1.015	-1.015	0.000	0.000	0.000	0.000
120	A	119	VAL	0	0.012	-0.002	15.358	0.579	0.579	0.000	0.000	0.000	0.000
121	A	120	ALA	0	0.018	0.006	18.350	0.356	0.356	0.000	0.000	0.000	0.000
122	A	121	ALA	0	-0.018	-0.008	20.092	-0.279	-0.279	0.000	0.000	0.000	0.000
123	A	122	HIS	0	0.024	0.015	22.820	0.392	0.392	0.000	0.000	0.000	0.000
124	A	123	VAL	0	-0.032	-0.014	24.799	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	124	SER	0	0.042	0.027	27.980	0.314	0.314	0.000	0.000	0.000	0.000
126	A	125	LEU	0	-0.011	-0.004	30.410	-0.095	-0.095	0.000	0.000	0.000	0.000
127	A	126	MET	0	-0.026	-0.002	31.836	-0.294	-0.294	0.000	0.000	0.000	0.000
128	A	127	SER	-1	-0.829	-0.896	33.102	-8.395	-8.395	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)