FMO DATABASE

FMODB ID: 196RZ

Calculation Name: 2D4P-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D4P

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIW0

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1071821.0702
FMO2-HF: Nuclear repulsion	1022318.053071
FMO2-HF: Total energy	-49503.017129
FMO2-MP2: Total energy	-49649.88547

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-240.675	-229.385	41.893	-20.297	-32.884	-0.22

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / 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	3	PHE	0	0.047	0.019	2.754	-4.734	-0.377	2.919	-2.544	-4.731	-0.015
4	A	4	ARG	1	0.736	0.819	5.325	27.224	27.245	-0.001	-0.003	-0.017	0.000
40	A	40	ALA	0	0.006	0.006	2.836	-2.235	-1.831	0.981	-0.336	-1.050	0.000
41	A	41	GLU	-1	-0.796	-0.874	2.903	-26.763	-25.813	0.100	-0.287	-0.762	-0.001
42	A	42	GLU	-1	-0.801	-0.901	1.820	-168.098	-165.382	22.867	-13.289	-12.294	-0.157
43	A	43	GLY	0	0.011	0.008	3.447	10.502	10.656	0.029	0.031	-0.214	-0.001
47	A	47	MET	0	0.020	-0.001	2.309	3.495	2.547	5.617	-0.999	-3.670	0.002
48	A	48	GLY	0	0.050	0.001	4.931	1.074	1.221	-0.001	-0.023	-0.123	0.000
72	A	72	SER	0	0.078	0.042	2.584	-6.363	-5.305	0.771	-0.652	-1.176	-0.011
73	A	73	VAL	0	0.061	0.035	4.985	-0.376	-0.285	-0.001	-0.003	-0.087	0.000
74	A	74	GLU	-1	-0.934	-0.966	2.554	-96.239	-91.075	3.470	-3.548	-5.086	-0.040
75	A	75	ALA	0	-0.008	-0.018	2.562	0.082	0.852	5.080	-2.608	-3.242	0.004
76	A	76	LEU	0	0.009	0.001	3.522	4.265	0.671	0.062	3.964	-0.432	-0.001
5	A	5	PRO	0	0.054	0.021	8.750	0.306	0.306	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.047	-0.013	11.332	-0.815	-0.815	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.001	-0.031	12.878	0.690	0.690	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.775	-0.864	16.158	-12.460	-12.460	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.834	-0.899	16.738	-14.709	-14.709	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.761	-0.838	12.480	-21.748	-21.748	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.001	-0.002	14.207	-0.466	-0.466	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.857	-0.924	16.288	-14.754	-14.754	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.786	0.885	9.784	22.548	22.548	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.009	-0.005	11.429	-0.776	-0.776	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.015	-0.042	13.239	0.375	0.375	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.857	0.914	11.232	22.238	22.238	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.058	-0.007	7.839	-0.560	-0.560	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.037	0.008	11.922	0.309	0.309	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.054	0.030	15.182	0.634	0.634	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.929	0.949	16.679	12.155	12.155	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.916	0.970	17.034	14.178	14.178	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.079	0.051	18.607	-0.636	-0.636	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.003	0.002	15.719	0.327	0.327	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.028	0.018	18.992	-0.089	-0.089	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.081	0.030	20.848	-0.290	-0.290	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.004	0.006	22.125	-0.041	-0.041	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.016	0.004	20.498	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.002	0.022	16.584	-0.145	-0.145	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.860	0.872	18.841	11.216	11.216	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.065	-0.018	21.462	0.197	0.197	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.043	0.003	16.894	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.026	0.038	16.625	-0.353	-0.353	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.891	0.939	17.646	11.362	11.362	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.047	-0.026	17.997	0.110	0.110	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.000	0.011	17.692	0.285	0.285	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.836	0.901	15.918	14.116	14.116	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.014	0.021	13.786	-0.220	-0.220	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.038	-0.013	8.850	-0.382	-0.382	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.003	-0.003	7.283	1.136	1.136	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.864	-0.931	6.177	-24.170	-24.170	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.781	-0.848	6.511	-22.137	-22.137	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.013	-0.012	5.400	-4.741	-4.741	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.032	-0.013	6.517	-0.826	-0.826	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.015	0.009	9.229	0.772	0.772	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.033	-0.014	11.740	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.023	0.003	15.452	0.464	0.464	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.019	-0.025	17.454	0.217	0.217	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.010	0.005	20.873	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.017	-0.007	23.458	0.266	0.266	0.000	0.000	0.000	0.000
56	A	56	TRP	0	-0.021	-0.008	26.601	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.012	-0.022	28.728	0.146	0.146	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.008	0.005	31.563	0.223	0.223	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.961	-0.984	33.437	-8.165	-8.165	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.050	0.042	29.733	-0.200	-0.200	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.003	-0.012	25.025	0.117	0.117	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.005	0.002	23.508	-0.124	-0.124	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.034	-0.020	18.369	0.045	0.045	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.006	0.013	20.353	-0.264	-0.264	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.021	-0.015	14.431	-0.226	-0.226	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.055	-0.015	17.483	0.562	0.562	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.727	0.827	14.704	15.481	15.481	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.024	0.025	9.283	-0.451	-0.451	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.777	-0.851	10.673	-15.297	-15.297	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.020	-0.014	6.853	-1.164	-1.164	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.744	0.866	5.099	28.653	28.653	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.874	0.925	7.228	26.061	26.061	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.013	-0.007	5.418	1.034	1.034	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.039	-0.014	5.942	1.333	1.333	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.017	0.002	8.133	1.530	1.530	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.891	0.940	5.880	32.956	32.956	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.025	0.006	9.048	1.078	1.078	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.013	-0.007	11.096	1.466	1.466	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.051	0.029	14.017	1.027	1.027	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.821	0.905	13.486	18.672	18.672	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.021	-0.014	15.141	1.119	1.119	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.003	-0.006	16.909	0.818	0.818	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.032	0.008	17.795	0.827	0.827	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.858	-0.922	17.813	-15.793	-15.793	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.066	-0.029	20.971	0.451	0.451	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.012	0.005	23.027	0.445	0.445	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.090	-0.042	22.039	0.390	0.390	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.032	-0.002	24.084	-0.147	-0.147	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.865	-0.918	22.909	-11.219	-11.219	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.003	-0.010	16.652	-0.153	-0.153	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.025	0.019	20.097	0.049	0.049	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.017	-0.010	14.618	-0.502	-0.502	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.020	-0.008	19.083	0.272	0.272	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.018	-0.007	16.554	-0.261	-0.261	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.839	-0.913	18.401	-12.324	-12.324	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.024	0.005	18.149	-0.643	-0.643	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.911	-0.949	19.244	-11.802	-11.802	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.820	0.903	12.071	15.897	15.897	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.833	0.889	14.593	12.550	12.550	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.860	-0.935	8.006	-23.649	-23.649	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.021	-0.018	10.798	-1.067	-1.067	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.843	-0.912	12.406	-13.316	-13.316	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.935	-0.968	11.914	-20.511	-20.511	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.024	-0.034	9.717	-0.201	-0.201	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.005	-0.006	11.614	-0.163	-0.163	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.980	0.999	14.930	14.238	14.238	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.050	-0.030	12.561	0.350	0.350	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.818	-0.881	10.737	-25.153	-25.153	0.000	0.000	0.000	0.000
114	A	114	GLY	0	-0.008	0.003	14.546	0.496	0.496	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.017	-0.009	14.813	0.661	0.661	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.006	0.003	19.066	0.014	0.014	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.028	-0.025	19.069	-0.055	-0.055	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.030	0.029	23.105	0.363	0.363	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.039	-0.024	26.733	-0.234	-0.234	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.014	-0.002	28.016	0.275	0.275	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.027	0.016	27.753	-0.309	-0.309	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.014	-0.001	24.342	0.120	0.120	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.010	0.012	28.128	0.099	0.099	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.010	-0.008	27.500	-0.112	-0.112	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.960	0.980	30.933	7.730	7.730	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.009	0.007	29.814	-0.094	-0.094	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.022	-0.022	32.522	0.251	0.251	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.012	0.018	33.216	0.181	0.181	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.068	-0.036	31.914	-0.222	-0.222	0.000	0.000	0.000	0.000
130	A	130	ARG	0	0.071	0.046	34.187	-0.207	-0.207	0.000	0.000	0.000	0.000

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