FMO DATABASE

FMODB ID: 4G24N

Calculation Name: 1UB4-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1UB4

Chain ID: A

ChEMBL ID:

UniProt ID: P0AE72

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-821264.487169
FMO2-HF: Nuclear repulsion	778662.34624
FMO2-HF: Total energy	-42602.140929
FMO2-MP2: Total energy	-42723.930764

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
42.665	45.996	1.328	-1.413	-3.247	-0.01

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / q_NPA : 0.926

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	4	ARG	1	0.919	0.945	2.595	45.693	48.987	1.329	-1.405	-3.219	-0.010
4	A	5	TYR	0	0.005	-0.009	4.889	0.323	0.360	-0.001	-0.008	-0.028	0.000
5	A	6	VAL	0	-0.032	-0.017	8.660	-0.943	-0.943	0.000	0.000	0.000	0.000
6	A	7	PRO	0	-0.001	0.017	11.287	0.550	0.550	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.822	-0.917	14.797	-17.634	-17.634	0.000	0.000	0.000	0.000
8	A	9	MET	0	-0.018	0.029	17.617	0.799	0.799	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.019	0.007	21.404	0.168	0.168	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.750	-0.847	16.602	-17.239	-17.239	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.022	-0.003	20.032	0.396	0.396	0.000	0.000	0.000	0.000
12	A	13	ILE	0	-0.021	-0.019	16.256	-0.727	-0.727	0.000	0.000	0.000	0.000
13	A	14	TRP	0	0.053	0.027	17.066	0.771	0.771	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.028	-0.026	16.425	-1.146	-1.146	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.791	-0.891	14.583	-16.842	-16.842	0.000	0.000	0.000	0.000
16	A	17	PHE	0	-0.095	-0.058	17.753	0.056	0.056	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.803	-0.890	19.291	-13.638	-13.638	0.000	0.000	0.000	0.000
18	A	19	PRO	0	-0.029	-0.027	20.738	0.395	0.395	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.077	-0.031	19.240	0.423	0.423	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.785	0.896	13.816	17.202	17.202	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.061	0.024	14.409	0.236	0.236	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.020	-0.048	11.923	-0.934	-0.934	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.826	-0.890	14.023	-15.277	-15.277	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.030	-0.017	17.509	-0.136	-0.136	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.000	-0.006	20.069	0.444	0.444	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.005	0.008	19.586	0.402	0.402	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.018	-0.002	18.958	-0.323	-0.323	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.871	0.929	20.932	11.436	11.436	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.016	0.010	21.449	-0.516	-0.516	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.002	-0.008	21.385	0.574	0.574	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.041	0.030	21.573	-0.535	-0.535	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.033	-0.015	18.131	0.193	0.193	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.009	-0.006	21.471	0.301	0.301	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.021	-0.014	19.956	0.482	0.482	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.035	0.016	20.464	-0.496	-0.496	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.124	0.053	11.984	-0.252	-0.252	0.000	0.000	0.000	0.000
37	A	38	MET	0	-0.010	-0.003	15.978	-1.016	-1.016	0.000	0.000	0.000	0.000
38	A	39	TYR	0	0.000	0.000	17.061	-0.512	-0.512	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.018	0.014	15.501	0.226	0.226	0.000	0.000	0.000	0.000
40	A	41	ASN	0	0.046	0.017	10.682	-2.308	-2.308	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.929	0.977	12.885	14.570	14.570	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.005	-0.015	15.468	0.017	0.017	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.034	-0.010	13.549	-0.139	-0.139	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.009	0.007	14.365	0.139	0.139	0.000	0.000	0.000	0.000
45	A	46	CYS	0	-0.063	-0.029	17.483	-0.578	-0.578	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.052	0.025	19.354	0.400	0.400	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.058	-0.021	21.472	-0.375	-0.375	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.078	0.047	23.557	0.417	0.417	0.000	0.000	0.000	0.000
49	A	50	PRO	0	0.003	0.014	25.390	-0.357	-0.357	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.005	0.004	25.652	0.388	0.388	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.035	-0.008	27.632	-0.090	-0.090	0.000	0.000	0.000	0.000
52	A	53	THR	0	0.060	0.026	30.031	-0.065	-0.065	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.058	-0.027	32.290	0.391	0.391	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.002	0.006	35.255	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.880	0.920	36.673	8.078	8.078	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.025	0.022	39.371	0.206	0.206	0.000	0.000	0.000	0.000
57	A	58	TYR	0	-0.080	-0.062	36.487	0.273	0.273	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.033	0.012	38.909	-0.176	-0.176	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.013	0.009	35.443	-0.077	-0.077	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.767	-0.865	34.492	-8.463	-8.463	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.048	-0.016	32.042	0.225	0.225	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.022	0.010	32.097	-0.261	-0.261	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.045	-0.018	26.688	-0.186	-0.186	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.016	-0.008	30.312	0.168	0.168	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.030	-0.022	29.119	-0.311	-0.311	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.052	-0.018	24.653	-0.788	-0.788	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.911	-0.965	23.046	-12.039	-12.039	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.883	0.945	26.588	11.015	11.015	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.862	-0.919	29.188	-9.137	-9.137	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.034	-0.037	30.743	-0.161	-0.161	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.043	-0.006	31.461	0.059	0.059	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.036	0.010	28.396	-0.245	-0.245	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.042	-0.025	29.908	0.358	0.358	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.009	-0.010	30.869	-0.225	-0.225	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.753	-0.866	32.064	-8.852	-8.852	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.081	-0.027	30.299	-0.279	-0.279	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.003	-0.005	27.744	-0.468	-0.468	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.933	0.969	24.207	11.673	11.673	0.000	0.000	0.000	0.000
79	A	80	SER	0	0.003	0.009	23.010	-0.630	-0.630	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.006	-0.022	18.503	0.298	0.298	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.065	0.016	17.058	-0.459	-0.459	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.016	-0.010	9.800	-1.066	-1.066	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.851	0.929	9.753	26.059	26.059	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.031	-0.019	11.188	-1.242	-1.242	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.843	0.919	13.731	14.654	14.654	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.015	0.020	10.667	0.046	0.046	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.021	-0.006	11.661	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.019	0.020	11.746	-2.054	-2.054	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.831	0.916	13.150	18.506	18.506	0.000	0.000	0.000	0.000
90	A	91	LYS	0	-0.006	-0.003	15.148	-0.381	-0.381	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.046	0.026	18.431	0.395	0.395	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.041	-0.018	19.831	-0.800	-0.800	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.009	0.014	22.511	0.366	0.366	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.036	0.017	26.024	-0.223	-0.223	0.000	0.000	0.000	0.000
95	A	96	PRO	0	0.001	-0.020	28.225	0.050	0.050	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.837	-0.915	29.736	-8.786	-8.786	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.777	-0.872	29.583	-10.019	-10.019	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.006	-0.014	25.788	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.058	-0.031	29.313	-0.101	-0.101	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.013	0.008	32.661	0.187	0.187	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.020	-0.014	28.155	0.136	0.136	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.868	0.895	26.652	11.432	11.432	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.024	0.017	32.047	0.136	0.136	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.826	0.898	34.842	8.502	8.502	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.002	0.000	29.680	0.080	0.080	0.000	0.000	0.000	0.000
106	A	107	ASN	0	-0.022	-0.013	34.035	-0.035	-0.035	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.044	-0.013	36.451	0.210	0.210	0.000	0.000	0.000	0.000
108	A	109	LEU	0	-0.071	-0.031	35.750	0.176	0.176	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.085	-0.049	31.661	0.006	0.006	0.000	0.000	0.000	0.000
110	A	111	GLY	-1	-0.927	-0.936	35.503	-8.411	-8.411	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)