FMO DATABASE

FMODB ID: 1324Z

Calculation Name: 2HW2-A-Xray549

Preferred Name:

Target Type:

Ligand Name: rifampicin

Ligand 3-letter code: RFP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HW2

Chain ID: A

ChEMBL ID:

UniProt ID: A0QRS5

Base Structure: X-ray

Registration Date: 2025-10-12

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1218979.6128
FMO2-HF: Nuclear repulsion	1165806.953875
FMO2-HF: Total energy	-53172.658925
FMO2-MP2: Total energy	-53330.253711

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:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
-157.352	-145.688	10.153	-7.434	-14.382	-0.081

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / 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	8	PRO	0	0.032	0.011	3.871	2.631	4.465	-0.012	-0.813	-1.009	-0.002
49	A	54	LEU	0	0.045	0.018	2.392	-2.080	-1.131	0.549	-0.357	-1.141	-0.002
50	A	55	ASP	-1	-0.843	-0.922	2.214	-76.657	-73.269	4.353	-3.619	-4.121	-0.030
51	A	56	ALA	0	0.037	0.019	2.834	3.166	1.700	0.189	1.608	-0.331	0.000
53	A	58	VAL	0	-0.004	0.000	2.298	0.856	1.573	2.144	-0.683	-2.178	-0.005
54	A	59	TRP	0	-0.023	-0.019	4.354	4.093	4.223	-0.001	-0.028	-0.101	0.000
110	A	115	TRP	0	-0.044	-0.021	4.382	-5.825	-5.669	-0.001	-0.014	-0.140	0.000
111	A	116	VAL	0	-0.041	-0.021	3.192	4.265	4.819	0.070	-0.158	-0.467	-0.001
112	A	117	GLY	0	0.044	0.002	2.543	-16.297	-14.050	1.247	-1.503	-1.991	-0.018
113	A	118	HIS	1	0.709	0.814	2.600	40.090	43.099	1.615	-1.850	-2.774	-0.023
114	A	119	PRO	0	-0.020	0.009	4.101	4.230	4.376	0.000	-0.017	-0.129	0.000
4	A	9	PHE	0	-0.021	-0.027	5.662	1.778	1.778	0.000	0.000	0.000	0.000
5	A	10	GLU	-1	-0.947	-0.952	5.477	-38.875	-38.875	0.000	0.000	0.000	0.000
6	A	11	VAL	0	-0.019	-0.027	6.487	-2.284	-2.284	0.000	0.000	0.000	0.000
7	A	12	HIS	0	0.024	0.030	6.520	0.822	0.822	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.887	-0.945	8.819	-19.922	-19.922	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.045	-0.040	11.400	2.003	2.003	0.000	0.000	0.000	0.000
10	A	15	GLY	0	-0.015	0.000	12.708	1.344	1.344	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.005	0.007	13.395	0.789	0.789	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.006	-0.002	12.495	-1.256	-1.256	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.019	-0.008	7.578	-0.221	-0.221	0.000	0.000	0.000	0.000
14	A	19	HIS	0	-0.012	-0.030	11.400	0.599	0.599	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.002	0.014	9.389	-0.311	-0.311	0.000	0.000	0.000	0.000
16	A	21	THR	0	-0.014	-0.014	10.276	1.413	1.413	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.853	0.912	12.288	19.835	19.835	0.000	0.000	0.000	0.000
18	A	23	ALA	0	-0.014	0.007	15.068	0.878	0.878	0.000	0.000	0.000	0.000
19	A	24	GLU	-1	-0.889	-0.941	17.264	-14.138	-14.138	0.000	0.000	0.000	0.000
20	A	25	LEU	0	-0.021	-0.012	17.428	0.621	0.621	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.817	0.890	19.088	13.691	13.691	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.014	-0.003	18.995	0.053	0.053	0.000	0.000	0.000	0.000
23	A	28	GLY	0	0.007	0.003	21.291	0.540	0.540	0.000	0.000	0.000	0.000
24	A	29	ASP	-1	-0.855	-0.913	21.939	-12.524	-12.524	0.000	0.000	0.000	0.000
25	A	30	ARG	1	0.784	0.859	23.225	10.265	10.265	0.000	0.000	0.000	0.000
26	A	31	LEU	0	-0.041	-0.010	18.833	0.317	0.317	0.000	0.000	0.000	0.000
27	A	32	VAL	0	0.008	-0.011	22.905	0.080	0.080	0.000	0.000	0.000	0.000
28	A	33	PRO	0	0.010	-0.002	23.523	-0.340	-0.340	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.013	0.015	24.562	0.351	0.351	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.919	0.961	21.508	13.155	13.155	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-0.821	-0.905	23.137	-11.814	-11.814	0.000	0.000	0.000	0.000
32	A	37	SER	0	0.004	-0.001	20.365	-0.961	-0.961	0.000	0.000	0.000	0.000
33	A	38	ASN	0	0.000	-0.001	15.585	0.339	0.339	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.032	-0.013	12.950	-0.459	-0.459	0.000	0.000	0.000	0.000
35	A	40	GLU	-1	-0.787	-0.883	18.897	-11.751	-11.751	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.031	0.016	22.753	0.158	0.158	0.000	0.000	0.000	0.000
37	A	42	GLY	0	-0.010	-0.008	24.742	0.353	0.353	0.000	0.000	0.000	0.000
38	A	43	ARG	1	0.789	0.880	23.123	12.201	12.201	0.000	0.000	0.000	0.000
39	A	44	ILE	0	-0.003	-0.004	24.621	-0.432	-0.432	0.000	0.000	0.000	0.000
40	A	45	MET	0	-0.049	-0.005	19.750	0.095	0.095	0.000	0.000	0.000	0.000
41	A	46	ASN	0	-0.050	-0.055	24.067	0.529	0.529	0.000	0.000	0.000	0.000
42	A	47	HIS	0	-0.069	-0.049	21.394	0.514	0.514	0.000	0.000	0.000	0.000
43	A	48	ILE	0	-0.028	0.006	18.114	-0.388	-0.388	0.000	0.000	0.000	0.000
44	A	49	TYR	0	-0.036	-0.047	15.316	0.013	0.013	0.000	0.000	0.000	0.000
45	A	50	ILE	0	-0.018	-0.002	13.761	-0.589	-0.589	0.000	0.000	0.000	0.000
46	A	51	THR	0	0.001	-0.009	8.689	-0.530	-0.530	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.055	0.039	10.735	0.736	0.736	0.000	0.000	0.000	0.000
48	A	53	THR	0	-0.024	-0.008	5.937	-1.967	-1.967	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.028	0.025	6.093	2.271	2.271	0.000	0.000	0.000	0.000
55	A	60	GLY	0	0.007	0.014	6.488	3.158	3.158	0.000	0.000	0.000	0.000
56	A	61	ALA	0	0.020	0.014	7.334	2.104	2.104	0.000	0.000	0.000	0.000
57	A	62	GLU	-1	-0.825	-0.889	5.541	-42.517	-42.517	0.000	0.000	0.000	0.000
58	A	63	LEU	0	-0.061	-0.037	9.067	2.569	2.569	0.000	0.000	0.000	0.000
59	A	64	ALA	0	-0.025	0.016	11.561	1.595	1.595	0.000	0.000	0.000	0.000
60	A	65	ALA	0	0.043	0.028	13.819	-0.178	-0.178	0.000	0.000	0.000	0.000
61	A	66	GLY	0	0.005	0.006	17.255	-0.109	-0.109	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.916	-0.963	17.526	-15.154	-15.154	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.002	0.005	17.407	0.004	0.004	0.000	0.000	0.000	0.000
64	A	69	ARG	1	0.872	0.930	8.356	28.183	28.183	0.000	0.000	0.000	0.000
65	A	70	GLY	0	0.031	0.022	10.230	0.742	0.742	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.813	0.895	11.075	17.183	17.183	0.000	0.000	0.000	0.000
67	A	72	ILE	0	0.030	0.002	5.895	-1.005	-1.005	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.002	0.014	10.467	0.221	0.221	0.000	0.000	0.000	0.000
69	A	74	ILE	0	-0.012	-0.005	11.905	-1.251	-1.251	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.037	-0.034	14.097	1.088	1.088	0.000	0.000	0.000	0.000
71	A	76	GLU	-1	-0.881	-0.943	17.058	-13.945	-13.945	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.031	-0.031	18.964	0.434	0.434	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.768	-0.835	21.967	-10.532	-10.532	0.000	0.000	0.000	0.000
74	A	79	GLY	0	0.037	0.023	25.005	0.420	0.420	0.000	0.000	0.000	0.000
75	A	80	ALA	0	-0.060	-0.011	24.438	-0.471	-0.471	0.000	0.000	0.000	0.000
76	A	81	ILE	0	-0.031	-0.010	18.352	-0.287	-0.287	0.000	0.000	0.000	0.000
77	A	82	GLU	-1	-0.839	-0.892	21.180	-11.901	-11.901	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.845	-0.923	18.118	-15.934	-15.934	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.782	-0.892	15.464	-16.844	-16.844	0.000	0.000	0.000	0.000
80	A	85	PRO	0	-0.013	0.002	17.610	-0.415	-0.415	0.000	0.000	0.000	0.000
81	A	86	ASN	0	-0.061	-0.059	16.941	0.639	0.639	0.000	0.000	0.000	0.000
82	A	87	VAL	0	-0.065	-0.037	12.641	-0.474	-0.474	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.018	0.002	15.322	-0.759	-0.759	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.879	-0.929	17.722	-13.026	-13.026	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.848	0.928	17.730	14.506	14.506	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.931	0.960	13.210	20.741	20.741	0.000	0.000	0.000	0.000
87	A	92	LEU	0	-0.031	-0.011	13.307	-0.216	-0.216	0.000	0.000	0.000	0.000
88	A	93	PRO	0	0.027	0.022	17.461	0.159	0.159	0.000	0.000	0.000	0.000
89	A	94	GLY	0	0.049	0.015	17.813	-0.687	-0.687	0.000	0.000	0.000	0.000
90	A	95	ASN	0	-0.007	-0.033	14.030	-1.588	-1.588	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.004	0.003	12.261	-0.732	-0.732	0.000	0.000	0.000	0.000
92	A	97	THR	0	-0.016	-0.012	9.280	-1.692	-1.692	0.000	0.000	0.000	0.000
93	A	98	ARG	1	0.889	0.953	9.605	17.651	17.651	0.000	0.000	0.000	0.000
94	A	99	SER	0	0.040	0.012	11.010	-1.104	-1.104	0.000	0.000	0.000	0.000
95	A	100	TYR	0	0.011	0.015	12.946	0.674	0.674	0.000	0.000	0.000	0.000
96	A	101	ARG	1	0.805	0.892	16.352	12.535	12.535	0.000	0.000	0.000	0.000
97	A	102	THR	0	0.034	0.001	19.134	0.526	0.526	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.905	0.957	22.326	10.747	10.747	0.000	0.000	0.000	0.000
99	A	104	GLU	-1	-0.909	-0.945	24.910	-10.214	-10.214	0.000	0.000	0.000	0.000
100	A	105	PRO	0	-0.014	-0.021	23.979	-0.491	-0.491	0.000	0.000	0.000	0.000
101	A	106	VAL	0	-0.020	0.003	18.662	-0.148	-0.148	0.000	0.000	0.000	0.000
102	A	107	TRP	0	-0.012	-0.018	21.873	0.256	0.256	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.042	-0.019	17.706	-0.862	-0.862	0.000	0.000	0.000	0.000
104	A	109	VAL	0	0.036	0.011	18.054	0.503	0.503	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.017	0.004	16.268	0.240	0.240	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.858	-0.917	13.642	-19.179	-19.179	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.021	-0.004	7.830	0.016	0.016	0.000	0.000	0.000	0.000
108	A	113	THR	0	0.001	-0.016	10.925	-0.641	-0.641	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.932	-0.954	9.168	-28.145	-28.145	0.000	0.000	0.000	0.000
115	A	120	PRO	0	0.037	-0.001	7.145	0.801	0.801	0.000	0.000	0.000	0.000
116	A	121	GLU	-1	-0.843	-0.927	10.251	-27.206	-27.206	0.000	0.000	0.000	0.000
117	A	122	GLN	0	0.026	0.012	5.808	-3.252	-3.252	0.000	0.000	0.000	0.000
118	A	123	LEU	0	-0.015	-0.007	8.234	1.282	1.282	0.000	0.000	0.000	0.000
119	A	124	ALA	0	0.006	0.003	9.798	1.707	1.707	0.000	0.000	0.000	0.000
120	A	125	ALA	0	-0.010	-0.004	12.251	1.228	1.228	0.000	0.000	0.000	0.000
121	A	126	MET	0	-0.029	-0.001	9.043	1.936	1.936	0.000	0.000	0.000	0.000
122	A	127	ARG	1	0.887	0.936	11.882	23.053	23.053	0.000	0.000	0.000	0.000
123	A	128	GLN	0	0.092	0.036	14.853	0.483	0.483	0.000	0.000	0.000	0.000
124	A	129	GLY	0	0.041	0.025	16.034	0.951	0.951	0.000	0.000	0.000	0.000
125	A	130	LEU	0	-0.020	-0.017	13.528	1.002	1.002	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.927	-0.960	17.452	-14.256	-14.256	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.956	-0.969	20.105	-13.352	-13.352	0.000	0.000	0.000	0.000
128	A	133	LEU	0	-0.002	-0.013	17.824	0.696	0.696	0.000	0.000	0.000	0.000
129	A	134	ARG	1	0.842	0.914	18.058	15.594	15.594	0.000	0.000	0.000	0.000
130	A	135	ARG	1	0.880	0.942	22.948	13.286	13.286	0.000	0.000	0.000	0.000
131	A	136	LYS	1	0.894	0.944	25.285	11.551	11.551	0.000	0.000	0.000	0.000
132	A	137	GLY	0	0.024	0.023	26.393	0.291	0.291	0.000	0.000	0.000	0.000
133	A	138	LEU	0	-0.024	-0.021	23.336	0.142	0.142	0.000	0.000	0.000	0.000
134	A	139	ALA	0	-0.053	-0.015	21.141	-0.385	-0.385	0.000	0.000	0.000	0.000
135	A	140	VAL	0	-0.005	-0.002	22.201	0.149	0.149	0.000	0.000	0.000	0.000
136	A	141	ILE	0	-0.016	0.003	19.909	-0.636	-0.636	0.000	0.000	0.000	0.000
137	A	142	TYR	0	-0.046	-0.027	21.485	0.716	0.716	0.000	0.000	0.000	0.000
138	A	143	ASP	-2	-1.579	-1.744	21.810	-24.979	-24.979	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:6:PRO)