FMO DATABASE

FMODB ID: JVLQ9

Calculation Name: 1TW4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cholic acid

Ligand 3-letter code: CHD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TW4

Chain ID: A

ChEMBL ID:

UniProt ID: P80226

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1061456.069244
FMO2-HF: Nuclear repulsion	1012104.807176
FMO2-HF: Total energy	-49351.262068
FMO2-MP2: Total energy	-49495.110581

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:ALA)

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

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.
-15.088	-12.423	10.574	-7.125	-6.112	-0.085

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.878

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	3	SER	0	0.005	0.012	3.117	6.511	9.134	-0.008	-1.232	-1.383	-0.003
4	A	4	GLY	0	0.014	0.013	4.967	-0.479	-0.438	-0.001	-0.006	-0.034	0.000
42	A	42	GLN	0	0.049	0.038	1.791	-38.809	-39.329	10.477	-5.754	-4.203	-0.081
43	A	43	LYS	1	0.883	0.920	5.197	23.031	23.078	-0.001	-0.002	-0.043	0.000
47	A	47	PHE	0	-0.033	-0.035	4.787	-7.241	-7.176	-0.001	-0.006	-0.058	0.000
102	A	102	VAL	0	0.004	0.003	2.929	1.165	1.574	0.108	-0.125	-0.391	-0.001
5	A	5	THR	0	0.020	0.024	8.379	0.307	0.307	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.017	-0.013	6.482	0.797	0.797	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.016	-0.006	12.911	1.074	1.074	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.006	0.008	16.403	-0.355	-0.355	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.021	-0.047	15.513	1.429	1.429	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.025	-0.011	19.011	1.049	1.049	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.004	-0.020	19.299	-1.583	-1.583	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.908	-0.934	21.519	-11.235	-11.235	0.000	0.000	0.000	0.000
13	A	13	ASN	0	0.003	-0.018	23.670	0.095	0.095	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.016	0.008	22.217	-0.233	-0.233	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.818	-0.929	25.533	-10.808	-10.808	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.803	-0.888	28.973	-9.462	-9.462	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.010	0.008	21.551	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.024	-0.021	24.630	0.038	0.038	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.834	0.895	27.646	9.529	9.529	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.003	0.011	27.898	0.220	0.220	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.089	-0.040	24.199	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.030	-0.015	27.955	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.038	-0.008	26.329	0.093	0.093	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.042	0.007	30.830	0.247	0.247	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.851	-0.934	33.249	-8.503	-8.503	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.916	-0.953	35.072	-8.538	-8.538	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.016	-0.011	28.314	-0.149	-0.149	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.001	0.000	30.200	-0.299	-0.299	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.841	0.911	31.087	8.493	8.493	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.037	-0.003	31.929	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.002	-0.014	26.966	-0.213	-0.213	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.907	0.967	26.959	9.189	9.189	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.867	-0.938	26.941	-10.789	-10.789	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.088	-0.036	23.761	-0.321	-0.321	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.912	0.963	21.323	12.918	12.918	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.022	-0.004	18.923	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.023	0.018	15.788	-0.630	-0.630	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.022	-0.016	12.049	0.500	0.500	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.849	-0.914	11.950	-22.579	-22.579	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.016	-0.009	6.253	0.437	0.437	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.035	0.014	7.477	-1.898	-1.898	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.035	0.026	5.860	4.447	4.447	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.832	-0.928	5.482	-40.813	-40.813	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.874	-0.901	8.099	-23.309	-23.309	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.003	0.010	8.847	3.385	3.385	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.017	-0.015	9.564	-2.779	-2.779	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.025	0.022	11.973	2.218	2.218	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.006	0.012	15.113	-0.585	-0.585	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.858	0.907	16.246	20.023	20.023	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.004	-0.011	19.829	0.118	0.118	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.032	-0.001	23.309	0.026	0.026	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.957	0.988	26.342	11.040	11.040	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.010	0.002	24.373	0.371	0.371	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.002	0.000	20.107	-0.304	-0.304	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.022	0.016	19.413	0.543	0.543	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.023	-0.023	15.453	-0.611	-0.611	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.001	0.004	15.294	1.537	1.537	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.001	-0.027	13.205	-1.163	-1.163	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.024	0.020	9.262	1.440	1.440	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.012	-0.027	11.107	-1.241	-1.241	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.062	-0.028	6.374	1.127	1.127	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.010	-0.010	11.040	0.946	0.946	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.925	0.964	14.291	21.205	21.205	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.883	-0.934	16.062	-14.452	-14.452	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.003	0.001	16.294	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.873	-0.930	18.319	-13.247	-13.247	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.041	-0.020	16.291	-0.803	-0.803	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.004	-0.015	19.935	1.222	1.222	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.025	-0.042	20.324	-0.790	-0.790	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.016	-0.012	20.377	0.392	0.392	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.783	-0.851	23.353	-11.846	-11.846	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.005	0.011	25.644	0.460	0.460	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.869	0.923	25.132	11.888	11.888	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.948	0.972	24.389	11.233	11.233	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.042	-0.019	20.707	0.480	0.480	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.877	0.941	21.162	12.893	12.893	0.000	0.000	0.000	0.000
80	A	80	CYS	0	-0.051	-0.014	16.990	-0.139	-0.139	0.000	0.000	0.000	0.000
81	A	81	THR	0	0.049	0.040	15.750	-0.289	-0.289	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.011	0.020	10.258	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.022	-0.019	10.953	0.102	0.102	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.020	0.005	5.502	-1.846	-1.846	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.010	0.005	9.104	2.314	2.314	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.011	-0.017	10.418	-0.904	-0.904	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.007	0.014	6.673	-0.196	-0.196	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.862	0.940	5.542	16.077	16.077	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.013	0.006	6.218	0.774	0.774	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.009	-0.005	7.912	2.178	2.178	0.000	0.000	0.000	0.000
91	A	91	THR	0	0.001	-0.016	11.711	0.028	0.028	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.951	0.974	14.755	16.835	16.835	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.019	-0.003	18.250	0.255	0.255	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.854	-0.931	21.958	-11.826	-11.826	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.851	0.942	23.351	13.119	13.119	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.018	-0.006	18.701	0.172	0.172	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.005	-0.007	17.587	-0.428	-0.428	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.010	0.006	11.750	1.759	1.759	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.851	-0.924	12.344	-20.141	-20.141	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.008	-0.021	8.182	1.902	1.902	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.852	-0.929	7.367	-27.758	-27.758	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.889	0.939	5.692	23.116	23.116	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.050	0.023	6.670	3.157	3.157	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.000	-0.005	7.474	-4.553	-4.553	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.808	-0.865	10.146	-18.250	-18.250	0.000	0.000	0.000	0.000
107	A	107	MET	0	-0.003	0.033	7.040	-3.869	-3.869	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.038	-0.020	10.115	2.613	2.613	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.786	-0.864	11.397	-23.299	-23.299	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.022	-0.012	13.522	1.586	1.586	0.000	0.000	0.000	0.000
111	A	111	ILE	0	0.000	0.002	16.169	-0.464	-0.464	0.000	0.000	0.000	0.000
112	A	112	THR	0	0.002	0.015	18.398	0.831	0.831	0.000	0.000	0.000	0.000
113	A	113	PHE	0	0.032	0.003	21.628	-0.337	-0.337	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.028	0.024	24.500	0.215	0.215	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.020	-0.004	27.008	0.341	0.341	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.007	0.013	25.788	0.060	0.060	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.022	-0.034	20.608	-0.260	-0.260	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.007	0.017	19.766	0.287	0.287	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.002	-0.009	16.925	-0.751	-0.751	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.831	0.883	14.985	19.702	19.702	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.927	0.973	14.798	16.279	16.279	0.000	0.000	0.000	0.000
122	A	122	SER	0	0.040	0.015	12.818	1.677	1.677	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.887	0.938	12.942	18.506	18.506	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.806	0.890	5.645	39.118	39.118	0.000	0.000	0.000	0.000
125	A	125	VAL	-1	-0.908	-0.952	12.108	-20.678	-20.678	0.000	0.000	0.000	0.000

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