FMO DATABASE

FMODB ID: G4611

Calculation Name: 3NPD-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 3-cyclohexyl-1-propylsulfonic acid | 1,2-ethanediol

Ligand 3-letter code: CXS | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NPD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HY15

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	112
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-853323.211273
FMO2-HF: Nuclear repulsion	809124.23077
FMO2-HF: Total energy	-44198.980503
FMO2-MP2: Total energy	-44326.598986

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.
-16.7	-15.985	0.006	-0.373	-0.348	-0.001

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 : 0.852 / q_NPA : 0.913

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	21	SER	0	-0.009	-0.023	3.819	-4.871	-4.156	0.006	-0.373	-0.348	-0.001
4	A	22	LEU	0	0.031	-0.003	6.370	1.631	1.631	0.000	0.000	0.000	0.000
5	A	23	LYS	1	1.012	1.001	8.595	22.527	22.527	0.000	0.000	0.000	0.000
6	A	24	ASP	-1	-0.812	-0.870	7.485	-33.796	-33.796	0.000	0.000	0.000	0.000
7	A	25	PHE	0	-0.015	-0.009	6.110	1.624	1.624	0.000	0.000	0.000	0.000
8	A	26	GLU	-1	-0.940	-0.969	8.375	-18.610	-18.610	0.000	0.000	0.000	0.000
9	A	27	LEU	0	0.013	0.005	11.952	1.715	1.715	0.000	0.000	0.000	0.000
10	A	28	SER	0	-0.006	-0.028	9.881	0.351	0.351	0.000	0.000	0.000	0.000
11	A	29	LYS	1	0.797	0.887	10.926	24.918	24.918	0.000	0.000	0.000	0.000
12	A	30	MET	0	-0.055	-0.025	13.900	1.426	1.426	0.000	0.000	0.000	0.000
13	A	31	LEU	0	0.001	0.004	14.464	1.337	1.337	0.000	0.000	0.000	0.000
14	A	32	GLU	-1	-0.795	-0.891	12.773	-20.843	-20.843	0.000	0.000	0.000	0.000
15	A	33	LYS	1	0.772	0.900	16.928	13.717	13.717	0.000	0.000	0.000	0.000
16	A	34	VAL	0	0.059	0.026	19.933	0.643	0.643	0.000	0.000	0.000	0.000
17	A	35	ALA	0	0.045	0.025	18.986	0.674	0.674	0.000	0.000	0.000	0.000
18	A	36	LYS	1	0.928	0.979	19.252	15.685	15.685	0.000	0.000	0.000	0.000
19	A	37	GLU	-1	-0.858	-0.931	22.328	-11.978	-11.978	0.000	0.000	0.000	0.000
20	A	38	SER	0	-0.024	-0.021	24.377	0.599	0.599	0.000	0.000	0.000	0.000
21	A	39	SER	0	0.005	-0.013	23.422	0.329	0.329	0.000	0.000	0.000	0.000
22	A	40	VAL	0	-0.016	0.016	26.155	0.296	0.296	0.000	0.000	0.000	0.000
23	A	41	GLY	0	-0.004	0.000	29.004	0.222	0.222	0.000	0.000	0.000	0.000
24	A	42	THR	0	-0.085	-0.029	27.769	0.106	0.106	0.000	0.000	0.000	0.000
25	A	43	PRO	0	-0.005	-0.014	29.469	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	44	ARG	1	0.828	0.914	29.962	10.414	10.414	0.000	0.000	0.000	0.000
27	A	45	ALA	0	-0.005	-0.003	33.331	-0.195	-0.195	0.000	0.000	0.000	0.000
28	A	46	ILE	0	-0.025	-0.007	32.390	0.034	0.034	0.000	0.000	0.000	0.000
29	A	47	ASN	0	0.000	-0.018	35.814	0.212	0.212	0.000	0.000	0.000	0.000
30	A	48	GLU	-1	-0.861	-0.930	37.943	-7.553	-7.553	0.000	0.000	0.000	0.000
31	A	49	ASP	-1	-0.890	-0.943	37.495	-7.959	-7.959	0.000	0.000	0.000	0.000
32	A	50	ILE	0	-0.030	-0.009	32.173	-0.233	-0.233	0.000	0.000	0.000	0.000
33	A	51	LEU	0	-0.004	0.000	31.640	0.195	0.195	0.000	0.000	0.000	0.000
34	A	52	ASP	-1	-0.751	-0.883	28.116	-11.207	-11.207	0.000	0.000	0.000	0.000
35	A	53	GLN	0	-0.030	-0.045	26.256	0.129	0.129	0.000	0.000	0.000	0.000
36	A	54	GLY	0	0.039	0.045	25.330	-0.211	-0.211	0.000	0.000	0.000	0.000
37	A	55	TYR	0	-0.029	-0.026	20.944	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	56	THR	0	-0.022	0.005	16.559	0.154	0.154	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.015	-0.016	12.765	0.470	0.470	0.000	0.000	0.000	0.000
40	A	58	GLU	-1	-0.920	-0.942	11.422	-23.803	-23.803	0.000	0.000	0.000	0.000
41	A	59	GLY	0	-0.005	-0.006	9.005	-0.351	-0.351	0.000	0.000	0.000	0.000
42	A	60	ASN	0	0.023	0.012	9.758	0.453	0.453	0.000	0.000	0.000	0.000
43	A	61	GLN	0	0.058	0.043	12.810	3.104	3.104	0.000	0.000	0.000	0.000
44	A	62	LEU	0	0.005	0.013	15.186	-0.476	-0.476	0.000	0.000	0.000	0.000
45	A	63	ILE	0	-0.019	-0.014	15.681	0.661	0.661	0.000	0.000	0.000	0.000
46	A	64	ASN	0	-0.035	-0.013	19.391	0.420	0.420	0.000	0.000	0.000	0.000
47	A	65	HIS	0	0.001	-0.025	19.004	0.385	0.385	0.000	0.000	0.000	0.000
48	A	66	LEU	0	-0.005	-0.001	24.133	0.422	0.422	0.000	0.000	0.000	0.000
49	A	67	SER	0	0.004	0.016	27.812	0.024	0.024	0.000	0.000	0.000	0.000
50	A	68	VAL	0	0.022	0.000	30.174	0.269	0.269	0.000	0.000	0.000	0.000
51	A	69	ARG	1	0.871	0.947	33.115	8.161	8.161	0.000	0.000	0.000	0.000
52	A	70	ALA	0	0.070	0.033	36.359	0.056	0.056	0.000	0.000	0.000	0.000
53	A	71	SER	0	0.002	-0.001	37.312	0.001	0.001	0.000	0.000	0.000	0.000
54	A	72	HIS	0	0.020	0.019	35.115	0.300	0.300	0.000	0.000	0.000	0.000
55	A	73	ALA	0	0.010	0.003	33.662	-0.129	-0.129	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.836	-0.916	34.817	-8.654	-8.654	0.000	0.000	0.000	0.000
57	A	75	ARG	1	0.838	0.914	37.413	7.869	7.869	0.000	0.000	0.000	0.000
58	A	76	MET	0	-0.036	-0.010	30.608	0.013	0.013	0.000	0.000	0.000	0.000
59	A	77	ARG	1	0.801	0.868	31.320	9.292	9.292	0.000	0.000	0.000	0.000
60	A	78	SER	0	-0.086	-0.040	34.261	0.065	0.065	0.000	0.000	0.000	0.000
61	A	79	ASN	0	-0.014	-0.012	36.164	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	80	PRO	0	0.073	0.041	30.959	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	81	ASP	-1	-0.864	-0.929	31.957	-9.741	-9.741	0.000	0.000	0.000	0.000
64	A	82	SER	0	-0.018	-0.011	33.517	-0.082	-0.082	0.000	0.000	0.000	0.000
65	A	83	VAL	0	-0.026	-0.004	30.312	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	84	ARG	1	0.845	0.898	24.781	11.893	11.893	0.000	0.000	0.000	0.000
67	A	85	SER	0	0.002	0.003	30.350	-0.173	-0.173	0.000	0.000	0.000	0.000
68	A	86	GLN	0	-0.028	-0.010	32.700	0.004	0.004	0.000	0.000	0.000	0.000
69	A	87	LEU	0	-0.045	-0.023	27.852	-0.077	-0.077	0.000	0.000	0.000	0.000
70	A	88	GLY	0	0.052	0.031	28.749	-0.294	-0.294	0.000	0.000	0.000	0.000
71	A	89	ASP	-1	-0.869	-0.942	29.772	-9.226	-9.226	0.000	0.000	0.000	0.000
72	A	90	SER	0	-0.048	0.006	30.640	0.046	0.046	0.000	0.000	0.000	0.000
73	A	91	VAL	0	-0.007	-0.022	24.832	-0.117	-0.117	0.000	0.000	0.000	0.000
74	A	92	CYS	0	-0.107	-0.044	25.936	0.028	0.028	0.000	0.000	0.000	0.000
75	A	93	SER	0	-0.017	-0.015	29.479	0.157	0.157	0.000	0.000	0.000	0.000
76	A	94	ASN	0	0.018	0.019	28.718	0.071	0.071	0.000	0.000	0.000	0.000
77	A	95	THR	0	0.024	-0.004	28.665	-0.413	-0.413	0.000	0.000	0.000	0.000
78	A	96	GLY	0	0.019	0.018	27.072	-0.274	-0.274	0.000	0.000	0.000	0.000
79	A	97	TYR	0	0.040	0.007	24.187	-0.536	-0.536	0.000	0.000	0.000	0.000
80	A	98	ARG	1	0.945	0.963	23.971	10.110	10.110	0.000	0.000	0.000	0.000
81	A	99	GLN	0	-0.052	-0.024	24.689	-0.595	-0.595	0.000	0.000	0.000	0.000
82	A	100	LEU	0	-0.001	0.016	19.713	-0.534	-0.534	0.000	0.000	0.000	0.000
83	A	101	LEU	0	0.029	0.025	19.876	-0.806	-0.806	0.000	0.000	0.000	0.000
84	A	102	ALA	0	-0.052	-0.025	21.012	-0.439	-0.439	0.000	0.000	0.000	0.000
85	A	103	ARG	1	0.830	0.903	18.460	14.255	14.255	0.000	0.000	0.000	0.000
86	A	104	GLY	0	0.022	0.022	16.554	-1.096	-1.096	0.000	0.000	0.000	0.000
87	A	105	ALA	0	-0.032	-0.012	15.857	-1.303	-1.303	0.000	0.000	0.000	0.000
88	A	106	ILE	0	-0.040	-0.024	15.416	0.792	0.792	0.000	0.000	0.000	0.000
89	A	107	LEU	0	0.001	0.008	18.250	-0.351	-0.351	0.000	0.000	0.000	0.000
90	A	108	THR	0	-0.025	-0.032	17.717	0.301	0.301	0.000	0.000	0.000	0.000
91	A	109	TYR	0	0.011	0.015	20.747	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	110	SER	0	-0.013	-0.006	21.370	0.096	0.096	0.000	0.000	0.000	0.000
93	A	111	PHE	0	0.047	0.021	23.466	0.292	0.292	0.000	0.000	0.000	0.000
94	A	112	THR	0	-0.011	-0.014	25.125	0.028	0.028	0.000	0.000	0.000	0.000
95	A	113	GLU	-1	-0.799	-0.905	28.068	-8.792	-8.792	0.000	0.000	0.000	0.000
96	A	114	TYR	0	-0.034	-0.026	31.063	0.027	0.027	0.000	0.000	0.000	0.000
97	A	115	LYS	1	0.914	0.946	33.008	8.072	8.072	0.000	0.000	0.000	0.000
98	A	116	THR	0	0.005	-0.007	31.818	0.021	0.021	0.000	0.000	0.000	0.000
99	A	117	ASN	0	0.018	0.024	24.380	-0.125	-0.125	0.000	0.000	0.000	0.000
100	A	118	GLN	0	0.032	0.022	26.714	-0.687	-0.687	0.000	0.000	0.000	0.000
101	A	119	PRO	0	0.028	0.009	24.708	0.163	0.163	0.000	0.000	0.000	0.000
102	A	120	VAL	0	-0.050	0.002	27.169	0.419	0.419	0.000	0.000	0.000	0.000
103	A	121	ALA	0	0.044	0.017	27.657	0.202	0.202	0.000	0.000	0.000	0.000
104	A	122	THR	0	-0.079	-0.050	20.930	-0.455	-0.455	0.000	0.000	0.000	0.000
105	A	123	GLU	-1	-0.828	-0.881	23.665	-11.945	-11.945	0.000	0.000	0.000	0.000
106	A	124	ARG	1	0.879	0.935	17.292	15.940	15.940	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.045	0.030	21.851	0.435	0.435	0.000	0.000	0.000	0.000
108	A	126	ASP	-1	-0.787	-0.881	19.815	-15.302	-15.302	0.000	0.000	0.000	0.000
109	A	127	ALA	0	0.017	-0.008	21.379	0.663	0.663	0.000	0.000	0.000	0.000
110	A	128	GLY	0	-0.078	-0.034	22.760	0.573	0.573	0.000	0.000	0.000	0.000
111	A	129	SER	0	-0.022	-0.045	23.453	0.518	0.518	0.000	0.000	0.000	0.000
112	A	131	ARG	0	0.015	0.040	25.606	1.763	1.763	0.000	0.000	0.000	0.000

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