FMO DATABASE

FMODB ID: Q51LY

Calculation Name: 6SMF-C-Xray547

Preferred Name:

Target Type:

Ligand Name: citrate anion | 2-amino-2-hydroxymethyl-propane-1,3-diol | sulfate ion | glycerol

Ligand 3-letter code: FLC | TRS | SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SMF

Chain ID: C

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1273017.86304
FMO2-HF: Nuclear repulsion	1219654.276268
FMO2-HF: Total energy	-53363.586773
FMO2-MP2: Total energy	-53524.32724

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-219.002	-210.45	2.392	-4.929	-6.015	-0.06

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.784 / q_NPA : 1.888

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	5	PRO	0	0.033	0.019	2.498	-19.731	-15.748	1.169	-2.300	-2.852	-0.026
4	A	6	THR	0	-0.005	0.008	2.810	2.258	2.854	0.099	-0.143	-0.552	-0.002
68	A	70	VAL	0	-0.026	-0.014	3.528	-5.976	-5.700	0.000	-0.098	-0.178	-0.001
69	A	71	LYS	1	0.854	0.923	2.368	24.842	27.884	1.120	-2.003	-2.159	-0.028
70	A	72	ALA	0	-0.005	0.010	3.547	-14.607	-13.952	0.004	-0.385	-0.274	-0.003
5	A	7	ILE	0	0.046	0.021	5.590	1.027	1.027	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.026	0.017	7.089	1.323	1.323	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.013	-0.007	11.233	2.110	2.110	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.005	0.010	13.592	1.079	1.079	0.000	0.000	0.000	0.000
9	A	11	ASN	0	0.006	0.004	17.056	2.056	2.056	0.000	0.000	0.000	0.000
10	A	12	GLY	0	0.097	0.042	20.826	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.006	0.006	23.530	0.116	0.116	0.000	0.000	0.000	0.000
12	A	14	ASN	0	-0.037	-0.025	26.880	0.410	0.410	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.011	0.017	23.916	0.361	0.361	0.000	0.000	0.000	0.000
14	A	16	ASN	0	0.012	-0.002	25.644	-0.158	-0.158	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.029	-0.014	26.966	0.301	0.301	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.038	-0.020	26.487	0.627	0.627	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.027	0.024	30.156	-0.244	-0.244	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.020	0.003	31.265	0.218	0.218	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.845	0.909	34.566	15.606	15.606	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.798	-0.894	37.543	-15.115	-15.115	0.000	0.000	0.000	0.000
21	A	23	PRO	0	0.056	0.034	36.607	0.091	0.091	0.000	0.000	0.000	0.000
22	A	24	THR	0	-0.051	-0.034	38.157	-0.199	-0.199	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.034	-0.007	40.676	0.291	0.291	0.000	0.000	0.000	0.000
24	A	26	TYR	0	-0.043	-0.031	37.045	0.006	0.006	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.005	0.017	35.348	-0.456	-0.456	0.000	0.000	0.000	0.000
26	A	28	HIS	0	0.025	-0.016	34.304	-0.286	-0.286	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.054	-0.004	26.661	0.056	0.056	0.000	0.000	0.000	0.000
28	A	30	THR	0	0.044	-0.003	27.517	-0.279	-0.279	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.006	-0.021	22.308	-0.506	-0.506	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.871	-0.922	22.892	-25.704	-25.704	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.807	-0.884	22.921	-22.912	-22.912	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.065	-0.032	21.334	-0.548	-0.548	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.012	-0.005	19.036	-1.319	-1.319	0.000	0.000	0.000	0.000
34	A	36	ASN	0	-0.034	-0.032	18.576	-2.869	-2.869	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.938	0.966	20.178	23.136	23.136	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.012	0.004	16.565	-0.984	-0.984	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.930	0.975	14.005	34.538	34.538	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.065	0.040	15.323	-1.700	-1.700	0.000	0.000	0.000	0.000
39	A	41	GLN	0	-0.066	-0.048	17.206	-0.427	-0.427	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.012	-0.017	11.901	-0.958	-0.958	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.953	-0.969	12.298	-39.725	-39.725	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.924	0.964	13.683	31.022	31.022	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.082	-0.044	13.390	1.119	1.119	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.853	-0.902	8.971	-59.747	-59.747	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.056	-0.021	7.576	-8.490	-8.490	0.000	0.000	0.000	0.000
46	A	48	THR	0	-0.037	-0.030	5.996	2.153	2.153	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.025	-0.004	8.407	-0.658	-0.658	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.929	-0.954	9.530	-47.423	-47.423	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.056	-0.014	11.528	1.515	1.515	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.828	0.896	10.956	43.699	43.699	0.000	0.000	0.000	0.000
51	A	53	GLN	0	-0.051	-0.053	17.167	0.509	0.509	0.000	0.000	0.000	0.000
52	A	54	SER	0	0.049	0.029	20.624	0.429	0.429	0.000	0.000	0.000	0.000
53	A	55	ASN	0	0.034	0.006	22.496	-0.174	-0.174	0.000	0.000	0.000	0.000
54	A	56	HIS	0	0.007	0.019	23.606	0.892	0.892	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.816	-0.878	22.952	-22.504	-22.504	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.024	0.007	22.057	-0.850	-0.850	0.000	0.000	0.000	0.000
57	A	59	ALA	0	0.042	0.028	19.305	-0.979	-0.979	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.017	-0.014	17.621	-1.654	-1.654	0.000	0.000	0.000	0.000
59	A	61	ILE	0	0.023	0.015	16.897	-1.686	-1.686	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.900	-0.949	16.165	-30.558	-30.558	0.000	0.000	0.000	0.000
61	A	63	TRP	0	-0.006	-0.028	13.079	-2.174	-2.174	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.006	0.011	11.994	-3.332	-3.332	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.008	-0.002	12.149	-1.585	-1.585	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.855	-0.904	9.118	-47.630	-47.630	0.000	0.000	0.000	0.000
65	A	67	ALA	0	0.029	0.013	7.745	-6.126	-6.126	0.000	0.000	0.000	0.000
66	A	68	GLN	0	0.057	0.045	6.927	-7.111	-7.111	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.043	-0.017	7.609	-4.244	-4.244	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.763	0.873	5.628	57.039	57.039	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.025	0.005	7.713	5.163	5.163	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.009	-0.006	10.387	-2.653	-2.653	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.007	0.012	12.954	2.222	2.222	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.021	0.007	16.177	-0.063	-0.063	0.000	0.000	0.000	0.000
76	A	78	ASN	0	0.033	0.022	18.655	2.000	2.000	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.067	0.020	22.125	0.245	0.245	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.015	-0.001	23.246	0.820	0.820	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.006	0.007	26.668	0.242	0.242	0.000	0.000	0.000	0.000
80	A	82	TYR	0	0.029	-0.003	24.841	0.506	0.506	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.030	-0.026	25.885	-0.517	-0.517	0.000	0.000	0.000	0.000
82	A	84	HIS	0	-0.052	-0.026	26.804	0.081	0.081	0.000	0.000	0.000	0.000
83	A	85	THR	0	-0.031	-0.018	29.265	0.360	0.360	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.032	-0.044	25.195	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.040	0.013	25.788	-0.670	-0.670	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.040	0.027	24.117	-0.567	-0.567	0.000	0.000	0.000	0.000
87	A	89	ILE	0	0.013	-0.004	20.431	-1.101	-1.101	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.020	0.000	20.996	-1.102	-1.102	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.888	-0.957	22.064	-23.493	-23.493	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.046	-0.023	18.075	-1.002	-1.002	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.035	-0.031	17.213	-1.820	-1.820	0.000	0.000	0.000	0.000
92	A	94	ARG	1	0.927	0.966	17.566	22.731	22.731	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.023	0.011	18.307	0.139	0.139	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.117	-0.046	12.597	-1.737	-1.737	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.014	-0.032	11.597	-0.417	-0.417	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.051	-0.005	8.626	-0.643	-0.643	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.016	0.012	11.195	2.861	2.861	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.028	0.013	13.422	-1.701	-1.701	0.000	0.000	0.000	0.000
99	A	101	ILE	0	0.007	0.009	16.090	1.648	1.648	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.725	-0.801	18.591	-23.427	-23.427	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.008	-0.006	20.344	0.464	0.464	0.000	0.000	0.000	0.000
102	A	104	HIS	1	0.772	0.861	22.882	23.493	23.493	0.000	0.000	0.000	0.000
103	A	105	LEU	0	0.042	0.035	26.078	0.122	0.122	0.000	0.000	0.000	0.000
104	A	106	SER	0	0.037	0.021	28.119	0.403	0.403	0.000	0.000	0.000	0.000
105	A	107	ASN	0	0.076	0.016	30.344	-0.774	-0.774	0.000	0.000	0.000	0.000
106	A	108	PRO	0	-0.035	-0.014	29.654	0.542	0.542	0.000	0.000	0.000	0.000
107	A	109	HIS	0	0.088	0.026	31.591	0.825	0.825	0.000	0.000	0.000	0.000
108	A	110	ALA	0	-0.072	-0.014	35.323	0.475	0.475	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.856	0.927	33.158	17.969	17.969	0.000	0.000	0.000	0.000
110	A	112	GLU	-1	-0.728	-0.844	37.092	-16.515	-16.515	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.074	0.034	37.232	-0.397	-0.397	0.000	0.000	0.000	0.000
112	A	114	PHE	0	-0.009	-0.007	34.949	-0.245	-0.245	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.777	0.850	32.487	17.287	17.287	0.000	0.000	0.000	0.000
114	A	116	HIS	0	-0.024	-0.003	32.472	-0.521	-0.521	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.813	0.908	30.861	18.678	18.678	0.000	0.000	0.000	0.000
116	A	118	SER	0	-0.006	-0.043	26.491	-0.356	-0.356	0.000	0.000	0.000	0.000
117	A	119	TYR	0	0.047	0.021	26.212	0.099	0.099	0.000	0.000	0.000	0.000
118	A	120	VAL	0	-0.013	-0.003	21.106	-0.683	-0.683	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.046	0.014	23.130	-0.783	-0.783	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.895	-0.922	25.462	-19.621	-19.621	0.000	0.000	0.000	0.000
121	A	123	ALA	0	-0.050	-0.027	21.634	0.174	0.174	0.000	0.000	0.000	0.000
122	A	124	ALA	0	-0.052	-0.013	19.727	-1.161	-1.161	0.000	0.000	0.000	0.000
123	A	125	LEU	0	-0.013	0.003	16.943	0.649	0.649	0.000	0.000	0.000	0.000
124	A	126	GLY	0	0.015	0.004	20.075	0.959	0.959	0.000	0.000	0.000	0.000
125	A	127	THR	0	-0.039	-0.040	21.852	-0.963	-0.963	0.000	0.000	0.000	0.000
126	A	128	ILE	0	0.003	0.022	21.430	0.704	0.704	0.000	0.000	0.000	0.000
127	A	129	SER	0	-0.041	-0.058	25.074	0.081	0.081	0.000	0.000	0.000	0.000
128	A	130	GLY	0	-0.043	-0.011	27.913	0.423	0.423	0.000	0.000	0.000	0.000
129	A	131	PHE	0	0.023	0.023	27.211	0.595	0.595	0.000	0.000	0.000	0.000
130	A	132	GLY	0	0.024	0.018	28.550	-0.144	-0.144	0.000	0.000	0.000	0.000
131	A	133	ALA	0	0.027	-0.007	25.281	-0.753	-0.753	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.845	-0.903	23.914	-25.643	-25.643	0.000	0.000	0.000	0.000
133	A	135	SER	0	-0.071	-0.036	24.153	-0.396	-0.396	0.000	0.000	0.000	0.000
134	A	136	TYR	0	-0.001	-0.021	19.426	-0.312	-0.312	0.000	0.000	0.000	0.000
135	A	137	SER	0	-0.013	-0.013	19.407	-1.636	-1.636	0.000	0.000	0.000	0.000
136	A	138	LEU	0	0.032	0.018	19.881	-1.475	-1.475	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.019	0.009	18.674	-0.812	-0.812	0.000	0.000	0.000	0.000
138	A	140	LEU	0	-0.005	0.000	13.114	-1.929	-1.929	0.000	0.000	0.000	0.000
139	A	141	ASP	-1	-0.813	-0.917	15.437	-34.225	-34.225	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.026	-0.002	17.342	-0.806	-0.806	0.000	0.000	0.000	0.000
141	A	143	ALA	0	0.027	0.010	13.157	-1.151	-1.151	0.000	0.000	0.000	0.000
142	A	144	ALA	0	-0.027	-0.022	12.060	-3.382	-3.382	0.000	0.000	0.000	0.000
143	A	145	LYS	1	0.733	0.850	12.826	32.085	32.085	0.000	0.000	0.000	0.000
144	A	146	LEU	-1	-0.805	-0.862	12.417	-45.551	-45.551	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)