FMO DATABASE

FMODB ID: RML98

Calculation Name: 4FDF-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4FDF

Chain ID: A

ChEMBL ID:

UniProt ID: P9WJR7

Base Structure: X-ray

Registration Date: 2025-10-04

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1080103.29637
FMO2-HF: Nuclear repulsion	1028841.520549
FMO2-HF: Total energy	-51261.775821
FMO2-MP2: Total energy	-51410.177883

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:22:GLY)

Summations of interaction energy for fragment #1(A:22: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.
-30.97	-30.011	-0.016	-0.401	-0.542	-0.001

Interaction energy analysis for fragmet #1(A:22:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.911

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	24	ALA	0	0.039	0.022	3.830	1.866	2.825	-0.016	-0.401	-0.542	-0.001
4	A	25	HIS	0	-0.032	-0.016	7.214	-0.164	-0.164	0.000	0.000	0.000	0.000
5	A	26	MET	0	0.059	0.045	10.689	0.466	0.466	0.000	0.000	0.000	0.000
6	A	27	VAL	0	0.000	0.000	14.229	-0.216	-0.216	0.000	0.000	0.000	0.000
7	A	28	ASP	-1	-0.784	-0.885	16.924	-13.289	-13.289	0.000	0.000	0.000	0.000
8	A	29	ILE	0	0.017	0.006	20.050	0.289	0.289	0.000	0.000	0.000	0.000
9	A	30	THR	0	0.030	0.001	23.085	0.259	0.259	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.834	-0.918	25.286	-11.516	-11.516	0.000	0.000	0.000	0.000
11	A	32	LYS	1	0.769	0.888	24.266	13.016	13.016	0.000	0.000	0.000	0.000
12	A	33	ALA	0	0.008	0.005	28.833	-0.101	-0.101	0.000	0.000	0.000	0.000
13	A	34	THR	0	-0.025	-0.028	29.057	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	35	THR	0	0.001	0.006	31.831	0.134	0.134	0.000	0.000	0.000	0.000
15	A	36	LYS	1	0.860	0.929	32.526	8.719	8.719	0.000	0.000	0.000	0.000
16	A	37	ARG	1	0.832	0.909	28.256	11.012	11.012	0.000	0.000	0.000	0.000
17	A	38	THR	0	-0.003	-0.012	32.263	0.230	0.230	0.000	0.000	0.000	0.000
18	A	39	ALA	0	0.003	0.022	28.686	-0.180	-0.180	0.000	0.000	0.000	0.000
19	A	40	VAL	0	0.003	0.005	30.727	0.213	0.213	0.000	0.000	0.000	0.000
20	A	41	ALA	0	0.006	0.007	27.865	-0.291	-0.291	0.000	0.000	0.000	0.000
21	A	42	ALA	0	0.024	0.014	29.815	0.322	0.322	0.000	0.000	0.000	0.000
22	A	43	GLY	0	0.027	0.014	29.494	-0.476	-0.476	0.000	0.000	0.000	0.000
23	A	44	ILE	0	-0.046	-0.014	30.812	0.303	0.303	0.000	0.000	0.000	0.000
24	A	45	LEU	0	0.009	0.020	32.128	-0.265	-0.265	0.000	0.000	0.000	0.000
25	A	46	ARG	1	0.827	0.890	32.841	9.479	9.479	0.000	0.000	0.000	0.000
26	A	47	THR	0	-0.051	-0.055	35.837	-0.133	-0.133	0.000	0.000	0.000	0.000
27	A	48	SER	0	0.032	0.006	38.627	0.234	0.234	0.000	0.000	0.000	0.000
28	A	49	ALA	0	0.071	0.022	42.283	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	50	GLN	0	-0.035	-0.009	44.913	0.184	0.184	0.000	0.000	0.000	0.000
30	A	51	VAL	0	0.035	0.014	39.969	0.084	0.084	0.000	0.000	0.000	0.000
31	A	52	VAL	0	0.017	0.022	41.091	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	53	ALA	0	0.024	0.021	43.279	0.055	0.055	0.000	0.000	0.000	0.000
33	A	54	LEU	0	-0.022	0.001	44.929	0.077	0.077	0.000	0.000	0.000	0.000
34	A	55	ILE	0	-0.019	-0.013	39.476	0.006	0.006	0.000	0.000	0.000	0.000
35	A	56	SER	0	-0.043	-0.030	43.571	0.019	0.019	0.000	0.000	0.000	0.000
36	A	57	THR	0	-0.082	-0.061	46.018	0.116	0.116	0.000	0.000	0.000	0.000
37	A	58	GLY	0	0.000	0.015	46.357	0.110	0.110	0.000	0.000	0.000	0.000
38	A	59	GLY	0	-0.012	-0.002	47.418	0.061	0.061	0.000	0.000	0.000	0.000
39	A	60	LEU	0	-0.014	-0.003	41.390	0.002	0.002	0.000	0.000	0.000	0.000
40	A	61	PRO	0	0.008	-0.001	44.292	0.026	0.026	0.000	0.000	0.000	0.000
41	A	62	LYS	1	0.775	0.861	36.819	8.592	8.592	0.000	0.000	0.000	0.000
42	A	63	GLY	0	0.015	0.021	42.806	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	64	ASP	-1	-0.827	-0.924	43.148	-7.477	-7.477	0.000	0.000	0.000	0.000
44	A	65	ALA	0	0.039	0.019	38.930	-0.176	-0.176	0.000	0.000	0.000	0.000
45	A	66	LEU	0	0.032	0.025	38.542	-0.262	-0.262	0.000	0.000	0.000	0.000
46	A	67	ALA	0	-0.016	-0.011	39.251	-0.175	-0.175	0.000	0.000	0.000	0.000
47	A	68	THR	0	-0.018	-0.028	36.571	-0.171	-0.171	0.000	0.000	0.000	0.000
48	A	69	ALA	0	0.016	0.002	34.780	-0.259	-0.259	0.000	0.000	0.000	0.000
49	A	70	ARG	1	0.862	0.918	34.352	7.610	7.610	0.000	0.000	0.000	0.000
50	A	71	VAL	0	-0.017	-0.012	35.434	-0.189	-0.189	0.000	0.000	0.000	0.000
51	A	72	ALA	0	0.003	0.002	32.076	-0.202	-0.202	0.000	0.000	0.000	0.000
52	A	73	GLY	0	0.035	0.018	30.594	-0.366	-0.366	0.000	0.000	0.000	0.000
53	A	74	ILE	0	-0.005	-0.016	30.676	-0.294	-0.294	0.000	0.000	0.000	0.000
54	A	75	MET	0	-0.091	-0.055	31.292	-0.112	-0.112	0.000	0.000	0.000	0.000
55	A	76	ALA	0	-0.007	0.001	26.895	-0.298	-0.298	0.000	0.000	0.000	0.000
56	A	77	ALA	0	0.046	0.037	26.372	-0.442	-0.442	0.000	0.000	0.000	0.000
57	A	78	LYS	1	0.923	0.956	26.711	9.285	9.285	0.000	0.000	0.000	0.000
58	A	79	ARG	1	0.907	0.961	25.166	11.633	11.633	0.000	0.000	0.000	0.000
59	A	80	THR	0	0.041	0.014	21.433	-0.567	-0.567	0.000	0.000	0.000	0.000
60	A	81	SER	0	0.020	0.005	20.138	-0.510	-0.510	0.000	0.000	0.000	0.000
61	A	82	ASP	-1	-0.923	-0.947	19.645	-13.801	-13.801	0.000	0.000	0.000	0.000
62	A	83	LEU	0	-0.055	-0.021	19.733	-0.432	-0.432	0.000	0.000	0.000	0.000
63	A	84	ILE	0	0.006	0.003	16.055	-1.058	-1.058	0.000	0.000	0.000	0.000
64	A	85	PRO	0	0.008	-0.010	12.697	0.045	0.045	0.000	0.000	0.000	0.000
65	A	86	LEU	0	-0.059	-0.025	10.327	-0.749	-0.749	0.000	0.000	0.000	0.000
66	A	87	CYS	0	-0.035	0.003	14.772	0.681	0.681	0.000	0.000	0.000	0.000
67	A	88	HIS	0	0.041	-0.002	18.506	0.209	0.209	0.000	0.000	0.000	0.000
68	A	89	GLN	0	-0.013	-0.012	20.901	0.093	0.093	0.000	0.000	0.000	0.000
69	A	90	LEU	0	-0.006	0.014	24.034	0.176	0.176	0.000	0.000	0.000	0.000
70	A	91	ALA	0	0.013	0.009	26.884	0.230	0.230	0.000	0.000	0.000	0.000
71	A	92	LEU	0	-0.016	0.001	28.056	0.285	0.285	0.000	0.000	0.000	0.000
72	A	93	THR	0	-0.052	-0.030	31.893	0.264	0.264	0.000	0.000	0.000	0.000
73	A	94	GLY	0	-0.041	-0.024	34.599	0.361	0.361	0.000	0.000	0.000	0.000
74	A	95	VAL	0	-0.014	-0.006	31.718	-0.264	-0.264	0.000	0.000	0.000	0.000
75	A	96	ASP	-1	-0.796	-0.845	34.582	-8.144	-8.144	0.000	0.000	0.000	0.000
76	A	97	VAL	0	-0.002	-0.007	33.108	-0.290	-0.290	0.000	0.000	0.000	0.000
77	A	98	ASP	-1	-0.841	-0.908	35.821	-7.485	-7.485	0.000	0.000	0.000	0.000
78	A	99	PHE	0	-0.018	-0.011	36.249	-0.271	-0.271	0.000	0.000	0.000	0.000
79	A	100	THR	0	-0.002	0.011	39.011	0.280	0.280	0.000	0.000	0.000	0.000
80	A	101	VAL	0	-0.029	-0.014	40.042	-0.193	-0.193	0.000	0.000	0.000	0.000
81	A	102	GLY	0	0.047	0.036	41.741	0.158	0.158	0.000	0.000	0.000	0.000
82	A	103	GLN	0	-0.036	-0.040	43.160	0.157	0.157	0.000	0.000	0.000	0.000
83	A	104	LEU	0	-0.014	-0.020	40.967	0.080	0.080	0.000	0.000	0.000	0.000
84	A	105	ASP	-1	-0.875	-0.944	37.449	-8.309	-8.309	0.000	0.000	0.000	0.000
85	A	106	ILE	0	-0.012	0.002	37.438	0.250	0.250	0.000	0.000	0.000	0.000
86	A	107	GLU	-1	-0.835	-0.895	34.629	-9.204	-9.204	0.000	0.000	0.000	0.000
87	A	108	ILE	0	-0.033	-0.013	32.608	0.233	0.233	0.000	0.000	0.000	0.000
88	A	109	THR	0	0.022	-0.002	33.339	-0.233	-0.233	0.000	0.000	0.000	0.000
89	A	110	ALA	0	-0.031	-0.009	30.685	0.188	0.188	0.000	0.000	0.000	0.000
90	A	111	THR	0	0.006	-0.002	32.300	-0.110	-0.110	0.000	0.000	0.000	0.000
91	A	112	VAL	0	0.001	0.005	29.131	0.152	0.152	0.000	0.000	0.000	0.000
92	A	113	ARG	1	0.812	0.861	32.125	8.567	8.567	0.000	0.000	0.000	0.000
93	A	114	SER	0	0.006	-0.020	30.473	-0.149	-0.149	0.000	0.000	0.000	0.000
94	A	115	THR	0	0.000	-0.016	32.459	0.251	0.251	0.000	0.000	0.000	0.000
95	A	116	ASP	-1	-0.756	-0.870	27.958	-11.279	-11.279	0.000	0.000	0.000	0.000
96	A	117	ARG	1	0.789	0.918	22.774	12.941	12.941	0.000	0.000	0.000	0.000
97	A	118	THR	0	-0.062	-0.026	22.247	-0.277	-0.277	0.000	0.000	0.000	0.000
98	A	119	GLY	0	0.010	0.015	24.301	0.456	0.456	0.000	0.000	0.000	0.000
99	A	120	VAL	0	0.021	0.001	24.763	-0.213	-0.213	0.000	0.000	0.000	0.000
100	A	121	GLU	-1	-0.878	-0.962	23.152	-12.718	-12.718	0.000	0.000	0.000	0.000
101	A	122	MET	0	-0.013	0.002	18.765	-0.036	-0.036	0.000	0.000	0.000	0.000
102	A	123	GLU	-1	-0.844	-0.930	22.995	-13.035	-13.035	0.000	0.000	0.000	0.000
103	A	124	ALA	0	-0.011	-0.004	25.882	0.361	0.361	0.000	0.000	0.000	0.000
104	A	125	LEU	0	0.028	0.008	22.201	0.220	0.220	0.000	0.000	0.000	0.000
105	A	126	THR	0	-0.015	-0.007	22.458	0.228	0.228	0.000	0.000	0.000	0.000
106	A	127	ALA	0	-0.023	0.000	25.024	0.234	0.234	0.000	0.000	0.000	0.000
107	A	128	VAL	0	0.024	0.011	28.056	0.257	0.257	0.000	0.000	0.000	0.000
108	A	129	SER	0	-0.010	-0.019	24.757	0.082	0.082	0.000	0.000	0.000	0.000
109	A	130	VAL	0	-0.009	-0.010	26.084	0.144	0.144	0.000	0.000	0.000	0.000
110	A	131	ALA	0	0.007	0.028	28.410	0.318	0.318	0.000	0.000	0.000	0.000
111	A	132	ALA	0	0.045	0.012	29.392	0.290	0.290	0.000	0.000	0.000	0.000
112	A	133	LEU	0	-0.003	-0.011	25.258	0.194	0.194	0.000	0.000	0.000	0.000
113	A	134	THR	0	-0.053	-0.028	29.970	0.211	0.211	0.000	0.000	0.000	0.000
114	A	135	LEU	0	-0.012	-0.008	33.072	0.291	0.291	0.000	0.000	0.000	0.000
115	A	136	TYR	0	0.000	-0.016	31.727	0.152	0.152	0.000	0.000	0.000	0.000
116	A	137	ASP	-1	-0.834	-0.910	32.640	-9.024	-9.024	0.000	0.000	0.000	0.000
117	A	138	MET	0	-0.062	-0.014	34.350	0.186	0.186	0.000	0.000	0.000	0.000
118	A	139	ILE	0	0.025	0.025	36.135	0.252	0.252	0.000	0.000	0.000	0.000
119	A	140	LYS	1	0.854	0.935	33.717	9.383	9.383	0.000	0.000	0.000	0.000
120	A	141	ALA	0	-0.038	-0.023	37.005	0.000	0.000	0.000	0.000	0.000	0.000
121	A	142	VAL	0	-0.056	-0.023	40.226	0.185	0.185	0.000	0.000	0.000	0.000
122	A	143	ASP	-1	-0.775	-0.877	38.759	-8.107	-8.107	0.000	0.000	0.000	0.000
123	A	144	PRO	0	-0.007	0.004	35.734	-0.211	-0.211	0.000	0.000	0.000	0.000
124	A	145	GLY	0	-0.015	0.007	34.280	-0.324	-0.324	0.000	0.000	0.000	0.000
125	A	146	ALA	0	-0.026	0.002	34.645	-0.110	-0.110	0.000	0.000	0.000	0.000
126	A	147	LEU	0	-0.012	-0.005	30.316	-0.316	-0.316	0.000	0.000	0.000	0.000
127	A	148	ILE	0	-0.017	-0.013	27.683	0.223	0.223	0.000	0.000	0.000	0.000
128	A	149	ASP	-1	-0.817	-0.899	28.226	-10.631	-10.631	0.000	0.000	0.000	0.000
129	A	150	ASP	-1	-0.898	-0.959	28.283	-10.106	-10.106	0.000	0.000	0.000	0.000
130	A	151	ILE	0	-0.008	-0.001	25.284	0.235	0.235	0.000	0.000	0.000	0.000
131	A	152	ARG	1	0.789	0.898	25.467	9.288	9.288	0.000	0.000	0.000	0.000
132	A	153	VAL	0	-0.001	-0.013	24.745	0.236	0.236	0.000	0.000	0.000	0.000
133	A	154	LEU	0	-0.049	-0.027	27.553	0.113	0.113	0.000	0.000	0.000	0.000
134	A	155	HIS	0	-0.047	-0.029	30.566	0.173	0.173	0.000	0.000	0.000	0.000
135	A	156	LYS	1	0.915	0.970	24.654	11.940	11.940	0.000	0.000	0.000	0.000
136	A	157	GLU	-2	-1.635	-1.779	29.670	-19.440	-19.440	0.000	0.000	0.000	0.000
137	A	165	THR	0	-0.039	-0.038	25.841	0.049	0.049	0.000	0.000	0.000	0.000
138	A	166	ARG	1	0.822	0.897	28.140	8.950	8.950	0.000	0.000	0.000	0.000
139	A	167	ARG	0	0.126	0.076	29.198	-0.849	-0.849	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:GLY)