FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Z724N

Calculation Name: 3A7M-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A7M

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1N2

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -804979.937214
FMO2-HF: Nuclear repulsion 759333.138294
FMO2-HF: Total energy -45646.79892
FMO2-MP2: Total energy -45779.901092


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-11.762-9.5814.195-2.5-3.8730.019
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.039
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   
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].
4A3SER0-0.0070.0654.399-0.376-0.200-0.001-0.062-0.1130.000
5A4THR00.014-0.0782.902-5.706-3.3220.284-1.288-1.3810.012
6A4THR0-0.0190.0584.1650.3490.5670.004-0.085-0.1360.000
7A5VAL00.086-0.0912.628-1.544-2.6120.4751.327-0.7330.001
8A5VAL0-0.0520.1112.162-0.217-0.1783.421-2.247-1.2110.005
9A6GLU00.104-0.1023.442-0.786-0.5180.013-0.119-0.1620.001
10A6GLU-1-0.925-0.8124.302-1.767-1.603-0.001-0.026-0.1370.000
11A7PHE00.049-0.0755.491-0.363-0.3630.0000.0000.0000.000
12A7PHE0-0.0390.0967.2870.0820.0820.0000.0000.0000.000
13A8ILE00.084-0.1057.006-0.366-0.3660.0000.0000.0000.000
14A8ILE0-0.0920.0837.3350.0170.0170.0000.0000.0000.000
15A9ASN00.068-0.0767.437-0.195-0.1950.0000.0000.0000.000
16A9ASN0-0.1120.0767.428-0.202-0.2020.0000.0000.0000.000
17A10ARG00.151-0.0789.041-0.164-0.1640.0000.0000.0000.000
18A10ARG10.7731.0288.4780.5520.5520.0000.0000.0000.000
19A11TRP00.110-0.08911.274-0.115-0.1150.0000.0000.0000.000
20A11TRP0-0.0290.12212.342-0.018-0.0180.0000.0000.0000.000
21A12GLN00.071-0.08512.270-0.049-0.0490.0000.0000.0000.000
22A12GLN0-0.0780.07410.742-0.042-0.0420.0000.0000.0000.000
23A13ARG00.120-0.05613.075-0.027-0.0270.0000.0000.0000.000
24A13ARG10.8391.04413.5000.0940.0940.0000.0000.0000.000
25A14ILE00.064-0.12114.907-0.056-0.0560.0000.0000.0000.000
26A14ILE0-0.0660.10815.3990.0020.0020.0000.0000.0000.000
27A15ALA00.168-0.06316.929-0.043-0.0430.0000.0000.0000.000
28A15ALA0-0.0680.10817.3750.0120.0120.0000.0000.0000.000
29A16LEU00.038-0.09417.593-0.010-0.0100.0000.0000.0000.000
30A16LEU0-0.1120.07615.888-0.007-0.0070.0000.0000.0000.000
31A17LEU00.069-0.10618.975-0.011-0.0110.0000.0000.0000.000
32A17LEU0-0.0640.09618.766-0.007-0.0070.0000.0000.0000.000
33A18SER00.012-0.07620.960-0.023-0.0230.0000.0000.0000.000
34A18SER00.0060.08121.6490.0110.0110.0000.0000.0000.000
35A19GLN00.135-0.08922.379-0.010-0.0100.0000.0000.0000.000
36A19GLN0-0.1190.09022.7410.0160.0160.0000.0000.0000.000
37A20SER0-0.044-0.10823.444-0.004-0.0040.0000.0000.0000.000
38A20SER0-0.0820.04122.733-0.010-0.0100.0000.0000.0000.000
39A21LEU00.093-0.11125.205-0.009-0.0090.0000.0000.0000.000
40A21LEU0-0.0680.11024.870-0.001-0.0010.0000.0000.0000.000
41A22LEU00.135-0.05426.955-0.010-0.0100.0000.0000.0000.000
42A22LEU0-0.1370.08527.6180.0030.0030.0000.0000.0000.000
43A23GLU00.081-0.12628.262-0.004-0.0040.0000.0000.0000.000
44A23GLU-1-0.903-0.78627.6360.0630.0630.0000.0000.0000.000
45A24LEU00.050-0.11529.584-0.002-0.0020.0000.0000.0000.000
46A24LEU0-0.0870.09028.497-0.002-0.0020.0000.0000.0000.000
47A25ALA00.131-0.07731.432-0.008-0.0080.0000.0000.0000.000
48A25ALA0-0.0380.09332.4700.0010.0010.0000.0000.0000.000
49A26GLN00.020-0.12132.884-0.003-0.0030.0000.0000.0000.000
50A26GLN0-0.0950.08231.350-0.002-0.0020.0000.0000.0000.000
51A27ARG00.019-0.09234.2000.0000.0000.0000.0000.0000.000
52A27ARG10.7731.00130.814-0.031-0.0310.0000.0000.0000.000
53A28GLY0-0.021-0.09635.583-0.003-0.0030.0000.0000.0000.000
54A29GLU00.0680.01834.644-0.003-0.0030.0000.0000.0000.000
55A29GLU-1-1.032-0.88133.764-0.007-0.0070.0000.0000.0000.000
56A30TRP00.043-0.13733.932-0.002-0.0020.0000.0000.0000.000
57A30TRP0-0.0330.09934.5250.0020.0020.0000.0000.0000.000
58A31ASP00.103-0.08534.6640.0010.0010.0000.0000.0000.000
59A31ASP-1-0.950-0.84036.746-0.013-0.0130.0000.0000.0000.000
60A32LEU00.036-0.12331.986-0.007-0.0070.0000.0000.0000.000
61A32LEU0-0.0480.11030.9350.0000.0000.0000.0000.0000.000
62A33LEU00.078-0.09530.054-0.008-0.0080.0000.0000.0000.000
63A33LEU0-0.1060.10730.0370.0010.0010.0000.0000.0000.000
64A34LEU00.130-0.07130.1430.0000.0000.0000.0000.0000.000
65A34LEU0-0.0980.09534.0600.0000.0000.0000.0000.0000.000
66A35GLN00.025-0.08730.859-0.002-0.0020.0000.0000.0000.000
67A35GLN0-0.1370.04530.509-0.008-0.0080.0000.0000.0000.000
68A36GLN00.047-0.11626.737-0.011-0.0110.0000.0000.0000.000
69A36GLN0-0.0970.06725.541-0.007-0.0070.0000.0000.0000.000
70A37GLU00.107-0.09225.761-0.003-0.0030.0000.0000.0000.000
71A37GLU-1-1.006-0.84328.5700.0080.0080.0000.0000.0000.000
72A38VAL00.115-0.09925.9790.0090.0090.0000.0000.0000.000
73A38VAL0-0.0510.12126.551-0.001-0.0010.0000.0000.0000.000
74A39SER00.056-0.06923.5500.0000.0000.0000.0000.0000.000
75A39SER0-0.0290.06722.939-0.006-0.0060.0000.0000.0000.000
76A40TYR00.065-0.06521.739-0.018-0.0180.0000.0000.0000.000
77A40TYR0-0.1330.03721.3830.0050.0050.0000.0000.0000.000
78A41LEU00.063-0.12721.5780.0150.0150.0000.0000.0000.000
79A41LEU0-0.0210.12225.3270.0020.0020.0000.0000.0000.000
80A42GLN00.160-0.04622.3130.0160.0160.0000.0000.0000.000
81A42GLN0-0.1230.08020.9860.0020.0020.0000.0000.0000.000
82A43SER00.001-0.10318.186-0.009-0.0090.0000.0000.0000.000
83A43SER0-0.1090.02417.444-0.016-0.0160.0000.0000.0000.000
84A44ILE00.074-0.06217.6500.0040.0040.0000.0000.0000.000
85A44ILE0-0.0700.10919.1880.0060.0060.0000.0000.0000.000
86A45GLU00.083-0.12019.2090.0470.0470.0000.0000.0000.000
87A45GLU-1-0.951-0.83121.7850.0640.0640.0000.0000.0000.000
88A46THR0-0.006-0.09417.5600.0320.0320.0000.0000.0000.000
89A46THR0-0.1060.01915.647-0.027-0.0270.0000.0000.0000.000
90A47VAL00.027-0.11514.574-0.047-0.0470.0000.0000.0000.000
91A47VAL0-0.1060.10013.5260.0030.0030.0000.0000.0000.000
92A48MET00.062-0.12014.9830.0790.0790.0000.0000.0000.000
93A48MET0-0.0750.10118.5420.0180.0180.0000.0000.0000.000
94A49GLU00.108-0.15117.7930.0370.0370.0000.0000.0000.000
95A49GLU-1-0.936-0.80917.264-0.095-0.0950.0000.0000.0000.000
96A50LYS0-0.068-0.04913.072-0.019-0.0190.0000.0000.0000.000
97A50LYS10.7090.99811.6700.1360.1360.0000.0000.0000.000
98A51GLN00.182-0.11312.7250.0470.0470.0000.0000.0000.000
99A51GLN0-0.1190.10412.189-0.099-0.0990.0000.0000.0000.000
100A52THR0-0.009-0.12711.3280.0960.0960.0000.0000.0000.000
101A52THR0-0.0150.10112.593-0.001-0.0010.0000.0000.0000.000
102A53PRO0-0.068-0.1177.474-0.103-0.1030.0000.0000.0000.000
103A54PRO00.0240.0027.713-0.106-0.1060.0000.0000.0000.000
104A55GLY00.0140.0078.703-0.260-0.2600.0000.0000.0000.000
105A56ILE0-0.006-0.0349.3630.5560.5560.0000.0000.0000.000
106A56ILE0-0.0370.12711.0790.0000.0000.0000.0000.0000.000
107A57THR00.051-0.04511.147-0.223-0.2230.0000.0000.0000.000
108A57THR00.0110.07210.932-0.004-0.0040.0000.0000.0000.000
109A58ARG00.246-0.04713.2690.0640.0640.0000.0000.0000.000
110A58ARG10.7350.98817.470-0.589-0.5890.0000.0000.0000.000
111A59SER00.001-0.05714.419-0.105-0.1050.0000.0000.0000.000
112A59SER0-0.0240.04313.356-0.002-0.0020.0000.0000.0000.000
113A60ILE00.080-0.07610.921-0.166-0.1660.0000.0000.0000.000
114A60ILE0-0.0710.0878.4360.0530.0530.0000.0000.0000.000
115A61GLN00.168-0.05012.113-0.040-0.0400.0000.0000.0000.000
116A61GLN0-0.1350.07015.2750.0060.0060.0000.0000.0000.000
117A62ASP00.062-0.11715.026-0.030-0.0300.0000.0000.0000.000
118A62ASP-1-0.915-0.78617.5320.6090.6090.0000.0000.0000.000
119A63MET00.145-0.06913.984-0.133-0.1330.0000.0000.0000.000
120A63MET0-0.1170.07412.1020.0750.0750.0000.0000.0000.000
121A64VAL00.053-0.10813.333-0.110-0.1100.0000.0000.0000.000
122A64VAL0-0.0880.10911.2290.0210.0210.0000.0000.0000.000
123A65ALA00.105-0.10014.261-0.091-0.0910.0000.0000.0000.000
124A65ALA0-0.0740.11518.213-0.004-0.0040.0000.0000.0000.000
125A66GLY0-0.048-0.12617.623-0.079-0.0790.0000.0000.0000.000
126A67TYR00.0960.01316.180-0.073-0.0730.0000.0000.0000.000
127A67TYR0-0.0880.09612.7260.0430.0430.0000.0000.0000.000
128A68ILE00.130-0.06917.453-0.072-0.0720.0000.0000.0000.000
129A68ILE0-0.0880.09016.0440.0050.0050.0000.0000.0000.000
130A69LYS00.116-0.08118.975-0.048-0.0480.0000.0000.0000.000
131A69LYS10.7270.98022.140-0.242-0.2420.0000.0000.0000.000
132A70GLN00.065-0.10220.724-0.034-0.0340.0000.0000.0000.000
133A70GLN0-0.0730.09319.7480.0350.0350.0000.0000.0000.000
134A71THR0-0.002-0.11320.757-0.030-0.0300.0000.0000.0000.000
135A71THR0-0.0450.07219.0370.0030.0030.0000.0000.0000.000
136A72LEU00.098-0.09421.981-0.036-0.0360.0000.0000.0000.000
137A72LEU0-0.0870.11223.3560.0040.0040.0000.0000.0000.000
138A73ASP00.085-0.12424.429-0.022-0.0220.0000.0000.0000.000
139A73ASP-1-0.892-0.77326.1330.2200.2200.0000.0000.0000.000
140A74ASN00.077-0.10025.274-0.017-0.0170.0000.0000.0000.000
141A74ASN0-0.1040.09023.7230.0110.0110.0000.0000.0000.000
142A75GLU00.139-0.10526.014-0.019-0.0190.0000.0000.0000.000
143A75GLU-1-0.889-0.75724.7210.1070.1070.0000.0000.0000.000
144A76GLN00.074-0.08327.674-0.017-0.0170.0000.0000.0000.000
145A76GLN0-0.0790.10429.4970.0110.0110.0000.0000.0000.000
146A77LEU00.013-0.14429.918-0.010-0.0100.0000.0000.0000.000
147A77LEU0-0.0740.11229.3690.0000.0000.0000.0000.0000.000
148A78LEU00.132-0.08630.236-0.009-0.0090.0000.0000.0000.000
149A78LEU0-0.1260.11128.7730.0000.0000.0000.0000.0000.000
150A79LYS0-0.007-0.14631.533-0.012-0.0120.0000.0000.0000.000
151A79LYS10.8221.04028.648-0.083-0.0830.0000.0000.0000.000
152A80GLY00.026-0.09633.425-0.007-0.0070.0000.0000.0000.000
153A81LEU00.0840.02235.078-0.004-0.0040.0000.0000.0000.000
154A81LEU0-0.0710.09633.4250.0000.0000.0000.0000.0000.000
155A82LEU00.151-0.08435.472-0.005-0.0050.0000.0000.0000.000
156A82LEU0-0.0960.10534.0500.0000.0000.0000.0000.0000.000
157A83GLN00.083-0.12236.876-0.007-0.0070.0000.0000.0000.000
158A83GLN0-0.1160.07638.0330.0020.0020.0000.0000.0000.000
159A84GLN00.112-0.09739.156-0.003-0.0030.0000.0000.0000.000
160A84GLN0-0.0940.11040.4540.0010.0010.0000.0000.0000.000
161A85ARG00.076-0.09840.168-0.002-0.0020.0000.0000.0000.000
162A85ARG10.7250.99839.644-0.024-0.0240.0000.0000.0000.000
163A86LEU00.070-0.10441.052-0.004-0.0040.0000.0000.0000.000
164A86LEU0-0.0610.11039.149-0.001-0.0010.0000.0000.0000.000
165A87ASP00.087-0.09642.775-0.004-0.0040.0000.0000.0000.000
166A87ASP-1-0.965-0.82043.9270.0480.0480.0000.0000.0000.000
167A88GLU00.062-0.13345.096-0.002-0.0020.0000.0000.0000.000
168A88GLU-1-0.888-0.77644.5270.0300.0300.0000.0000.0000.000
169A89LEU00.059-0.12645.632-0.002-0.0020.0000.0000.0000.000
170A89LEU0-0.0610.10943.068-0.001-0.0010.0000.0000.0000.000
171A90SER00.019-0.08846.882-0.004-0.0040.0000.0000.0000.000
172A90SER0-0.0830.04546.2380.0000.0000.0000.0000.0000.000
173A91SER0-0.008-0.11148.676-0.002-0.0020.0000.0000.0000.000
174A91SER0-0.0360.07950.0080.0010.0010.0000.0000.0000.000
175A92LEU0-0.047-0.11550.5050.0000.0000.0000.0000.0000.000
176A92LEU0-0.0800.09349.265-0.001-0.0010.0000.0000.0000.000
177A93ILE00.074-0.08451.138-0.001-0.0010.0000.0000.0000.000
178A93ILE0-0.1060.09748.5040.0000.0000.0000.0000.0000.000
179A94GLY00.016-0.08152.630-0.001-0.0010.0000.0000.0000.000
180A95GLN00.059-0.01953.3780.0000.0000.0000.0000.0000.000
181A95GLN0-0.0930.07852.6390.0010.0010.0000.0000.0000.000
182A96SER00.070-0.03554.301-0.001-0.0010.0000.0000.0000.000
183A96SER0-0.0250.05653.9300.0000.0000.0000.0000.0000.000
184A97THR00.059-0.09056.1960.0020.0020.0000.0000.0000.000
185A97THR00.0020.07659.8240.0000.0000.0000.0000.0000.000
186A98ARG00.076-0.05356.0420.0010.0010.0000.0000.0000.000
187A98ARG10.9191.06654.821-0.016-0.0160.0000.0000.0000.000
188A99GLN00.194-0.07053.1020.0020.0020.0000.0000.0000.000
189A99GLN0-0.0660.13349.669-0.002-0.0020.0000.0000.0000.000
190A100LYS00.101-0.10153.8250.0020.0020.0000.0000.0000.000
191A100LYS10.8751.07956.725-0.022-0.0220.0000.0000.0000.000
192A101SER00.019-0.08356.4600.0020.0020.0000.0000.0000.000
193A101SER0-0.0580.06158.169-0.001-0.0010.0000.0000.0000.000
194A102LEU00.008-0.11253.6650.0010.0010.0000.0000.0000.000
195A102LEU0-0.0830.10552.3620.0000.0000.0000.0000.0000.000
196A103ASN00.127-0.05952.1130.0020.0020.0000.0000.0000.000
197A103ASN0-0.1080.06350.5300.0020.0020.0000.0000.0000.000
198A104ASN00.115-0.06553.0770.0030.0030.0000.0000.0000.000
199A104ASN0-0.1120.06057.6320.0000.0000.0000.0000.0000.000
200A105ALA00.104-0.08755.8640.0010.0010.0000.0000.0000.000
201A105ALA0-0.0880.10054.9740.0000.0000.0000.0000.0000.000
202A106TYR00.088-0.09151.1260.0010.0010.0000.0000.0000.000
203A106TYR0-0.0610.10846.4770.0000.0000.0000.0000.0000.000
204A107GLY00.017-0.10452.2120.0030.0030.0000.0000.0000.000
205A108ARG00.1470.04153.3480.0020.0020.0000.0000.0000.000
206A108ARG10.8121.05457.018-0.035-0.0350.0000.0000.0000.000
207A109LEU00.067-0.10353.388-0.001-0.0010.0000.0000.0000.000
208A109LEU0-0.1140.08050.8290.0000.0000.0000.0000.0000.000
209A110SER00.061-0.06150.4120.0010.0010.0000.0000.0000.000
210A110SER0-0.0660.06949.6350.0000.0000.0000.0000.0000.000
211A111GLY0-0.048-0.11551.5280.0020.0020.0000.0000.0000.000
212A112MET00.099-0.02954.229-0.002-0.0020.0000.0000.0000.000
213A112MET0-0.1230.09355.244-0.001-0.0010.0000.0000.0000.000
214A113LEU00.047-0.08354.6120.0030.0030.0000.0000.0000.000
215A113LEU0-0.0790.09856.6570.0000.0000.0000.0000.0000.000
216A114LEU00.075-0.12155.451-0.003-0.0030.0000.0000.0000.000
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