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: 37GNL

Calculation Name: 3DLV-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DLV

Chain ID: B

ChEMBL ID:

UniProt ID: Q8TZT9

Base Structure: X-ray

Registration Date: 2025-07-08

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 OptH
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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -801270.619017
FMO2-HF: Nuclear repulsion 760223.671908
FMO2-HF: Total energy -41046.94711
FMO2-MP2: Total energy -41169.268676


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(B:2:GLY)


Summations of interaction energy for fragment #1(B:2: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.
-3.38-5.92414.127-6.639-4.944-0.033
Interaction energy analysis for fragmet #1(B:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.019
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].
3B3ARG10.8181.0524.6362.0202.2800.000-0.125-0.1340.000
4B4PHE00.017-0.0783.7930.3362.025-0.017-0.878-0.7940.004
5B4PHE0-0.0710.0572.7930.1080.6740.072-0.189-0.4490.001
6B5VAL00.069-0.1246.448-0.238-0.2380.0000.0000.0000.000
7B5VAL0-0.0480.13410.3590.0270.0270.0000.0000.0000.000
8B6VAL00.055-0.1239.7880.0680.0680.0000.0000.0000.000
9B6VAL0-0.0850.1059.059-0.011-0.0110.0000.0000.0000.000
10B7TRP00.150-0.09311.3200.0120.0120.0000.0000.0000.000
11B7TRP0-0.0670.12314.7540.0050.0050.0000.0000.0000.000
12B8PRO00.047-0.08314.9100.0180.0180.0000.0000.0000.000
13B9SER00.0670.00217.2160.0150.0150.0000.0000.0000.000
14B9SER0-0.0100.10118.8250.0010.0010.0000.0000.0000.000
15B10GLU00.111-0.09914.4830.0680.0680.0000.0000.0000.000
16B10GLU-1-0.890-0.77812.448-0.640-0.6400.0000.0000.0000.000
17B11LEU00.068-0.10015.8930.0550.0550.0000.0000.0000.000
18B11LEU0-0.0820.08513.707-0.010-0.0100.0000.0000.0000.000
19B12ASP00.133-0.11516.8140.0030.0030.0000.0000.0000.000
20B12ASP-1-0.810-0.74720.338-0.227-0.2270.0000.0000.0000.000
21B13SER0-0.013-0.12420.4910.0210.0210.0000.0000.0000.000
22B13SER0-0.0380.08022.5620.0070.0070.0000.0000.0000.000
23B14ARG00.078-0.13322.9540.0220.0220.0000.0000.0000.000
24B14ARG10.7941.06024.4750.1930.1930.0000.0000.0000.000
25B15LEU00.025-0.10523.2130.0190.0190.0000.0000.0000.000
26B15LEU0-0.0630.15121.3270.0000.0000.0000.0000.0000.000
27B16SER00.024-0.07823.7830.0030.0030.0000.0000.0000.000
28B16SER00.0180.09125.7940.0020.0020.0000.0000.0000.000
29B17ARG00.118-0.06621.090-0.020-0.0200.0000.0000.0000.000
30B17ARG10.7901.02017.1680.0470.0470.0000.0000.0000.000
31B18LYS00.068-0.08121.299-0.007-0.0070.0000.0000.0000.000
32B18LYS10.8951.07325.4060.0400.0400.0000.0000.0000.000
33B19TYR00.059-0.11923.3970.0040.0040.0000.0000.0000.000
34B19TYR0-0.1460.05924.118-0.002-0.0020.0000.0000.0000.000
35B20GLY00.042-0.08619.344-0.020-0.0200.0000.0000.0000.000
36B21ARG00.1530.03017.665-0.037-0.0370.0000.0000.0000.000
37B21ARG10.6730.98918.7710.1350.1350.0000.0000.0000.000
38B22ILE00.007-0.16814.5980.0520.0520.0000.0000.0000.000
39B22ILE0-0.0560.13012.6980.0030.0030.0000.0000.0000.000
40B23VAL0-0.004-0.14215.5570.0710.0710.0000.0000.0000.000
41B23VAL0-0.0330.15613.8920.0000.0000.0000.0000.0000.000
42B24PRO0-0.040-0.13016.2450.0150.0150.0000.0000.0000.000
43B25ARG00.1400.03419.314-0.026-0.0260.0000.0000.0000.000
44B25ARG10.9241.07923.7050.0420.0420.0000.0000.0000.000
45B26SER00.076-0.06122.424-0.016-0.0160.0000.0000.0000.000
46B26SER0-0.0440.07122.7930.0020.0020.0000.0000.0000.000
47B27ILE00.093-0.08018.5830.0020.0020.0000.0000.0000.000
48B27ILE0-0.1160.07416.6290.0010.0010.0000.0000.0000.000
49B28ALA00.120-0.08918.733-0.038-0.0380.0000.0000.0000.000
50B28ALA0-0.1100.10119.2760.0050.0050.0000.0000.0000.000
51B29VAL00.025-0.11619.7190.0330.0330.0000.0000.0000.000
52B29VAL0-0.0570.11719.1710.0000.0000.0000.0000.0000.000
53B30GLU00.112-0.13421.614-0.017-0.0170.0000.0000.0000.000
54B30GLU-1-0.968-0.79925.831-0.155-0.1550.0000.0000.0000.000
55B31SER0-0.072-0.10223.524-0.012-0.0120.0000.0000.0000.000
56B31SER00.0170.08925.1660.0040.0040.0000.0000.0000.000
57B32PRO00.020-0.08218.594-0.003-0.0030.0000.0000.0000.000
58B33ARG00.1270.01120.575-0.006-0.0060.0000.0000.0000.000
59B33ARG10.8231.04822.1100.3050.3050.0000.0000.0000.000
60B34VAL00.076-0.12818.015-0.034-0.0340.0000.0000.0000.000
61B34VAL00.0220.16717.496-0.002-0.0020.0000.0000.0000.000
62B35GLU00.048-0.07217.814-0.075-0.0750.0000.0000.0000.000
63B35GLU-1-0.839-0.83221.818-0.358-0.3580.0000.0000.0000.000
64B36GLU00.100-0.09219.368-0.024-0.0240.0000.0000.0000.000
65B36GLU-1-0.858-0.75719.767-0.311-0.3110.0000.0000.0000.000
66B37ILE00.101-0.07115.4100.0020.0020.0000.0000.0000.000
67B37ILE0-0.1000.07713.400-0.010-0.0100.0000.0000.0000.000
68B38VAL00.028-0.11114.320-0.132-0.1320.0000.0000.0000.000
69B38VAL0-0.0500.11615.647-0.005-0.0050.0000.0000.0000.000
70B39ARG00.150-0.06415.268-0.080-0.0800.0000.0000.0000.000
71B39ARG10.7901.03519.0710.3780.3780.0000.0000.0000.000
72B40ALA00.089-0.07815.5460.0150.0150.0000.0000.0000.000
73B40ALA0-0.0790.08414.9500.0040.0040.0000.0000.0000.000
74B41ALA00.047-0.11511.6720.0450.0450.0000.0000.0000.000
75B41ALA0-0.0610.09310.930-0.049-0.0490.0000.0000.0000.000
76B42GLU00.061-0.13411.879-0.141-0.1410.0000.0000.0000.000
77B42GLU-1-0.976-0.82714.731-0.622-0.6220.0000.0000.0000.000
78B43GLU00.078-0.13914.2370.0150.0150.0000.0000.0000.000
79B43GLU-1-0.943-0.81316.290-0.376-0.3760.0000.0000.0000.000
80B44LEU0-0.044-0.13811.8520.1210.1210.0000.0000.0000.000
81B44LEU0-0.0980.08311.0480.0060.0060.0000.0000.0000.000
82B45LYS0-0.028-0.12310.884-0.073-0.0730.0000.0000.0000.000
83B45LYS10.8571.06911.3070.5570.5570.0000.0000.0000.000
84B46PHE00.070-0.0997.877-0.089-0.0890.0000.0000.0000.000
85B46PHE0-0.0750.0767.713-0.105-0.1050.0000.0000.0000.000
86B47LYS00.155-0.0657.6360.3610.3610.0000.0000.0000.000
87B47LYS10.8311.0708.1931.1801.1800.0000.0000.0000.000
88B48VAL00.057-0.1548.957-0.516-0.5160.0000.0000.0000.000
89B48VAL0-0.0330.15212.1100.0070.0070.0000.0000.0000.000
90B49ILE00.027-0.11010.6720.1830.1830.0000.0000.0000.000
91B49ILE0-0.1330.0538.1180.0390.0390.0000.0000.0000.000
92B50ARG00.139-0.08411.6760.1680.1680.0000.0000.0000.000
93B50ARG10.7621.02213.6390.5040.5040.0000.0000.0000.000
94B51VAL00.007-0.13513.933-0.142-0.1420.0000.0000.0000.000
95B51VAL0-0.0340.13215.304-0.004-0.0040.0000.0000.0000.000
96B52GLU00.085-0.11316.5960.0420.0420.0000.0000.0000.000
97B52GLU-1-0.927-0.78917.802-0.427-0.4270.0000.0000.0000.000
98B53GLU00.115-0.12619.167-0.028-0.0280.0000.0000.0000.000
99B53GLU-1-1.060-0.86221.103-0.355-0.3550.0000.0000.0000.000
100B54ASP00.054-0.14921.9190.0080.0080.0000.0000.0000.000
101B54ASP-1-0.964-0.81124.333-0.238-0.2380.0000.0000.0000.000
102B55LYS00.050-0.08325.058-0.003-0.0030.0000.0000.0000.000
103B55LYS10.7971.02226.1310.2700.2700.0000.0000.0000.000
104B56LEU00.153-0.11328.0120.0040.0040.0000.0000.0000.000
105B56LEU0-0.0440.14429.5050.0020.0020.0000.0000.0000.000
106B57ASN00.143-0.06630.9070.0010.0010.0000.0000.0000.000
107B57ASN0-0.1340.06335.4700.0000.0000.0000.0000.0000.000
108B58PRO0-0.164-0.13932.0100.0060.0060.0000.0000.0000.000
109B59ARG00.3110.09133.247-0.010-0.0100.0000.0000.0000.000
110B59ARG10.6380.93730.9020.1340.1340.0000.0000.0000.000
111B60LEU00.063-0.09035.5670.0040.0040.0000.0000.0000.000
112B60LEU0-0.0500.10438.8110.0000.0000.0000.0000.0000.000
113B61SER00.036-0.07038.3660.0070.0070.0000.0000.0000.000
114B61SER0-0.0130.07237.206-0.002-0.0020.0000.0000.0000.000
115B62GLY00.004-0.09538.1520.0040.0040.0000.0000.0000.000
116B63ILE00.0380.01836.8890.0030.0030.0000.0000.0000.000
117B63ILE0-0.1020.07235.6600.0000.0000.0000.0000.0000.000
118B64ASP00.098-0.09632.5760.0040.0040.0000.0000.0000.000
119B64ASP-1-0.935-0.84431.554-0.133-0.1330.0000.0000.0000.000
120B65GLU00.028-0.12031.789-0.001-0.0010.0000.0000.0000.000
121B65GLU-1-0.905-0.81432.734-0.108-0.1080.0000.0000.0000.000
122B66GLU00.045-0.13128.390-0.012-0.0120.0000.0000.0000.000
123B66GLU-1-0.909-0.77427.345-0.133-0.1330.0000.0000.0000.000
124B67LEU0-0.021-0.11726.669-0.019-0.0190.0000.0000.0000.000
125B67LEU0-0.0300.12425.794-0.001-0.0010.0000.0000.0000.000
126B68ARG00.174-0.06427.883-0.006-0.0060.0000.0000.0000.000
127B68ARG10.8021.04129.3170.1810.1810.0000.0000.0000.000
128B69THR00.002-0.08525.701-0.001-0.0010.0000.0000.0000.000
129B69THR0-0.0800.03623.5790.0070.0070.0000.0000.0000.000
130B70PHE00.085-0.09422.3650.0030.0030.0000.0000.0000.000
131B70PHE0-0.0300.13519.105-0.009-0.0090.0000.0000.0000.000
132B71GLY00.003-0.11519.5310.0010.0010.0000.0000.0000.000
133B72MET00.051-0.03515.5350.0120.0120.0000.0000.0000.000
134B72MET0-0.0860.12214.8320.0080.0080.0000.0000.0000.000
135B73ILE00.115-0.09613.0790.0680.0680.0000.0000.0000.000
136B73ILE0-0.0800.11611.531-0.012-0.0120.0000.0000.0000.000
137B74VAL00.073-0.09410.039-0.123-0.1230.0000.0000.0000.000
138B74VAL0-0.0840.0968.8740.0090.0090.0000.0000.0000.000
139B75LEU00.034-0.1337.7620.3640.3640.0000.0000.0000.000
140B75LEU0-0.0250.1317.1490.0000.0000.0000.0000.0000.000
141B76GLU00.095-0.1224.456-1.028-0.985-0.001-0.0720.0300.000
142B76GLU-1-0.948-0.7944.341-2.235-1.9720.000-0.032-0.2310.000
143B77SER00.012-0.0902.9931.4082.2740.030-0.407-0.4900.001
144B77SER0-0.0400.0693.7090.4080.5510.003-0.048-0.0980.000
145B78PRO00.039-0.0661.768-5.052-12.23813.950-4.543-2.221-0.036
146B79TYR00.0770.0124.0752.0072.2290.001-0.036-0.1880.000
147B79TYR0-0.0980.0776.1500.0750.0750.0000.0000.0000.000
148B80GLY00.085-0.0613.114-1.604-1.0330.091-0.308-0.354-0.003
149B81LYS00.1440.0024.836-1.075-1.056-0.002-0.001-0.0150.000
150B81LYS10.7571.0325.8070.8650.8650.0000.0000.0000.000
151B82SER00.077-0.0586.116-0.141-0.1410.0000.0000.0000.000
152B82SER0-0.0470.0579.8790.0060.0060.0000.0000.0000.000
153B83LYS00.055-0.0978.475-0.084-0.0840.0000.0000.0000.000
154B83LYS10.9301.0828.112-0.368-0.3680.0000.0000.0000.000
155B84SER00.034-0.0836.7720.2120.2120.0000.0000.0000.000
156B84SER0-0.0060.0865.328-0.398-0.3980.0000.0000.0000.000
157B85LEU00.089-0.1048.052-0.047-0.0470.0000.0000.0000.000
158B85LEU0-0.0790.1039.4010.0270.0270.0000.0000.0000.000
159B86LYS00.113-0.05410.8270.0230.0230.0000.0000.0000.000
160B86LYS10.8241.03012.6890.0220.0220.0000.0000.0000.000
161B87LEU00.066-0.11411.6820.0810.0810.0000.0000.0000.000
162B87LEU0-0.0710.1179.655-0.002-0.0020.0000.0000.0000.000
163B88ILE00.100-0.06411.9350.0630.0630.0000.0000.0000.000
164B88ILE0-0.0650.0919.718-0.014-0.0140.0000.0000.0000.000
165B89ALA00.121-0.09213.3880.0270.0270.0000.0000.0000.000
166B89ALA0-0.0920.09915.9040.0100.0100.0000.0000.0000.000
167B90GLN0-0.008-0.12216.0410.0330.0330.0000.0000.0000.000
168B90GLN0-0.0780.07916.155-0.014-0.0140.0000.0000.0000.000
169B91LYS00.120-0.10416.3260.0630.0630.0000.0000.0000.000
170B91LYS10.7791.07915.8750.3500.3500.0000.0000.0000.000
171B92ILE00.135-0.08217.6090.0280.0280.0000.0000.0000.000
172B92ILE0-0.0880.09616.7850.0020.0020.0000.0000.0000.000
173B93ARG00.113-0.07719.4900.0240.0240.0000.0000.0000.000
174B93ARG10.7351.00820.4930.2020.2020.0000.0000.0000.000
175B94GLU00.035-0.14121.0810.0310.0310.0000.0000.0000.000
176B94GLU-1-0.907-0.80220.640-0.268-0.2680.0000.0000.0000.000
177B95PHE00.016-0.13621.6120.0280.0280.0000.0000.0000.000
178B95PHE0-0.0790.08618.2940.0090.0090.0000.0000.0000.000
179B96ARG00.099-0.07223.1430.0150.0150.0000.0000.0000.000
180B96ARG10.6410.91522.9510.2680.2680.0000.0000.0000.000
181B97ARG00.102-0.07225.5960.0130.0130.0000.0000.0000.000
182B97ARG10.8571.05225.6670.1440.1440.0000.0000.0000.000
183B98ARG00.128-0.06226.4080.0190.0190.0000.0000.0000.000
184B98ARG10.7931.04323.0390.2280.2280.0000.0000.0000.000
185B99SER00.001-0.07927.6100.0120.0120.0000.0000.0000.000
186B99SER0-0.0820.03927.002-0.004-0.0040.0000.0000.0000.000
187B100ALA00.104-0.08229.4110.0070.0070.0000.0000.0000.000
188B100ALA0-0.0930.10230.7790.0000.0000.0000.0000.0000.000
189B101GLY0-0.005-0.09231.1260.0090.0090.0000.0000.0000.000
190B102THR00.001-0.01532.6070.0090.0090.0000.0000.0000.000
191B102THR0-0.0270.08334.3190.0030.0030.0000.0000.0000.000
192B103LEU00.109-0.07832.263-0.011-0.0110.0000.0000.0000.000
193B103LEU0-0.1280.08632.2580.0010.0010.0000.0000.0000.000
194B104VAL00.038-0.11332.951-0.006-0.0060.0000.0000.0000.000
195B104VAL0-0.0690.10435.9590.0010.0010.0000.0000.0000.000
196B105PRO00.000-0.09034.4890.0010.0010.0000.0000.0000.000