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: N263Q

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 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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -801032.938764
FMO2-HF: Nuclear repulsion 759984.378539
FMO2-HF: Total energy -41048.560225
FMO2-MP2: Total energy -41170.820665


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.
-2.757-5.63115.508-7.446-5.187-0.036
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 : 0.056 / q_NPA : 0.017
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].
3B3ARG10.7830.9964.5481.8752.1390.000-0.123-0.1400.000
4B4PHE00.020-0.0653.7930.0491.852-0.017-0.951-0.8350.005
5B4PHE0-0.0820.0552.6560.0510.7440.133-0.269-0.5580.001
6B5VAL00.069-0.1226.481-0.193-0.1930.0000.0000.0000.000
7B5VAL0-0.0460.13410.2620.0260.0260.0000.0000.0000.000
8B6VAL00.078-0.1069.8270.0480.0480.0000.0000.0000.000
9B6VAL0-0.0980.0999.060-0.009-0.0090.0000.0000.0000.000
10B7TRP00.171-0.08211.3920.0240.0240.0000.0000.0000.000
11B7TRP0-0.0500.13214.9340.0050.0050.0000.0000.0000.000
12B8PRO00.054-0.08914.9650.0150.0150.0000.0000.0000.000
13B9SER00.063-0.00517.2850.0160.0160.0000.0000.0000.000
14B9SER0-0.0100.09418.7090.0010.0010.0000.0000.0000.000
15B10GLU00.109-0.08414.5010.0710.0710.0000.0000.0000.000
16B10GLU-1-0.905-0.77312.402-0.725-0.7250.0000.0000.0000.000
17B11LEU00.065-0.08715.8710.0510.0510.0000.0000.0000.000
18B11LEU0-0.0950.07713.968-0.011-0.0110.0000.0000.0000.000
19B12ASP00.132-0.11216.8480.0060.0060.0000.0000.0000.000
20B12ASP-1-0.811-0.75720.458-0.243-0.2430.0000.0000.0000.000
21B13SER00.030-0.12520.5300.0180.0180.0000.0000.0000.000
22B13SER0-0.0300.08922.605-0.003-0.0030.0000.0000.0000.000
23B14ARG00.045-0.13822.9790.0230.0230.0000.0000.0000.000
24B14ARG10.8081.04724.7670.2010.2010.0000.0000.0000.000
25B15LEU0-0.002-0.08623.2240.0210.0210.0000.0000.0000.000
26B15LEU0-0.0690.13721.295-0.002-0.0020.0000.0000.0000.000
27B16SER00.041-0.07923.7750.0020.0020.0000.0000.0000.000
28B16SER00.0200.08325.7480.0020.0020.0000.0000.0000.000
29B17ARG00.127-0.07421.046-0.020-0.0200.0000.0000.0000.000
30B17ARG10.7630.99616.8320.1060.1060.0000.0000.0000.000
31B18LYS00.053-0.06021.247-0.011-0.0110.0000.0000.0000.000
32B18LYS10.8861.06025.3590.0650.0650.0000.0000.0000.000
33B19TYR00.088-0.10823.3480.0020.0020.0000.0000.0000.000
34B19TYR0-0.1720.04723.807-0.002-0.0020.0000.0000.0000.000
35B20GLY00.039-0.09219.311-0.019-0.0190.0000.0000.0000.000
36B21ARG00.1490.03117.644-0.043-0.0430.0000.0000.0000.000
37B21ARG10.6591.00318.4730.1730.1730.0000.0000.0000.000
38B22ILE00.012-0.16414.5820.0550.0550.0000.0000.0000.000
39B22ILE0-0.0630.13212.7240.0000.0000.0000.0000.0000.000
40B23VAL00.034-0.12715.5280.0690.0690.0000.0000.0000.000
41B23VAL0-0.0460.14913.918-0.001-0.0010.0000.0000.0000.000
42B24PRO0-0.007-0.11916.2080.0180.0180.0000.0000.0000.000
43B25ARG00.1340.04719.285-0.026-0.0260.0000.0000.0000.000
44B25ARG10.9281.07023.6510.0630.0630.0000.0000.0000.000
45B26SER00.070-0.06622.413-0.015-0.0150.0000.0000.0000.000
46B26SER0-0.0380.06722.7770.0010.0010.0000.0000.0000.000
47B27ILE00.093-0.06918.6190.0050.0050.0000.0000.0000.000
48B27ILE0-0.1230.07016.6250.0000.0000.0000.0000.0000.000
49B28ALA00.142-0.06318.770-0.036-0.0360.0000.0000.0000.000
50B28ALA0-0.1240.09519.2720.0040.0040.0000.0000.0000.000
51B29VAL00.008-0.11319.7510.0350.0350.0000.0000.0000.000
52B29VAL0-0.0560.10519.3060.0000.0000.0000.0000.0000.000
53B30GLU00.158-0.07621.676-0.020-0.0200.0000.0000.0000.000
54B30GLU-1-0.999-0.82725.896-0.163-0.1630.0000.0000.0000.000
55B31SER0-0.026-0.10223.584-0.011-0.0110.0000.0000.0000.000
56B31SER00.0110.09325.2620.0060.0060.0000.0000.0000.000
57B32PRO0-0.007-0.09318.623-0.002-0.0020.0000.0000.0000.000
58B33ARG00.1420.03220.670-0.010-0.0100.0000.0000.0000.000
59B33ARG10.7501.00222.3100.3020.3020.0000.0000.0000.000
60B34VAL00.059-0.13518.143-0.036-0.0360.0000.0000.0000.000
61B34VAL00.0090.15617.587-0.003-0.0030.0000.0000.0000.000
62B35GLU00.082-0.09117.958-0.075-0.0750.0000.0000.0000.000
63B35GLU-1-0.813-0.76921.872-0.337-0.3370.0000.0000.0000.000
64B36GLU00.097-0.11819.527-0.021-0.0210.0000.0000.0000.000
65B36GLU-1-0.840-0.74619.958-0.311-0.3110.0000.0000.0000.000
66B37ILE00.088-0.08415.5500.0050.0050.0000.0000.0000.000
67B37ILE0-0.1120.08513.514-0.012-0.0120.0000.0000.0000.000
68B38VAL00.053-0.10414.473-0.128-0.1280.0000.0000.0000.000
69B38VAL0-0.0790.11315.486-0.004-0.0040.0000.0000.0000.000
70B39ARG00.186-0.06115.182-0.073-0.0730.0000.0000.0000.000
71B39ARG10.7811.03519.0280.3690.3690.0000.0000.0000.000
72B40ALA00.087-0.08415.6800.0210.0210.0000.0000.0000.000
73B40ALA0-0.0900.07515.1850.0030.0030.0000.0000.0000.000
74B41ALA00.054-0.10511.5950.0480.0480.0000.0000.0000.000
75B41ALA0-0.0670.09010.872-0.046-0.0460.0000.0000.0000.000
76B42GLU00.072-0.13011.777-0.124-0.1240.0000.0000.0000.000
77B42GLU-1-0.958-0.82414.629-0.588-0.5880.0000.0000.0000.000
78B43GLU00.040-0.12314.1370.0260.0260.0000.0000.0000.000
79B43GLU-1-0.901-0.78816.343-0.338-0.3380.0000.0000.0000.000
80B44LEU00.005-0.12211.7640.1260.1260.0000.0000.0000.000
81B44LEU0-0.1020.07710.9560.0000.0000.0000.0000.0000.000
82B45LYS0-0.040-0.09810.824-0.068-0.0680.0000.0000.0000.000
83B45LYS10.7981.02011.4120.5320.5320.0000.0000.0000.000
84B46PHE00.082-0.0897.812-0.059-0.0590.0000.0000.0000.000
85B46PHE0-0.0660.0707.653-0.108-0.1080.0000.0000.0000.000
86B47LYS00.200-0.0547.5540.3310.3310.0000.0000.0000.000
87B47LYS10.7411.0248.0161.2021.2020.0000.0000.0000.000
88B48VAL00.029-0.1588.853-0.513-0.5130.0000.0000.0000.000
89B48VAL0-0.0240.13312.0850.0070.0070.0000.0000.0000.000
90B49ILE00.040-0.07910.5980.1890.1890.0000.0000.0000.000
91B49ILE0-0.1430.0478.2090.0260.0260.0000.0000.0000.000
92B50ARG00.147-0.07611.6800.1630.1630.0000.0000.0000.000
93B50ARG10.7600.98413.8420.4870.4870.0000.0000.0000.000
94B51VAL0-0.001-0.13413.933-0.143-0.1430.0000.0000.0000.000
95B51VAL0-0.0300.11715.558-0.003-0.0030.0000.0000.0000.000
96B52GLU00.085-0.09816.6680.0460.0460.0000.0000.0000.000
97B52GLU-1-0.898-0.77317.390-0.449-0.4490.0000.0000.0000.000
98B53GLU00.111-0.09919.238-0.030-0.0300.0000.0000.0000.000
99B53GLU-1-0.968-0.82521.244-0.346-0.3460.0000.0000.0000.000
100B54ASP00.025-0.14122.0370.0090.0090.0000.0000.0000.000
101B54ASP-1-0.934-0.81524.607-0.244-0.2440.0000.0000.0000.000
102B55LYS00.059-0.09225.161-0.005-0.0050.0000.0000.0000.000
103B55LYS10.7190.97125.7760.2810.2810.0000.0000.0000.000
104B56LEU00.146-0.09928.1140.0050.0050.0000.0000.0000.000
105B56LEU0-0.0450.14829.5150.0010.0010.0000.0000.0000.000
106B57ASN00.132-0.06330.9970.0000.0000.0000.0000.0000.000
107B57ASN0-0.1370.06035.5600.0000.0000.0000.0000.0000.000
108B58PRO0-0.154-0.16632.4840.0060.0060.0000.0000.0000.000
109B59ARG00.3270.09933.316-0.010-0.0100.0000.0000.0000.000
110B59ARG10.6390.94030.9480.1430.1430.0000.0000.0000.000
111B60LEU00.069-0.08835.6030.0030.0030.0000.0000.0000.000
112B60LEU0-0.0480.10338.9200.0000.0000.0000.0000.0000.000
113B61SER00.019-0.06238.6060.0070.0070.0000.0000.0000.000
114B61SER0-0.0250.06537.479-0.002-0.0020.0000.0000.0000.000
115B62GLY00.013-0.09238.1850.0040.0040.0000.0000.0000.000
116B63ILE00.0330.00537.0360.0020.0020.0000.0000.0000.000
117B63ILE0-0.0920.07635.8270.0000.0000.0000.0000.0000.000
118B64ASP00.089-0.09432.8270.0030.0030.0000.0000.0000.000
119B64ASP-1-0.934-0.84731.717-0.142-0.1420.0000.0000.0000.000
120B65GLU00.041-0.13531.7910.0000.0000.0000.0000.0000.000
121B65GLU-1-0.916-0.79732.721-0.118-0.1180.0000.0000.0000.000
122B66GLU00.042-0.11428.463-0.011-0.0110.0000.0000.0000.000
123B66GLU-1-0.896-0.78027.429-0.151-0.1510.0000.0000.0000.000
124B67LEU0-0.008-0.12926.715-0.021-0.0210.0000.0000.0000.000
125B67LEU0-0.0430.12425.915-0.001-0.0010.0000.0000.0000.000
126B68ARG00.170-0.06627.931-0.005-0.0050.0000.0000.0000.000
127B68ARG10.8051.04429.3750.1890.1890.0000.0000.0000.000
128B69THR00.029-0.05525.910-0.001-0.0010.0000.0000.0000.000
129B69THR0-0.0890.02823.8760.0050.0050.0000.0000.0000.000
130B70PHE00.073-0.10722.4360.0010.0010.0000.0000.0000.000
131B70PHE0-0.0470.13219.433-0.008-0.0080.0000.0000.0000.000
132B71GLY00.014-0.11619.6260.0040.0040.0000.0000.0000.000
133B72MET00.031-0.03015.6170.0080.0080.0000.0000.0000.000
134B72MET0-0.0500.11014.7080.0040.0040.0000.0000.0000.000
135B73ILE00.063-0.08813.2420.0720.0720.0000.0000.0000.000
136B73ILE0-0.0810.10611.979-0.006-0.0060.0000.0000.0000.000
137B74VAL00.097-0.08410.099-0.139-0.1390.0000.0000.0000.000
138B74VAL0-0.0880.0938.9800.0060.0060.0000.0000.0000.000
139B75LEU00.055-0.1197.9000.3660.3660.0000.0000.0000.000
140B75LEU0-0.0180.1227.279-0.001-0.0010.0000.0000.0000.000
141B76GLU00.102-0.1014.455-1.081-1.034-0.001-0.0740.0280.000
142B76GLU-1-0.846-0.7254.275-1.756-1.5290.000-0.029-0.1980.000
143B77SER00.036-0.0932.8761.3232.2230.037-0.421-0.5150.001
144B77SER0-0.0370.0623.6140.4500.6420.007-0.080-0.1200.000
145B78PRO00.011-0.0661.737-4.840-12.70615.257-5.106-2.285-0.040
146B79TYR00.0580.0044.1131.9862.2160.001-0.041-0.1900.000
147B79TYR0-0.0810.0846.1130.0430.0430.0000.0000.0000.000
148B80GLY00.067-0.0643.119-1.881-1.2670.093-0.351-0.355-0.003
149B81LYS00.1370.0054.738-0.847-0.825-0.002-0.001-0.0190.000
150B81LYS10.7451.0005.7050.9930.9930.0000.0000.0000.000
151B82SER00.093-0.0586.074-0.061-0.0610.0000.0000.0000.000
152B82SER0-0.0530.0539.8470.0200.0200.0000.0000.0000.000
153B83LYS00.017-0.0998.410-0.059-0.0590.0000.0000.0000.000
154B83LYS10.9351.0758.107-0.294-0.2940.0000.0000.0000.000
155B84SER00.034-0.0886.8790.2360.2360.0000.0000.0000.000
156B84SER0-0.0180.1116.271-0.311-0.3110.0000.0000.0000.000
157B85LEU00.098-0.0978.108-0.020-0.0200.0000.0000.0000.000
158B85LEU0-0.0860.0939.4940.0240.0240.0000.0000.0000.000
159B86LYS00.125-0.05610.8700.0340.0340.0000.0000.0000.000
160B86LYS10.8291.03512.5940.0750.0750.0000.0000.0000.000
161B87LEU00.077-0.09611.7340.0820.0820.0000.0000.0000.000
162B87LEU0-0.0790.1049.832-0.004-0.0040.0000.0000.0000.000
163B88ILE00.105-0.06512.0270.0720.0720.0000.0000.0000.000
164B88ILE0-0.0670.0919.820-0.019-0.0190.0000.0000.0000.000
165B89ALA00.120-0.08113.4920.0330.0330.0000.0000.0000.000
166B89ALA0-0.0950.08715.8960.0080.0080.0000.0000.0000.000
167B90GLN0-0.003-0.12616.1140.0350.0350.0000.0000.0000.000
168B90GLN0-0.0690.08016.004-0.016-0.0160.0000.0000.0000.000
169B91LYS00.135-0.08616.4260.0630.0630.0000.0000.0000.000
170B91LYS10.7191.01016.0140.3230.3230.0000.0000.0000.000
171B92ILE00.124-0.08517.7270.0310.0310.0000.0000.0000.000
172B92ILE0-0.0790.09816.7030.0000.0000.0000.0000.0000.000
173B93ARG00.116-0.07019.6070.0240.0240.0000.0000.0000.000
174B93ARG10.7170.97020.5510.2120.2120.0000.0000.0000.000
175B94GLU00.050-0.13521.1900.0300.0300.0000.0000.0000.000
176B94GLU-1-0.888-0.75620.629-0.260-0.2600.0000.0000.0000.000
177B95PHE0-0.008-0.12921.7330.0270.0270.0000.0000.0000.000
178B95PHE0-0.0700.09218.6230.0030.0030.0000.0000.0000.000
179B96ARG00.141-0.05423.2130.0160.0160.0000.0000.0000.000
180B96ARG10.6540.92323.1340.2710.2710.0000.0000.0000.000
181B97ARG00.114-0.07025.7100.0120.0120.0000.0000.0000.000
182B97ARG10.8611.04526.1320.1430.1430.0000.0000.0000.000
183B98ARG00.118-0.04626.4680.0180.0180.0000.0000.0000.000
184B98ARG10.7500.99522.5500.2220.2220.0000.0000.0000.000
185B99SER0-0.022-0.08927.6660.0130.0130.0000.0000.0000.000
186B99SER0-0.0910.02426.880-0.006-0.0060.0000.0000.0000.000
187B100ALA00.109-0.07029.4600.0070.0070.0000.0000.0000.000
188B100ALA0-0.1000.09130.8420.0000.0000.0000.0000.0000.000
189B101GLY0-0.002-0.09431.2220.0090.0090.0000.0000.0000.000
190B102THR0-0.001-0.00532.7170.0090.0090.0000.0000.0000.000
191B102THR0-0.0170.07934.5890.0020.0020.0000.0000.0000.000
192B103LEU00.094-0.06532.354-0.011-0.0110.0000.0000.0000.000
193B103LEU0-0.1220.07632.2130.0010.0010.0000.0000.0000.000
194B104VAL00.042-0.12133.035-0.007-0.0070.0000.0000.0000.000
195B104VAL0-0.0730.10236.0390.0010.0010.0000.0000.0000.000
196B105PRO00.007-0.08734.3790.0010.0010.0000.0000.0000.000